WorldWideScience

Sample records for joint genome institute

  1. Joint Genome Institute's Automation Approach and History

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Simon

    2006-07-05

    Department of Energy/Joint Genome Institute (DOE/JGI) collaborates with DOE national laboratories and community users, to advance genome science in support of the DOE missions of clean bio-energy, carbon cycling, and bioremediation.

  2. A Taste of Algal Genomes from the Joint Genome Institute

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2012-06-17

    Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

  3. The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

    Energy Technology Data Exchange (ETDEWEB)

    Nordberg, Henrik [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Cantor, Michael [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dusheyko, Serge [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hua, Susan [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Poliakov, Alexander [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Shabalov, Igor [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Smirnova, Tatyana [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dubchak, Inna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

    2013-11-12

    The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. In this paper, we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

  4. 2012 U.S. Department of Energy: Joint Genome Institute: Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, David [DOE JGI Public Affairs Manager

    2013-01-01

    The mission of the U.S. Department of Energy Joint Genome Institute (DOE JGI) is to serve the diverse scientific community as a user facility, enabling the application of large-scale genomics and analysis of plants, microbes, and communities of microbes to address the DOE mission goals in bioenergy and the environment. The DOE JGI's sequencing efforts fall under the Eukaryote Super Program, which includes the Plant and Fungal Genomics Programs; and the Prokaryote Super Program, which includes the Microbial Genomics and Metagenomics Programs. In 2012, several projects made news for their contributions to energy and environment research.

  5. DOE Joint Genome Institute 2008 Progress Report

    International Nuclear Information System (INIS)

    Gilbert, David

    2009-01-01

    While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic technological change is presently underway at the JGI. The Sanger capillary-based sequencing process that

  6. DOE Joint Genome Institute 2008 Progress Report

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, David

    2009-03-12

    While initially a virtual institute, the driving force behind the creation of the DOE Joint Genome Institute in Walnut Creek, California in the Fall of 1999 was the Department of Energy's commitment to sequencing the human genome. With the publication in 2004 of a trio of manuscripts describing the finished 'DOE Human Chromosomes', the Institute successfully completed its human genome mission. In the time between the creation of the Department of Energy Joint Genome Institute (DOE JGI) and completion of the Human Genome Project, sequencing and its role in biology spread to fields extending far beyond what could be imagined when the Human Genome Project first began. Accordingly, the targets of the DOE JGI's sequencing activities changed, moving from a single human genome to the genomes of large numbers of microbes, plants, and other organisms, and the community of users of DOE JGI data similarly expanded and diversified. Transitioning into operating as a user facility, the DOE JGI modeled itself after other DOE user facilities, such as synchrotron light sources and supercomputer facilities, empowering the science of large numbers of investigators working in areas of relevance to energy and the environment. The JGI's approach to being a user facility is based on the concept that by focusing state-of-the-art sequencing and analysis capabilities on the best peer-reviewed ideas drawn from a broad community of scientists, the DOE JGI will effectively encourage creative approaches to DOE mission areas and produce important science. This clearly has occurred, only partially reflected in the fact that the DOE JGI has played a major role in more than 45 papers published in just the past three years alone in Nature and Science. The involvement of a large and engaged community of users working on important problems has helped maximize the impact of JGI science. A seismic technological change is presently underway at the JGI. The Sanger capillary

  7. 2013 Progress Report -- DOE Joint Genome Institute

    Energy Technology Data Exchange (ETDEWEB)

    None

    2013-11-01

    In October 2012, we introduced a 10-Year Strategic Vision [http://bit.ly/JGI-Vision] for the Institute. A central focus of this Strategic Vision is to bridge the gap between sequenced genomes and an understanding of biological functions at the organism and ecosystem level. This involves the continued massive-scale generation of sequence data, complemented by orthogonal new capabilities to functionally annotate these large sequence data sets. Our Strategic Vision lays out a path to guide our decisions and ensure that the evolving set of experimental and computational capabilities available to DOE JGI users will continue to enable groundbreaking science.

  8. Joint Quantum Institute

    Data.gov (United States)

    Federal Laboratory Consortium — The Joint Quantum Institute (JQI) is pursuing that goal through the work of leading quantum scientists from the Department of Physics of the University of Maryland...

  9. Joint Global Change Research Institute (JGCRI)

    Data.gov (United States)

    Federal Laboratory Consortium — The Joint Global Change Research Institute (JGCRI) is dedicated to understanding the problems of global climate change and their potential solutions. The Institute...

  10. The integrated microbial genome resource of analysis.

    Science.gov (United States)

    Checcucci, Alice; Mengoni, Alessio

    2015-01-01

    Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.

  11. 75 FR 8374 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-02-24

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Officer, Scientific Review Branch, National Human Genome Research Institute, National Institutes of Health...

  12. 78 FR 21382 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-04-10

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... applications. Place: National Human Genome Research Institute, Suite 4076, 5635 Fisher's Lane, Bethesda, MD..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4075...

  13. 77 FR 8268 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-02-14

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... applications. Place: National Human Genome Research Institute, 5635 Fisher's Lane, Room 4076, Rockville, MD..., CIDR, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite...

  14. 77 FR 71604 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-12-03

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special..., Scientific Review Branch, National Human Genome Research Institute, National Institutes of Health, 5635...

  15. 75 FR 53703 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-09-01

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., Scientific Review Branch, National Human Genome Research Institute, National Institutes of Health, 5635.... (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  16. 77 FR 74676 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-12-17

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4075, Bethesda.... 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: December 11, 2012. David...

  17. 76 FR 10909 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-02-28

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, MSC..., Human Genome Research, National Institutes of Health, HHS). Dated: February 18, 2011. Jennifer S. Spaeth...

  18. 77 FR 35991 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-06-15

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4075, Bethesda.... 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: June 8, 2012. Jennifer S...

  19. 75 FR 8977 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-02-26

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4076, MSC..., Human Genome Research, National Institutes of Health, HHS) Dated: February 18, 2010. Jennifer Spaeth...

  20. 75 FR 67380 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-11-02

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Review Branch, National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane.... (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  1. 76 FR 29772 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2011-05-23

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research... of Scientific Review, National Human Genome Research Institute, National Institutes of Health...

  2. 77 FR 5035 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-02-01

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research... Officer, Scientific Review Branch, National Human Genome Research Institute, National Institutes of Health...

  3. 78 FR 107 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-01-02

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... evaluate grant applications. Place: National Human Genome Research Institute, 3rd Floor Conference Room....D., Scientific Review Officer, Scientific Review Branch, National Human Genome Research Institute...

  4. 78 FR 64222 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2013-10-28

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research... Review, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, 301...

  5. 78 FR 20933 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-04-08

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... review and evaluate grant applications. Place: National Human Genome Research Institute, Room 3055, 5635...

  6. 78 FR 31953 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-05-28

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... review and evaluate grant applications. Place: National Human Genome Research Institute, 3rd Floor...

  7. 77 FR 22332 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-04-13

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special.... Agenda: To review and evaluate grant applications. Place: National Human Genome Research Institute, 5635...

  8. 75 FR 19984 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2010-04-16

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute, National Institutes of Health, 5635 Fishers Lane, Suite 4075... Nakamura, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome Research...

  9. 76 FR 28056 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-05-13

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Counselors, National Human Genome Research Institute. The meeting will be closed to the public as indicated... National Human Genome Research Institute, including consideration of personnel qualifications and...

  10. 76 FR 17930 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-03-31

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Review Officer, Scientific Review Branch, National Human Genome Research Institute, 5635 Fishers Lane...

  11. 76 FR 58023 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-09-19

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Initial..., Scientific Review Officer, Office of Scientific Review, National Human Genome Research Institute, National...

  12. 77 FR 28888 - National Human Genome Research Institute Notice of Closed Meeting

    Science.gov (United States)

    2012-05-16

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Initial...: To review and evaluate grant applications. Place: National Human Genome Research Institute, 3635...

  13. 78 FR 70063 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-11-22

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Counselors, National Human Genome Research Institute. The meeting will be closed to the public as indicated... NATIONAL HUMAN GENOME RESEARCH INSTITUTE, including consideration of personnel qualifications and...

  14. 76 FR 5390 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-01-31

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Place: National Human Genome Research Institute Special Emphasis... Officer, Scientific Review Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076...

  15. 75 FR 13558 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-03-22

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Counselors, National Human Genome Research Institute. The meeting will be closed to the public as indicated... National Human Genome Research Institute, including consideration of personnel qualifications and...

  16. 76 FR 19780 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-04-08

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research Institute, National... . (Catalogue of Federal Domestic Assistance Program No. 93.172, Human Genome Research, National Institutes of...

  17. 76 FR 3917 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-01-21

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9306, Rockville, MD...

  18. 75 FR 56115 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-09-15

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS...

  19. 76 FR 3643 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-01-20

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Initial... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  20. 78 FR 24223 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-04-24

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Initial...: To review and evaluate grant applications. Place: National Human Genome Research Institute, 3rd floor...

  1. 76 FR 22407 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-04-21

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special.... (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  2. 75 FR 26762 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-05-12

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Initial... . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research, National Institutes of...

  3. 77 FR 31863 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-05-30

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special..., Human Genome Research, National Institutes of Health, HHS) Dated: May 22, 2012. Jennifer S. Spaeth...

  4. 76 FR 66731 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-10-27

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: October 21, 2011...

  5. 76 FR 36930 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-06-23

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special..., Human Genome Research, National Institutes of Health, HHS) Dated: June 17, 2011. Jennifer S. Spaeth...

