Science.gov

Sample records for annual publication ngs

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 77 FR 26585 - Annual Public Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-04

    ... created by Congress to advance the mission of FDA to modernize medical, veterinary, food, food ingredient... 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...

  6. 78 FR 23960 - Annual Public Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-23

    ... Food and Drug Amendments of 2007, is announcing an annual open public meeting. The Foundation will...: The open public meeting will be held on May 23, 2013, from 10 a.m. until 12 noon. Interested persons..., and cosmetic product development; accelerate innovation; and enhance product safety. With the...

  7. 75 FR 39034 - Public Housing Annual Contributions Contract

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-07

    ... URBAN DEVELOPMENT Public Housing Annual Contributions Contract AGENCY: Office of the Chief Information... conditions contained in an Annual Contributions Contract (ACC) with certain requirements applicable to all...: Public Housing Annual Contributions Contract. OMB Approval Number: 2577-New. Form Numbers:...

  8. Alabama Public Library Service Annual Report, 1992.

    ERIC Educational Resources Information Center

    Alabama Public Library Service, Montgomery.

    This annual report summarizes activities of the Alabama Public Library Service for the fiscal year 1992. The following general areas are discussed: (1) agency services, including agency restructuring and personnel lay-offs, children's summer library program, the state union list of serials, automated systems, and production of a second edition of…

  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, 1995.

    ERIC Educational Resources Information Center

    Alabama Public Library Service, Montgomery.

    This annual report summarizes activities of the Alabama Public Library Service (APLS) for the fiscal year 1995. The APLS is charged with improving library services throughout the state to ensure that all citizens have access to quality library and information services. During fiscal year 1995, major building renovations were completed with 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. 77 FR 43618 - Sunshine Act Meetings; OPIC Annual Public Hearing

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-07-25

    ... CORPORATION Sunshine Act Meetings; OPIC Annual Public Hearing TIME AND DATE: 2:00 p.m., Thursday, September 6..., DC. STATUS: Hearing OPEN to the Public at 2:00 p.m. PURPOSE: Annual Public Hearing to afford an... presentations may not exceed ten (10) minutes. The time for individual presentations may be...

  14. 78 FR 5516 - Sunshine Act: OPIC Annual Public Hearing

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-25

    ... CORPORATION Sunshine Act: OPIC Annual Public Hearing TIME AND DATE: 2 p.m., Wednesday, March 13, 2013. PLACE...: Hearing open to the public at 2 p.m. PURPOSE: Annual Public Hearing to afford an opportunity for any... INFORMATION: OPIC is a U.S. Government agency that provides, on a commercial basis, political risk...

  15. 75 FR 76758 - Sunshine Act; OPIC Annual Public Hearing

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-09

    ... CORPORATION Sunshine Act; OPIC Annual Public Hearing Time and Date: 3:30 p.m., Thursday, January 20, 2011.... Status: Hearing OPEN to the Public at 3:30 p.m. Purpose: Annual Public Hearing to afford an opportunity...: OIC is a U.S. Government agency that provides, on a commercial basis, political risk insurance...

  16. Utah Public Library Service: 1995. An Annual Report.

    ERIC Educational Resources Information Center

    Long, Sandi

    This annual report of public library services is part of "The Upgrade Process," a tool for Utah's public librarians and library trustees to use as they work to improve the quality and effectiveness of public library service. The process has three major components: public library service standards; a flexible planning process for public library…

  17. 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.

  18. 77 FR 4568 - Annual Computational Science Symposium; Public Conference

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-30

    ... HUMAN SERVICES Food and Drug Administration Annual Computational Science Symposium; Public Conference... announcing a public conference entitled ``The FDA/PhUSE Annual Computational Science Symposium.'' The purpose... computational science. At the conference, which will bring together FDA, industry, and academia, FDA will...

  19. 75 FR 9427 - Notice of Proposed Information Collection for Public Comment; Public Housing Annual Contributions...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-02

    ... Contributions Contract AGENCY: Office of the Assistant Secretary for Public and Indian Housing, HUD. ACTION... lists the following information: Title of Proposal: Public Housing Annual Contributions Contract. OMB... HUD to make annual contributions to public housing agencies (PHAs) to achieve and maintain the...

  20. Publication rate of presentations at an annual military orthopaedic meeting.

    PubMed

    Schoenfeld, Andrew J; Carey, Paul A; Frye, Brandon D; Weaver, Courtney R; Belmont, Philip J

    2012-01-01

    Many research abstracts presented at orthopaedic conferences do not undergo a formal editorial, or peer-review process; however, abstracts are frequently referenced in textbooks and influence clinical practice. The purpose of this study was to determine the publication rate of abstracts formally presented at the Society of Military Orthopaedic Surgeons (SOMOS) annual meetings from 1998 to 2006 that went to full-text publication. Using Google Scholar and PubMed, a literature search was performed for each abstract presented at the annual SOMOS meeting in the years 1998-2006, to calculate the overall full-text publication rate, the average duration from presentation to publication, and the distribution of publications in the various journals. A total of 770 abstracts were presented at the annual SOMOS meetings. The overall full-text publication rate at a minimum of 3 years was 45.7% (352 publications). The average time from presentation to publication was 2.7 years. The published articles appeared in 65 peer-reviewed journals, with notable distribution in Spine (10.0%), The American Journal of Sports Medicine (9.4%), and The Journal of Bone and Joint Surgery (9.4%). The full-text publication rate of abstracts presented at the annual SOMOS meetings compares favorably with that of other major orthopaedic conferences in the United States. Nonetheless, more than half of abstracts presented at the SOMOS meetings remain unpublished. PMID:23327844

  1. Alabama Public Library Service. Annual Report, 1978.

    ERIC Educational Resources Information Center

    Alabama Public Library Service, Montgomery.

    This report on Alabama public and regional libraries and their services includes brief discussions of the year's state and federal aid, public library development, interlibrary cooperation, library automation, summer reading programs, services for the blind and physically handicapped, planning and research, library services to institutions,…

  2. 78 FR 67168 - Sixth Annual Sentinel Initiative; Public Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-08

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration Sixth Annual Sentinel Initiative; Public Workshop AGENCY: Food and Drug Administration, HHS. ACTION: Notice of public workshop. The Food and Drug...

  3. Annual State of Public Education Report, SY 2006-2007

    ERIC Educational Resources Information Center

    Guam Public School System, 2007

    2007-01-01

    The report addresses the reporting requirements of Public Law 26-26 and the programs and activities that affect student achievement as described in the Guam Public School System's Board-adopted District Action Plan (DAP). This is an annual report on progress towards increasing student achievement with the ultimate aim of Preparing Students for…

  4. 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…

  5. Annual State of Public Education Report, SY 2005-2006

    ERIC Educational Resources Information Center

    Guam Public School System, 2007

    2007-01-01

    The purpose of this Annual School Progress Report is twofold: (1) to share information about the progress of Guam Public School System towards meeting education goals, which are embodied in the District Action Plan (DAP); and (2) to inform educators and the community at large about programs and activities that affect the quality of educational…

  6. 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…

  7. The Condition of Connecticut's Public School Facilities. Annual Report.

    ERIC Educational Resources Information Center

    Connecticut State Dept. of Education, Hartford.

    This is the second annual report on the condition of Connecticut's public school facilities required pursuant to Section 10-220 of the Connecticut General Statutes. The data in this report reflect the responses of school district officials to various survey questions. The report includes tables which list school-by-school responses to all survey…

  8. Annual Report on the Condition of Connecticut's Public Schools, 2002.

    ERIC Educational Resources Information Center

    Connecticut State Dept. of Education, Hartford.

    This is the fourth annual report on the condition of Connecticut's public school facilities required pursuant to Section 10-220 of the Connecticut General Statutes. The data in this report reflect the responses of school district officials to various survey questions. Summary data are discussed in fairly broad categories--education reference…

  9. Annual Report on the Condition of Connecticut's Public Schools.

    ERIC Educational Resources Information Center

    Connecticut State Dept. of Education, Hartford.

    This is the third annual report on the condition of Connecticut's public school facilities required pursuant to Section 10-220 of the Connecticut General Statutes. The data in this report reflect the responses of school district officials to various survey questions. Summary data are discussed in fairly broad categories--education reference groups…

  10. 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.

  11. 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…

  12. 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

  13. NGS-based deep bisulfite sequencing.

    PubMed

    Lee, Suman; Kim, Joomyeong

    2016-01-01

    We have developed an NGS-based deep bisulfite sequencing protocol for the DNA methylation analysis of genomes. This approach allows the rapid and efficient construction of NGS-ready libraries with a large number of PCR products that have been individually amplified from bisulfite-converted DNA. This approach also employs a bioinformatics strategy to sort the raw sequence reads generated from NGS platforms and subsequently to derive DNA methylation levels for individual loci. The results demonstrated that this NGS-based deep bisulfite sequencing approach provide not only DNA methylation levels but also informative DNA methylation patterns that have not been seen through other existing methods.•This protocol provides an efficient method generating NGS-ready libraries from individually amplified PCR products.•This protocol provides a bioinformatics strategy sorting NGS-derived raw sequence reads.•This protocol provides deep bisulfite sequencing results that can measure DNA methylation levels and patterns of individual loci.

  14. The 33rd 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.

    2001-01-01

    Presents results of the 33rd Annual Phi Delta Kappa/Gallup Poll on the public's attitudes toward the public schools. Includes a summary of key findings and tables showing percentage distributions of responses to each question. (PKP)

  15. 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... Public Water Systems Compliance Report; ICR Numbers: EPA ICR Number 1812.05, OMB Control Number...

  16. Toward Better Oversight of NGS Tests.

    PubMed

    2016-09-01

    The FDA has published two draft guidance documents aimed at streamlining its oversight of tests based on next-generation sequencing (NGS). One contains preliminary recommendations addressing the analytic validity of NGS-based tests for hereditary diseases; the other explains how test developers can obtain official recognition of their genetic variant databases, potentially speeding marketing clearance or approval. PMID:27457361

  17. Toward Better Oversight of NGS Tests.

    PubMed

    2016-09-01

    The FDA has published two draft guidance documents aimed at streamlining its oversight of tests based on next-generation sequencing (NGS). One contains preliminary recommendations addressing the analytic validity of NGS-based tests for hereditary diseases; the other explains how test developers can obtain official recognition of their genetic variant databases, potentially speeding marketing clearance or approval.

  18. 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.

  19. 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... Network (MDEpiNet) 2011: Second Annual Public Workshop.'' The purpose of the public workshop is to provide... establishment of a network that works with FDA experts to determine the evidence gaps and questions,...

  20. 40 CFR 256.61 - Requirements for public participation in the annual State work program.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... program. (a) A public participation work plan in accord with 40 CFR 25.11 shall be included in the annual... required by 40 CFR part 35, the draft work program shall be made available to the public at the State... in the annual State work program. 256.61 Section 256.61 Protection of Environment...

  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

    ... HUMAN SERVICES Food and Drug Administration Division of Cardiovascular Devices 30-Day Notices and Annual... following public workshop entitled ``Division of Cardiovascular Devices 30-Day Notices and Annual Reports..., specifically for cardiovascular devices. DATES: Date and Time: The public workshop will be held on August...

  2. 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...

  3. 77 FR 53935 - Sunshine Act Cancellation Notice-OPIC's September 6, 2012 Annual Public Hearing

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-04

    ... From the Federal Register Online via the Government Publishing Office OVERSEAS PRIVATE INVESTMENT CORPORATION Sunshine Act Cancellation Notice--OPIC's September 6, 2012 Annual Public Hearing OPIC's Sunshine... statements for the record; therefore, OPIC's Annual Public Hearing scheduled for 2 p.m., September 6,...

  4. The 39th 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.

    2007-01-01

    In this article, the authors report the results of the 39th Annual Phi Delta Kappa/Gallup Poll of the public's attitudes toward the public schools. This year's report examined the public's assessment of the No Child Left Behind (NCLB) and its principal strategy, standardized testing. The authors include a summary of key findings and tables showing…

  5. 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…

  6. The 34th 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.

    2002-01-01

    Results of the 34th Annual Phi Delta Kappa/Gallup Poll of the public's attitudes toward the public schools. Reports, for example, that school-age parents continue to regard local schools favorably, 71 percent of whom give the school attended by their oldest child a grade of A or B. (PKP)

  7. Measuring Changes in Salaries and Wages in Public Schools. [Annual Edition].

    ERIC Educational Resources Information Center

    Educational Research Service, Arlington, VA.

    The Educational Research Service reports annually a statistical measure of salaries of public school system employees called the Composite Indicator of Changes (CIC) in Average Salaries and Wages Paid by Public School Systems. Each edition can be used to analyze trends in average salaries and wages paid to public school employees over the past 10…

  8. 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

    ... URBAN DEVELOPMENT Notice of Extension of Information Collection for Public Comment; Consolidated Plan... proposed extension of information collection requirements for Consolidated Planning for Community Planning... forms of information submission of responses. Title of Proposal: Consolidated Plan & Annual...

  9. 78 FR 59662 - Annual Public Meeting of the Interagency Steering Committee on Multimedia Environmental Modeling

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-27

    ...) Citizen science, crowd sourcing, and social media; (2) environmental evaluation and remediation; (3... From the Federal Register Online via the Government Publishing Office ] DEPARTMENT OF ENERGY Annual Public Meeting of the Interagency Steering Committee on Multimedia Environmental Modeling...

  10. 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…

  11. 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 Superintendent…

  12. Second Annual Report: Program of Research and Evaluation for Public Schools (PREPS), 1977-1978.

    ERIC Educational Resources Information Center

    Saterfiel, Thomas H.

    This document is the second annual report of the activities of the Program of Research and Evaluation for Public Schools (PREPS). The mission of PREPS, a consortium of public school districts in Mississippi, is to aid member schools in obtaining quality data from which curricular and administrative decisions can be made. Technical assistance…

  13. 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…

  14. 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…

  15. Guam Department of Education Annual State of Public Education Report, SY 2003-2004

    ERIC Educational Resources Information Center

    Guam Public School System, 2005

    2005-01-01

    This report addresses the reporting requirements of Public Law 26-26 and the provisions of the No Child Left Behind (NCLB) as described in the Department of Education's Board-adopted District Action Plan (DAP). The law specifically requires Guam Department of Education to include the following information in the Annual State of Public Education…

  16. 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

    ..., Release No. 68921/February 13, 2013] Order Approving Public Company Accounting Oversight Board Budget and Annual Accounting Support Fee for Calendar Year 2013 The Sarbanes-Oxley Act of 2002, as amended (the ``Sarbanes-Oxley Act''),\\1\\ established the Public Company Accounting Oversight Board (``PCAOB'') to...

  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. Occupational radiation exposures in Canada, 1987. Annual publication

    SciTech Connect

    Not Available

    1989-01-01

    The information in this tenth annual report is derived from the National Dose Registry of the Bureau of Radiation and Medical Devices, Dept. of National Health and Welfare. It provides statistics on occupational radiation exposures of all monitored workers in Canada from NDR records as well as from data submitted by nuclear power generating stations, Atomic Energy of Canada Ltd. and uranium mines. This report presents by occupation: Average yearly whole body doses by region, dose distributions, and variations of the average doses with time. Statistical data are tabulated in summary form.

  19. 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... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF HEALTH AND.... Department of Health and Human Services efforts that use distributed systems of automated health care...

  20. 18 CFR 141.2 - FERC Form No. 1-F, Annual report for Nonmajor public utilities and licensees.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ..., Annual report for Nonmajor public utilities and licensees. 141.2 Section 141.2 Conservation of Power and... ACT AND PUBLIC UTILITY REGULATORY POLICIES ACT OF 1978 STATEMENTS AND REPORTS (SCHEDULES) § 141.2 FERC Form No. 1-F, Annual report for Nonmajor public utilities and licensees. (a) Prescription. The form...

  1. The potential of whole genome NGS for infectious disease diagnosis.

    PubMed

    Lecuit, Marc; Eloit, Marc

    2015-01-01

    Non-targeted identification of microbes is now possible directly in biological samples, based on whole-genome-NGS (WG-NGS) techniques that allow deep sequencing of nucleic acids, data mining and sorting out of sequences of pathogens without any a priori hypothesis. WG-NGS was first only used as a research tool due to its cost, complexity and lack of standardization. Recent improvements in sample preparation and bioinformatics pipelines and decrease in cost now allow actionable diagnostics in patients. The potency and limits of WG-NGS and possible future indications are discussed here. WG-NGS will likely soon become a standard procedure in microbiological diagnosis.

  2. Annual New Hampshire Public Library Personnel Data Survey, 1998.

    ERIC Educational Resources Information Center

    New Hampshire State Library, Concord.

    This document presents data on personnel in New Hampshire public libraries in 1998. Libraries are arranged by town in alphabetical order and by the following ranges of population served: 30,001 and over, 18,001-30,000, 12,001-18,000, 9,001=12,000, 6,001-9,000, 3,001-6,000, 1,001-3,000, and under 1,000. The following data are provided for each…

  3. 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

  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. The Education Alliance: Business and Community for Public Schools. Annual Report, 1997.

    ERIC Educational Resources Information Center

    Education Alliance, Charleston, WV.

    Formerly the West Virginia Education Fund, the Education Alliance is a nonprofit organization that serves as a catalyst for business and community involvement in West Virginia public schools. This annual report describes the following Education Alliance activities during 1997: (1) Mini-Grants for Classroom Projects (grants to 195 teachers of up to…

  6. 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...

  7. 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....

  8. 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...

  9. 78 FR 17937 - Notice of Proposed Information Collection for Public Comment; FHA Lender Approval, Annual Renewal...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-25

    ... 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,...

  10. 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...

  11. 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,...

  12. 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,...

  13. 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…

  14. 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

    ... discussions of PCAOB budget matters. \\2\\ 17 CFR 202.190. See Release No. 33-8724 (July 18, 2006) [71 FR 41998...; 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...

  15. 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...

  16. Measuring Changes in Salaries and Wages in Public Schools: 2000 Edition. 27th Annual Edition.

    ERIC Educational Resources Information Center

    Williams, Alicia R.; Cooke, Willa D.; Davis, Andrea M.; Miller, Oronde A.; Lewis, JoAnn

    This annual survey reports comparable salary data for 22 professional positions. The purpose of this edition is to aid in the analysis of trends in average salaries and wages paid public-school employees in the six component groups of school personnel over the previous 10 years. This report shows how the Composite Indicator of Changes (CIC) in…

  17. The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis.

    PubMed

    Ruark, Elise; Renwick, Anthony; Clarke, Matthew; Snape, Katie; Ramsay, Emma; Elliott, Anna; Hanks, Sandra; Strydom, Ann; Seal, Sheila; Rahman, Nazneen

    2016-01-01

    To provide a useful community resource for orthogonal assessment of NGS analysis software, we present the ICR142 NGS validation series. The dataset includes high-quality exome sequence data from 142 samples together with Sanger sequence data at 730 sites; 409 sites with variants and 321 sites at which variants were called by an NGS analysis tool, but no variant is present in the corresponding Sanger sequence. The dataset includes 286 indel variants and 275 negative indel sites, and thus the ICR142 validation dataset is of particular utility in evaluating indel calling performance. The FASTQ files and Sanger sequence results can be accessed in the European Genome-phenome Archive under the accession number EGAS00001001332.

  18. The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis

    PubMed Central

    Ruark, Elise; Renwick, Anthony; Clarke, Matthew; Snape, Katie; Ramsay, Emma; Elliott, Anna; Hanks, Sandra; Strydom, Ann; Seal, Sheila; Rahman, Nazneen

    2016-01-01

    To provide a useful community resource for orthogonal assessment of NGS analysis software, we present the ICR142 NGS validation series. The dataset includes high-quality exome sequence data from 142 samples together with Sanger sequence data at 730 sites; 409 sites with variants and 321 sites at which variants were called by an NGS analysis tool, but no variant is present in the corresponding Sanger sequence. The dataset includes 286 indel variants and 275 negative indel sites, and thus the ICR142 validation dataset is of particular utility in evaluating indel calling performance. The FASTQ files and Sanger sequence results can be accessed in the European Genome-phenome Archive under the accession number EGAS00001001332. PMID:27158454

  19. Publication rates of abstracts presented at the annual meeting of the Society of Military Orthopaedic Surgeons.

    PubMed

    Fuller, Brian C; Dowd, Thomas C; Masini, Brendan D; Gerlinger, Tad L

    2012-01-01

    Previous studies have reported publication rates of abstracts presented at orthopaedic meetings from 22 to 68 percent. The objective of this study was to determine the publication rate of papers presented at the Society of Military Orthopaedic Surgeons (SOMOS) meetings from 1999 to 2003. A database was created including all abstracts presented at SOMOS meetings from 1999 to 2003 as listed in official program books. To assess whether each abstract resulted in publication in a peer-reviewed journal, a computerized PubMed search of the presenting author and appropriate keywords from the title was conducted. Overall, 191 of the 435 abstracts presented at SOMOS from 1999 to 2003 were published in a peer-reviewed journal, giving a publication rate of 44%. The publication rate of abstract presentations at annual SOMOS meetings compares favorably with the rates for other orthopaedic meetings. However, less than 50% result in peer-reviewed publication. PMID:22995357

  20. Patenting genetic diagnostic methods: NGS, GWAS, SNPs and patents.

    PubMed

    Lawson, Charles

    2015-06-01

    This article reviews the problems posed by patent claims to genetic diagnostic methods associated with genome-wide association studies (GWAS) adopting methodologies using next-generation sequencing (NGS) and single nucleotide polymorphisms (SNP). These problems are essentially about experimental reproducibility and the credibility and veracity of reported developments. An analysis of the relevant law demonstrates that the current Australian and United States laws about suitable patentable subject matter differ, and that the current reproducibility (sufficiency, enablement and inutility) standards are unlikely to address these problems. The article concludes that following the United States approach excluding these genetic diagnostic method claims from patenting is one solution. Failing this, improving analysis and quality controls that are now being adopted in the basic research will reduce the nature of the problems, although this will remain problematic for patent examiners and the broader public.

  1. 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. PMID:27115642

  2. 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.

  3. NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL.

    PubMed

    May, Ali; Abeln, Sanne; Buijs, Mark J; Heringa, Jaap; Crielaard, Wim; Brandt, Bernd W

    2015-07-01

    Massively parallel sequencing of microbial genetic markers (MGMs) is used to uncover the species composition in a multitude of ecological niches. These sequencing runs often contain a sample with known composition that can be used to evaluate the sequencing quality or to detect novel sequence variants. With NGS-eval, the reads from such (mock) samples can be used to (i) explore the differences between the reads and their references and to (ii) estimate the sequencing error rate. This tool maps these reads to references and calculates as well as visualizes the different types of sequencing errors. Clearly, sequencing errors can only be accurately calculated if the reference sequences are correct. However, even with known strains, it is not straightforward to select the correct references from databases. We previously analysed a pyrosequencing dataset from a mock sample to estimate sequencing error rates and detected sequence variants in our mock community, allowing us to obtain an accurate error estimation. Here, we demonstrate the variant detection and error analysis capability of NGS-eval with Illumina MiSeq reads from the same mock community. While tailored towards the field of metagenomics, this server can be used for any type of MGM-based reads. NGS-eval is available at http://www.ibi.vu.nl/programs/ngsevalwww/.

  4. 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,…

  5. 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)…

  6. 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.

  7. 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

    ... around idea exchanges and sharing of case studies and examples, fostered efficient information sharing... August 1, 2013 Part II Department of Health and Human Services Secretarial Review and Publication of the...; ] DEPARTMENT OF HEALTH AND HUMAN SERVICES Secretarial Review and Publication of the Annual Report to...

  8. 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

  9. 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.

  10. 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/ngshome.html.

  11. 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

  12. 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

  13. Development of a high-resolution NGS-based HLA-typing and analysis pipeline

    PubMed Central

    Wittig, Michael; Anmarkrud, Jarl A.; Kässens, Jan C.; Koch, Simon; Forster, Michael; Ellinghaus, Eva; Hov, Johannes R.; Sauer, Sascha; Schimmler, Manfred; Ziemann, Malte; Görg, Siegfried; Jacob, Frank; Karlsen, Tom H.; Franke, Andre

    2015-01-01

    The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions. PMID:25753671

  14. Development of a high-resolution NGS-based HLA-typing and analysis pipeline.

    PubMed

    Wittig, Michael; Anmarkrud, Jarl A; Kässens, Jan C; Koch, Simon; Forster, Michael; Ellinghaus, Eva; Hov, Johannes R; Sauer, Sascha; Schimmler, Manfred; Ziemann, Malte; Görg, Siegfried; Jacob, Frank; Karlsen, Tom H; Franke, Andre

    2015-06-23

    The human leukocyte antigen (HLA) complex contains the most polymorphic genes in the human genome. The classical HLA class I and II genes define the specificity of adaptive immune responses. Genetic variation at the HLA genes is associated with susceptibility to autoimmune and infectious diseases and plays a major role in transplantation medicine and immunology. Currently, the HLA genes are characterized using Sanger- or next-generation sequencing (NGS) of a limited amplicon repertoire or labeled oligonucleotides for allele-specific sequences. High-quality NGS-based methods are in proprietary use and not publicly available. Here, we introduce the first highly automated open-kit/open-source HLA-typing method for NGS. The method employs in-solution targeted capturing of the classical class I (HLA-A, HLA-B, HLA-C) and class II HLA genes (HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1). The calling algorithm allows for highly confident allele-calling to three-field resolution (cDNA nucleotide variants). The method was validated on 357 commercially available DNA samples with known HLA alleles obtained by classical typing. Our results showed on average an accurate allele call rate of 0.99 in a fully automated manner, identifying also errors in the reference data. Finally, our method provides the flexibility to add further enrichment target regions.

  15. Orthogonal NGS for High Throughput Clinical Diagnostics.

    PubMed

    Chennagiri, Niru; White, Eric J; Frieden, Alexander; Lopez, Edgardo; Lieber, Daniel S; Nikiforov, Anastasia; Ross, Tristen; Batorsky, Rebecca; Hansen, Sherry; Lip, Va; Luquette, Lovelace J; Mauceli, Evan; Margulies, David; Milos, Patrice M; Napolitano, Nichole; Nizzari, Marcia M; Yu, Timothy; Thompson, John F

    2016-04-19

    Next generation sequencing is a transformative technology for discovering and diagnosing genetic disorders. However, high-throughput sequencing remains error-prone, necessitating variant confirmation in order to meet the exacting demands of clinical diagnostic sequencing. To address this, we devised an orthogonal, dual platform approach employing complementary target capture and sequencing chemistries to improve speed and accuracy of variant calls at a genomic scale. We combined DNA selection by bait-based hybridization followed by Illumina NextSeq reversible terminator sequencing with DNA selection by amplification followed by Ion Proton semiconductor sequencing. This approach yields genomic scale orthogonal confirmation of ~95% of exome variants. Overall variant sensitivity improves as each method covers thousands of coding exons missed by the other. We conclude that orthogonal NGS offers improvements in variant calling sensitivity when two platforms are used, better specificity for variants identified on both platforms, and greatly reduces the time and expense of Sanger follow-up, thus enabling physicians to act on genomic results more quickly.

  16. Orthogonal NGS for High Throughput Clinical Diagnostics

    PubMed Central

    Chennagiri, Niru; White, Eric J.; Frieden, Alexander; Lopez, Edgardo; Lieber, Daniel S.; Nikiforov, Anastasia; Ross, Tristen; Batorsky, Rebecca; Hansen, Sherry; Lip, Va; Luquette, Lovelace J.; Mauceli, Evan; Margulies, David; Milos, Patrice M.; Napolitano, Nichole; Nizzari, Marcia M.; Yu, Timothy; Thompson, John F.

    2016-01-01

    Next generation sequencing is a transformative technology for discovering and diagnosing genetic disorders. However, high-throughput sequencing remains error-prone, necessitating variant confirmation in order to meet the exacting demands of clinical diagnostic sequencing. To address this, we devised an orthogonal, dual platform approach employing complementary target capture and sequencing chemistries to improve speed and accuracy of variant calls at a genomic scale. We combined DNA selection by bait-based hybridization followed by Illumina NextSeq reversible terminator sequencing with DNA selection by amplification followed by Ion Proton semiconductor sequencing. This approach yields genomic scale orthogonal confirmation of ~95% of exome variants. Overall variant sensitivity improves as each method covers thousands of coding exons missed by the other. We conclude that orthogonal NGS offers improvements in variant calling sensitivity when two platforms are used, better specificity for variants identified on both platforms, and greatly reduces the time and expense of Sanger follow-up, thus enabling physicians to act on genomic results more quickly. PMID:27090146

  17. 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.

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

    DOE PAGESBeta

    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 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

  19. 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.

  20. 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…

  1. 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. PMID:27008019

  2. 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.

  3. NGS-Logistics: federated analysis of NGS sequence variants across multiple locations.

    PubMed

    Ardeshirdavani, Amin; Souche, Erika; Dehaspe, Luc; Van Houdt, Jeroen; Vermeesch, Joris Robert; Moreau, Yves

    2014-01-01

    As many personal genomes are being sequenced, collaborative analysis of those genomes has become essential. However, analysis of personal genomic data raises important privacy and confidentiality issues. We propose a methodology for federated analysis of sequence variants from personal genomes. Specific base-pair positions and/or regions are queried for samples to which the user has access but also for the whole population. The statistics results do not breach data confidentiality but allow further exploration of the data; researchers can negotiate access to relevant samples through pseudonymous identifiers. This approach minimizes the impact on data confidentiality while enabling powerful data analysis by gaining access to important rare samples. Our methodology is implemented in an open source tool called NGS-Logistics, freely available at https://ngsl.esat.kuleuven.be.

  4. 78 FR 4378 - Annual List of Newspapers To Be Used by the Alaska Region for Publication of Legal Notices of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-22

    ... Forest Service Annual List of Newspapers To Be Used by the Alaska Region for Publication of Legal Notices... Ranger Districts, Forests, and the Regional Office of the Alaska Region will use to publish legal... the Federal Register. ADDRESSES: Robin Dale, Alaska Region Group Leader for Appeals, Litigation...

  5. 75 FR 32737 - Annual List of Newspapers To Be Used by the Alaska Region for Publication of Legal Notices of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-09

    ... Forest Service Annual List of Newspapers To Be Used by the Alaska Region for Publication of Legal Notices... Districts, Forests, and the Regional Office of the Alaska Region will use to publish legal notice of all.... ADDRESSES: Ken Post, Appeals Specialist; Forest Service, Alaska Region; P.O. Box 21628; Juneau, Alaska...

  6. 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…

  7. 75 FR 65340 - Secretarial Review and Publication of the Annual Report to Congress Submitted by the Contracted...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-22

    ... mandate for review and publication of the annual report on September 10, 2009 (74 FR 46594). In March 2010... in any order of priority) are: Acute myocardial infarction Alzheimer's disease and related disorders...: Phase I: Cardiovascular diseases, including acute myocardial infarction, ischemic heart...

  8. 77 FR 56919 - Secretarial Review and Publication of the Annual Report to Congress Submitted by the Contracted...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-09-14

    ... reasons. NQF shall consider measures that assist consumers and patients in making informed health care... including hospitals and physicians. Maintenance of Consensus Endorsed Measures--NQF shall establish and... publication of the annual report on September 10, 2009 (74 FR 46594). In March 2010, NQF submitted to...

  9. Genetic counselors' (GC) knowledge, awareness, understanding of clinical next-generation sequencing (NGS) genomic testing.

    PubMed

    Boland, P M; Ruth, K; Matro, J M; Rainey, K L; Fang, C Y; Wong, Y N; Daly, M B; Hall, M J

    2015-12-01

    Genomic tests are increasingly complex, less expensive, and more widely available with the advent of next-generation sequencing (NGS). We assessed knowledge and perceptions among genetic counselors pertaining to NGS genomic testing via an online survey. Associations between selected characteristics and perceptions were examined. Recent education on NGS testing was common, but practical experience limited. Perceived understanding of clinical NGS was modest, specifically concerning tumor testing. Greater perceived understanding of clinical NGS testing correlated with more time spent in cancer-related counseling, exposure to NGS testing, and NGS-focused education. Substantial disagreement about the role of counseling for tumor-based testing was seen. Finally, a majority of counselors agreed with the need for more education about clinical NGS testing, supporting this approach to optimizing implementation.

  10. 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…

  11. Annual Progress Report, 1975. Southern Rural Development Center, Mississippi State University. SRDC Series Publication No. 10.

    ERIC Educational Resources Information Center

    Southern Rural Development Center, State College, MS.

    Included in this second annual report on the Southern Rural Development Center's (SRDC) 1974-75 plan of work are data re: orientation visits; regional workshops; technical consultants; liaison with regional agencies and organizations; information dissemination; annual evaluation; functional networks in the areas of land use issues, citizen…

  12. Maryland's Public Charter School Program: Providing High Quality Choices in Public Education. Charter School Annual Report, 2008

    ERIC Educational Resources Information Center

    Maryland State Department of Education, 2009

    2009-01-01

    The Maryland General Assembly enacted Maryland's charter school law in 2003. This current school year (2008-2009) marks the sixth year of Maryland's public charter school program. This paper presents the statistics representing the performance of Maryland's public charter schools for the school year 2008-2009.

  13. 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. PMID:26009315

  14. 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.

  15. Multiple Object Adaptive Optics: Mixed NGS/LGS tomography

    NASA Astrophysics Data System (ADS)

    Morris, Tim; Gendron, Eric; Basden, Alastair; Martin, Olivier; Osborn, James; Henry, David; Hubert, Zoltan; Sivo, Gaetano; Gratadour, Damien; Chemla, Fanny; Sevin, Arnaud; Cohen, Matthieu; Younger, Eddy; Vidal, Fabrice; Wilson, Richard; Batterley, Tim; Bitenc, Urban; Reeves, Andrew; Bharmal, Nazim; Raynaud, Henri-François; Kulcsar, Caroline; Conan, Jean-Marc; Guzman, Dani; De Cos Juez, Javier; Huet, Jean-Michel; Perret, Denis; Dickson, Colin; Atkinson, David; Baillie, Tom; Longmore, Andy; Todd, Stephen; Talbot, Gordon; Morris, Simon; Myers, Richard; Rousset, Gérard

    2013-12-01

    Open-loop adaptive optics has been successfully demonstrated on-sky by several groups, including the fully tomographic MOAO demonstration made using CANARY. MOAO instrumentation such as RAVEN will deliver the first astronomical science and other planned instruments aim to extend both open-loop AO performance and the number of corrected fields. Many of these planned systems rely on the use of tomographic open-loop LGS wavefront sensing. Here we present results from the combined NGS/LGS tomographic CANARY system and then compare the NGS- and LGS-based tomographic system performance. We identify the major system performance drivers, and highlight some potential routes for further exploitation of open-loop tomographic AO.

  16. 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

  17. 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.

  18. Next generation sequencing (NGS): a golden tool in forensic toolkit.

    PubMed

    Aly, S M; Sabri, D M

    2015-01-01

    The DNA analysis is a cornerstone in contemporary forensic sciences. DNA sequencing technologies are powerful tools that enrich molecular sciences in the past based on Sanger sequencing and continue to glowing these sciences based on Next generation sequencing (NGS). Next generation sequencing has excellent potential to flourish and increase the molecular applications in forensic sciences by jumping over the pitfalls of the conventional method of sequencing. The main advantages of NGS compared to conventional method that it utilizes simultaneously a large number of genetic markers with high-resolution of genetic data. These advantages will help in solving several challenges such as mixture analysis and dealing with minute degraded samples. Based on these new technologies, many markers could be examined to get important biological data such as age, geographical origins, tissue type determination, external visible traits and monozygotic twins identification. It also could get data related to microbes, insects, plants and soil which are of great medico-legal importance. Despite the dozens of forensic research involving NGS, there are requirements before using this technology routinely in forensic cases. Thus, there is a great need to more studies that address robustness of these techniques. Therefore, this work highlights the applications of forensic sciences in the era of massively parallel sequencing.

  19. 16(th) IHIW : review of HLA typing by NGS.

    PubMed

    De Santis, D; Dinauer, D; Duke, J; Erlich, H A; Holcomb, C L; Lind, C; Mackiewicz, K; Monos, D; Moudgil, A; Norman, P; Parham, P; Sasson, A; Allcock, R J N

    2013-02-01

    Human leucocyte antigen (HLA) genes play an important role in the success of organ transplantation and are associated with autoimmune and infectious diseases. Current DNA-based genotyping methods, including Sanger sequence-based typing (SSBT), have identified a high degree of polymorphism. This level of polymorphism makes high-resolution HLA genotyping challenging, resulting in ambiguous typing results due to an inability to resolve phase and/or defining polymorphisms lying outside the region amplified. Next-generation sequencing (NGS) may resolve the issue through the combination of clonal amplification, which provides phase information, and the ability to sequence larger regions of genes, including introns, without the additional effort or cost associated with current methods. The NGS HLA sequencing project of the 16IHIW aimed to discuss the different approaches to (i) template preparation including short- and long-range PCR amplicons, exome capture and whole genome; (ii) sequencing platforms, including GS 454 FLX, Ion Torrent PGM, Illumina MiSeq/HiSeq and Pacific Biosciences SMRT; (iii) data analysis, specifically allele-calling software. The pilot studies presented at the workshop demonstrated that although individual sequencers have very different performance characteristics, all produced sequence data suitable for the resolution of HLA genotyping ambiguities. The developments presented at this workshop clearly highlight the potential benefits of NGS in the HLA laboratory.

  20. 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" (David…

  1. ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines

    PubMed Central

    Wolfinger, Michael T.; Fallmann, Jörg; Eggenhofer, Florian; Amman, Fabian

    2015-01-01

    Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools. PMID:26236465

  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... information collection requirements for Consolidated Planning for Community Planning and Development (CPD) programs described below will be submitted to the Office of Management and Budget (OMB) for review,...

  3. 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

  4. 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.

  5. 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: Hispanic/Latino,…

  6. Strategic Plan to Ensure Racial and Ethnic Diversity in Connecticut Public Higher Education, 2010. Annual Report

    ERIC Educational Resources Information Center

    Connecticut Department of Higher Education (NJ1), 2010

    2010-01-01

    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: Hispanic/Latino, African…

  7. Strategic Plan to Ensure Racial and Ethnic Diversity in Connecticut Public Higher Education, 2009. Annual Report

    ERIC Educational Resources Information Center

    Connecticut Department of Higher Education (NJ1), 2009

    2009-01-01

    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: Hispanic/Latino, African…

  8. Strategic Plan to Ensure Racial and Ethnic Diversity in Connecticut Public Higher Education, 2008. Annual Report

    ERIC Educational Resources Information Center

    Connecticut Department of Higher Education (NJ1), 2008

    2008-01-01

    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: Hispanic/Latino,…

  9. Denver Public Schools, Division of Health Services. Forty-Sixth Annual Report, 1970-1971.

    ERIC Educational Resources Information Center

    Denver Public Schools, CO.