  6. 77 FR 61770 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-10-11

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) [[Page 61771...

  7. 76 FR 63932 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-10-14

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: October 7...

  8. 77 FR 2735 - National Human Genome Research Institute; Notice of Meetings

    Science.gov (United States)

    2012-01-19

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... personal privacy. Name of Committee: National Advisory Council for Human Genome Research. Date: February 13... Extramural Research National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9305...

  9. 75 FR 51828 - National Human Genome Research Institute; Notice of Meetings

    Science.gov (United States)

    2010-08-23

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... personal privacy. Name of Committee: National Advisory Council for Human Genome Research. Date: February 7... Research, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9305, Bethesda, MD...

  10. 78 FR 66752 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2013-11-06

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... National Human Genome Research Institute Special Emphasis Panel, October 15, 2013, 01:00 p.m. to October 15, 2013, 02:30 p.m., National Human Genome Research Institute, 5635 Fishers Lane, Suite 3055, Rockville...

  11. 77 FR 2304 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2012-01-17

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome....S.C. 281(d)(4)), notice is hereby given that the National Human Genome Research Institute (NHGRI... meeting of the National Advisory Council for Human Genome Research. Background materials on the proposed...

  12. 77 FR 64816 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2012-10-23

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute. The meeting will be open to the public as indicated below, with... invasion of personal privacy. Name of Committee: Board of Scientific Counselors, National Human Genome...

  13. 75 FR 2147 - National Human Genome Research Institute; Notice of Meetings

    Science.gov (United States)

    2010-01-14

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Council for Human Genome Research. The meetings will be open to the public as indicated below, with... Extramural Research, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076, MSC 9305...

  14. 76 FR 65204 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2011-10-20

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute. The meeting will be open to the public as indicated below, with... invasion of personal privacy. Name of Committee: Board of Scientific Counselors, National Human Genome...

  15. 75 FR 60467 - National Human Genome Research Institute; Notice of Meeting

    Science.gov (United States)

    2010-09-30

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., National Human Genome Research Institute. The meeting will be open to the public as indicated below, with... invasion of personal privacy. Name of Committee: Board of Scientific Counselors, National Human Genome...

  16. 77 FR 59933 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-10-01

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research....D., Scientific Review Officer, Scientific Review Branch, National Human Genome Research Institute...

  17. 77 FR 58402 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-09-20

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research...: To review and evaluate grant applications. Place: National Human Genome Research Institute, 5635...

  18. 77 FR 60706 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-10-04

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special.... Nakamura, Ph.D., Scientific Review Officer, Scientific Review Branch, National Human Genome Research...

  19. 77 FR 20646 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-04-05

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research.... Agenda: To review and evaluate grant applications. Place: National Human Genome Research Institute, 5635...

  20. 76 FR 22112 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-04-20

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special....nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  1. 75 FR 10488 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2010-03-08

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research...- 4280, [email protected]gov . Name of Committee: National Human Genome Research Institute Special...

  2. 76 FR 65204 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2011-10-20

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... constitute a clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome... Review Officer, Scientific Review Branch, National Human Genome Research Institute, 5635 Fishers Lane...

  3. 75 FR 8373 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-02-24

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute [email protected] . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  4. 77 FR 12604 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-03-01

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. >Name of Committee: National Human Genome Research... review and evaluate contract proposals. Place: National Human Genome Reseach Institute, 5635 Fishers Lane...

  5. 76 FR 3642 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2011-01-20

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research....nih.gov . Name of Committee: National Human Genome Research Institute Special Emphasis Panel eMERGE...

  6. 75 FR 52537 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-08-26

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Initial....nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  7. 75 FR 2148 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-01-14

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Initial....nih.gov . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  8. 78 FR 9707 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2013-02-11

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research... Officer, Scientific Review Branch, National Human Genome Research Institute, 5635 Fishers Lane, Suite 4076...

  9. 75 FR 32957 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-06-10

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... funding cycle. (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  10. 78 FR 14806 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-03-07

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... p.m. Agenda: To review and evaluate grant applications. Place: National Human Genome Research...

  11. 75 FR 52538 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-08-26

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Person: Ken D. Nakamura, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome...

  12. 76 FR 35223 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-06-16

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... Person: Rudy O. Pozzatti, PhD, Scientific Review Officer, Scientific Review Branch, National Human Genome...

  13. 76 FR 66076 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-10-25

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Call). Contact Person: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: October 19...

  14. 78 FR 61851 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-10-04

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research Institute Special... a.m. to 4:00 p.m. Agenda: To review and evaluate grant applications. Place: National Human Genome...

  15. 75 FR 80509 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-12-22

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Call). Contact Person: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome... Assistance Program Nos. 93.172, Human Genome Research, National Institutes of Health, HHS) Dated: December 16...

  16. Institute for Genomics and Systems Biology

    Science.gov (United States)

    Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

  17. 77 FR 67385 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2012-11-09

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research Institute Special Emphasis Panel, October 29, 2012, 8:00 a.m. to October 30...

  18. 78 FR 65342 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2013-10-31

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research Institute Special Emphasis Panel, October 17, 2013, 08:00 a.m. to October 17...

  19. 76 FR 65738 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2011-10-24

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research Institute Special Emphasis Panel, November 29, 2011, 8 a.m. to November 29...

  20. 76 FR 71581 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2011-11-18

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Human Genome Research Institute Special Emphasis Panel, November 22, 2011, 12 p.m. to November 22...

  1. Bayesian methods for jointly estimating genomic breeding values of one continuous and one threshold trait.

    Directory of Open Access Journals (Sweden)

    Chonglong Wang

    Full Text Available Genomic selection has become a useful tool for animal and plant breeding. Currently, genomic evaluation is usually carried out using a single-trait model. However, a multi-trait model has the advantage of using information on the correlated traits, leading to more accurate genomic prediction. To date, joint genomic prediction for a continuous and a threshold trait using a multi-trait model is scarce and needs more attention. Based on the previously proposed methods BayesCπ for single continuous trait and BayesTCπ for single threshold trait, we developed a novel method based on a linear-threshold model, i.e., LT-BayesCπ, for joint genomic prediction of a continuous trait and a threshold trait. Computing procedures of LT-BayesCπ using Markov Chain Monte Carlo algorithm were derived. A simulation study was performed to investigate the advantages of LT-BayesCπ over BayesCπ and BayesTCπ with regard to the accuracy of genomic prediction on both traits. Factors affecting the performance of LT-BayesCπ were addressed. The results showed that, in all scenarios, the accuracy of genomic prediction obtained from LT-BayesCπ was significantly increased for the threshold trait compared to that from single trait prediction using BayesTCπ, while the accuracy for the continuous trait was comparable with that from single trait prediction using BayesCπ. The proposed LT-BayesCπ could be a method of choice for joint genomic prediction of one continuous and one threshold trait.

  2. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  3. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  4. Joint Institute for Nanoscience Annual Report 2004

    Energy Technology Data Exchange (ETDEWEB)

    Baer, Donald R.; Campbell, Charles

    2005-02-01

    Due to the inherently interdisciplinary nature of nanoscience and nanotechnology, research in this arena is often significantly enhanced through creative cooperative activities. The Joint Institute for Nanoscience (JIN) is a venture of the University of Washington (UW) and Pacific Northwest National Laboratory (PNNL) to encourage and enhance high impact and high quality nanoscience and nanotechnology research that leverages the strengths and capabilities of both institutions, and to facilitate education in these areas. This report summarizes JIN award activities that took place during fiscal year 2004 and provides a historical list of JIN awardees, their resulting publications, and JIN-related meetings. Major portions of the JIN efforts and resources are dedicated to funding graduate students and postdoctoral research associates to perform research in collaborations jointly directed by PNNL staff scientists and UW professors. JIN fellowships are awarded on the basis of applications that include research proposals. They have been very successful in expanding collaborations between PNNL and UW, which have led to many excellent joint publications and presentations and enhanced the competitiveness of both institutions for external grant funding. JIN-based interactions are playing a significant role in creating new research directions and reshaping existing research programs at both the UW and PNNL. The JIN also co-sponsors workshops on Nanoscale Science and Technology, four of which have been held in Seattle and one in Richland. In addition to involving PNNL staff in various UW nanoscience courses and seminars, a National Science Foundation grant, Development of UW-PNL Collaborative Curriculums in Nano-Science and Technology, has allowed the development of three intensive short courses that are taught by UW faculty, PNNL staff, and faculty from other institutions, including Washington State University, the University of Idaho, Stanford University, and the University of

  5. 77 FR 64816 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-10-23

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., Human Genome Research, National Institutes of Health, HHS) Dated: October 16, 2012. David Clary, Program... Conference Call). Contact Person: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human...

  6. 78 FR 11898 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-02-20

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome....172, Human Genome Research, National Institutes of Health, HHS) Dated: February 13, 2013. David Clary... Conference Call). Contact Person: Camilla E. Day, Ph.D., Scientific Review Officer CIDR, National Human...

  7. 78 FR 77477 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-12-23

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., Human Genome Research, National Institutes of Health, HHS). Dated: December 17, 2013. David Clary... Conference Call). Contact Person: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human...

  8. 77 FR 50140 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2012-08-20

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome..., Human Genome Research, National Institutes of Health, HHS) Dated: August 13, 2012. Anna Snouffer, Deputy..., Bethesda, MD 20892. Contact Person: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human...

  9. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

    Science.gov (United States)

    Manolio, Teri A

    2016-10-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

  10. 77 FR 55853 - National Human Genome Research Institute; Amended Notice of Meeting

    Science.gov (United States)

    2012-09-11

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Advisory Council for Human Genome Research, September 10, 2012, 8:30 a.m. to September 11, 2012, 5...