    This publication from the Division of Health Services in the Denver Public Schools details new projects initiated in 1970-71. Some of these projects include a) extension of dental care in kindergarten through seventh grade and among pupils in the Neighborhood Youth Corps, b) initiation of rubella immunization centers in the elementary schools, c)…

  10. A slow death or eternal life? Future directions for annual public health reports.

    PubMed

    Bruce, N; Price, C; Whincup, P

    1994-11-01

    Several years after their reintroduction, district public health reports continue to face questions about purpose, content and evaluation. As public health embraces the wider vision of the World Health Organisation's 'Health for All' strategy, and the consequent need for collaboration with other sectors and participation with communities, there is a need for the reports to respond accordingly. This theme is explored in relation to the needs of the report's diverse audience, the type of local research required to make the report relevant and effective, and approaches to evaluation. A growing local research function has resource and training implications for Departments of Public Health. The demands of producing a report every year suggest that biennial publication of the main report, with other targeted products over the intervening period, would be a more realistic and effective option. PMID:7997494

  11. 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

  12. 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

  13. Radiogenic age and isotopic studies, Report 3. Paper No. 89-02. Annual publication

    SciTech Connect

    Not Available

    1990-01-01

    Annual collection of reports presenting data from the Geochronology Section of the Continental Geoscience Division. Reports make full presentation of the data, relate these to field settings, and make comparatively short interpretations. The reports cover Rb-Sr and Sm-Nd procedures currently in use at the laboratory using high performance liquid chromatography methods; 40Ar/39Ar analyses, including that on the age of the New Quebec Crater; a summary of studies in N.B.; and studies in the northwest Canadian Shield, Baffin Island, Ontario, and Yukon Territory.

  14. 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.

  15. HCV genotyping from NGS short reads and its application in genotype detection from HCV mixed infected plasma.

    PubMed

    Qiu, Ping; Stevens, Richard; Wei, Bo; Lahser, Fred; Howe, Anita Y M; Klappenbach, Joel A; Marton, Matthew J

    2015-01-01

    Genotyping of hepatitis C virus (HCV) plays an important role in the treatment of HCV. As new genotype-specific treatment options become available, it has become increasingly important to have accurate HCV genotype and subtype information to ensure that the most appropriate treatment regimen is selected. Most current genotyping methods are unable to detect mixed genotypes from two or more HCV infections. Next generation sequencing (NGS) allows for rapid and low cost mass sequencing of viral genomes and provides an opportunity to probe the viral population from a single host. In this paper, the possibility of using short NGS reads for direct HCV genotyping without genome assembly was evaluated. We surveyed the publicly-available genetic content of three HCV drug target regions (NS3, NS5A, NS5B) in terms of whether these genes contained genotype-specific regions that could predict genotype. Six genotypes and 38 subtypes were included in this study. An automated phylogenetic analysis based HCV genotyping method was implemented and used to assess different HCV target gene regions. Candidate regions of 250-bp each were found for all three genes that have enough genetic information to predict HCV genotypes/subtypes. Validation using public datasets shows 100% genotyping accuracy. To test whether these 250-bp regions were sufficient to identify mixed genotypes, we developed a random primer-based method to sequence HCV plasma samples containing mixtures of two HCV genotypes in different ratios. We were able to determine the genotypes without ambiguity and to quantify the ratio of the abundances of the mixed genotypes in the samples. These data provide a proof-of-concept that this random primed, NGS-based short-read genotyping approach does not need prior information about the viral population and is capable of detecting mixed viral infection.

  16. Clinical validation of NGS technology for HLA: An early adopter's perspective.

    PubMed

    Weimer, Eric T

    2016-10-01

    Clinical validation of NGS for HLA typing has been a topic of interest with many laboratories investigating the merits. NGS has proven effective at reducing ambiguities and costs while providing more detailed information on HLA genes not previously sequenced. The ability of NGS to multiplex many patients within a single run presents unique challenges and sequencing new regions of HLA genes requires application of our knowledge of genetics to accurately determine HLA typing. This review represents my laboratory's experience in validation of NGS for HLA typing. It describes the obstacles faced with validation of NGS and is broken down into pre-analytic, analytic, and post-analytic challenges. Each section includes solutions to address them.

  17. Student Charges at Public, Four-Year Institutions. Annual Survey, Fall 1992.

    ERIC Educational Resources Information Center

    Strand, Heather; And Others

    This report examines student charges at public, four-year institutions throughout the United States based on the responses from a survey of 513 responding institutions. Statistical data are presented in the appendix comprising nearly the entire report. Major findings include the following items: (1) the overall fall 1992 resident undergraduate…

  18. 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…

  19. 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…

  20. Annual Financial Reporting Requirements for Texas Public Community Colleges, Fiscal Year 1996.

    ERIC Educational Resources Information Center

    Texas State Higher Education Coordinating Board, Austin. Div. of Research, Planning and Finance.

    This manual provides a comprehensive set of definitions, rules, formats, and illustrations for use by public community and junior colleges in Texas to ensure consistent and uniform financial reporting. Chapter 1 provides an introduction to the manual, highlighting changes in requirements for Fiscal Year (FY) 1996. Chapter 2 presents general…

  1. 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…

  2. 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…

  3. 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…

  4. Normal and compound poisson approximations for pattern occurrences in NGS reads.

    PubMed

    Zhai, Zhiyuan; Reinert, Gesine; Song, Kai; Waterman, Michael S; Luan, Yihui; Sun, Fengzhu

    2012-06-01

    Next generation sequencing (NGS) technologies are now widely used in many biological studies. In NGS, sequence reads are randomly sampled from the genome sequence of interest. Most computational approaches for NGS data first map the reads to the genome and then analyze the data based on the mapped reads. Since many organisms have unknown genome sequences and many reads cannot be uniquely mapped to the genomes even if the genome sequences are known, alternative analytical methods are needed for the study of NGS data. Here we suggest using word patterns to analyze NGS data. Word pattern counting (the study of the probabilistic distribution of the number of occurrences of word patterns in one or multiple long sequences) has played an important role in molecular sequence analysis. However, no studies are available on the distribution of the number of occurrences of word patterns in NGS reads. In this article, we build probabilistic models for the background sequence and the sampling process of the sequence reads from the genome. Based on the models, we provide normal and compound Poisson approximations for the number of occurrences of word patterns from the sequence reads, with bounds on the approximation error. The main challenge is to consider the randomness in generating the long background sequence, as well as in the sampling of the reads using NGS. We show the accuracy of these approximations under a variety of conditions for different patterns with various characteristics. Under realistic assumptions, the compound Poisson approximation seems to outperform the normal approximation in most situations. These approximate distributions can be used to evaluate the statistical significance of the occurrence of patterns from NGS data. The theory and the computational algorithm for calculating the approximate distributions are then used to analyze ChIP-Seq data using transcription factor GABP. Software is available online (www-rcf.usc.edu/∼fsun/Programs/NGS_motif_power/NGS

  5. 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.

  6. 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.

  7. VizieR Online Data Catalog: DUSTiNGS. I. The Good Source Catalog (Boyer+, 2015)

    NASA Astrophysics Data System (ADS)

    Boyer, M. L.; McQuinn, K. B. W.; Barmby, P.; Bonanos, A. Z.; Gehrz, R. D.; Gordon, K. D.; Groenewegen, M. A. T.; Lagadec, E.; Lennon, D.; Marengo, M.; Meixner, M.; Skillman, E.; Sloan, G. C.; Sonneborn, G.; van Loon, J. Th.; Zijlstra, A.

    2015-07-01

    The DUSTiNGS (DUST in Nearby Galaxies with Spitzer) survey includes uniform 3.6 and 4.5um Spitzer/IRAC imaging of 50 nearby galaxies (see table 1) between 2011 Jun 19 and 2012 Jun 23 (see table 2). The final Vega magnitudes of the high-quality point sources are reported in the DUSTiNGS "Good"-Source Catalog (GSC), which is described in Table 5 (see section 5). A full point source catalog is available at: http://irsa.ipac.caltech.edu/data/SPITZER/DUSTiNGS/ (3 data files).

  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. The NGS WikiBook: a dynamic collaborative online training effort with long-term sustainability.

    PubMed

    Li, Jing-Woei; Bolser, Dan; Manske, Magnus; Giorgi, Federico Manuel; Vyahhi, Nikolay; Usadel, Björn; Clavijo, Bernardo J; Chan, Ting-Fung; Wong, Nathalie; Zerbino, Daniel; Schneider, Maria Victoria

    2013-09-01

    Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

  10. 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.

  11. 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.

  12. 78 FR 48421 - Publication of North American Datum of 1983 (2011) Epoch 2010.00, North American Datum of 1983...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-08

    ..., 54 FR 25318, June 14, 1989). DATES: Individuals or organizations wishing to submit comments on the...) Epoch 2010.00 AGENCY: National Geodetic Survey (NGS), National Ocean Service (NOS), National Oceanic and... Geodetic Survey (NGS) has finalized the publication of new realizations of three geodetic references...

  13. 76 FR 55473 - Secretarial Review and Publication of the Annual Report to Congress Submitted by the Contracted...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-07

    ... annual report on September 10, 2009 (74 FR 46594). In March 2010, NQF submitted to Congress and the..., 2010. The second annual report was published in the Federal Register on October 22, 2010 (75 FR 65340... obstructive pulmonary disease (9) Acute myocardial infarction (10) Colorectal cancer (11) Hip/pelvic...

  14. Publications.

    ERIC Educational Resources Information Center

    Aviation/Space, 1980

    1980-01-01

    Presents a variety of publications available from government and nongovernment sources. The government publications are from the Federal Aviation Administration (FAA) and the National Aeronautics and Space Administration (NASA) and are designed for educators, students, and the public. (Author/SA)

  15. 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.

  16. Targeted NGS meets expert clinical characterization: Efficient diagnosis of spastic paraplegia type 11.

    PubMed

    Castro-Fernández, Cristina; Arias, Manuel; Blanco-Arias, Patricia; Santomé-Collazo, Luis; Amigo, Jorge; Carracedo, Ángel; Sobrido, Maria-Jesús

    2015-06-01

    Next generation sequencing (NGS) is transforming the diagnostic approach for neurological disorders, since it allows simultaneous analysis of hundreds of genes, even based on just a broad, syndromic patient categorization. However, such an approach bears a high risk of incidental and uncertain genetic findings. We report a patient with spastic paraplegia whose comprehensive neurological and imaging examination raised a high clinical suspicion of SPG11. Thus, although our NGS pipeline for this group of disorders includes gene panel and exome sequencing, in this sample only the spatacsin gene region was captured and subsequently searched for mutations. Two probably pathogenic variants were quickly and clearly identified, confirming the diagnosis of SPG11. This case illustrates how combination of expert clinical characterization with highly oriented NGS protocols leads to a fast, cost-efficient diagnosis, minimizing the risk of findings with unclear significance.

  17. 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…

  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. 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.

  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. 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…

  2. 78 FR 4377 - Annual List of Newspapers To Be Used by the Alaska Region for Publication of Legal Notices of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-22

    ...; ] DEPARTMENT OF AGRICULTURE Forest Service Annual List of Newspapers To Be Used by the Alaska Region for...: This notice lists the newspapers that Ranger Districts, Forests, and the Regional Office of the Alaska...: Robin Dale, Alaska Region Group Leader for Appeals, Litigation and FOIA; Forest Service, Alaska...

  3. 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)

  4. 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…

  5. Annual Fund. Estate Planning.

    ERIC Educational Resources Information Center

    Stuhr, Robert L.; Jarc, Jerry A.

    The first of a series, this publication consists of two symposium presentations. The first paper, "Annual Fund: Cornerstone of Development," by Robert L. Stuhr, defines the annual fund concept in the context of institutional development and provides five requisites for a successful annual fund: it must (1) be part of an ongoing development…

  6. RepARK--de novo creation of repeat libraries from whole-genome NGS reads.

    PubMed

    Koch, Philipp; Platzer, Matthias; Downie, Bryan R

    2014-05-01

    Generation of repeat libraries is a critical step for analysis of complex genomes. In the era of next-generation sequencing (NGS), such libraries are usually produced using a whole-genome shotgun (WGS) derived reference sequence whose completeness greatly influences the quality of derived repeat libraries. We describe here a de novo repeat assembly method--RepARK (Repetitive motif detection by Assembly of Repetitive K-mers)--which avoids potential biases by using abundant k-mers of NGS WGS reads without requiring a reference genome. For validation, repeat consensuses derived from simulated and real Drosophila melanogaster NGS WGS reads were compared to repeat libraries generated by four established methods. RepARK is orders of magnitude faster than the other methods and generates libraries that are: (i) composed almost entirely of repetitive motifs, (ii) more comprehensive and (iii) almost completely annotated by TEclass. Additionally, we show that the RepARK method is applicable to complex genomes like human and can even serve as a diagnostic tool to identify repetitive sequences contaminating NGS datasets.

  7. 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.

  8. 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.

  9. 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…

  10. 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…

  11. 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 by the…

  12. 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. PMID:26280812

  13. 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

  14. Annual Evaluation Report for 1969-70: ESEA Title I, Public Law 89-10, As Amended.

    ERIC Educational Resources Information Center

    Billings Public Schools, MT.

    This evaluation attempts to measure the extent and effectiveness of ESEA Title I programs designed to meet the needs of disadvantaged children and apprizes the public and the legislature of program outcomes. In keeping with USOE requirements for evaluating Title I programs, this document is constructed of (1) responses to USOE probes by…

  15. Excellence in Higher Education as Defined by Legislators and Public and Private Institutions Administrators. AIR 1991 Annual Forum Paper.

    ERIC Educational Resources Information Center

    Munoz, Grisel; And Others

    This report presents the results of a delphi study used to determine the criteria for defining excellence in higher education. An open questionnaire was administered to the commissions on education of the Puerto Rico Legislature, the administrators and governing boards of the major public and private postsecondary institutions in Puerto Rico, and…

  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. Implementation of Public Law 94-142: The Education for All Handicapped Children Act. Sixth Annual Report to Congress.

    ERIC Educational Resources Information Center

    Special Education Programs (ED/OSERS), Washington, DC. Div. of Educational Services.

    The report examines progress for the school years 1981-82 and 1982-83 in implementing P.L. 94-142, The Education for All Handicapped Children Act. Following an executive summary, an analysis of four major aspects of the law's implementation is detailed. A section on students receiving a free appropriate public education cites data on the number of…

  18. Implementation of Public Law 94-142: The Education for All Handicapped Children Act. Fifth Annual Report to Congress.

    ERIC Educational Resources Information Center

    Special Education Programs (ED/OSERS), Washington, DC. Div. of Educational Services.

    The report examines progress for school years 1980-81 and 1981-82 in implementing P.L. 94-142, The Education for All Handicapped Children Act. Following an executive summary, an analysis of three major aspects of the law's implementation is detailed. A section on progress toward a free appropriate public education cites data on the number of…

  19. State Financial Control Practices and Public Universities: Results of a National Study. Revised. ASHE 1984 Annual Meeting Paper.

    ERIC Educational Resources Information Center

    Volkwein, J. Fredericks

    Results of a national study of budgetary control imposed upon 88 Ph.D. granting public universities by 49 state governments (excluding Alaska) are presented. A comparative analysis is provided of financial control practices in each state, along with an index that places these practices along a continuum. Information is included on the nature and…

  20. 26 CFR 301.6104(d)-1 - Public inspection and distribution of applications for tax exemption and annual information...

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... day care, health care or scientific or medical research); and (B) The site does not serve as an office... days from the date it receives the request, notify the requester of its prepayment policy and the... 26 Internal Revenue 18 2014-04-01 2014-04-01 false Public inspection and distribution...

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

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... day care, health care or scientific or medical research); and (B) The site does not serve as an office... days from the date it receives the request, notify the requester of its prepayment policy and the... 26 Internal Revenue 18 2013-04-01 2013-04-01 false Public inspection and distribution...

  2. 26 CFR 301.6104(d)-1 - Public inspection and distribution of applications for tax exemption and annual information...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... day care, health care or scientific or medical research); and (B) The site does not serve as an office... days from the date it receives the request, notify the requester of its prepayment policy and the... 26 Internal Revenue 18 2012-04-01 2012-04-01 false Public inspection and distribution...

  3. Next generation sequencing (NGS) strategies for the genetic testing of myopathies.

    PubMed

    Nigro, Vincenzo; Piluso, Giulio

    2012-12-01

    Next generation sequencing (NGS) technologies offer the possibility to map entire genomes at affordable costs. This brings the genetic testing procedure to a higher level of complexity. The positive aspect is the ease to cope with the complex diagnosis of genetically heterogeneous disorders and to identify novel disease genes. Worries arise from the management of too many DNA variations with unpredictable meaning and incidental findings that can cause ethical and clinical dilemmas. The technology of enrichment makes possible to focus the sequencing to the exome or to a more specific DNA target. This is being used to provide insights into the genetics underlying Mendelian traits involved in myopathies and to set up cost-effective diagnostic tests. This huge potential of the NGS applications makes likely that these will soon become the first approach in genetic diagnostic laboratories.

  4. 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

  5. Parallel WGA and WTA for Comparative Genome and Transcriptome NGS Analysis Using Tiny Cell Numbers.

    PubMed

    Korfhage, Christian; Fricke, Evelyn; Meier, Andreas

    2015-07-01

    Genomic DNA determines how and when the transcriptome is changed by a trigger or environmental change and how cellular metabolism is influenced. Comparative genome and transcriptome analysis of the same cell sample links a defined genome with all changes in the bases, structure, or numbers of the transcriptome. However, comparative genome and transcriptome analysis using next-generation sequencing (NGS) or real-time PCR is often limited by the small amount of sample available. In mammals, the amount of DNA and RNA in a single cell is ∼10 picograms, but deep analysis of the genome and transcriptome currently requires several hundred nanograms of nucleic acids for library preparation for NGS sequencing. Consequently, accurate whole-genome amplification (WGA) and whole-transcriptome amplification (WTA) is required for such quantitative analysis. This unit describes how the genome and the transcriptome of a tiny number of cells can be amplified in a highly parallel and comparable process. Protocols for quality control of amplified DNA and application of amplified DNA for NGS are included.

  6. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species.

    PubMed

    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.

  7. Functional genomics of tomato: opportunities and challenges in post-genome NGS era.

    PubMed

    Kumar, Rahul; Khurana, Ashima

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies.

  8. 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.

  9. HLA-genotyping of clinical specimens using Ion Torrent-based NGS.

    PubMed

    Barone, Jonathan C; Saito, Katsuyuki; Beutner, Karl; Campo, Maria; Dong, Wei; Goswami, Chirayu P; Johnson, Erica S; Wang, Zi-Xuan; Hsu, Susan

    2015-12-01

    We have evaluated and validated the NXType™ workflow (One Lambda, Inc.) and the accompanying TypeStream™ software on the Ion Torrent Next Generation Sequencing (NGS) platform using a comprehensive testing panel. The panel consisted of 285 genomic DNA (gDNA) samples derived from four major ethnic populations and contained 59 PT samples and 226 clinical specimens. The total number of alleles from the six loci interrogated by NGS was 3420. This validation panel provided a wide range of HLA sequence variations including many rare alleles, new variants and homozygous alleles. The NXType™ system (reagents and software) was able to correctly genotype the vast majority of these specimens. The concordance rate between SBT-derived genotypes and those generated by TypeStream™ auto-analysis ranged from 99.5% to 99.8% for the HLA-A, B, C, DRB1 and DQB1 loci, and was 98.9% for HLA-DPB1. A strategy for data review was developed that would allow correction of most of the few remaining typing errors. The entire NGS workflow from gDNA amplification to genotype assignment could be completed within 3 working days. Through this validation study, the limitations and shortcomings of the platform, specific assay system, and software algorithm were also revealed for further evaluation and improvement.

  10. Functional genomics of tomato: opportunities and challenges in post-genome NGS era.

    PubMed

    Kumar, Rahul; Khurana, Ashima

    2014-12-01

    The Tomato Genome Sequencing Project represented a landmark venture in the history of sequencing projects where both Sanger's and next-generation sequencing (NGS) technologies were employed, and a highly accurate and one of the best assembled plant genomes along with a draft of the wild relative, Solanum pimpinellifolium, were released in 2012. However, the functional potential of the major portion of this newly generated resource is still undefined. The very first challenge before scientists working on tomato functional biology is to exploit this high-quality reference sequence for tapping of the wealth of genetic variants for improving agronomic traits in cultivated tomatoes. The sequence data generated recently by 150 Tomato Genome Consortium would further uncover the natural alleles present in different tomato genotypes. Therefore, we found it relevant to have a fresh outlook on tomato functional genomics in the context of application of NGS technologies in its post-genome sequencing phase. Herein, we provide an overview how NGS technologies vis-a-vis available reference sequence have assisted each other for their mutual improvement and how their combined use could further facilitate the development of other 'omics' tools, required to propel the Solanaceae research. Additionally, we highlight the challenges associated with the application of these cutting-edge technologies. PMID:25431420

  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. Development of Bioinformatics Pipeline for Analyzing Clinical Pediatric NGS Data

    PubMed Central

    Crowgey, Erin L.; Kolb, Anders; Wu, Cathy H.

    2015-01-01

    Using an Illumina exome sequencing dataset generated from pediatric Acute Myeloid Leukemia patients (AML; type FLT3/ITD+) a comprehensive bioinformatics pipeline was developed to aid in a better clinical understanding of the genetic data associated with the clinical phenotype. The pipeline starts with raw next generation sequencing reads and using both publicly available resources and custom scripts, analyzes the genomic data for variants associated with pediatric AML. By incorporating functional information such as Gene Ontology annotation and protein-protein interactions, the methodology prioritizes genomic variants and returns disease specific results and knowledge maps. Furthermore, it compares the somatic mutations at diagnosis with the somatic mutations at relapse and outputs variants and functional annotations that are specific for the relapse state. PMID:26306272

  13. 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 thee-year…

  14. 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…

  15. 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…

  16. 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

    2015-01-01

    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. PMID:25641679

  17. 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.

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

    PubMed

    Golosova, Olga; Henderson, Ross; Vaskin, Yuriy; Gabrielian, Andrei; Grekhov, German; Nagarajan, Vijayaraj; 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.

  19. 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

  20. 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.

  1. New genes and pathomechanisms in mitochondrial disorders unraveled by NGS technologies.

    PubMed

    Legati, Andrea; Reyes, Aurelio; Nasca, Alessia; Invernizzi, Federica; Lamantea, Eleonora; Tiranti, Valeria; Garavaglia, Barbara; Lamperti, Costanza; Ardissone, Anna; Moroni, Isabella; Robinson, Alan; Ghezzi, Daniele; Zeviani, Massimo

    2016-08-01

    Next Generation Sequencing (NGS) technologies are revolutionizing the diagnostic screening for rare disease entities, including primary mitochondrial disorders, particularly those caused by nuclear gene defects. NGS approaches are able to identify the causative gene defects in small families and even single individuals, unsuitable for investigation by traditional linkage analysis. These technologies are contributing to fill the gap between mitochondrial disease cases defined on the basis of clinical, neuroimaging and biochemical readouts, which still outnumber by approximately 50% the cases for which a molecular-genetic diagnosis is attained. We have been using a combined, two-step strategy, based on targeted genes panel as a first NGS screening, followed by whole exome sequencing (WES) in still unsolved cases, to analyze a large cohort of subjects, that failed to show mutations in mtDNA and in ad hoc sets of specific nuclear genes, sequenced by the Sanger's method. Not only this approach has allowed us to reach molecular diagnosis in a significant fraction (20%) of these difficult cases, but it has also revealed unexpected and conceptually new findings. These include the possibility of marked variable penetrance of recessive mutations, the identification of large-scale DNA rearrangements, which explain spuriously heterozygous cases, and the association of mutations in known genes with unusual, previously unreported clinical phenotypes. Importantly, WES on selected cases has unraveled the presence of pathogenic mutations in genes encoding non-mitochondrial proteins (e.g. the transcription factor E4F1), an observation that further expands the intricate genetics of mitochondrial disease and suggests a new area of investigation in mitochondrial medicine. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.

  2. Critical review of NGS analyses for de novo genotyping multigene families.

    PubMed

    Lighten, Jackie; van Oosterhout, Cock; Bentzen, Paul

    2014-08-01

    The genotyping of highly polymorphic multigene families across many individuals used to be a particularly challenging task because of methodological limitations associated with traditional approaches. Next-generation sequencing (NGS) can overcome most of these limitations, and it is increasingly being applied in population genetic studies of multigene families. Here, we critically review NGS bioinformatic approaches that have been used to genotype the major histocompatibility complex (MHC) immune genes, and we discuss how the significant advances made in this field are applicable to population genetic studies of gene families. Increasingly, approaches are introduced that apply thresholds of sequencing depth and sequence similarity to separate alleles from methodological artefacts. We explain why these approaches are particularly sensitive to methodological biases by violating fundamental genotyping assumptions. An alternative strategy that utilizes ultra-deep sequencing (hundreds to thousands of sequences per amplicon) to reconstruct genotypes and applies statistical methods on the sequencing depth to separate alleles from artefacts appears to be more robust. Importantly, the 'degree of change' (DOC) method avoids using arbitrary cut-off thresholds by looking for statistical boundaries between the sequencing depth for alleles and artefacts, and hence, it is entirely repeatable across studies. Although the advances made in generating NGS data are still far ahead of our ability to perform reliable processing, analysis and interpretation, the community is developing statistically rigorous protocols that will allow us to address novel questions in evolution, ecology and genetics of multigene families. Future developments in third-generation single molecule sequencing may potentially help overcome problems that still persist in de novo multigene amplicon genotyping when using current second-generation sequencing approaches.

  3. 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.

  4. 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.

  5. 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

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

    PubMed

    Someswara Rao, Chinta; Raju, S Viswanadha

    2016-03-01

    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.

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

    PubMed

    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-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

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

    PubMed

    Someswara Rao, Chinta; Raju, S Viswanadha

    2016-03-01

    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

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

    DOE PAGESBeta

    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 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

  10. 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

  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. PMID:26441948

  12. 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

  13. Fast and Cost-Effective Mining of Microsatellite Markers Using NGS Technology: An Example of a Korean Water Deer Hydropotes inermis argyropus

    PubMed Central

    Yu, Jeong-Nam; Won, Changman; Jun, Jumin; Lim, YoungWoon; Kwak, Myounghai

    2011-01-01

    Background Microsatellites, a special class of repetitive DNA sequence, have become one of the most popular genetic markers for population/conservation genetic studies. However, its application to endangered species has been impeded by high development costs, a lack of available sequences, and technical difficulties. The water deer Hydropotes inermis is the sole existing endangered species of the subfamily Capreolinae. Although population genetics studies are urgently required for conservation management, no species-specific microsatellite marker has been reported. Methods We adopted next-generation sequencing (NGS) to elucidate the microsatellite markers of Korean water deer and overcome these impediments on marker developments. We performed genotyping to determine the efficiency of this method as applied to population genetics. Results We obtained 98 Mbp of nucleotide information from 260,467 sequence reads. A total of 20,101 di-/tri-nucleotide repeat motifs were identified; di-repeats were 5.9-fold more common than tri-repeats. [CA]n and [AAC]n/[AAT]n repeats were the most frequent di- and tri-repeats, respectively. Of the 17,206 di-repeats, 12,471 microsatellite primer pairs were derived. PCR amplification of 400 primer pairs yielded 106 amplicons and 79 polymorphic markers from 20 individual Korean water deer. Polymorphic rates of the 79 new microsatellites varied from 2 to 11 alleles per locus (He: 0.050–0.880; Ho: 0.000–1.000), while those of known microsatellite markers transferred from cattle to Chinese water deer ranged from 4 to 6 alleles per locus (He: 0.279–0.714; Ho: 0.300–0.400). Conclusions Polymorphic microsatellite markers from Korean water deer were successfully identified using NGS without any prior sequence information and deposited into the public database. Thus, the methods described herein represent a rapid and low-cost way to investigate the population genetics of endangered/non-model species. PMID:22069476

  14. 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

  15. 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. PMID:27192129

  16. 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.

  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. PMID:27200084

  18. NGS-Based Assay for the Identification of Individuals Carrying Recessive Genetic Mutations in Reproductive Medicine.

    PubMed

    Abulí, Anna; Boada, Montserrat; Rodríguez-Santiago, Benjamín; Coroleu, Buenaventura; Veiga, Anna; Armengol, Lluís; Barri, Pedro N; Pérez-Jurado, Luis A; Estivill, Xavier

    2016-06-01

    Next-generation sequencing (NGS) has the capacity of carrier screening in gamete donation (GD) programs. We have developed and validated an NGS carrier-screening test (qCarrier test) that includes 200 genes associated with 368 disorders (277 autosomal recessive and 37 X-linked). Carrier screening is performed on oocyte donation candidates and the male partner of oocyte recipient. Carriers of X-linked conditions are excluded from the GD program, whereas donors are chosen who do not carry mutations for the same gene/disease as the recipients. The validation phase showed a high sensitivity (>99% sensitivity) detecting all single-nucleotide variants, 13 indels, and 25 copy-number variants included in the validation set. A total of 1,301 individuals were analysed with the qCarrier test, including 483 candidate oocyte donors and 635 receptor couples, 105 females receiving sperm donation, and 39 couples seeking pregnancy. We identified 56% of individuals who are carriers for at least one genetic condition and 1.7% of female donors who were excluded from the program due to a carrier state of X-linked conditions. Globally, 3% of a priori assigned donations had a high reproductive risk that could be minimized after testing. Genetic counselling at different stages is essential for helping to facilitate a successful and healthy pregnancy.

  19. Panel-based NGS Reveals Novel Pathogenic Mutations in Autosomal Recessive Retinitis Pigmentosa.

    PubMed

    Perez-Carro, Raquel; Corton, Marta; Sánchez-Navarro, Iker; Zurita, Olga; Sanchez-Bolivar, Noelia; Sánchez-Alcudia, Rocío; Lelieveld, Stefan H; Aller, Elena; Lopez-Martinez, Miguel Angel; López-Molina, Ma Isabel; Fernandez-San Jose, Patricia; Blanco-Kelly, Fiona; Riveiro-Alvarez, Rosa; Gilissen, Christian; Millan, Jose M; Avila-Fernandez, Almudena; Ayuso, Carmen

    2016-01-25

    Retinitis pigmentosa (RP) is a group of inherited progressive retinal dystrophies (RD) characterized by photoreceptor degeneration. RP is highly heterogeneous both clinically and genetically, which complicates the identification of causative genes and mutations. Targeted next-generation sequencing (NGS) has been demonstrated to be an effective strategy for the detection of mutations in RP. In our study, an in-house gene panel comprising 75 known RP genes was used to analyze a cohort of 47 unrelated Spanish families pre-classified as autosomal recessive or isolated RP. Disease-causing mutations were found in 27 out of 47 cases achieving a mutation detection rate of 57.4%. In total, 33 pathogenic mutations were identified, 20 of which were novel mutations (60.6%). Furthermore, not only single nucleotide variations but also copy-number variations, including three large deletions in the USH2A and EYS genes, were identified. Finally seven out of 27 families, displaying mutations in the ABCA4, RP1, RP2 and USH2A genes, could be genetically or clinically reclassified. These results demonstrate the potential of our panel-based NGS strategy in RP diagnosis.

  20. 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.

  1. 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(®).

  2. 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

  3. 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.

  4. NGS-Based Assay for the Identification of Individuals Carrying Recessive Genetic Mutations in Reproductive Medicine.

    PubMed

    Abulí, Anna; Boada, Montserrat; Rodríguez-Santiago, Benjamín; Coroleu, Buenaventura; Veiga, Anna; Armengol, Lluís; Barri, Pedro N; Pérez-Jurado, Luis A; Estivill, Xavier

    2016-06-01

    Next-generation sequencing (NGS) has the capacity of carrier screening in gamete donation (GD) programs. We have developed and validated an NGS carrier-screening test (qCarrier test) that includes 200 genes associated with 368 disorders (277 autosomal recessive and 37 X-linked). Carrier screening is performed on oocyte donation candidates and the male partner of oocyte recipient. Carriers of X-linked conditions are excluded from the GD program, whereas donors are chosen who do not carry mutations for the same gene/disease as the recipients. The validation phase showed a high sensitivity (>99% sensitivity) detecting all single-nucleotide variants, 13 indels, and 25 copy-number variants included in the validation set. A total of 1,301 individuals were analysed with the qCarrier test, including 483 candidate oocyte donors and 635 receptor couples, 105 females receiving sperm donation, and 39 couples seeking pregnancy. We identified 56% of individuals who are carriers for at least one genetic condition and 1.7% of female donors who were excluded from the program due to a carrier state of X-linked conditions. Globally, 3% of a priori assigned donations had a high reproductive risk that could be minimized after testing. Genetic counselling at different stages is essential for helping to facilitate a successful and healthy pregnancy. PMID:26990548

  5. 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

  6. Characterization of oxides on Bruce A NGS liner tubes and steam generator tubes

    SciTech Connect

    Miller, D.G.; Burrill, K.A.

    1998-12-31

    Oxide deposits on end-fitting liner tubes and steam generator tubes from the Bruce A Nuclear Generating Station (NGS) were characterized in advance of the decontamination of the heat transport system (HTS) of Bruce Unit 2. Oxide loadings, and Co-60 surface activities and specific activities were determined for the oxides on inlet and outlet end-fitting liner tubes from Bruce Unit l, Bruce Unit 2 and Bruce Unit 4. Oxides on the inner surfaces of steam generator tubes from Bruce NGS Units 1 and 2 were also characterized. The consistency in the deposit characteristics on the inlet liner tubes and steam generator tubes from Bruce A, along with the absence of magnetite on the outlet liner tubes has led to the development of a model for iron transport in the HTS of pressurized heavy water reactors (PHWRs). The activity transport/fouling mechanism involves flow-accelerated corrosion of the outlet feeder pipes, followed by deposition of iron in the steam generators, along the inlet feeder pipes, on the inlet end fittings, on the inlet fuel bundles and on the inlet region of the pressure tube. The results of loop experiments using decontamination solutions indicated that the oxide was rapidly removed from inlet liner tubes. However, removal of the Cr-rich oxide from the outlet liner tubes was less efficient, requiring the Alkaline Permangante (AP) oxidizing pre-treatment that is typically used in light water reactors (LWRs). The steam generator tubes were effectively decontaminated.

  7. 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

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

    PubMed Central

    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. PMID:26840129

  9. ngs (notochord granular surface) gene encodes a novel type of intermediate filament family protein essential for notochord maintenance in zebrafish.

    PubMed

    Tong, Xiangjun; Xia, Zhidan; Zu, Yao; Telfer, Helena; Hu, Jing; Yu, Jingyi; Liu, Huan; Zhang, Quan; Sodmergen; Lin, Shuo; Zhang, Bo

    2013-01-25

    The notochord is an important organ involved in embryonic patterning and locomotion. In zebrafish, the mature notochord consists of a single stack of fully differentiated, large vacuolated cells called chordocytes, surrounded by a single layer of less differentiated notochordal epithelial cells called chordoblasts. Through genetic analysis of zebrafish lines carrying pseudo-typed retroviral insertions, a mutant exhibiting a defective notochord with a granular appearance was isolated, and the corresponding gene was identified as ngs (notochord granular surface), which was specifically expressed in the notochord. In the mutants, the notochord started to degenerate from 32 hours post-fertilization, and the chordocytes were then gradually replaced by smaller cells derived from chordoblasts. The granular notochord phenotype was alleviated by anesthetizing the mutant embryos with tricaine to prevent muscle contraction and locomotion. Phylogenetic analysis showed that ngs encodes a new type of intermediate filament (IF) family protein, which we named chordostatin based on its function. Under the transmission electron microcopy, bundles of 10-nm-thick IF-like filaments were enriched in the chordocytes of wild-type zebrafish embryos, whereas the chordocytes in ngs mutants lacked IF-like structures. Furthermore, chordostatin-enhanced GFP (EGFP) fusion protein assembled into a filamentous network specifically in chordocytes. Taken together, our work demonstrates that ngs encodes a novel type of IF protein and functions to maintain notochord integrity for larval development and locomotion. Our work sheds light on the mechanisms of notochord structural maintenance, as well as the evolution and biological function of IF family proteins.

  10. 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.

  11. 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... ENDOWMENT FOR THE HUMANITIES PART-TIME CAREER EMPLOYMENT § 1176.5 Annual plan. (a) An agencywide plan for promoting part-time employment opportunities will be developed annually. This plan will establish...

  12. 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,...

  13. 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... 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,...

  14. 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,...

  15. 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,...

  16. 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... 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,...

  17. 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 901.5 Parks, Forests, and Public Property PENNSYLVANIA AVENUE DEVELOPMENT CORPORATION BYLAWS OF THE CORPORATION § 901.5 Annual report. The Executive Director shall prepare annually a comprehensive and...

  18. 36 CFR 901.5 - Annual report.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 3 2011-07-01 2011-07-01 false Annual report. 901.5 Section 901.5 Parks, Forests, and Public Property PENNSYLVANIA AVENUE DEVELOPMENT CORPORATION BYLAWS OF THE CORPORATION § 901.5 Annual report. The Executive Director shall prepare annually a comprehensive and...

  19. 42 CFR 419.50 - Annual review.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 3 2012-10-01 2012-10-01 false Annual review. 419.50 Section 419.50 Public Health....50 Annual review. (a) General rule. Not less often than annually, CMS reviews and updates groups... composed of an appropriate selection of representatives of providers to review (and advise CMS...

  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... Designation of Banned Substances; Reclassification of Pollutants § 671.14 Annual review. The Director shall review the list of banned substances and designated pollutants at least annually, and may propose...

  1. 45 CFR 671.14 - Annual review.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 3 2011-10-01 2011-10-01 false Annual review. 671.14 Section 671.14 Public... Designation of Banned Substances; Reclassification of Pollutants § 671.14 Annual review. The Director shall review the list of banned substances and designated pollutants at least annually, and may propose...

  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. PMID:26599467

  3. 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.

  4. 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.