  11. What does it mean to be genomically literate?: National Human Genome Research Institute Meeting Report.

    Science.gov (United States)

    Hurle, Belen; Citrin, Toby; Jenkins, Jean F; Kaphingst, Kimberly A; Lamb, Neil; Roseman, Jo Ellen; Bonham, Vence L

    2013-08-01

    Genomic discoveries will increasingly advance the science of medicine. Limited genomic literacy may adversely impact the public's understanding and use of the power of genetics and genomics in health care and public health. In November 2011, a meeting was held by the National Human Genome Research Institute to examine the challenge of achieving genomic literacy for the general public, from kindergarten to grade 12 to adult education. The role of the media in disseminating scientific messages and in perpetuating or reducing misconceptions was also discussed. Workshop participants agreed that genomic literacy will be achieved only through active engagement between genomics experts and the varied constituencies that comprise the public. This report summarizes the background, content, and outcomes from this meeting, including recommendations for a research agenda to inform decisions about how to advance genomic literacy in our society.

  12. 77 FR 27471 - National Human Genome Research Institute Amended Notice of Meeting

    Science.gov (United States)

    2012-05-10

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome Research Institute Amended Notice of Meeting Notice is hereby given of a change in the meeting of the National Advisory Council for Human Genome Research, May 21, 2012, 8:30 a.m. to May 22, 2012, 5:00 p.m...

  13. 78 FR 55752 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2013-09-11

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research.... Pozzatti, Ph.D., Scientific Review Officer, Scientific Review Branch, National Human Genome Research...

  14. 78 FR 56905 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-09-16

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research....m. Agenda: To review and evaluate grant applications. Place: National Human Genome Research...

  15. 76 FR 28056 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2011-05-13

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... clearly unwarranted invasion of personal privacy. Name of Committee: National Human Genome Research... D. Nakamura, PhD, Scientific Review Officer, Office of Scientific Review, National Human Genome...

  16. 76 FR 35224 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-06-16

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome...). Contact Person: Camilla E. Day, PhD, Scientific Review Officer, CIR, National Human Genome Research..., [email protected] . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  17. 75 FR 48977 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-08-12

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome.... Contact Person: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research..., [email protected] . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  18. 75 FR 35821 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-06-23

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Person: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome Research [email protected] . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  19. 78 FR 47715 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-08-06

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Person: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research [email protected] . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  20. 76 FR 79199 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-12-21

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome.... Contact Person: Camilla E. Day, Ph.D., Scientific Review Officer, CIDR, National Human Genome Research..., [email protected] . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human Genome Research...

  1. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  2. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  3. 78 FR 68856 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2013-11-15

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Nakamura, Ph.D., Scientific Review Officer, Scientific Review Branch, National Human Genome Research...-402-0838. [[Page 68857

  4. 75 FR 44800 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-07-29

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... for Human Genome Research. The meeting will be closed to the public in accordance with the provisions... Committee: National Advisory Council for Human Genome Research. Date: August 18, 2010. Time: 1 p.m. to 3 p.m...

  5. Joint Genomic Prediction of Canine Hip Dysplasia in UK and US Labrador Retrievers

    Directory of Open Access Journals (Sweden)

    Stefan M. Edwards

    2018-03-01

    Full Text Available Canine hip dysplasia, a debilitating orthopedic disorder that leads to osteoarthritis and cartilage degeneration, is common in several large-sized dog breeds and shows moderate heritability suggesting that selection can reduce prevalence. Estimating genomic breeding values require large reference populations, which are expensive to genotype for development of genomic prediction tools. Combining datasets from different countries could be an option to help build larger reference datasets without incurring extra genotyping costs. Our objective was to evaluate genomic prediction based on a combination of UK and US datasets of genotyped dogs with records of Norberg angle scores, related to canine hip dysplasia. Prediction accuracies using a single population were 0.179 and 0.290 for 1,179 and 242 UK and US Labrador Retrievers, respectively. Prediction accuracies changed to 0.189 and 0.260, with an increased bias of genomic breeding values when using a joint training set (biased upwards for the US population and downwards for the UK population. Our results show that in this study of canine hip dysplasia, little or no benefit was gained from using a joint training set as compared to using a single population as training set. We attribute this to differences in the genetic background of the two populations as well as the small sample size of the US dataset.

  6. Joint Institute for Nanoscience Annual Report 2003

    Energy Technology Data Exchange (ETDEWEB)

    Baer, Donald R.; Campbell, Charles

    2004-02-01

    The Joint Institute for Nanoscience (JIN) is a cooperative venture of the University of Washington and Pacific Northwest National Laboratory to encourage and enhance high-impact and high-quality nanoscience and nanotechnology of all types. This first annual report for the JIN summarizes activities beginning in 2001 and ending at the close of fiscal year 2003 and therefore represents somewhat less than two years of activities. Major portions of the JIN resources are dedicated to funding graduate students and postdoctoral research associates to perform research in collaborations jointly directed by Pacific Northwest National Laboratory (PNNL) staff scientists and University of Washington (UW) professors. These fellowships were awarded on the basis of applications that included research proposals. JIN co-sponsors an annual Nanoscale Science and Technology Workshop held in Seattle. In addition to involving PNNL staff in various UW nanoscience courses and seminars, a National Science Foundation grant Development of UW-PNL Collaborative Curriculums in Nano-Science and Technology has allowed the development of three intensive short courses that are taught by UW faculty, PNNL staff, and faculty from other institutions, including Washington State University, the University of Idaho, Stanford University, and the University of Alaska. The initial JIN agreement recognized that expansion of cooperation beyond UW and PNNL would be highly valuable. Starting in early 2003, efforts were initiated to form a regional communication link called the Northwest Nanoscience and Nanotechnology Network (N₄). In concept, N₄ is a tool to encourage communication and help identify regional resources and nanoscience and technology activities.

  7. 76 FR 9031 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-02-16

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Call). Contact Person: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome...- 402-8837, [email protected] . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human...

  8. 75 FR 62548 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2010-10-12

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Call). Contact Person: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome...- 402-8837, [email protected] . Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human...

  9. 76 FR 50486 - National Human Genome Research Institute; Notice of Closed Meeting

    Science.gov (United States)

    2011-08-15

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES National Institutes of Health National Human Genome... Conference Call). Contact Person: Camilla E. Day, PhD, Scientific Review Officer, CIDR, National Human Genome...- 402-8837, [email protected] . (Catalogue of Federal Domestic Assistance Program Nos. 93.172, Human...

  10. Improving genomic prediction for Danish Jersey using a joint Danish-US reference population

    DEFF Research Database (Denmark)

    Su, Guosheng; Nielsen, Ulrik Sander; Wiggans, G

    Accuracy of genomic prediction depends on the information in the reference population. Achieving an adequate sized reference population is a challenge for genomic prediction in small cattle populations. One way to increase the size of reference population is to combine reference data from different...... populations. The objective of this study was to assess the gain of genomic prediction accuracy when including US Jersey bulls in the Danish Jersey reference population. The data included 1,262 Danish progeny-tested bulls and 1,157 US progeny-tested bulls. Genomic breeding values (GEBV) were predicted using...... a GBLUP model from the Danish reference population and the joint Danish-US reference population. The traits in the analysis were milk yield, fat yield, protein yield, fertility, mastitis, longevity, body conformation, feet & legs, and longevity. Eight of the nine traits benefitted from the inclusion of US...

  11. Complete Genome Sequence of the Hyperthermophilic Sulfate-Reducing Bacterium Thermodesulfobacterium geofontis OPF15T.

    Science.gov (United States)

    Elkins, James G; Hamilton-Brehm, Scott D; Lucas, Susan; Han, James; Lapidus, Alla; Cheng, Jan-Fang; Goodwin, Lynne A; Pitluck, Sam; Peters, Lin; Mikhailova, Natalia; Davenport, Karen W; Detter, John C; Han, Cliff S; Tapia, Roxanne; Land, Miriam L; Hauser, Loren; Kyrpides, Nikos C; Ivanova, Natalia N; Pagani, Ioanna; Bruce, David; Woyke, Tanja; Cottingham, Robert W

    2013-04-11

    Thermodesulfobacterium geofontis OPF15(T) (ATCC BAA-2454, JCM 18567) was isolated from Obsidian Pool, Yellowstone National Park, and grows optimally at 83°C. The 1.6-Mb genome sequence was finished at the Joint Genome Institute and has been deposited for future genomic studies pertaining to microbial processes and nutrient cycles in high-temperature environments.

  12. The accelerators of the Joint Institute for Nuclear Research at Dubna

    International Nuclear Information System (INIS)

    Kuehn, B.

    1981-01-01

    History, state-of-the-art, and the planned development of the high-energy and heavy-ion accelerators at the Joint Institute for Nuclear Research at Dubna are reviewed. Data on the particle beams available at present and in the future are given. (author)

  13. The report of joint research over 20 years of the Bulgarian Academy of Sciences and Hiroshima Institute of Technology

    OpenAIRE

    Tanaka,Takeshi; Vutova,Katia

    2014-01-01

    The Department of Electronics and Computer Engineering, Hiroshima Institute of Technology (EC-HIT) started the international joint research with the Laboratory “Physical Problems of Electron Beam technologies” of the Institute of Electronics, Bulgarian Academy of Sciences (IE-BAS) from 1994. 20 papers, included a book chapter, were published by implementing the international joint research under 5 Agreements for Academic Cooperation and Exchange between HIT and IEBAS. Our international joint ...

  14. Conceptualizing a Genomics Software Institute (GSI).

    Science.gov (United States)

    Gilbert, Jack A; Catlett, Charlie; Desai, Narayan; Knight, Rob; White, Owen; Robbins, Robert; Sankaran, Rajesh; Sansone, Susanna-Assunta; Field, Dawn; Meyer, Folker

    2012-03-19

    Microbial ecology has been enhanced greatly by the ongoing 'omics revolution, bringing half the world's biomass and most of its biodiversity into analytical view for the first time; indeed, it feels almost like the invention of the microscope and the discovery of the new world at the same time. With major microbial ecology research efforts accumulating prodigious quantities of sequence, protein, and metabolite data, we are now poised to address environmental microbial research at macro scales, and to begin to characterize and understand the dimensions of microbial biodiversity on the planet. What is currently impeding progress is the need for a framework within which the research community can develop, exchange and discuss predictive ecosystem models that describe the biodiversity and functional interactions. Such a framework must encompass data and metadata transparency and interoperation; data and results validation, curation, and search; application programming interfaces for modeling and analysis tools; and human and technical processes and services necessary to ensure broad adoption. Here we discuss the need for focused community interaction to augment and deepen established community efforts, beginning with the Genomic Standards Consortium (GSC), to create a science-driven strategic plan for a Genomic Software Institute (GSI).

  15. Joint Institute for Nuclear Research Exhibition Science Bringing Nations Together

    CERN Multimedia

    2000-01-01

    The JOINT INSTITUTE FOR NUCLEAR RESEARCH, JINR, was established by its founding countries in 1956 with the purpose of joining together the scientific and material potential of Member States in studies of the fundamental properties of matter. JINR is an international inter-governmental scientific research organization, whose activities are based on the principles of openness for participation to all interested states and of their equal, mutually beneficial collaboration.

  16. Joint Institute for Nuclear Research Exhibition Science Bringing Nations Together

    CERN Multimedia

    1999-01-01

    The JOINT INSTITUTE FOR NUCLEAR RESEARCH, JINR, was established by its founding countries in 1956 with the purpose of joining together the scientific and material potential of Member States in studies of the fundamental properties of matter. JINR is an international inter-governmental scientific research organization, the activities of which are based on the principles of openness for participation to all interested states of their equal, mutually beneficial collaboration.

  17. 25 years of the Joint Institute for Nuclear Research in Dubna and Czechoslovakia's part in its activities

    International Nuclear Information System (INIS)

    Simane, C.; Tucek, J.

    1981-01-01

    The main tasks and results attained by the individual units of the Joint Institute for Nuclear Research in Dubna are briefly described: by the high energy laboratory, the nuclear problems laboratory, the laboratory of theoretical physics, the laboratory of neutron physics, the laboratory of nuclear reactions, the laboratory of computer technology and automation, and by the unit responsible for the implementation of the project for accelerators of positively charged ions based on the principle of collective acceleration using electron rings. Czechoslovakia contributes approximately 6% to the financing of the Institute. Also briefly described are the main fields of cooperation between Czechoslovak research institutes and the laboratories of the Joint Institute for Nuclear Research. (Z.M.)

  18. Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

    OpenAIRE

    Wright, James C.; Sugden, Deana; Francis-McIntyre, Sue; Riba Garcia, Isabel; Gaskell, Simon J.; Grigoriev, Igor V.; Baker, Scott E.; Beynon, Robert J.; Hubbard, Simon J.

    2009-01-01

    Abstract Background Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were ac...

  19. Impact of transgene genome location on gene migration from herbicide-resistant wheat (Triticum aestivum L.) to jointed goatgrass (Aegilops cylindrica Host).

    Science.gov (United States)

    Rehman, Maqsood; Hansen, Jennifer L; Mallory-Smith, Carol A; Zemetra, Robert S

    2017-08-01

    Wheat (Triticum aestivum) (ABD) and jointed goatgrass (Aegilops cylindrica) (CD) can cross and produce hybrids that can backcross to either parent. Such backcrosses can result in progeny with chromosomes and/or chromosome segments retained from wheat. Thus, a herbicide resistance gene could migrate from wheat to jointed goatgrass. In theory, the risk of gene migration from herbicide-resistant wheat to jointed goatgrass is more likely if the gene is located on the D genome and less likely if the gene is located on the A or B genome of wheat. BC 1 populations (jointed goatgrass as a recurrent parent) were analyzed for chromosome numbers and transgene transmission rates under sprayed and non-sprayed conditions. Transgene retention in the non-sprayed BC 1 generation for the A, B and D genomes was 84, 60 and 64% respectively. In the sprayed populations, the retention was 81, 59 and 74% respectively. The gene transmission rates were higher than the expected 50% or less under sprayed and non-sprayed conditions, possibly owing to meiotic chromosome restitution and/or chromosome non-disjunction. Such high transmission rates in the BC 1 generation negates the benefits of gene placement for reducing the potential of gene migration from wheat to jointed goatgrass. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  20. GAViT: Genome Assembly Visualization Tool for Short Read Data

    Energy Technology Data Exchange (ETDEWEB)

    Syed, Aijazuddin; Shapiro, Harris; Tu, Hank; Pangilinan, Jasmyn; Trong, Stephan

    2008-03-14

    It is a challenging job for genome analysts to accurately debug, troubleshoot, and validate genome assembly results. Genome analysts rely on visualization tools to help validate and troubleshoot assembly results, including such problems as mis-assemblies, low-quality regions, and repeats. Short read data adds further complexity and makes it extremely challenging for the visualization tools to scale and to view all needed assembly information. As a result, there is a need for a visualization tool that can scale to display assembly data from the new sequencing technologies. We present Genome Assembly Visualization Tool (GAViT), a highly scalable and interactive assembly visualization tool developed at the DOE Joint Genome Institute (JGI).

  1. Fungal Genomics for Energy and Environment

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2013-03-11

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  2. Genome Improvement at JGI-HAGSC

    Energy Technology Data Exchange (ETDEWEB)

    Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

    2012-03-03

    Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

  3. Joint analysis of three genome-wide association studies of esophageal squamous cell carcinoma in Chinese populations

    Science.gov (United States)

    Zhan, Qimin; Hu, Zhibin; He, Zhonghu; Jia, Weihua; Zhou, Yifeng; Yu, Kai; Shu, Xiao-Ou; Yuan, Jian-Min; Zheng, Wei; Zhao, Xue-Ke; Gao, She-Gan; Yuan, Zhi-Qing; Zhou, Fu-You; Fan, Zong-Min; Cui, Ji-Li; Lin, Hong-Li; Han, Xue-Na; Li, Bei; Chen, Xi; Dawsey, Sanford M.; Liao, Linda; Lee, Maxwell P.; Ding, Ti; Qiao, You-Lin; Liu, Zhihua; Liu, Yu; Yu, Dianke; Chang, Jiang; Wei, Lixuan; Gao, Yu-Tang; Koh, Woon-Puay; Xiang, Yong-Bing; Tang, Ze-Zhong; Fan, Jin-Hu; Han, Jing-Jing; Zhou, Sheng-Li; Zhang, Peng; Zhang, Dong-Yun; Yuan, Yuan; Huang, Ying; Liu, Chunling; Zhai, Kan; Qiao, Yan; Jin, Guangfu; Guo, Chuanhai; Fu, Jianhua; Miao, Xiaoping; Lu, Changdong; Yang, Haijun; Wang, Chaoyu; Wheeler, William A.; Gail, Mitchell; Yeager, Meredith; Yuenger, Jeff; Guo, Er-Tao; Li, Ai-Li; Zhang, Wei; Li, Xue-Min; Sun, Liang-Dan; Ma, Bao-Gen; Li, Yan; Tang, Sa; Peng, Xiu-Qing; Liu, Jing; Hutchinson, Amy; Jacobs, Kevin; Giffen, Carol; Burdette, Laurie; Fraumeni, Joseph F.; Shen, Hongbing; Ke, Yang; Zeng, Yixin; Wu, Tangchun; Kraft, Peter; Chung, Charles C.; Tucker, Margaret A.; Hou, Zhi-Chao; Liu, Ya-Li; Hu, Yan-Long; Liu, Yu; Wang, Li; Yuan, Guo; Chen, Li-Sha; Liu, Xiao; Ma, Teng; Meng, Hui; Sun, Li; Li, Xin-Min; Li, Xiu-Min; Ku, Jian-Wei; Zhou, Ying-Fa; Yang, Liu-Qin; Wang, Zhou; Li, Yin; Qige, Qirenwang; Yang, Wen-Jun; Lei, Guang-Yan; Chen, Long-Qi; Li, En-Min; Yuan, Ling; Yue, Wen-Bin; Wang, Ran; Wang, Lu-Wen; Fan, Xue-Ping; Zhu, Fang-Heng; Zhao, Wei-Xing; Mao, Yi-Min; Zhang, Mei; Xing, Guo-Lan; Li, Ji-Lin; Han, Min; Ren, Jing-Li; Liu, Bin; Ren, Shu-Wei; Kong, Qing-Peng; Li, Feng; Sheyhidin, Ilyar; Wei, Wu; Zhang, Yan-Rui; Feng, Chang-Wei; Wang, Jin; Yang, Yu-Hua; Hao, Hong-Zhang; Bao, Qi-De; Liu, Bao-Chi; Wu, Ai-Qun; Xie, Dong; Yang, Wan-Cai; Wang, Liang; Zhao, Xiao-Hang; Chen, Shu-Qing; Hong, Jun-Yan; Zhang, Xue-Jun; Freedman, Neal D; Goldstein, Alisa M.; Lin, Dongxin; Taylor, Philip R.; Wang, Li-Dong; Chanock, Stephen J.