  5. 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

  6. HapTree: a novel Bayesian framework for single individual polyplotyping using NGS data.

    PubMed

    Berger, Emily; Yorukoglu, Deniz; Peng, Jian; Berger, Bonnie

    2014-03-01

    As the more recent next-generation sequencing (NGS) technologies provide longer read sequences, the use of sequencing datasets for complete haplotype phasing is fast becoming a reality, allowing haplotype reconstruction of a single sequenced genome. Nearly all previous haplotype reconstruction studies have focused on diploid genomes and are rarely scalable to genomes with higher ploidy. Yet computational investigations into polyploid genomes carry great importance, impacting plant, yeast and fish genomics, as well as the studies of the evolution of modern-day eukaryotes and (epi)genetic interactions between copies of genes. In this paper, we describe a novel maximum-likelihood estimation framework, HapTree, for polyploid haplotype assembly of an individual genome using NGS read datasets. We evaluate the performance of HapTree on simulated polyploid sequencing read data modeled after Illumina sequencing technologies. For triploid and higher ploidy genomes, we demonstrate that HapTree substantially improves haplotype assembly accuracy and efficiency over the state-of-the-art; moreover, HapTree is the first scalable polyplotyping method for higher ploidy. As a proof of concept, we also test our method on real sequencing data from NA12878 (1000 Genomes Project) and evaluate the quality of assembled haplotypes with respect to trio-based diplotype annotation as the ground truth. The results indicate that HapTree significantly improves the switch accuracy within phased haplotype blocks as compared to existing haplotype assembly methods, while producing comparable minimum error correction (MEC) values. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2-5.

  7. 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.

  8. 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. PMID:26427785

  9. 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

    2016-07-01

    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.

  10. Administration of Public Laws 81-874 & 81-815. Twenty-Sixth Annual Report of the Commissioner of Education, June 30, 1976. (Appendix A of the Annual Report of the U.S. Commissioner of Education, Fiscal Year 1976.)

    ERIC Educational Resources Information Center

    Office of Education (DHEW), Washington, DC.

    This is the 26th report concerning administration of Public Law 81-874 and Public Law 81-815, as amended, including a detailed statement of receipts and disbursements, for the fiscal year ending June 30, l976. The laws are concerned with aid to federally impacted areas, specifically for maintenance and operation, construction, and disaster relief.…

  11. 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 §§...

  12. 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 §§...

  13. 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 §§...

  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 §§...

  15. 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 §§...

  16. 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...

  17. 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...

  18. 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 RESOURCES § 1620.5 Annual review. (a) Priorities shall be set periodically and shall be reviewed by...

  19. 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...

  20. 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...

  1. 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...

  2. 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...

  3. 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...

  4. 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" (Terence (Terry)…

  5. 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 Effect of World View on…

  6. 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 Learning" (Jennifer…

  7. 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 Relations" (Patricia T.…

  8. 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.

  9. 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.

  10. e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.

    PubMed

    Bruno, Fosso; Marinella, Marzano; Santamaria, Monica

    2015-01-01

    In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to investigate both organisms and genes diversity. Anyway, if the purpose is limited to explore the taxonomic complexity, an amplicon-based approach, based on PCR-targeted sequencing of selected genetic species markers, commonly named "meta-barcodes", is desirable. Among the genomic regions most widely used for the discrimination of bacterial organisms, in some cases up to the species level, some hypervariable domains of the gene coding for the 16S rRNA occupy a prominent place. The amplification of a certain meta-barcode from a microbial community through the use of PCR primers able to work in the entire considered taxonomic group is the first task after the extraction of the total DNA. Generally, this step is followed by the high-throughput sequencing of the resulting amplicons libraries by means of a selected NGS platform. Finally, the interpretation of the huge amount of produced data requires appropriate bioinformatics tools and know-how in addition to efficient computational resources. Here a computational methodology suitable for the taxonomic characterization of 454 meta-barcode sequences is described in detail. In particular, a dataset covering the V1-V3 region belonging to the bacterial 16S rRNA coding gene and produced in the Human Microbiome Project (HMP) from a palatine tonsils sample is analyzed. The proposed exercise includes the

  11. e-DNA meta-barcoding: from NGS raw data to taxonomic profiling.

    PubMed

    Bruno, Fosso; Marinella, Marzano; Santamaria, Monica

    2015-01-01

    In recent years, thanks to the essential support provided by the Next-Generation Sequencing (NGS) technologies, Metagenomics is enabling the direct access to the taxonomic and functional composition of mixed microbial communities living in any environmental niche, without the prerequisite to isolate or culture the single organisms. This approach has already been successfully applied for the analysis of many habitats, such as water or soil natural environments, also characterized by extreme physical and chemical conditions, food supply chains, and animal organisms, including humans. A shotgun sequencing approach can lead to investigate both organisms and genes diversity. Anyway, if the purpose is limited to explore the taxonomic complexity, an amplicon-based approach, based on PCR-targeted sequencing of selected genetic species markers, commonly named "meta-barcodes", is desirable. Among the genomic regions most widely used for the discrimination of bacterial organisms, in some cases up to the species level, some hypervariable domains of the gene coding for the 16S rRNA occupy a prominent place. The amplification of a certain meta-barcode from a microbial community through the use of PCR primers able to work in the entire considered taxonomic group is the first task after the extraction of the total DNA. Generally, this step is followed by the high-throughput sequencing of the resulting amplicons libraries by means of a selected NGS platform. Finally, the interpretation of the huge amount of produced data requires appropriate bioinformatics tools and know-how in addition to efficient computational resources. Here a computational methodology suitable for the taxonomic characterization of 454 meta-barcode sequences is described in detail. In particular, a dataset covering the V1-V3 region belonging to the bacterial 16S rRNA coding gene and produced in the Human Microbiome Project (HMP) from a palatine tonsils sample is analyzed. The proposed exercise includes the

  12. 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.

  13. 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.

  14. The Community Care Program Makes a Difference. Annual Report to the Governor and the Illinois General Assembly on Public Act 81-202, Fiscal Year 1986.

    ERIC Educational Resources Information Center

    Illinois State Dept. on Aging, Springfield.

    This document contains an annual report on Illinois' Community Care Program (CCP), a program which provides in-home and other support services to help older persons to remain living at home and avoid premature institutionalization. Three levels of care provided by the CCP are described: (1) chore housekeeping, consisting of basic household tasks…

  15. 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.

  16. An NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry.

    PubMed

    Xiong, Yun; Guo, Yufeng; Xiao, Weidi; Cao, Qichen; Li, Shanshan; Qi, Xianni; Zhang, Zhidan; Wang, Qinhong; Shui, Wenqing

    2016-03-01

    Detection of proteins containing single amino acid polymorphisms (SAPs) encoded by nonsynonymous SNPs (nsSNPs) can aid researchers in studying the functional significance of protein variants. Most proteogenomic approaches for large-scale SAPs mapping require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. Searching shotgun proteomic data sets against these NGS-derived databases allowed for identification of SAP peptides, thus validating the proteome-level sequence variation. Contrary to the conventional approaches, our study presents a novel strategy for proteome-wide SAP detection without relying on sample-specific NGS data. By searching a deep-coverage proteomic data set from an industrial thermotolerant yeast strain using our strategy, we identified 337 putative SAPs compared to the reference genome. Among the SAP peptides identified with stringent criteria, 85.2% of SAP sites were validated using whole-genome sequencing data obtained for this organism, which indicates high accuracy of SAP identification with our strategy. More interestingly, for certain SAP peptides that cannot be predicted by genomic sequencing, we used synthetic peptide standards to verify expression of peptide variants in the proteome. Our study has provided a unique tool for proteogenomics to enable proteome-wide direct SAP identification and capture nongenetic protein variants not linked to nsSNPs.

  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. |SE|S|AM|E| Barcode: NGS-oriented software for amplicon characterization--application to species and environmental barcoding.

    PubMed

    Piry, S; Guivier, E; Realini, A; Martin, J-F

    2012-11-01

    Progress in NGS technologies has opened up new opportunities for characterizing biodiversity, both for individual specimen identification and for environmental barcoding. Although the amount of data available to biologist is increasing, user-friendly tools to facilitate data analysis have yet to be developed. Our aim, with |SE|S|AM|E| Barcode, is to provide such support through a unified platform. The sequences are analysed through a pipeline that (i) processes NGS amplicon runs, filtering markers and samples, (ii) builds reference libraries and finally (iii) identifies (barcodes) the sequences in each amplicon from the reference library. We use a simulated data set for specimen identification and a recently published data set for environmental barcoding to validate the method. The results obtained are consistent with the expected characterizations (in silico and previously published, respectively). |SE|S|AM|E| Barcode and its documentation are freely available under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported Licence for Windows and Linux from http://www1.montpellier.inra.fr/CBGP/NGS/.

  19. 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.

  20. 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

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

    PubMed

    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.

  2. 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 events, by…

  3. 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.

  4. 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 and Top…

  5. 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.

  6. 22 CFR 62.15 - Annual reports.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 22 Foreign Relations 1 2012-04-01 2012-04-01 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....

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 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.

  13. 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. PMID:26658062

  14. 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.

  15. 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

  16. 42 CFR 419.50 - Annual review.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Annual review. 419.50 Section 419.50 Public Health... review. (a) General rule. Not less often than annually, CMS reviews and updates groups, relative payment... selection of representatives of providers to review (and advise CMS concerning) the clinical integrity...

  17. 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…

  18. 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 for University…

  19. The Map, the Mission and the Mandate: Personnel Preparation and Public Law 94-142. Second Annual Regional Conferences. A Report.

    ERIC Educational Resources Information Center

    Smith, Judy, Ed.

    Presented are nine papers on the issues and directions presented at meetings on the implementation of Public Law 94-142 (Education for All Handicapped Children Act) through the preparation of professionals in special education. Entries include the following titles and authors: "Regional Collaboration" by J. Harvey; "The Education for All…

  20. Third Annual Desegregation Status Report for Public Postsecondary Education Institutions in the State of Maryland. Volume IV: Employees and Board Members.

    ERIC Educational Resources Information Center

    Maryland State Board for Higher Education, Annapolis.

    The data in this volume were collected in accordance with the 1974 Maryland plan for the desegregation of public post secondary education institutions. Presented are employee related data for Maryland colleges, universities and state agencies, and data on members of boards associated with higher education. The statistics for institutions include…

  1. 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....”

  2. 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.

  3. 1987 annual report on low-level radioactive waste management progress: Report to Congress in response to Public Law 99-240

    SciTech Connect

    Not Available

    1988-08-01

    In response to Section 7(b) of the Low-Level Radioactive Waste Policy Amendments Act of 1985 (Public Law 99-240), this report summarizes the progress of states and low-level radioactive waste compacts in 1987 in establishing new low-level waste disposal facilities. It also reports the volume of low-level waste received for disposal in 1987 by commercially operated low-level waste disposal facilities.

  4. 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.

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

    PubMed Central

    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. PMID:26460497

  6. 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.

  7. 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 contains…

  8. Administration of the Radiation Control for Health and Safety Act of 1968, Public Law 90-602, (1987 annual report). Report for January-December 1987

    SciTech Connect

    Not Available

    1988-04-01

    This document is an annual report submitted to the President for transmittal to the Congress. The Food and Drug Administration, through its Center for Devices and Radiological Health, is responsible for the day-to-day administration of the Radiation Control for Health and Safety Act of 1968. The report provides a summary of the operations of the Center in carrying out that responsibility for calendar year 1987. In reviewing the operations of the CDRH as reported in the document, it should be kept in mind that the day-to-day administration of the Act is only part of the Center's function. Other responsibilities include the administration and enforcement of the 1976 Medical Device Amendments to the Federal Food, Drug, and Cosmetic Act (not covered in the report). Manufacturers of electronic products are required by 21 CFR 1002.20 to report accidental radiation occurrences to the CDRH. The Center no longer maintains a Radiation Incidents Registry, since accidental radiation occurrences are reported through the Device Experience Network (DEN) and through the requirements of the Medical Device Reporting (MDR) regulations.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Live Genomics for Pathogen Monitoring in Public Health

    PubMed Central

    D’Auria, Giuseppe; Schneider, Maria Victoria; Moya, Andrés

    2014-01-01

    Whole genome analysis based on next generation sequencing (NGS) now represents an affordable framework in public health systems. Robust analytical pipelines of genomic data provides in a short lapse of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. Pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, virulence, persistence factors, mobile elements and adaptation features. Such information can be obtained not only at large spectra, but also at the “local” level, such as in the event of a recurrent or emergency outbreak. This paper reviews the state of the art in infection diagnostics in the context of modern NGS methodologies. We describe how actuation protocols in a public health environment will benefit from a “streaming approach” (pipeline). Such pipeline would include NGS data quality assessment, data mining for comparative analysis, searching differential genetic features, such as virulence, resistance persistence factors and mutation profiles (SNPs and InDels) and formatted “comprehensible” results. Such analytical protocols will enable a quick response to the needs of locally circumscribed outbreaks, providing information on the causes of resistance and genetic tracking elements for rapid detection, and monitoring actuations for present and future occurrences. PMID:25437609

  16. Annual report on the administration of the Radiation Control for health and Safety Act of 1968, Public Law 90-602, April 1, 1991. Rept. for Jan-Dec 90

    SciTech Connect

    Not Available

    1991-04-01

    The Secretary of Health and Human Services is required by Subpart 3, Part F of Title III of the Public Health Service Act; 42 USC 263b et seq. (Public Law 90-602) to submit an annual report to the President for transmittal to the Congress on or before April 1 on the administration of the Radiation Control for Health and Safety Act. The detailed information required in the report is outlined in Section 360D of the Public Health Service Act. The Food and Drug Administration, through its Center for Devices and Radiological Health, is responsible for the day-to-day administration of the Radiation Control for Health and Safety Act of 1968. The report provides a summary of the operations of the Center in carrying out that responsibility for calendar year 1990. In reviewing the operations of the Center for Devices and Radiological Health as reported in the document, it should be kept in mind that the day-to-day administration of the Act is only part of the Center's function. Other responsibilities include the administration and enforcement of the 1976 Medical Device Amendments to the Federal Food, Drug, and Cosmetic Act (not covered in the report). Manufacturers of electronic products are required by 21 CFR 1002.20 to report accidental radiation occurrences to the Center for Devices and Radiological Health. The Center no longer maintains a Radiation Incidents Registry, since accidental radiation occurrences are reported through the Device Experience Network (DEN) and through the requirements of the Medical Device Reporting (MDR) Regulations.

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Points to consider in the clinical use of NGS panels for mitochondrial disease: an analysis of gene inclusion and consent forms.

    PubMed

    Platt, Julia; Cox, Rachel; Enns, Gregory M

    2014-08-01

    Mitochondrial next generation sequencing (NGS) panels offer single-step analysis of the numerous nuclear genes involved in the structure, function, and maintenance of mitochondria. However, the complexities of mitochondrial biology and genetics raise points for consideration in clinical use of these tests. To understand the current status of mitochondrial genetic testing, we assessed the gene offerings and consent forms of mitochondrial NGS panels available from seven US-based clinical laboratories. The NGS panels varied markedly in number of genes (101-1204 genes), and the proportion of genes causing "classic" mitochondrial diseases and their phenocopies ranged widely between labs (18 %-94 % of panel contents). All panels included genes not associated with classic mitochondrial diseases (6 %-28 % of panel contents), including genes causing adult-onset neurodegenerative disorders, cancer predisposition, and other genetic syndromes or inborn errors of metabolism. Five of the panels included genes that are not listed in OMIM to be associated with a disease phenotype (5 %-49 % of panel contents). None of the consent documents reviewed had options for patient preference regarding receipt of incidental findings. These findings raise points of discussion applicable to mitochondrial diagnostics, but also to the larger arenas of exome and genome sequencing, including the need to consider the boundaries between clinical and research testing, the necessity of appropriate informed consent, and the responsibilities of clinical laboratories and clinicians. Based on these findings, we recommend careful evaluation by laboratories of the genes offered on NGS panels, clear communication of the predicted phenotypes, and revised consent forms to allow patients to make choices about receiving incidental findings. We hope that our analysis and recommendations will help to maximize the considerable clinical utility of NGS panels for the diagnosis of mitochondrial disease.

  3. 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.

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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...

  9. 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...

  10. 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...

  11. 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...

  12. 24 CFR 982.151 - Annual contributions contract.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... DEVELOPMENT (CONTINUED) OFFICE OF ASSISTANT SECRETARY FOR PUBLIC AND INDIAN HOUSING, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT SECTION 8 TENANT BASED ASSISTANCE: HOUSING CHOICE VOUCHER PROGRAM Annual...

  13. 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.

  14. 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...

  15. 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.

  16. 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.

  17. Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples

    PubMed Central

    Al-Hebshi, Nezar Noor; Nasher, Akram Thabet; Idris, Ali Mohamed; Chen, Tsute

    2015-01-01

    Background Usefulness of next-generation sequencing (NGS) in assessing bacteria associated with oral squamous cell carcinoma (OSCC) has been undermined by inability to classify reads to the species level. Objective The purpose of this study was to develop a robust algorithm for species-level classification of NGS reads from oral samples and to pilot test it for profiling bacteria within OSCC tissues. Methods Bacterial 16S V1-V3 libraries were prepared from three OSCC DNA samples and sequenced using 454's FLX chemistry. High-quality, well-aligned, and non-chimeric reads ≥350 bp were classified using a novel, multi-stage algorithm that involves matching reads to reference sequences in revised versions of the Human Oral Microbiome Database (HOMD), HOMD extended (HOMDEXT), and Greengene Gold (GGG) at alignment coverage and percentage identity ≥98%, followed by assignment to species level based on top hit reference sequences. Priority was given to hits in HOMD, then HOMDEXT and finally GGG. Unmatched reads were subject to operational taxonomic unit analysis. Results Nearly, 92.8% of the reads were matched to updated-HOMD 13.2, 1.83% to trusted-HOMDEXT, and 1.36% to modified-GGG. Of all matched reads, 99.6% were classified to species level. A total of 228 species-level taxa were identified, representing 11 phyla; the most abundant were Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria. Thirty-five species-level taxa were detected in all samples. On average, Prevotella oris, Neisseria flava, Neisseria flavescens/subflava, Fusobacterium nucleatum ss polymorphum, Aggregatibacter segnis, Streptococcus mitis, and Fusobacterium periodontium were the most abundant. Bacteroides fragilis, a species rarely isolated from the oral cavity, was detected in two samples. Conclusion This multi-stage algorithm maximizes the fraction of reads classified to the species level while ensuring reliable classification by giving priority to the human, oral reference

  18. 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.

  19. 14 CFR 1206.900 - Requirements for annual report.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 5 2011-01-01 2010-01-01 true Requirements for annual report. 1206.900 Section 1206.900 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION AVAILABILITY OF AGENCY RECORDS TO MEMBERS OF THE PUBLIC Annual Report § 1206.900 Requirements for annual report. On...

  20. 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 Section 1206.900 Aeronautics and Space NATIONAL AERONAUTICS AND SPACE ADMINISTRATION AVAILABILITY OF AGENCY RECORDS TO MEMBERS OF THE PUBLIC Annual Report § 1206.900 Requirements for annual report. On...

  1. 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

  2. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST.

    PubMed

    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(®) 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.

  3. 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.

  4. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST.

    PubMed

    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(®) 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

  5. 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.

  6. 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.

  7. 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.

  8. Neurofibromatosis type 1 molecular diagnosis: what can NGS do for you when you have a large gene with loss of function mutations?

    PubMed

    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

    2015-05-01

    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[euro ] 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.

  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. 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.

  11. 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.

  12. 41 CFR 105-69.600 - Semi-annual compilation.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Semi-annual compilation. 105-69.600 Section 105-69.600 Public Contracts and Property Management Federal Property Management... Administration 69-NEW RESTRICTIONS ON LOBBYING Agency Reports § 105-69.600 Semi-annual compilation. (a) The...

  13. 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

  14. ACCJC 1996-1997 Annual Report.

    ERIC Educational Resources Information Center

    Accrediting Commission for Community and Junior Colleges, Santa Rosa, CA.