    2014-01-01

    We conducted a joint (pooled) analysis of three genome-wide association studies (GWAS) 1-3 of esophageal squamous cell carcinoma (ESCC) in ethnic Chinese (5,337 ESCC cases and 5,787 controls) with 9,654 ESCC cases and 10,058 controls for follow-up. In a logistic regression model adjusted for age, sex, study, and two eigenvectors, two new loci achieved genome-wide significance, marked by rs7447927 at 5q31.2 (per-allele odds ratio (OR) = 0.85, 95% CI 0.82-0.88; P=7.72x10−20) and rs1642764 at 17p13.1 (per-allele OR= 0.88, 95% CI 0.85-0.91; P=3.10x10−13). rs7447927 is a synonymous single nucleotide polymorphism (SNP) in TMEM173 and rs1642764 is an intronic SNP in ATP1B2, near TP53. Furthermore, a locus in the HLA class II region at 6p21.32 (rs35597309) achieved genome-wide significance in the two populations at highest risk for ESSC (OR=1.33, 95% CI 1.22-1.46; P=1.99x10−10). Our joint analysis identified new ESCC susceptibility loci overall as well as a new locus unique to the ESCC high risk Taihang Mountain region. PMID:25129146

  4. National Human Genome Research Institute

    Science.gov (United States)

    ... Care Genomic Medicine Working Group New Horizons and Research Patient Management Policy and Ethics Issues Quick Links for Patient Care Education All About the Human Genome Project Fact Sheets Genetic Education Resources for ...

  5. 77 FR 6810 - National Human Genome Research Institute; Notice of Closed Meetings

    Science.gov (United States)

    2012-02-09

    .... Pozzatti, Ph.D., Scientific Review Officer, Scientific Review Branch, National Human Genome Research... Institute Special Emphasis Panel; ENCODE Production SEP (M1). Date: March 5, 2012. Time: 8 a.m. to 5 p.m... Potomac Avenue, Studio 6, Arlington, VA 22202. Contact Person: Keith McKenney, Ph.D., Scientific Review...

  6. Introduction to Metagenomics at DOE JGI: Program Overview and Program Informatics (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

    Energy Technology Data Exchange (ETDEWEB)

    Tringe, Susannah

    2011-10-12

    Susannah Tringe of the DOE Joint Genome Institute talks about the Program Overview and Program Informatics at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

  7. A Collection of Algal Genomes from the JGI

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2012-03-19

    Algae, defined as photosynthetic eukaryotes other than plants, constitute a major component of fundamental eukaryotic diversity. Acquisition of the ability to conduct oxygenic photosynthesis through endosymbiotic events has been a principal driver of eukaryotic evolution, and today algae continue to underpin aquatic food chains as primary producers. Algae play profound roles in the carbon cycle, can impose health and economic costs through toxic blooms, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE?s Joint Genome Institute (JGI). A collection of algal projects ongoing at JGI contributes to each of these areas and illustrates analyses employed in their genome exploration.

  8. A 'joint venture' model of recontacting in clinical genomics: challenges for responsible implementation.

    Science.gov (United States)

    Dheensa, Sandi; Carrieri, Daniele; Kelly, Susan; Clarke, Angus; Doheny, Shane; Turnpenny, Peter; Lucassen, Anneke

    2017-07-01

    Advances in genomics often lead healthcare professionals (HCPs) to learn new information, e.g., about reinterpreted variants that could have clinical significance for patients seen previously. A question arises of whether HCPs should recontact these former patients. We present some findings interrogating the views of patients (or parents of patients) with a rare or undiagnosed condition about how such recontacting might be organised ethically and practically. Forty-one interviews were analysed thematically. Participants suggested a 'joint venture' model in which efforts to recontact are shared with HCPs. Some proposed an ICT-approach involving an electronic health record that automatically alerts them to potentially relevant updates. The need for rigorous privacy controls and transparency about who could access their data was emphasised. Importantly, these findings highlight that the lack of clarity about recontacting is a symptom of a wider problem: the lack of necessary infrastructure to pool genomic data responsibly, to aggregate it with other health data, and to enable patients/parents to receive updates. We hope that our findings will instigate a debate about the way responsibilities for recontacting under any joint venture model could be allocated, as well as the limitations and normative implications of using ICT as a solution to this intractable problem. As a first step to delineating responsibilities in the clinical setting, we suggest HCPs should routinely discuss recontacting with patients/parents, including the new information that should trigger a HCP to initiate recontact, as part of the consent process for genetic testing. Copyright © 2017 The Authors. Published by Elsevier Masson SAS.. All rights reserved.

  9. A history of the collaboration between the European Organisation for Nuclear Research (CERN) and the Joint Institute for Nuclear Research (JINR), and with Soviet research institutes in the USSR 1955-1970

    International Nuclear Information System (INIS)

    Lock, W.O.

    1975-01-01

    The report describes in some detail the origins and development up to 1970 of the collaboration which now exists between the European Organization for Nuclear Research (CERN) and its counterpart the Joint Institute for Nuclear Research (JINR) at Dubna, USSR and also with the Institute for High Energy Physics, Serpukhov, USSR. Part 1 deals with the relations between JINR and CERN, their beginnings and the subsequent development of exchange of scientists, joint Summer Schools, and the organization of Seminars to discuss perspectives in high energy physics. Part 2 describes first the steps which led up to the signing of an Agreement between CERN and the State Committee of the USSR for the Utilization of Atomic Energy, governing collaboration between CERN and the Institute for High Energy Physics at Serpukhov. A brief account is then given of the subsequent installation of equipment built at CERN for the Institute's 76-Gev proton accelerator and the carrying out of joint physics experiments by teams from Western Europe and from the Soviet Union. Part 3 summarizes the origins of collaborative agreements which have been made by CERN with a few other leading Institutes in the Soviet Union. A number of Annexes reproduce some of the relevant documents and letters. (author)

  10. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes

    Energy Technology Data Exchange (ETDEWEB)

    Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard; Schoch, Conrad L.; Horwitz, Benjamin A.; Barry, Kerrie W.; Condon, Bradford J.; Copeland, Alex C.; Dhillon, Braham; Glaser, Fabian; Hesse, Cedar N.; Kosti, Idit; LaButti, Kurt; Lindquist, Erika A.; Lucas, Susan; Salamov, Asaf A.; Bradshaw, Rosie E.; Ciuffetti, Lynda; Hamelin, Richard C.; Kema, Gert H. J.; Lawrence, Christopher; Scott, James A.; Spatafora, Joseph W.; Turgeon, B. Gillian; de Wit, Pierre J. G. M.; Zhong, Shaobin; Goodwin, Stephen B.; Grigoriev, Igor V.

    2013-03-05

    The class of Dothideomycetes is one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops that are grown for biofuel, food or feed. Most Dothideomycetes have only a single host plant, and related species can have very diverse hosts. Eighteen genomes of Dothideomycetes have currently been sequenced by the Joint Genome Institute and other sequencing centers. Here we describe the results of comparative analyses of the fungi in this group.

  11. Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Doethideomycetes Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard; Schoch, Conrad L.; Horwitz, Benjamin A.; Barry, Kerrie W.; Condon, Bradford J.; Copeland, Alex C.; Dhillon, Braham; Glaser, Fabien; Hesse, Cedar N.; Kosti, Idit; LaButti, Kurt; Lindquist, Erika A.; Lucas, Susan; Salamov, Asaf A.; Bradshaw, Rosie E.; Ciuffetti, Lynda; Hamelin, Richard C.; Kema, Gert H. J.; Lawrence, Christopher; Scott, James A.; Spatafora, Joseph W.; Turgeon, B. Gillian; de Wit, Pierre J. G. M.; Zhong, Shaobin; Goodwin, Stephen B.; Grigoriev, Igor V.

    2012-03-13

    The class of Dothideomycetes is one of the largest and most diverse groups of fungi. Many are plant pathogens and pose a serious threat to agricultural crops grown for biofuel, food or feed. Most Dothideomycetes have only a single host and related species can have very diverse host plants. Eighteen genomes of Dothideomycetes have currently been sequenced by the Joint Genome Institute and other sequencing centers. Here we describe the results of comparative analyses of the fungi in this group.

  12. Use of microsatellite markers derived from whole genome sequence data for identifying polymorphism in Phytophthora ramorum

    Science.gov (United States)

    Kelly Ivors; Matteo Garbelotto; Ineke De Vries; Peter Bonants

    2006-01-01

    Investigating the population genetics of Phytophthora ramorum, the causal agent of sudden oak death (SOD), is critical to understanding the biology and epidemiology of this important phytopathogen. Raw sequence data (445,000 reads) of P. ramorum was provided by the Joint Genome Institute. Our objective was to develop and utilize...

  13. Ploidy and genome composition of Musa germplasm at the International Institute of Tropical Agriculture (IITA)

    Czech Academy of Sciences Publication Activity Database

    Pillay, M.; Ogundiwin, E.; Tenkouano, A.; Doležel, Jaroslav

    2006-01-01

    Roč. 5, - (2006), s. 1224-1232 ISSN 1684-5315 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : Banana * plantain * genomes Subject RIV: EB - Genetics ; Molecular Biology

  14. Protecting genomic data analytics in the cloud: state of the art and opportunities.

    Science.gov (United States)

    Tang, Haixu; Jiang, Xiaoqian; Wang, Xiaofeng; Wang, Shuang; Sofia, Heidi; Fox, Dov; Lauter, Kristin; Malin, Bradley; Telenti, Amalio; Xiong, Li; Ohno-Machado, Lucila

    2016-10-13

    The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, but such techniques need to be rigorously evaluated for their ability to support the analysis of human genomic data in an efficient and cost-effective manner. With respect to public cloud environments, there are concerns about the inadvertent exposure of human genomic data to unauthorized users. In analyses involving multiple institutions, there is additional concern about data being used beyond agreed research scope and being prcoessed in untrused computational environments, which may not satisfy institutional policies. To systematically investigate these issues, the NIH-funded National Center for Biomedical Computing iDASH (integrating Data for Analysis, 'anonymization' and SHaring) hosted the second Critical Assessment of Data Privacy and Protection competition to assess the capacity of cryptographic technologies for protecting computation over human genomes in the cloud and promoting cross-institutional collaboration. Data scientists were challenged to design and engineer practical algorithms for secure outsourcing of genome computation tasks in working software, whereby analyses are performed only on encrypted data. They were also challenged to develop approaches to enable secure collaboration on data from genomic studies generated by multiple organizations (e.g., medical centers) to jointly compute aggregate statistics without sharing individual-level records. The results of the competition indicated that secure computation techniques can enable comparative analysis of human genomes, but greater efficiency (in terms of compute time and memory utilization) are needed before they are sufficiently practical for real world environments.

  15. Brief review of topmost scientific results obtained in 2016 at the Joint Institute for Nuclear Research

    International Nuclear Information System (INIS)

    Kravchenko, E.I.; Sabaeva, E.V.

    2017-01-01

    This brief review presents the topmost scientific results obtained in 2016 at the Joint Institute for Nuclear Research in such fields as theoretical and experimental physics, radiation and radiobiological research, accelerators, information technology and computer physics. It also provides information about the publications by JINR staff members and activities carried out at the JINR University Centre in 2016. [ru

  16. Ten years of maintaining and expanding a microbial genome and metagenome analysis system.

    Science.gov (United States)

    Markowitz, Victor M; Chen, I-Min A; Chu, Ken; Pati, Amrita; Ivanova, Natalia N; Kyrpides, Nikos C

    2015-11-01

    Launched in March 2005, the Integrated Microbial Genomes (IMG) system is a comprehensive data management system that supports multidimensional comparative analysis of genomic data. At the core of the IMG system is a data warehouse that contains genome and metagenome datasets sequenced at the Joint Genome Institute or provided by scientific users, as well as public genome datasets available at the National Center for Biotechnology Information Genbank sequence data archive. Genomes and metagenome datasets are processed using IMG's microbial genome and metagenome sequence data processing pipelines and are integrated into the data warehouse using IMG's data integration toolkits. Microbial genome and metagenome application specific data marts and user interfaces provide access to different subsets of IMG's data and analysis toolkits. This review article revisits IMG's original aims, highlights key milestones reached by the system during the past 10 years, and discusses the main challenges faced by a rapidly expanding system, in particular the complexity of maintaining such a system in an academic setting with limited budgets and computing and data management infrastructure. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Educational Research Centre of the Joint Institute for Nuclear Research and students training on the 'Medical Physics' speciality

    International Nuclear Information System (INIS)

    Ivanova, S.P.; )

    2005-01-01

    The Educational Research Centre (ERC) of the Joint Institute for Nuclear Research is the place of joint activity of the JINR, Moscow State University (MSU) and Moscow Engineering Physical Institute (MEFI) on students training by a broadened circle of specialities with introduction of new educational forms. Active application of medical accelerator beams of the JINR Laboratory of Nuclear Beams becomes a reason for implementation of a new training chair in the MEFI on the JINR base - the Physical methods in applied studies in the medicine chair. For the 'medical physics' trend development in 2003 the workshop on discussion both curricula and teaching methodic by the speciality was held. One the Educational Research Centre main activities is both organization and conducting an international scientific schools and training courses. The International student School 'Nuclear-Physical Methods and Accelerators is the most popular and traditional. The principal aim of these schools and courses is familiarization of students and postgraduates with last achievement and and contemporary problems of applied medical physics. The school audience is a students and postgraduates of ERC, MSU, MEFI, and an institutes of Poland, Hungary, Slovakia, France, Czech and Bulgaria

  18. Protecting genomic data analytics in the cloud: state of the art and opportunities

    Directory of Open Access Journals (Sweden)

    Haixu Tang

    2016-10-01

    Full Text Available Abstract The outsourcing of genomic data into public cloud computing settings raises concerns over privacy and security. Significant advancements in secure computation methods have emerged over the past several years, but such techniques need to be rigorously evaluated for their ability to support the analysis of human genomic data in an efficient and cost-effective manner. With respect to public cloud environments, there are concerns about the inadvertent exposure of human genomic data to unauthorized users. In analyses involving multiple institutions, there is additional concern about data being used beyond agreed research scope and being prcoessed in untrused computational environments, which may not satisfy institutional policies. To systematically investigate these issues, the NIH-funded National Center for Biomedical Computing iDASH (integrating Data for Analysis, ‘anonymization’ and SHaring hosted the second Critical Assessment of Data Privacy and Protection competition to assess the capacity of cryptographic technologies for protecting computation over human genomes in the cloud and promoting cross-institutional collaboration. Data scientists were challenged to design and engineer practical algorithms for secure outsourcing of genome computation tasks in working software, whereby analyses are performed only on encrypted data. They were also challenged to develop approaches to enable secure collaboration on data from genomic studies generated by multiple organizations (e.g., medical centers to jointly compute aggregate statistics without sharing individual-level records. The results of the competition indicated that secure computation techniques can enable comparative analysis of human genomes, but greater efficiency (in terms of compute time and memory utilization are needed before they are sufficiently practical for real world environments.

  19. The national cancer institute (NCI) and cancer biology in a 'post genome world'

    International Nuclear Information System (INIS)

    Klausner, Richard D.

    1996-01-01

    The National Cancer Institute (NCI) exists to reduce the burden of all cancers through research and discovery. Extensive restructuring of the NCI over the past year has been aimed at assuring that the institution functions in all ways to promote opportunities for discovery in the laboratory, in the clinic, and in the community. To do this well requires the difficult and almost paradoxical problem of planning for scientific discovery which, in turn is based on the freedom to pursue the unanticipated. The intellectual and structural landscape of science is changing and it places new challenges, new demands and new opportunities for facilitating discovery. The nature of cancer as a disease of genomic instability and of accumulated genetic change, coupled with a possibility of the development of new technologies for reading, utilizing, interpreting and manipulating the genome of single cells, provides unprecedented opportunities for a new type of high through-put biology that will change the nature of discovery, cancer detection, diagnosis, prognosis, therapeutic decision-making and therapeutic discovery. To capture these new opportunities will require attention to be paid to integrate the development of technology and new scientific discoveries with the ability to apply advances rapidly and efficiently through clinical trials

  20. Genome sequence of the dark pink pigmented Listia bainesii microsymbiont Methylobacterium sp. WSM2598.

    Science.gov (United States)

    Ardley, Julie; Tian, Rui; Howieson, John; Yates, Ron; Bräu, Lambert; Han, James; Lobos, Elizabeth; Huntemann, Marcel; Chen, Amy; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Pati, Amrita; Goodwin, Lynne; Woyke, Tanja; Kyrpides, Nikos; Reeve, Wayne

    2014-01-01

    Strains of a pink-pigmented Methylobacterium sp. are effective nitrogen- (N2) fixing microsymbionts of species of the African crotalarioid genus Listia. Strain WSM2598 is an aerobic, motile, Gram-negative, non-spore-forming rod isolated in 2002 from a Listia bainesii root nodule collected at Estcourt Research Station in South Africa. Here we describe the features of Methylobacterium sp. WSM2598, together with information and annotation of a high-quality draft genome sequence. The 7,669,765 bp draft genome is arranged in 5 scaffolds of 83 contigs, contains 7,236 protein-coding genes and 18 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 G enomic E ncyclopedia for B acteria and A rchaea- R oot N odule B acteria (GEBA-RNB) project.

  1. Isotope-based medical research in the post genome era: Gene-orchestrated life functions in medicine seen and affected by isotopes. Workshop report

    International Nuclear Information System (INIS)

    Feinendegen, L.E.

    1997-01-01

    The US Department of Energy (DOE) and the National Institutes of Health (NIH) conducted a workshop on Isotope-Based Medical Research in the Post Genome Era at NIH, Bethesda, Maryland, November 12--14, 1997. The workshop aimed at identifying the role of stable and radioisotopes for advanced diagnosis and therapy of a wide range of illnesses using the new information that comes from the human genome program. In this sense, the agenda addressed the challenge of functional genomics in humans. The workshop addressed: functional genomics in clinical medicine; new diagnostic potentials; new therapy potentials; challenge to tracer- and effector-pharmaceutical chemistry; and project plans for joint ventures

  2. Isotope-based medical research in the post genome era: Gene-orchestrated life functions in medicine seen and affected by isotopes. Workshop report

    Energy Technology Data Exchange (ETDEWEB)

    Feinendegen, L.E.

    1997-12-31

    The US Department of Energy (DOE) and the National Institutes of Health (NIH) conducted a workshop on Isotope-Based Medical Research in the Post Genome Era at NIH, Bethesda, Maryland, November 12--14, 1997. The workshop aimed at identifying the role of stable and radioisotopes for advanced diagnosis and therapy of a wide range of illnesses using the new information that comes from the human genome program. In this sense, the agenda addressed the challenge of functional genomics in humans. The workshop addressed: functional genomics in clinical medicine; new diagnostic potentials; new therapy potentials; challenge to tracer- and effector-pharmaceutical chemistry; and project plans for joint ventures.