    The 1996-97 Annual Report from the Accrediting Commission for Community and Junior Colleges (ACCJC) provides public disclosure of the Commission's procedures and policies to help renew public confidence in the importance and effectiveness of peer review and self-regulation in accreditation. The report begins with messages from the Commission's…

  15. 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.

  16. 42 CFR 1007.17 - Annual report.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 5 2011-10-01 2011-10-01 false Annual report. 1007.17 Section 1007.17 Public Health OFFICE OF INSPECTOR GENERAL-HEALTH CARE, DEPARTMENT OF HEALTH AND HUMAN SERVICES OIG AUTHORITIES... abuse and neglect of patients in health care facilities; the number of such complaints investigated...

  17. 42 CFR 1007.17 - Annual report.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 42 Public Health 5 2012-10-01 2012-10-01 false Annual report. 1007.17 Section 1007.17 Public Health OFFICE OF INSPECTOR GENERAL-HEALTH CARE, DEPARTMENT OF HEALTH AND HUMAN SERVICES OIG AUTHORITIES... abuse and neglect of patients in health care facilities; the number of such complaints investigated...

  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. 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. PMID:27459734

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 12 CFR 363.3 - Independent public accountant.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... POLICY ANNUAL INDEPENDENT AUDITS AND REPORTING REQUIREMENTS § 363.3 Independent public accountant. (a) Annual audit of financial statements. Each insured depository institution shall engage an independent public accountant to audit and report on its annual financial statements in accordance with...

  5. 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)

  6. 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)

  7. Public Education, Public Good.

    ERIC Educational Resources Information Center

    Tomlinson, John

    1986-01-01

    Criticizes policies which would damage or destroy a public education system. Examines the relationship between government-provided education and democracy. Concludes that privatization of public education would emphasize self-interest and selfishness, further jeopardizing the altruism and civic mindedness necessary for the public good. (JDH)

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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 'Excellent' Public…

  15. 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

  16. 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

  17. Ames Research Center publications, 1977

    NASA Technical Reports Server (NTRS)

    1979-01-01

    This bibliography lists 786 formal NASA publications, journal articles, books, chapters of books, patents, and contractor reports which appeared during 1977 or which were not included in previous annual bibliographies. Citations are arranged by directorate, type of publication, and author. Each NASA report is identified by a technical report and accession number to facilitate ordering. An author index is provided.

  18. 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…

  19. 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…

  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, 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…

  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, 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…

  2. 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. PMID:26125026

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 12 CFR 363.3 - Independent public accountant.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 4 2011-01-01 2011-01-01 false Independent public accountant. 363.3 Section... POLICY ANNUAL INDEPENDENT AUDITS AND REPORTING REQUIREMENTS § 363.3 Independent public accountant. (a... public accountant to audit and report on its annual financial statements in accordance with...

  8. 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...

  9. 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...

  10. 45 CFR 264.73 - What is an annual reconciliation?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false What is an annual reconciliation? 264.73 Section 264.73 Public Welfare Regulations Relating to Public Welfare OFFICE OF FAMILY ASSISTANCE (ASSISTANCE PROGRAMS), ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES OTHER ACCOUNTABILITY PROVISIONS What Are the...

  11. 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...

  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...

  13. 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...

  14. 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.

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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...

  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. 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....

  2. ISS Update: 1st Annual ISS R&D Conference

    NASA Video Gallery

    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...

  3. The 47th annual Florida pesticide residue workshop

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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....

  4. Oregon Migrant Health Project, 1971 Annual Report.

    ERIC Educational Resources Information Center

    Oregon State Board of Health, Portland.

    In its 9th year of providing migrant health services through a U.S. Public Health Service Continuing Migrant Health Act grant, this Oregon Migrant Health Project annual report is concerned with (1) the health services provided during the 1970-71 harvest season through a contractual arrangement between the Oregon State Health Division and 10 county…

  5. 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 in Public…

  6. 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…

  7. 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…

  8. Physical Fitness and Health. Annual Report 1977.

    ERIC Educational Resources Information Center

    Michigan State Dept. of Public Health, Lansing.

    This annual report from the Michigan Council on Physical Fitness and Health describes a project initiated by the Council in l977. "Project Fitness" serves to evaluate the physical fitness levels of all students in the public schools from grades kindergarten through twelve. Emphasis is placed upon early education of children in the importance of…

  9. 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.

  10. 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…

  11. 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…

  12. Nuclear medicine annual 1990

    SciTech Connect

    Freeman, L.M. )

    1990-01-01

    Two of the major areas of cutting-edge nuclear medicine research, single-photon emission computed tomography (SPECT) functional brain imaging and monoclonal antibody studies receive attention in this volume. Advances in these areas are critical to the continued growth of our specialty. Fortunately, the current outlook in both areas remains quite optimistic. As has been the policy in the first decade of publication, thorough state-of-the-art reviews on existing procedures are interspersed with chapters dealing with research developments. The editor wishes to express a particular note of appreciation to a very supportive British colleague, Dr. Ignac Fogelman, who is becoming a regular contributor. His exhaustive review of the role of nuclear medicine in the evaluation of osteoporotic patients is packed with extremely useful information that will prove to be fruitful to all readers. The author would like to thank the readers and colleagues who have taken the time to offer useful and constructive comments over the past ten years. The author continue to welcome suggestions that will help to further improve this Annual.

  13. Maryland's Achievements in Public Education, 2011

    ERIC Educational Resources Information Center

    Maryland State Department of Education, 2011

    2011-01-01

    This report presents Maryland's achievements in public education for 2011. Maryland's achievements include: (1) Maryland's public schools again ranked #1 in the nation in Education Week's 2011 Quality Counts annual report; (2) Maryland ranked 1st nationwide for a 3rd year in a row in the percentage of public school students scoring 3 or higher on…

  14. 1 CFR 10.10 - Publication required.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 1 General Provisions 1 2012-01-01 2012-01-01 false Publication required. 10.10 Section 10.10 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Annual Publication § 10.10 Publication required. The Director of the...

  15. 1 CFR 10.10 - Publication required.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 1 General Provisions 1 2014-01-01 2012-01-01 true Publication required. 10.10 Section 10.10 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Annual Publication § 10.10 Publication required. The Director of the...

  16. 1 CFR 10.10 - Publication required.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 1 General Provisions 1 2013-01-01 2012-01-01 true Publication required. 10.10 Section 10.10 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Annual Publication § 10.10 Publication required. The Director of the...

  17. 1 CFR 10.10 - Publication required.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 1 General Provisions 1 2010-01-01 2010-01-01 false Publication required. 10.10 Section 10.10 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Annual Publication § 10.10 Publication required. The Director of the...

  18. 1 CFR 10.10 - Publication required.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 1 General Provisions 1 2011-01-01 2011-01-01 false Publication required. 10.10 Section 10.10 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER SPECIAL EDITIONS OF THE FEDERAL REGISTER PRESIDENTIAL PAPERS Annual Publication § 10.10 Publication required. The Director of the...

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. LLNL NESHAPs 2003 Annual Report

    SciTech Connect

    Harrach, R J; Gallegos, G M; Peterson, S; Wilson, K R; Althouse, P E; Larson, J M; Bertoldo, N A; Tate, P J; Bowen, B

    2004-06-23

    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 2003 are summarized here. Livermore site: 0.044 mrem (0.44 {micro}Sv) (55% from point-source emissions, 45% 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. Site 300: 0.017 mrem (0.17 {micro}Sv) (98% from point-source emissions, 2% from diffuse-source emissions). The EDEs were calculated using the EPA-approved CAP88-PC air dispersion/dose-assessment model, except for doses for two diffuse sources that were estimated using 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.

  4. 45 CFR 265.9 - What information must the State file annually?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false What information must the State file annually? 265... COLLECTION AND REPORTING REQUIREMENTS § 265.9 What information must the State file annually? (a) Each State must file an annual report containing information on the TANF program and the State's MOE...

  5. 45 CFR 286.275 - What information must Tribes file annually?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false What information must Tribes file annually? 286... file annually? (a) Each Tribal TANF grantee must file an annual report containing information on its... category available in Tribal TANF grantee's locality) group child care provided by a nonrelative;...

  6. International Society for the Social Studies Annual Conference Proceedings (Orlando, Florida, February 25-26, 2010). Volume 2010, Issue 1

    ERIC Educational Resources Information Center

    Russell, William Benedict, III, Ed.

    2010-01-01

    The "ISSS Annual Conference Proceedings" is a peer-reviewed professional publication published once a year following the annual conference. (Individual papers contain references.) [For the 2009 proceedings, see ED504973.

  7. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (79th, Anaheim, CA, August 10-13, 1996). Advertising and Public Relations Division.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Advertising and Public Relations section of the proceedings contains the following 14 papers: "Toward an Understanding of Cultural Values Manifest in Advertising: A Content Analysis of Chinese Television Commercials from 1990 and 1995" (Hong Cheng); "The Impact of Advertising Distance on International Advertising: An Analysis of Creative…

  8. Public-Private Sector Collaboration in Education: Implications for Research, Policy, and the Education of Professional Educators. Proceedings of the Annual Rupert N. Evans Symposium (10th, Urbana, Illinois, May 2-3, 1989).

    ERIC Educational Resources Information Center

    Phelps, L. Allen, Ed.; Thurston, Paul W., Ed.

    These proceedings contain 11 papers that examine several diverse collaborative efforts designed to improve education and training programs through substantive involvement of the private sector. Authors and titles are as follows: "Public-Private Sector Collaboration in Education: Implications for Research, Policy, and the Education of Professional…

  9. High School Draw: Direct Entry Enrollment of Dade County Public High School Graduates--Annual Report Year Data 1992-93 through 1996-97. Research Report No. 97-06R.

    ERIC Educational Resources Information Center

    Baldwin, Anne

    For a number of years, analyses have been conducted each fall term to determine changes in the draw of high school graduates to Florida's Miami-Dade Community College (MDCC) from the Dade County Public Schools. Findings of the 1997 study, including comparisons with data from studies conducted over the past 5 years, include the following: (1) in…

  10. An Analysis of the Relationships between South Carolina Department of Education Annual School Report Card Variables of Public Elementary Schools and Student Achievement as Measured by 2008 PACT Data: With an Initial Emphasis on School Size

    ERIC Educational Resources Information Center

    Minolfo, Salvatore Andrew

    2010-01-01

    One purpose of this study was to determine whether a relationship exists between the size of South Carolina PreKindergarten-5 or Kindergarten-5 public elementary schools and student achievement while controlling for the effect of socioeconomic status. The independent variable school size, or 135-day average daily membership, the dependent variable…

  11. Proceedings of the Annual Meeting of the Association for Education in Journalism and Mass Communication (77th, Atlanta, Georgia, August 10-13, 1994). Part VIII: Advertising and Public Relations.

    ERIC Educational Resources Information Center

    Association for Education in Journalism and Mass Communication.

    The Advertising and Public Relations section of this collection of conference presentations contains the following 17 papers: "Using the FCB Grid and the 'Lost Quadrants' to Write Advertising Strategy" (Johan C. Yssel); "Antitrust and the Marketplace of Ideas: The Continuing Problem of Issue Advertising Access to Broadcast Television Networks"…

  12. International Federation of Library Associations Annual Conference Papers. Education and Research Division: Editors of Library Journals and Serial Publications Sections (47th, Leipzig, East Germany, August 17-22, 1981).

    ERIC Educational Resources Information Center

    Bankole, E. Bejide; And Others

    Four papers and two reports from three sections concerned with library science periodicals and serials publications in libraries include discussions of the role of library and information science journals and their coverage by indexing services as well as a description of an online system for serials, a report from the working group on newspapers,…

  13. Strategic Petroleum Reserve: Annual/quarterly report

    SciTech Connect

    Not Available

    1994-02-16

    Section 165 of the Energy Policy and Conservation Act (Public Law 94-163), as amended, requires the Secretary of Energy to submit annual and quarterly reports to the President and the Congress on activities of the Strategic Petroleum Reserve. This report combines the fourth quarter 1993 Quarterly Report with the 1993 Annual Report. Key activities described include appropriations; life extension planning; expansion planning; Strategic Petroleum Reserve oil acquisition; the oil stabilization program; and the refined petroleum product reserve test programs. Sections of this report also describe the program mission; the storage facility development program; environmental compliance; budget and finance; and drawdown and distribution.

  14. Annual Energy Review, 2008

    SciTech Connect

    2009-06-01

    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 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.

  15. Europlanet Prize for Public Engagement

    NASA Astrophysics Data System (ADS)

    Fouchet, Thierry

    2016-10-01

    The Europlanet Prize for Public Engagement with Planetary Science is awarded annually. Through the Prize, Europlanet aims to recognise achievements in engaging European citizens with planetary science and to raise the profile of outreach within the scientific community. It is awarded to individuals or groups who have developed innovative practices in planetary science communication and whose efforts have significantly contributed to a wider public engagement with planetary science.

  16. 12 CFR 325.207 - Publication of stress test results.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 5 2013-01-01 2013-01-01 false Publication of stress test results. 325.207... GENERAL POLICY CAPITAL MAINTENANCE Annual Stress Test § 325.207 Publication of stress test results. (a... annual stress test in the period starting June 15 and ending June 30. (2) An over $50 billion...

  17. 12 CFR 325.207 - Publication of stress test results.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 5 2014-01-01 2014-01-01 false Publication of stress test results. 325.207... GENERAL POLICY CAPITAL MAINTENANCE Annual Stress Test § 325.207 Publication of stress test results. (a... annual stress test in the period starting June 15 and ending June 30. (2) An over $50 billion...

  18. 78 FR 52997 - Connected Vehicle Research Program Public Meeting; Notice of Public Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-27

    ... Connected Vehicle Research Program Public Meeting; Notice of Public Meeting AGENCY: ITS Joint Program Office... JPO) will host its annual free public meeting to provide an overview of the ITS JPO Connected Vehicle... opportunity to learn details about the Connected Vehicle research program in anticipation of the...

  19. 1974 Annual Report of the Appalachian Regional Commission.

    ERIC Educational Resources Information Center

    Kendrick, Elise F., Ed.; And Others

    Created via the Regional Development Act of 1965, the Appalachian Regional Commission documents its contributions to Appalachian socioeconomic development in this 1974 annual report. General areas of concern are identified as: (1) extension of public services to outlying areas; (2) improvement of public service quality and quantity; (3) promotion…

  20. 45 CFR 604.600 - Semi-annual compilation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION NEW RESTRICTIONS ON LOBBYING Agency Reports § 604.600 Semi-annual compilation. (a) The head of each agency shall collect and compile the disclosure reports (see Appendix B) and, on May 31 and November 30 of each...

  1. 45 CFR 604.600 - Semi-annual compilation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION NEW RESTRICTIONS ON LOBBYING Agency Reports § 604.600 Semi-annual compilation. (a) The head of each agency shall collect and compile the disclosure reports (see Appendix B) and, on May 31 and November 30 of each...

  2. 45 CFR 604.600 - Semi-annual compilation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION NEW RESTRICTIONS ON LOBBYING Agency Reports § 604.600 Semi-annual compilation. (a) The head of each agency shall collect and compile the disclosure reports (see appendix B) and, on May 31 and November 30 of each...

  3. 45 CFR 604.600 - Semi-annual compilation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION NEW RESTRICTIONS ON LOBBYING Agency Reports § 604.600 Semi-annual compilation. (a) The head of each agency shall collect and compile the disclosure reports (see Appendix B) and, on May 31 and November 30 of each...

  4. 45 CFR 604.600 - Semi-annual compilation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Public Welfare Regulations Relating to Public Welfare (Continued) NATIONAL SCIENCE FOUNDATION NEW RESTRICTIONS ON LOBBYING Agency Reports § 604.600 Semi-annual compilation. (a) The head of each agency shall collect and compile the disclosure reports (see Appendix B) and, on May 31 and November 30 of each...

  5. 42 CFR 410.160 - Part B annual deductible.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 2 2010-10-01 2010-10-01 false Part B annual deductible. 410.160 Section 410.160 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES MEDICARE PROGRAM SUPPLEMENTARY MEDICAL INSURANCE (SMI) BENEFITS Payment of SMI Benefits § 410.160 Part B...

  6. Protecting America's Aged, Children, and Poor. Multi-Generational Needs; Multi-Generational Solutions. A Public Forum Presented by the Chairman of the Select Committee on Aging. House of Representatives, Ninety-Ninth Congress, Second Session, in Conjunction with the Annual Meeting of the American Public Health Association.

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. House Select Committee on Aging.

    This document contains materials from a Congressional public forum which focused on multigenerational approaches to the health and economic problems of Americans. Introductory remarks are included from Fernando Torres-Gil, staff director of the House Select Committee on Aging; Victor Sidel, president of the American Public Health Association…

  7. Public Education in the United States: A Nation Divided

    ERIC Educational Resources Information Center

    Bushaw, William J.; Lopez, Shane J.

    2012-01-01

    The 44th annual PDK/Gallup Poll of the Public's Attitudes Toward the Public Schools showed some sharp divisions among the public's attitude toward the public schools, but also some hopeful signs of broad agreement in some areas. Satisfaction with President Barack Obama declined in the last year, but remains ahead of two years ago and the public…

  8. Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

    PubMed Central

    2014-01-01

    Background Next-generation sequencing (NGS) technologies have resulted in petabytes of scattered data, decentralized in archives, databases and sometimes in isolated hard-disks which are inaccessible for browsing and analysis. It is expected that curated secondary databases will help organize some of this Big Data thereby allowing users better navigate, search and compute on it. Results To address the above challenge, we have implemented a NGS biocuration workflow and are analyzing short read sequences and associated metadata from cancer patients to better understand the human variome. Curation of variation and other related information from control (normal tissue) and case (tumor) samples will provide comprehensive background information that can be used in genomic medicine research and application studies. Our approach includes a CloudBioLinux Virtual Machine which is used upstream of an integrated High-performance Integrated Virtual Environment (HIVE) that encapsulates Curated Short Read archive (CSR) and a proteome-wide variation effect analysis tool (SNVDis). As a proof-of-concept, we have curated and analyzed control and case breast cancer datasets from the NCI cancer genomics program - The Cancer Genome Atlas (TCGA). Our efforts include reviewing and recording in CSR available clinical information on patients, mapping of the reads to the reference followed by identification of non-synonymous Single Nucleotide Variations (nsSNVs) and integrating the data with tools that allow analysis of effect nsSNVs on the human proteome. Furthermore, we have also developed a novel phylogenetic analysis algorithm that uses SNV positions and can be used to classify the patient population. The workflow described here lays the foundation for analysis of short read sequence data to identify rare and novel SNVs that are not present in dbSNP and therefore provides a more comprehensive understanding of the human variome. Variation results for single genes as well as the entire

  9. Electric power annual 1996. Volume 1

    SciTech Connect

    1997-08-01

    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 policy-makers, analysts, and the general public with data that may be used in understanding US 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); US Department of Energy. Volume 1--with a focus on US electric utilities--contains final 1996 data on net generation and fossil fuel consumption, stocks, receipts, and cost; preliminary 1996 data on generating unit capability, and retail sales of electricity, associated revenue, and the average revenue per kilowatthour of electricity sold. Additionally, information on net generation from renewable energy sources and on the associated generating capability is included in Volume 1 of the EPA. Data published in the Electric Power Annual Volume 1 are compiled from three statistical forms filed monthly and two forms filed annually by electric utilities. These forms are described in detail in the Technical Notes. 5 figs., 30 tabs.