  3. Brief review of topmost scientific results obtained in 2015 at the Joint Institute for Nuclear Research

    International Nuclear Information System (INIS)

    Sabaeva, E.V.; Krupko, E.I.

    2016-01-01

    This brief review presents the topmost scientific results obtained in 2015 at the Joint Institute for Nuclear Research in such fields as theoretical and experimental physics, radiation and radiobiological research, accelerators, information technology and computer physics. It also provides information about the publications by JINR staff members, awards given to JINR scientists, and activities carried out at the JINR University Centre in 2015. [ru

  4. Brief review of topmost scientific results obtained in 2013 at the Joint Institute for Nuclear Research

    International Nuclear Information System (INIS)

    Sabaeva, E.V.; Kravchenko, E.I.

    2014-01-01

    This brief review presents the topmost scientific results obtained in 2013 at the Joint Institute for Nuclear Research in such areas as theoretical physics, experimental physics, radiation and radiobiological research, accelerators, information technology and computer physics. It also provides information on the number of publications by JINR staff members, awards given to JINR scientists, and activities carried out at the JINR University Centre in 2013.

  5. Brief review of topmost scientific results obtained in 2014 at the Joint Institute for Nuclear Research

    International Nuclear Information System (INIS)

    Bulatova, V.V.; Sabaeva, E.V.

    2015-01-01

    This brief review presents the topmost scientific results obtained in 2014 at the Joint Institute for Nuclear Research in such fields as theoretical and experimental physics, radiation and radiobiological research, accelerators, information technology and computer physics. It also provides information about the publications by JINR staff members, patents for inventions, awards given to JINR scientists, and activities carried out at the JINR University Centre in 2014. [ru

  6. Report of results of joint research using facilities in Japan Atomic Energy Research Institute in fiscal year 1987

    International Nuclear Information System (INIS)

    1988-06-01

    The total themes of the joint research in fiscal year 1987 were 127. These are shown being classified into the general joint research in Tokai and Takasaki, neutron diffraction research and cooperative research. The general joint research is the standard utilization form using research reactors JRR-2 and JRR-4, Co-60 gamma irradiation facilities in Tokai and Takasaki, an electron beam irradiation facility in Takasaki, an electron beam linear accelator and hot laboratories, which are opened for common utilization by Japan Atomic Energy Research Institute. The cooperative research is carried out by concluding research cooperation contracts between the researchers of universities and JAERI. In the general joint research, radioactivation analysis, radiation chemistry, irradiation effect, neutron diffraction and so on are the main themes, and in the cooperative research, reactor technology, reactor materials, nuclear physics measurement and others are the main themes. The total number of visitors was 2629 man-day, and decreased due to the stop of JRR-2. Also other activities are reported. The abstracts of respective reports are collected in this book. (Kako, I.)

  7. Complete genome sequence of Rhodospirillum rubrum type strain (S1).

    Science.gov (United States)

    Munk, A Christine; Copeland, Alex; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Barry, Kerrie; Detter, John C; Hammon, Nancy; Israni, Sanjay; Pitluck, Sam; Brettin, Thomas; Bruce, David; Han, Cliff; Tapia, Roxanne; Gilna, Paul; Schmutz, Jeremy; Larimer, Frank; Land, Miriam; Kyrpides, Nikos C; Mavromatis, Konstantinos; Richardson, Paul; Rohde, Manfred; Göker, Markus; Klenk, Hans-Peter; Zhang, Yaoping; Roberts, Gary P; Reslewic, Susan; Schwartz, David C

    2011-07-01

    Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002.

  8. Senior Student Affairs Officers' Reports of Joint Intra-Institutional Efforts to Support College Students with Mental Illness

    Science.gov (United States)

    Scheidel, Sarah

    2016-01-01

    The purpose of this sequential mixed-methods study was to explore senior student affairs officers' reports of joint intra-institutional efforts within the past three years to achieve the common goal of supporting the academic and personal success of college students with mental illness. The 20 factors identified by Mattessich, Murray-Close, and…

  9. The Joint Institute for Nuclear Research in Experimental Physics of Elementary Particles

    Science.gov (United States)

    Bednyakov, V. A.; Russakovich, N. A.

    2018-05-01

    The year 2016 marks the 60th anniversary of the Joint Institute for Nuclear Research (JINR) in Dubna, an international intergovernmental organization for basic research in the fields of elementary particles, atomic nuclei, and condensed matter. Highly productive advances over this long road clearly show that the international basis and diversity of research guarantees successful development (and maintenance) of fundamental science. This is especially important for experimental research. In this review, the most significant achievements are briefly described with an attempt to look into the future (seven to ten years ahead) and show the role of JINR in solution of highly important problems in elementary particle physics, which is a fundamental field of modern natural sciences. This glimpse of the future is full of justified optimism.

  10. Institutional Responsibility and the Flawed Genomic Biomarkers at Duke University: A Missed Opportunity for Transparency and Accountability.

    Science.gov (United States)

    DeMets, David L; Fleming, Thomas R; Geller, Gail; Ransohoff, David F

    2017-08-01

    When there have been substantial failures by institutional leadership in their oversight responsibility to protect research integrity, the public should demand that these be recognized and addressed by the institution itself, or the funding bodies. This commentary discusses a case of research failures in developing genomic predictors for cancer risk assessment and treatment at a leading university. In its review of this case, the Office of Research Integrity, an agency within the US Department of Health and Human Services, focused their report entirely on one individual faculty member and made no comment on the institution's responsibility and its failure to provide adequate oversight and investigation. These actions missed an important opportunity to emphasize the institution's critical responsibilities in oversight of research integrity and the importance of institutional transparency and accountability.

  11. Joint Institute for Nuclear Research as an example of socialist integration in science

    International Nuclear Information System (INIS)

    Bogolyubov, N.N.

    1979-01-01

    History of establishing, main directions of works and some results of investigations which have been carried out in the Joint Institute of Nuclear Research according to the program of the JINR member-states are stated as well as directions of the JINR co-operation with other countries are given. In detail, main works are stated in the field of high energy physics, theoretical nuclear physics, investigation of interactions of elementary particles, nuclear spectroscopy of nuclides. Examples are given of joint researches which have been conducted by scientists from the JINR together with scientists from other scientific research centers of the JINR member-states and other countries. Content is stated of works in the field of synthesis of ultraheavy elements and development of methods of study as their chemical properties. Composition of the JINR computer center is given as well as the list of problems which are solved at this center. Some results are given of works conducted in the JINR in the field of development of equipment for nuclear-physical researches and improvement of accelerators. Some results are presented of the JINR activity and plans for future [ru

  12. Joint genome-wide association study for milk fatty acid traits in Chinese and Danish Holstein populations

    DEFF Research Database (Denmark)

    Li, Xiujin; Buitenhuis, Albert Johannes; Lund, Mogens Sandø

    2015-01-01

    is highly consistent between the Chinese and Danish Holstein populations, such that a joint genome-wide association study (GWAS) can be performed. In this study, a joint GWAS was performed for 16 milk FA traits based on data of 784 Chinese and 371 Danish Holstein cows genotyped by a high-density bovine...... different effects in the 2 populations. Ten FA were influenced by a quantitative trait loci (QTL) region including DGAT1. Both C14:1 and the C14 index were influenced by a QTL region including SCD1 in the combined population. Other QTL regions also showed significant associations with the studied FA....... A large region (14.9–24.9 Mbp) in BTA26 significantly influenced C14:1 and the C14 index in both populations, mostly likely due to the SNP in SCD1. A QTL region (69.97–73.69 Mbp) on BTA9 showed a significantly different effect on C18:0 between the 2 populations. Detection of these important SNP...

  13. Assembly, Annotation, and Analysis of Multiple Mycorrhizal Fungal Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Initiative Consortium, Mycorrhizal Genomics; Kuo, Alan; Grigoriev, Igor; Kohler, Annegret; Martin, Francis

    2013-03-08

    Mycorrhizal fungi play critical roles in host plant health, soil community structure and chemistry, and carbon and nutrient cycling, all areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI). To this end we are building on our earlier sequencing of the Laccaria bicolor genome by partnering with INRA-Nancy and the mycorrhizal research community in the MGI to sequence and analyze dozens of mycorrhizal genomes of all Basidiomycota and Ascomycota orders and multiple ecological types (ericoid, orchid, and ectomycorrhizal). JGI has developed and deployed high-throughput sequencing techniques, and Assembly, RNASeq, and Annotation Pipelines. In 2012 alone we sequenced, assembled, and annotated 12 draft or improved genomes of mycorrhizae, and predicted ~;;232831 genes and ~;;15011 multigene families, All of this data is publicly available on JGI MycoCosm (http://jgi.doe.gov/fungi/), which provides access to both the genome data and tools with which to analyze the data. Preliminary comparisons of the current total of 14 public mycorrhizal genomes suggest that 1) short secreted proteins potentially involved in symbiosis are more enriched in some orders than in others amongst the mycorrhizal Agaricomycetes, 2) there are wide ranges of numbers of genes involved in certain functional categories, such as signal transduction and post-translational modification, and 3) novel gene families are specific to some ecological types.