  10. Petroleum supply annual 1998: Volume 2

    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 monthly surveys. The PSA is divided into two volumes. The first volume contains three sections: Summary Statistics, Detailed Statistics, and Refinery Statistics; each with final annual data. This second volume contains final statistics for each month of 1998, 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. 35 tabs.

  11. Petroleum supply annual, 1997. Volume 2

    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 monthly surveys. The PSA is divided into two volumes. The 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. 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. 35 tabs.

  12. Petroleum supply annual 1995: Volume 2

    SciTech Connect

    1996-06-01

    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 1995 through monthly surveys. The PSA is divided into two volumes. This first volume contains three sections: Summary Statistics, Detailed Statistics, and selected Refinery Statistics each with final annual data. The second volume contains final statistics for each month of 1995, 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.

  13. Petroleum supply annual 1996: Volume 2

    SciTech Connect

    1997-06-01

    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 1996 through monthly surveys. The PSA is divided into two volumes. The first volume contains three sections: Summary Statistics, Detailed Statistics, and Refinery Capacity; each with final annual data. The second volume contains final statistics for each month of 1996, 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. 35 tabs.

  14. Electric power annual 1997. Volume 1

    SciTech Connect

    1998-07-01

    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 policy-makers, analysts, and the general public with data that may be used in understanding US electricity markets. The Electric Power Annual is prepared by the Electric Power Division; Office of Coal, Nuclear, Electric and Alternate Fuels; Energy Information Administration (EIA); US Department of Energy. Volume 1 -- with a focus on US electric utilities -- contains final 1997 data on net generation and fossil fuel consumption, stocks, receipts, and cost; preliminary 1997 data on generating unit capability, and retail sales of electricity, associated revenue, and the average revenue per kilowatthour of electricity sold (based on a monthly sample: Form EIA-826, ``Monthly Electric Utility Sales and Revenue Report with State Distributions``). Additionally, information on net generation from renewable energy sources and on the associated generating capability is included in Volume 1 of the EPA.

  15. Electric power annual 1997. Volume 2

    SciTech Connect

    1998-10-01

    The Electric Power Annual 1997, Volume 2 contains annual summary statistics at national, regional, and state levels for the electric power industry, including information on both electric utilities and nonutility power producers. Included are data for electric utility retail sales of electricity, associated revenue, and average revenue per kilowatthour of electricity sold; financial statistics; environmental statistics; power transactions; and demand-side management. Also included are data for US nonutility power producers on installed capacity; gross generation; emissions; and supply and disposition of energy. 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. 15 figs., 62 tabs.

  16. Journal publications by Australian chiropractic academics: are they enough?

    PubMed Central

    Hoskins, Wayne; Pollard, Henry; Reggars, John; Vitiello, Andrew; Bonello, Rod

    2006-01-01

    Purpose To document the number of journal publications attributed to the academic faculty of Australian chiropractic tertiary institutions. To provide a discussion of the significance of this output and to relate this to the difficulty the profession appears to be experiencing in the uptake of evidence based healthcare outcomes and cultures. Methods The departmental websites for the three Australian chiropractic tertiary institutions were accessed and a list of academic faculty compiled. It was noted whether each academic held a chiropractic qualification or research Doctoral (not professional) degree qualification A review of the literature was conducted using the names of the academics and cross-referencing to publications listed independently in the PubMed and Index to Chiropractic Literature (ICL) databases (from inception to February 27 2006). Publications were excluded that were duplicates, corrected reprints, conference abstracts/proceedings, books, monographs, letters to the editor/comments or editorials. Using this information an annual and recent publication rate was constructed. Results For the 41 academics there was a total of 155 PubMed listed publications (mean 3.8, annual rate per academic 0.31) and 415 ICL listed publications (mean 10.1, annual rate 0.62). Over the last five years there have been 50 PubMed listed publications (mean 1.2, annual rate 0.24) and 97 ICL listed publications (mean 2.4, annual rate 0.47). Chiropractor academics (n = 31) had 29 PubMed listed publications (mean 2.5, annual rate 0.27) and 265 ICL listed publications (mean 8.5, annual rate 0.57). Academics with a doctoral degree (n = 13) had 134 PubMed listed publications (mean 10.3, annual rate 0.70) and 311 ICL listed publications (mean 23.9, annual rate 1.44). Academics without a Doctoral degree (n = 28) had 21 PubMed listed publications (mean 0.8, annual rate 0.13) and 104 ICL listed publications (mean 3.7, annual rate 0.24). Conclusion While several academics have compiled

  17. 2010 Annual Report

    SciTech Connect

    2010-01-01

    This annual report includes: an overview of Western; approaches for future hydropower and transmission service; major achievements in FY 2010; FY 2010 customer Integrated Resource Planning, or IRP, survey; and financial data.

  18. Natural gas annual 1994

    SciTech Connect

    1995-11-17

    The Natural Gas Annual provides information on the supply and disposition of natural gas to a wide audience including industry, consumers, Federal and State agencies, and educational institutions. The 1994 data are presented in a sequence that follows natural gas (including supplemental supplies) from its production to its end use. This is followed by tables summarizing natural gas supply and disposition from 1990 to 1994 for each Census Division and each State. Annual historical data are shown at the national level.

  19. Natural gas annual 1995

    SciTech Connect

    1996-11-01

    The Natural Gas Annual provides information on the supply and disposition of natural gas to a wide audience including industry, consumers, Federal and State agencies, and educational institutions. The 1995 data are presented in a sequence that follows natural gas (including supplemental supplies) from its production to its end use. This is followed by tables summarizing natural gas supply and disposition from 1991 to 1995 for each Census Division and each State. Annual historical data are shown at the national level.

  20. Laser program annual report 1983

    SciTech Connect

    Hendricks, C.D.; Rufer, M.L.; Murphy, P.W.

    1984-06-01

    In the 1983 Laser Program Annual Report we present the accomplishments and unclassified activities of the Laser Program at Lawrence Livermore National laboratory (LLNL) for the year 1983. It should be noted that the report, of necessity, is a summary, and more detailed expositions of the research can be found in the many publications and reports authored by staff members in the Laser Program. The purpose of this report is to present our work in a brief form, but with sufficient depth to provide an overview of the analytical and experimental aspects of the LLNL Inertial-Confinement Fusion (ICF) Program. The format of this report is basically the same as that of previous years. Section 1 is an overview and highlights the important accomplishments and directions of the Program. Sections 2 through 7 provide the detailed information on the various major parts of the Program: Laser Systems and Operations, Target Design, Target Fabrication, Fusion Experiments, Laser Research and Development, and Energy Applications.

  1. Annual report to Congress, 1993

    SciTech Connect

    Not Available

    1994-03-31

    Created by Congress in 1977 as an independent entity within the Department of Energy, the Energy Information Administration (EIA) is the principal and authoritative source of comprehensive energy data for the Congress, the Federal Government, the States, and the public. With the mandate to ``collect, assemble, evaluate, analyze, and disseminate data and information,`` EIA`s mission has been defined to: maintain a comprehensive data and information program relevant to energy resources and reserves, energy production, energy demand, energy technologies, and related financial and statistical information relevant to the adequacy of energy resources to meet the Nation`s demands in the near and longer term future. Develop and maintain analytical tool and collection and processing systems; provide analyses that are accurate, timely, and objective; and provide information dissemination services. This annual report summarizes EIA`s activities and accomplishments in 1993.

  2. LLNL NESHAPs 1998 annual report

    SciTech Connect

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

    1999-06-14

    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 1998 operations are summarized here. (1) Livermore site: 0.055 mrem (0.55 {micro}Sv) (57% from point-source emissions, 43% from diffuse-source emissions). The point-source emissions include gaseous tritium modeled as tritiated water vapor as directed by EPA Region IX and is used for compliance purposes. LLNL believes a more realistic dose for the Livermore site is 0.049 mrem (0.49 {micro}Sv) (52% from point-source emissions, 48% from diffuse-source emissions). This dose is based on an assessment that represents a more realistic behavior of tritium gas in the environment. (2) Site 300: 0.024 mrem (0.24 {micro}Sv) (78% from point-source emissions, 22% 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.

  3. Academic and Public Library Buildings, 1986.

    ERIC Educational Resources Information Center

    Fox, Bette-Lee; And Others

    1986-01-01

    Three articles on library buildings present Library Journal's annual architectural survey of completed public and academic library buildings and library projects in progress; guidelines for leasing a shared library facility, and a description of a successful public library building project in Michigan are also discussed. (EM)

  4. Sexual Violence in America: Public Funding and Social Priority.

    PubMed

    Waechter, Randall; Ma, Van

    2015-12-01

    We compared lifetime risk, annual incidence, and annual economic burden of sexual violence with other major public health issues in the United States: cardiovascular disease, cancer, diabetes, and HIV/AIDS. With public funding data from 2013, we examined how much public funding is allocated to these public health issues as a proxy of the social priority of addressing each of them. Although sexual violence is as prevalent as and more costly than are these other major public health issues, it receives a fraction of the public funds that they receive. PMID:26469639

  5. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis.

    PubMed

    Wei, Qing-Zhen; Fu, Wen-Yuan; Wang, Yun-Zhu; Qin, Xiao-Dong; Wang, Jing; Li, Ji; Lou, Qun-Feng; Chen, Jin-Feng

    2016-06-07

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes.

  6. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis.

    PubMed

    Wei, Qing-Zhen; Fu, Wen-Yuan; Wang, Yun-Zhu; Qin, Xiao-Dong; Wang, Jing; Li, Ji; Lou, Qun-Feng; Chen, Jin-Feng

    2016-01-01

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes. PMID:27271557

  7. Detection and characterization of two co-infection variant strains of avian orthoreovirus (ARV) in young layer chickens using next-generation sequencing (NGS).

    PubMed

    Tang, Yi; Lin, Lin; Sebastian, Aswathy; Lu, Huaguang

    2016-04-19

    Using next-generation sequencing (NGS) for full genomic characterization studies of the newly emerging avian orthoreovirus (ARV) field strains isolated in Pennsylvania poultry, we identified two co-infection ARV variant strains from one ARV isolate obtained from ARV-affected young layer chickens. The de novo assembly of the ARV reads generated 19 contigs of two different ARV variant strains according to 10 genome segments of each ARV strain. The two variants had the same M2 segment. The complete genomes of each of the two variant strains were 23,493 bp in length, and 10 dsRNA segments ranged from 1192 bp (S4) to 3958 bp (L1), encoding 12 viral proteins. Sequence comparison of nucleotide (nt) and amino acid (aa) sequences of all 10 genome segments revealed 58.1-100% and 51.4-100% aa identity between the two variant strains, and 54.3-89.4% and 49.5-98.1% aa identity between the two variants and classic vaccine strains. Phylogenetic analysis revealed a moderate to significant nt sequence divergence between the two variant and ARV reference strains. These findings have demonstrated the first naturally occurring co-infection of two ARV variants in commercial young layer chickens, providing scientific evidence that multiple ARV strains can be simultaneously present in one host species of chickens.

  8. Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS): Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE) Samples

    PubMed Central

    Arreaza, Gladys; Qiu, Ping; Pang, Ling; Albright, Andrew; Hong, Lewis Z.; Marton, Matthew J.; Levitan, Diane

    2016-01-01

    In cancer drug discovery, it is important to investigate the genetic determinants of response or resistance to cancer therapy as well as factors that contribute to adverse events in the course of clinical trials. Despite the emergence of new technologies and the ability to measure more diverse analytes (e.g., circulating tumor cell (CTC), circulating tumor DNA (ctDNA), etc.), tumor tissue is still the most common and reliable source for biomarker investigation. Because of its worldwide use and ability to preserve samples for many decades at ambient temperature, formalin-fixed, paraffin-embedded tumor tissue (FFPE) is likely to be the preferred choice for tissue preservation in clinical practice for the foreseeable future. Multiple analyses are routinely performed on the same FFPE samples (such as Immunohistochemistry (IHC), in situ hybridization, RNAseq, DNAseq, TILseq, Methyl-Seq, etc.). Thus, specimen prioritization and optimization of the isolation of analytes is critical to ensure successful completion of each assay. FFPE is notorious for producing suboptimal DNA quality and low DNA yield. However, commercial vendors tend to request higher DNA sample mass than what is actually required for downstream assays, which restricts the breadth of biomarker work that can be performed. We evaluated multiple genomics service laboratories to assess the current state of NGS pre-analytical processing of FFPE. Significant differences in pre-analytical capabilities were observed. Key aspects are highlighted and recommendations are made to improve the current practice in translational research. PMID:27657050

  9. Detection and characterization of two co-infection variant strains of avian orthoreovirus (ARV) in young layer chickens using next-generation sequencing (NGS)

    PubMed Central

    Tang, Yi; Lin, Lin; Sebastian, Aswathy; Lu, Huaguang

    2016-01-01

    Using next-generation sequencing (NGS) for full genomic characterization studies of the newly emerging avian orthoreovirus (ARV) field strains isolated in Pennsylvania poultry, we identified two co-infection ARV variant strains from one ARV isolate obtained from ARV-affected young layer chickens. The de novo assembly of the ARV reads generated 19 contigs of two different ARV variant strains according to 10 genome segments of each ARV strain. The two variants had the same M2 segment. The complete genomes of each of the two variant strains were 23,493 bp in length, and 10 dsRNA segments ranged from 1192 bp (S4) to 3958 bp (L1), encoding 12 viral proteins. Sequence comparison of nucleotide (nt) and amino acid (aa) sequences of all 10 genome segments revealed 58.1–100% and 51.4–100% aa identity between the two variant strains, and 54.3–89.4% and 49.5–98.1% aa identity between the two variants and classic vaccine strains. Phylogenetic analysis revealed a moderate to significant nt sequence divergence between the two variant and ARV reference strains. These findings have demonstrated the first naturally occurring co-infection of two ARV variants in commercial young layer chickens, providing scientific evidence that multiple ARV strains can be simultaneously present in one host species of chickens. PMID:27089943

  10. Rapid identification of fruit length loci in cucumber (Cucumis sativus L.) using next-generation sequencing (NGS)-based QTL analysis

    PubMed Central

    Wei, Qing-zhen; Fu, Wen-yuan; Wang, Yun-zhu; Qin, Xiao-dong; Wang, Jing; Li, Ji; Lou, Qun-feng; Chen, Jin-feng

    2016-01-01

    The cucumber (Cucumis sativus L.) exhibits extensive variations in fruit size and shape. Fruit length is an important agronomic and domesticated trait controlled by quantitative trait loci (QTLs). Nonetheless, the underlying molecular and genetic mechanisms that determine cucumber fruit length remain unclear. QTL-seq is an efficient strategy for QTL identification that takes advantage of bulked-segregant analysis (BSA) and next-generation sequencing (NGS). In the present study, we conducted QTL mapping and QTL-seq of cucumber fruit length. QTL mapping identified 8 QTLs for immature and mature fruit length. A major-effect QTL fl3.2, which explained a maximum of 38.87% of the phenotypic variation, was detected. A genome-wide comparison of SNP profiles between two DNA bulks identified 6 QTLs for ovary length. QTLs ovl3.1 and ovl3.2 both had major effects on ovary length with a △ (SNP-index) of 0.80 (P < 0.01) and 0.74 (P < 0.01), respectively. Quantitative RT-PCR of fruit size-related homologous genes localized in the consensus QTL FL3.2 was conducted. Four candidate genes exhibited increased expression levels in long fruit genotypes. Our results demonstrated the power of the QTL-seq method in rapid QTL detection and provided reliable QTL regions for fine mapping of fruit length-related loci and for identifying candidate genes. PMID:27271557

  11. Use of Combined MSAP and NGS Techniques to Identify Differentially Methylated Regions in Somaclones: A Case Study of Two Stable Somatic Wheat Mutants

    PubMed Central

    Baránek, Miroslav; Čechová, Jana; Kovacs, Tamas; Eichmeier, Aleš; Wang, Shunli; Raddová, Jana; Nečas, Tomáš; Ye, Xingguo

    2016-01-01

    The appearance of somaclonal variability induced by in vitro cultivation is relatively frequent and can, in some cases, provide a valuable source of new genetic variation for crop improvement. The cause of this phenomenon remains unknown; however, there are a number of reports suggesting that epigenetics, including DNA methylations, are an important factor. In addition to the non-heritable DNA methylation changes caused by transient and reversible stress-responsive gene regulation, recent evidence supports the existence of mitotically and meiotically inherited changes. The induction of phenotypes via stable DNA methylation changes has occasionally great economical value; however, very little is known about the genetic or molecular basis of these phenotypes. We used a novel approach consisting of a standard MSAP analysis followed by deep amplicon sequencing to better understand this phenomenon. Our models included two wheat genotypes, and their somaclones induced using in vitro cultivation with a changed heritable phenotype (shortened stem height and silenced high molecular weight glutenin). Using this novel procedure, we obtained information on the dissimilarity of DNA methylation landscapes between the standard cultivar and its respective somaclones, and we extracted the sequences and genome regions that were differentially methylated between subjects. Transposable elements were identified as the most likely factor for producing changes in somaclone properties. In summary, the novel approach of combining MSAP and NGS is relatively easy and widely applicable, which is a rather unique feature compared with the currently available techniques in the epigenetics field. PMID:27792769

  12. Powerplant and Industrial Fuel Use Act annual report

    SciTech Connect

    1981-03-01

    This annual report was prepared for the Congress by the Secretary of the Department of Energy (DOE) in conjunction with the Acting Administrator of the Environmental Protection Agency (EPA) as required by Section 806 of the Powerplant and Industrial Fuel Use Act of 1978 (FUA), Public Law 95-620, enacted November 9, 1978. This annual report describes actions taken under the legislation, which was enacted to promote national energy self-sufficiency and encourage the use of the alternate energy resources in electric powerplants and major industrial fuel-burning installations (MFBI's) in the utility, industrial and Federal governmental sectors. Annual FUA implementation activities are discussed and legislative requirements are satisfied that the annual report discuss: actions taken under FUA and under Section 2 of the Energy Supply and Environmental Coordination Act of 1974 (ESECA) Public Law 93-319 during the preceding calendar year; and the effectiveness of the provisions of both laws in achieving their purposes.

  13. What's Up? Use the night sky to engage the public through amateur astronomy in IYA; What's Up monthly astronomy themed podcasts; Annual Saturn Observation Night worldwide celebration of Saturn Opposition

    NASA Astrophysics Data System (ADS)

    Houston Jones, Jane

    2008-09-01

    Abstract What's Up video podcasts: connecting "astronomy for everyone" monthly astronomical views with related NASA missions, science, images and handson education. Background: What's Up Podcasts are 2 minute video podcasts available through RSS feed, You tube, and NASA websites every month. They feature an astronomy related viewing target in the sky each month, targets visible to everyone, from city or country, just by looking up! No telescope is required to view these objects. Summary: Expand and broaden the scope of the existing "What's Up" public astronomy themed video podcasts. NASA builds partnerships and linkages between Science, Technology, Engineering and Mathematics formal and informal education providers. What's Up podcasts provides a link between astronomical views and events, or "what's up in the night sky this month" with current NASA missions, mission milestones and events, space telescope images or press releases. These podcasts, plus supporting star charts, hands-on activities, standards-based educational lessons and mission links will be used by museums, planetariums, astronomy clubs, civic and youth groups, as well as by classrooms and the general public. They can be translated to other languages, too. Providing the podcasts in high definition, through the NASA websites, You Tube, iTunes and other web video sharing sites reaches wide audiences of all ages. Third Saturn Observation Night - May 18, 2008 Centered on Saturn Opposition, when the Sun and Saturn are on opposite sides of the Earth, all IYA participants - in all countries around the world - will be encouraged to take their telescopes out and share the planet Saturn with their communities. NASA's International Saturn Observation Campaign network of astronomy enthusiasts has now conducted a Saturn Observation Night event for the past 2 years, and it succeeds by building an international community all sharing Saturn. This celebration has been successfully conducted in hundreds of locations

  14. The Oak Ridge Reservation Annual Site Environmental Report Summary, 2007

    SciTech Connect

    None, None

    2009-02-28

    The Oak Ridge Reservation Annual Site Environmental Report is prepared and published each year to inform the public of the environmental activities that take place on the reservation and in the surrounding areas. It is written to comply with DOE Order 231.1A, Environment, Safety, and Health Reporting. This document has been prepared to present the highlights of the Oak Ridge Reservation Annual Site Environmental Report 2007 in an easy-to-read, summary format.

  15. Introduction of the Python script STRinNGS for analysis of STR regions in FASTQ or BAM files and expansion of the Danish STR sequence database to 11 STRs.

    PubMed

    Friis, Susanne L; Buchard, Anders; Rockenbauer, Eszter; Børsting, Claus; Morling, Niels

    2016-03-01

    This work introduces the in-house developed Python application STRinNGS for analysis of STR sequence elements in BAM or FASTQ files. STRinNGS identifies sequence reads with STR loci by their flanking sequences, it analyses the STR sequence and the flanking regions, and generates a report with the assigned SNP-STR alleles. The main output file from STRinNGS contains all sequences with read counts above 1% of the total number of reads per locus. STR sequences are automatically named according to the nomenclature used previously and according to the repeat unit definitions in STRBase (http://www.cstl.nist.gov/strbase/). The sequences are named with (1) the locus name, (2) the length of the repeat region divided by the length of the repeat unit, (3) the sequence(s) of the repeat unit(s) followed by the number of repeats and (4) variations in the flanking regions. Lower case letters in the main output file are used to flag sequences with previously unknown variations in the STRs. SNPs in the flanking regions are named by their "rs" numbers and the nucleotides in the SNP position. Data from 207 Danes sequenced with the Ion Torrent™ HID STR 10-plex that amplified nine STRs (CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D16S539, TH01, TPOX, vWA), and Amelogenin was analysed with STRinNGS. Sequencing uncovered five common SNPs near four STRs and revealed 20 new alleles in the 207 Danes. Three short homopolymers in the D8S1179 flanking regions caused frequent sequencing errors. In 29 of 3726 allele calls (0.8%), sequences with homopolymer errors were falsely assigned as true alleles. An in-house developed script in R compensated for these errors by compiling sequence reads that had identical STR sequences and identical nucleotides in the five common SNPs. In the output file from the R script, all SNP-STR haplotype calls were correct. The 207 samples and six additional samples were sequenced for D3S1358, D12S391, and D21S11 using the 454 GS Junior platform in this and a

  16. International VLBI Service for Geodesy and Astrometry 2011 Annual Report

    NASA Technical Reports Server (NTRS)

    Baver, Karen D. (Editor); Behrend, Dirk

    2012-01-01

    This volume of reports is the 2011 Annual Report of the International VLBI Service for Geodesy and Astrometry (IVS). The individual reports were contributed by VLBI groups in the international geodetic and astrometric community who constitute the components of IVS. The 2011 Annual Report documents the work of these IVS components over the period January 1, 2011 through December 31, 2011. The reports document changes, activities, and progress of the IVS. The entire contents of this Annual Report also appear on the IVS Web site at http://ivscc.gsfc.nasa.gov/publications/ar2011.

  17. International VLBI Service for Geodesy and Astrometry 2007 Annual Report

    NASA Technical Reports Server (NTRS)

    Behrend, D. (Editor); Baver, K. D. (Editor)

    2008-01-01

    This volume of reports is the 2007 Annual Report of the International VLBI Service for Geodesy and Astrometry (IVS). The individual reports were contributed by VLBI groups in the international geodetic and astrometric community who constitute the components of IVS. The 2007 Annual Report documents the work of these IVS components over the period January 1, 2007 through December 31, 2007. The reports document changes, activities, and progress of the IVS. The entire contents of this Annual Report also appear on the IVS Web site at http://ivscc.gsfc.nasa.gov/publications/ar2007.

  18. International VLBI Service for Geodesy and Astrometry 2008 Annual Report

    NASA Technical Reports Server (NTRS)

    Behrend, Dirk; Baver, Karen D.

    2009-01-01

    This volume of reports is the 2008 Annual Report of the International VLBI Service for Geodesy and Astrometry (IVS). The individual reports were contributed by VLBI groups in the international geodetic and astrometric community who constitute the components of IVS. The 2008 Annual Report documents the work of these IVS components over the period January 1, 2008 through December 31, 2008. The reports document changes, activities, and progress of the IVS. The entire contents of this Annual Report also appear on the IVS Web site at http://ivscc.gsfc.nasa.gov/publications/ar2008.

  19. Financial statistics of major US publicly owned electric utilities 1993

    SciTech Connect

    Not Available

    1995-02-01

    The 1993 edition of the Financial Statistics of Major U.S. Publicly Owned Electric Utilities publication presents five years (1989 to 1993) of summary financial data and current year detailed financial data on the major publicly owned electric utilities. The objective of the publication is to provide Federal and State governments, industry, and the general public with current and historical data that can be used for policymaking and decision making purposes related to publicly owned electric utility issues. Generator and nongenerator summaries are presented in this publication. The primary source of publicly owned financial data is the Form EIA-412, the Annual Report of Public Electric Utilities, filed on a fiscal basis.

  20. Public Power 1981 directory

    SciTech Connect

    Not Available

    1981-01-01

    More than 2200 listings of local publicly owned electric systems, organizations of these utilities, and Federal power agencies are included in this directory. Not included are: privately owned electric companies and rural electric cooperatives. Listings cover the following information: name, address, and telephone number of the utility; chief officer; year the system was established; number of meters served; generation by type, including steam, gas, turbine, internal combustion engine, and hydroelectric in kilowatts of capacity; power purchased at wholesale for latest full year; and annual electric revenues for the latest-available full year. Publicly owned electric utilities in 48 states, the Canal Zone, Puerto Rico, the Virgin Islands, Guam, and American Samoa are listed. (JMT)

  1. LLNL NESHAPs 2001 Annual Report

    SciTech Connect

    Harrach, R.J.; Peterson, S.-R.; Gallegos, G.M.; Tate, P.J.; Bertoldo, N.A.; Althouse, P.E.

    2002-06-18

    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 2001 are summarized here: (1) Livermore site: 0.017 mrem (0.17 {micro}Sv) (34% from point-source emissions, 66% 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: 0.054 mrem (0.54 {micro}Sv) (93% from point-source emissions, 7% 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.

  2. LLNL NESHAPs 2008 Annual Report

    SciTech Connect

    Bertoldo, N; Gallegos, G; MacQueen, D; Wegrecki, A; Wilson, K

    2009-06-25

    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 {mu}Sv) 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 1.0, to calculate the dose to the maximally exposed individual for the Livermore site and Site 300. The dose for the LLNL site-wide maximally exposed members of the public from operations in 2008 are summarized here: {sm_bullet} Livermore site: 0.0013 mrem (0.013 {mu}Sv) (26% from point source emissions, 74% 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. {sm_bullet} Site 300: 0.000000044 mrem (0.00000044 {mu}Sv) (100% from point source emissions).

  3. LLNL NESHAPs 2000 Annual Report

    SciTech Connect

    Gallegos, G M; Harrach, R J; Berger, R L; Bertoldo, N A; Tate, P J; Peterson, S R

    2001-06-01

    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 2000 operations are summarized here. {sm_bullet} Livermore site: 0.038 mrem (0.38 {micro}Sv) (45% from point-source emissions, 55% from diffuse-source emissions). The point-source emissions include gaseous tritium modeled as tritiated water vapor as directed by EPA Region IX, and the resulting dose is used for compliance purposes. {sm_bullet} Site 300: 0.019 mrem (0.19 {micro}Sv) (79% from point-source emissions, 21% from diffuse-source emissions). The EDEs were calculated using the EPA-approved CAP88-PC air dispersion/dose-assessment model, except for doses for four 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 input to CAP88-PC for each modeled source.

  4. Natural gas annual 1997

    SciTech Connect

    1998-10-01

    The Natural Gas Annual provides information on the supply and disposition of natural gas to a wide audience including industry, consumers, Federal and State agencies, and educational institutions. The 1997 data are presented in a sequence that follows natural gas (including supplemental supplies) from its production to its end use. This is followed by tables summarizing natural gas supply and disposition from 1993 to 1997 for each Census Division and each State. Annual historical data are shown at the national level. 27 figs., 109 tabs.

  5. International energy annual 1996

    SciTech Connect

    1998-02-01

    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, geothermal, solar, and wind electric power, biofuels energy for the US, and biofuels electric power for Brazil. New in the 1996 edition are estimates of carbon dioxide emissions from the consumption of petroleum and coal, and the consumption and flaring of natural gas. 72 tabs.

  6. Annual Energy Outlook

    EIA Publications

    2015-01-01

    The projections in the U.S. Energy Information Administration's (EIA's) Annual Energy Outlook 2015 (AEO2015) focus on the factors that shape the U.S. energy system over the long term. For the first time, the Annual Energy Outlook (AEO) is presented as a shorter edition under a newly adopted two-year release cycle. With this approach, full editions and shorter editions of the AEO will be produced in alternating years. This approach will allow EIA to focus more resources on rapidly changing energy markets both in the United States and internationally, and to consider how they might evolve over the next few years.

  7. NGS-based approach to determine the presence of HPV and their sites of integration in human cancer genome

    PubMed Central

    Chandrani, P; Kulkarni, V; Iyer, P; Upadhyay, P; Chaubal, R; Das, P; Mulherkar, R; Singh, R; Dutt, A

    2015-01-01

    Background: Human papilloma virus (HPV) accounts for the most common cause of all virus-associated human cancers. Here, we describe the first graphic user interface (GUI)-based automated tool ‘HPVDetector', for non-computational biologists, exclusively for detection and annotation of the HPV genome based on next-generation sequencing data sets. Methods: We developed a custom-made reference genome that comprises of human chromosomes along with annotated genome of 143 HPV types as pseudochromosomes. The tool runs on a dual mode as defined by the user: a ‘quick mode' to identify presence of HPV types and an ‘integration mode' to determine genomic location for the site of integration. The input data can be a paired-end whole-exome, whole-genome or whole-transcriptome data set. The HPVDetector is available in public domain for download: http://www.actrec.gov.in/pi-webpages/AmitDutt/HPVdetector/HPVDetector.html. Results: On the basis of our evaluation of 116 whole-exome, 23 whole-transcriptome and 2 whole-genome data, we were able to identify presence of HPV in 20 exomes and 4 transcriptomes of cervical and head and neck cancer tumour samples. Using the inbuilt annotation module of HPVDetector, we found predominant integration of viral gene E7, a known oncogene, at known 17q21, 3q27, 7q35, Xq28 and novel sites of integration in the human genome. Furthermore, co-infection with high-risk HPVs such as 16 and 31 were found to be mutually exclusive compared with low-risk HPV71. Conclusions: HPVDetector is a simple yet precise and robust tool for detecting HPV from tumour samples using variety of next-generation sequencing platforms including whole genome, whole exome and transcriptome. Two different modes (quick detection and integration mode) along with a GUI widen the usability of HPVDetector for biologists and clinicians with minimal computational knowledge. PMID:25973533

  8. The International Society for the Social Studies Annual Conference Proceedings (Orlando, Florida, February 24-25, 2011). Volume 2011, Issue 1

    ERIC Educational Resources Information Center

    Russell, William Benedict, III, Ed.

    2011-01-01

    The "ISSS Annual Conference Proceedings" is a peer-reviewed professional publication published once a year following the annual conference. (Individual papers contain references.) [For the 2010 proceedings, see ED509647.

  9. The International Society for the Social Studies Annual Conference Proceedings (Orlando, Florida, March 1-2, 2012). Volume 2012, Issue 1

    ERIC Educational Resources Information Center

    Russell, William Benedict, III, Ed.

    2012-01-01

    The "ISSS Annual Conference Proceedings" is a peer-reviewed professional publication published once a year following the annual conference. (Individual papers contain references.) [For the 2011 proceedings, see ED518589.

  10. A NGS approach to the encrusting Mediterranean sponge Crella elegans (Porifera, Demospongiae, Poecilosclerida): transcriptome sequencing, characterization and overview of the gene expression along three life cycle stages.

    PubMed

    Pérez-Porro, A R; Navarro-Gómez, D; Uriz, M J; Giribet, G

    2013-05-01

    Sponges can be dominant organisms in many marine and freshwater habitats where they play essential ecological roles. They also represent a key group to address important questions in early metazoan evolution. Recent approaches for improving knowledge on sponge biological and ecological functions as well as on animal evolution have focused on the genetic toolkits involved in ecological responses to environmental changes (biotic and abiotic), development and reproduction. These approaches are possible thanks to newly available, massive sequencing technologies-such as the Illumina platform, which facilitate genome and transcriptome sequencing in a cost-effective manner. Here we present the first NGS (next-generation sequencing) approach to understanding the life cycle of an encrusting marine sponge. For this we sequenced libraries of three different life cycle stages of the Mediterranean sponge Crella elegans and generated de novo transcriptome assemblies. Three assemblies were based on sponge tissue of a particular life cycle stage, including non-reproductive tissue, tissue with sperm cysts and tissue with larvae. The fourth assembly pooled the data from all three stages. By aggregating data from all the different life cycle stages we obtained a higher total number of contigs, contigs with blast hit and annotated contigs than from one stage-based assemblies. In that multi-stage assembly we obtained a larger number of the developmental regulatory genes known for metazoans than in any other assembly. We also advance the differential expression of selected genes in the three life cycle stages to explore the potential of RNA-seq for improving knowledge on functional processes along the sponge life cycle.

  11. AN INFRARED CENSUS OF DUST IN NEARBY GALAXIES WITH SPITZER (DUSTiNGS). II. DISCOVERY OF METAL-POOR DUSTY AGB STARS

    SciTech Connect

    Boyer, Martha L.; Sonneborn, George; McQuinn, Kristen B. W.; Gehrz, Robert D.; Skillman, Evan; Barmby, Pauline; Bonanos, Alceste Z.; Gordon, Karl D.; Meixner, Margaret; Groenewegen, M. A. T.; Lagadec, Eric; Lennon, Daniel; Marengo, Massimo; McDonald, Iain; Zijlstra, Albert; Sloan, G. C.; Van Loon, Jacco Th.

    2015-02-10

    The DUSTiNGS survey (DUST in Nearby Galaxies with Spitzer) is a 3.6 and 4.5 μm imaging survey of 50 nearby dwarf galaxies designed to identify dust-producing asymptotic giant branch (AGB) stars and massive stars. Using two epochs, spaced approximately six months apart, we identify a total of 526 dusty variable AGB stars (sometimes called ''extreme'' or x-AGB stars; [3.6]-[4.5] > 0.1 mag). Of these, 111 are in galaxies with [Fe/H] < –1.5 and 12 are in galaxies with [Fe/H] < –2.0, making them the most metal-poor dust-producing AGB stars known. We compare these identifications to those in the literature and find that most are newly discovered large-amplitude variables, with the exception of ≈30 stars in NGC 185 and NGC 147, 1 star in IC 1613, and 1 star in Phoenix. The chemical abundances of the x-AGB variables are unknown, but the low metallicities suggest that they are more likely to be carbon-rich than oxygen-rich and comparisons with existing optical and near-IR photometry confirm that 70 of the x-AGB variables are confirmed or likely carbon stars. We see an increase in the pulsation amplitude with increased dust production, supporting previous studies suggesting that dust production and pulsation are linked. We find no strong evidence linking dust production with metallicity, indicating that dust can form in very metal-poor environments.

  12. Annual Conference Abstracts

    ERIC Educational Resources Information Center

    Engineering Education, 1976

    1976-01-01

    Presents the abstracts of 158 papers presented at the American Society for Engineering Education's annual conference at Knoxville, Tennessee, June 14-17, 1976. Included are engineering topics covering education, aerospace, agriculture, biomedicine, chemistry, computers, electricity, acoustics, environment, mechanics, and women. (SL)

  13. Carolinas Communication Annual, 1998.

    ERIC Educational Resources Information Center

    McLennan, David B.

    1998-01-01

    This 1998 issue of "Carolinas Communication Annual" contains the following articles: "Give Me That Old Time Religion?: A Study of Religious Themes in the Rhetoric of the Ku Klux Klan" (John S. Seiter); "The Three Stooges versus the Third Reich" (Roy Schwartzman); "Interdisciplinary Team Teaching: Implementing Collaborative Instruction in an…

  14. UNICEF Annual Report, 1996.

    ERIC Educational Resources Information Center

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

    At this time, the United Nations Children Fund (UNICEF) is commemorating its 50th anniversary, under the slogan "children first." This annual UNICEF report reviews the organization's activities during 1995. An introduction by the executive director states that the report will give readers a sense of what UNICEF is doing with partners to rise to…

  15. NERSC Annual Report 2004

    SciTech Connect

    Hules, John; Bashor, Jon; Yarris, Lynn; McCullough, Julie; Preuss, Paul; Bethel, Wes

    2005-04-15

    The National Energy Research Scientific Computing Center (NERSC) is the premier computational resource for scientific research funded by the DOE Office of Science. The Annual Report includes summaries of recent significant and representative computational science projects conducted on NERSC systems as well as information about NERSC's current and planned systems and services.

  16. 2010 AAUW Annual Report

    ERIC Educational Resources Information Center

    American Association of University Women, 2010

    2010-01-01

    This report highlights some of the outstanding accomplishments of AAUW (American Association of University Women) for fiscal year 2010. This year's annual report also features stories of remarkable women who are leading the charge to break through barriers and ensure that all women have a fair chance. Sharon is working to reduce the pay gap…

  17. Magnetic Resonance Annual, 1985

    SciTech Connect

    Kressel, H.Y.

    1985-01-01

    The inaugural volume of Magnetic Resonance Annual includes reviews of MRI of the posterior fossa, cerebral neoplasms, and the cardiovascular and genitourinary systems. A chapter on contrast materials outlines the mechanisms of paramagnetic contrast enhancement and highlights several promising contrast agents.

  18. Annual Conference Abstracts

    ERIC Educational Resources Information Center

    Journal of Engineering Education, 1972

    1972-01-01

    Includes abstracts of papers presented at the 80th Annual Conference of the American Society for Engineering Education. The broad areas include aerospace, affiliate and associate member council, agricultural engineering, biomedical engineering, continuing engineering studies, chemical engineering, civil engineering, computers, cooperative…

  19. UNICEF Annual Report, 1995.

    ERIC Educational Resources Information Center

    United Nations Children's Fund, New York, N.Y.

    This annual report for the United Nations Children's Fund (UNICEF) details the programs and services provided by this organization in 1994. Following an overview of the year and a remembrance of former UNICEF Executive Director James P. Grant, the report describes developments in seven world regions and in specific emergency countries. The report…

  20. Annual research briefs, 1994

    NASA Technical Reports Server (NTRS)

    1994-01-01

    Briefs of the 1994 annual progress reports of the Research Fellows and students of the Center for Turbulence Research are presented. Subjects covered include turbulence combustion, large eddy simulation, Reynolds-averaged turbulence modeling, turbulence control, postprocessing, sound generation, and turbulence physics.