  14. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  15. Statistical Methods in Integrative Genomics

    Science.gov (United States)

    Richardson, Sylvia; Tseng, George C.; Sun, Wei

    2016-01-01

    Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions. PMID:27482531

  16. Complete genome sequence of Tolumonas auensis type strain (TA 4T)

    Energy Technology Data Exchange (ETDEWEB)

    Chertkov, Olga; Copeland, Alex; Lucas1, Susa; Lapidus, Alla; Berry, KerrieW.; Detter, JohnC.; Glavina Del Rio, Tijana; Hammon, Nancy; Dalin, Eileen; Tice, Hope; Pitluck, Sam; Richardson, Paul; Bruce, David; Goodwin, Lynne; Han, Cliff; Tapia, Roxanne; Saunders, Elizabeth; Schmutz, Jeremy; Brettin, Thomas; Larimer, Frank; Land, Miriam; Hauser, Loren; Spring, Stefan; Rohde, Manfred; Kyrpides, NikosC.; Ivanova, Natalia; G& #246; ker, Markus; Beller, HarryR.; Klenk, Hans-Peter; Woyke, Tanja

    2011-10-04

    Tolumonas auensis (Fischer-Romero et al. 1996) is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4T is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292-bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.

  17. Complete genome sequence of Tolumonas auensis type strain (TA 4T)

    Energy Technology Data Exchange (ETDEWEB)

    Chertkov, Olga [Los Alamos National Laboratory (LANL); Copeland, A [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Berry, Alison M [California Institute of Technology, University of California, Davis; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Richardson, P M [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Schmutz, Jeremy [Stanford University; Brettin, Thomas S [ORNL; Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Rohde, Manfred [HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Beller, Harry R. [Lawrence Berkeley National Laboratory (LBNL); Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Oth- er than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4T is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.

  18. Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

    Energy Technology Data Exchange (ETDEWEB)

    Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang; Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinlzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

    2013-01-24

    The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.

  19. The Functional Genomics Initiative at Oak Ridge National Laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Dabney; Justice, Monica; Beattle, Ken; Buchanan, Michelle; Ramsey, Michael; Ramsey, Rose; Paulus, Michael; Ericson, Nance; Allison, David; Kress, Reid; Mural, Richard; Uberbacher, Ed; Mann, Reinhold

    1997-12-31

    The Functional Genomics Initiative at the Oak Ridge National Laboratory integrates outstanding capabilities in mouse genetics, bioinformatics, and instrumentation. The 50 year investment by the DOE in mouse genetics/mutagenesis has created a one-of-a-kind resource for generating mutations and understanding their biological consequences. It is generally accepted that, through the mouse as a surrogate for human biology, we will come to understand the function of human genes. In addition to this world class program in mammalian genetics, ORNL has also been a world leader in developing bioinformatics tools for the analysis, management and visualization of genomic data. Combining this expertise with new instrumentation technologies will provide a unique capability to understand the consequences of mutations in the mouse at both the organism and molecular levels. The goal of the Functional Genomics Initiative is to develop the technology and methodology necessary to understand gene function on a genomic scale and apply these technologies to megabase regions of the human genome. The effort is scoped so as to create an effective and powerful resource for functional genomics. ORNL is partnering with the Joint Genome Institute and other large scale sequencing centers to sequence several multimegabase regions of both human and mouse genomic DNA, to identify all the genes in these regions, and to conduct fundamental surveys to examine gene function at the molecular and organism level. The Initiative is designed to be a pilot for larger scale deployment in the post-genome era. Technologies will be applied to the examination of gene expression and regulation, metabolism, gene networks, physiology and development.

  20. Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T)

    Energy Technology Data Exchange (ETDEWEB)

    Copeland, A [U.S. Department of Energy, Joint Genome Institute; O' Connor, Kathleen [Purdue University; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute; Berry, Kerrie W. [United States Department of Energy Joint Genome Institute; Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Hammon, Nancy [U.S. Department of Energy, Joint Genome Institute; Dalin, Eileen [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Bruce, David [Los Alamos National Laboratory (LANL); Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Han, Cliff [Los Alamos National Laboratory (LANL); Tapia, Roxanne [Los Alamos National Laboratory (LANL); Saunders, Elizabeth H [Los Alamos National Laboratory (LANL); Schmutz, Jeremy [Stanford University; Brettin, Thomas S [ORNL; Larimer, Frank W [ORNL; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Vargas, Carmen [University of Seville; Nieto, Joaquin J. [University of Seville; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Csonka, Laszlo N. [Purdue University; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute

    2011-01-01

    Chromohalobacter salexigens is one of nine currently known species of the genus Chromoha- lobacter in the family Halomonadaceae. It is the most halotolerant of the so-called mod- erately halophilic bacteria currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11T and Halomonas elongata are the first and the second members of the family Halomonada- ceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.

  1. Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

    Science.gov (United States)

    O'Donnell, Christopher J; Nabel, Elizabeth G

    2008-10-01

    The inaugural issue of Circulation: Cardiovascular Genetics arrives at a remarkable time in the history of genetic research and cardiovascular medicine. Despite tremendous progress in knowledge gained, cardiovascular disease(CVD) remains the leading cause of death in the United States,1 and it has overcome infectious diseases as the leading cause of death worldwide.2 In addition, rates of CVD remain higher in black and Hispanic populations in the United States.1 The recent Strategic Plan of the National Heart, Lung,and Blood Institute (NHLBI) emphasizes research areas to fill the significant knowledge gaps needed to improve the diagnosis,treatment, and control of known risk factors and clinically apparent disease. Simultaneously, the NHLBI Strategic Plan recognizes a tremendous opportunity that is available for use of genetic and genomic research to generate new knowledge that might reduce the morbidity and mortality from CVD in US populations.3 Public availability of vast amounts of detailed sequence information about the human genome, completed sequence data on dozens of other animal genomes, and private sector development of high-throughput genetic technologies has transformed in a few short years the conduct of cardiovascular genetics and genomics research from a primary focus on mendelian disorders to a current emphasis on genome-wide association studies (GWAS; Figure1). In this review, we describe the rationale for the current emphasis on large-scale genomic studies, summarize the evolving approaches and progress to date, and identify immediate-term research needs. The National Institutes of Health (NIH) and the NHLBI are supporting a portfolio of large-scale genetic and genomic programs in diverse US populations with the longer-term objective of translating knowledge into the prediction, prevention, and preemption of CVD, as well as lung, sleep, and blood disorders. Underlying this portfolio is a strong commitment to make available participant-level data and

  2. Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.

    Directory of Open Access Journals (Sweden)

    Dana B Hancock

    Full Text Available Genome-wide association studies have identified numerous genetic loci for spirometic measures of pulmonary function, forced expiratory volume in one second (FEV(1, and its ratio to forced vital capacity (FEV(1/FVC. Given that cigarette smoking adversely affects pulmonary function, we conducted genome-wide joint meta-analyses (JMA of single nucleotide polymorphism (SNP and SNP-by-smoking (ever-smoking or pack-years associations on FEV(1 and FEV(1/FVC across 19 studies (total N = 50,047. We identified three novel loci not previously associated with pulmonary function. SNPs in or near DNER (smallest P(JMA = 5.00×10(-11, HLA-DQB1 and HLA-DQA2 (smallest P(JMA = 4.35×10(-9, and KCNJ2 and SOX9 (smallest P(JMA = 1.28×10(-8 were associated with FEV(1/FVC or FEV(1 in meta-analysis models including SNP main effects, smoking main effects, and SNP-by-smoking (ever-smoking or pack-years interaction. The HLA region has been widely implicated for autoimmune and lung phenotypes, unlike the other novel loci, which have not been widely implicated. We evaluated DNER, KCNJ2, and SOX9 and found them to be expressed in human lung tissue. DNER and SOX9 further showed evidence of differential expression in human airway epithelium in smokers compared to non-smokers. Our findings demonstrated that joint testing of SNP and SNP-by-environment interaction identified novel loci associated with complex traits that are missed when considering only the genetic main effects.

  3. Genome sequence of the Lotus spp. microsymbiont Mesorhizobium loti strain R7A.

    Science.gov (United States)

    Kelly, Simon; Sullivan, John; Ronson, Clive; Tian, Rui; Bräu, Lambert; Munk, Christine; Goodwin, Lynne; Han, Cliff; Woyke, Tanja; Reddy, Tatiparthi; Huntemann, Marcel; Pati, Amrita; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

    2014-01-01

    Mesorhizobium loti strain R7A was isolated in 1993 in Lammermoor, Otago, New Zealand from a Lotus corniculatus root nodule and is a reisolate of the inoculant strain ICMP3153 (NZP2238) used at the site. R7A is an aerobic, Gram-negative, non-spore-forming rod. The symbiotic genes in the strain are carried on a 502-kb integrative and conjugative element known as the symbiosis island or ICEMlSym(R7A). M. loti is the microsymbiont of the model legume Lotus japonicus and strain R7A has been used extensively in studies of the plant-microbe interaction. This report reveals that the genome of M. loti strain R7A does not harbor any plasmids and contains a single scaffold of size 6,529,530 bp which encodes 6,323 protein-coding genes and 75 RNA-only encoding genes. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

  4. Dana-Farber Cancer Institute: Identification of Therapeutic Targets Across Cancer Types | Office of Cancer Genomics

    Science.gov (United States)

    The Dana Farber Cancer Institute CTD2 Center focuses on the use of high-throughput genetic and bioinformatic approaches to identify and credential oncogenes and co-dependencies in cancers. This Center aims to provide the cancer research community with information that will facilitate the prioritization of targets based on both genomic and functional evidence, inform the most appropriate genetic context for downstream mechanistic and validation studies, and enable the translation of this information into therapeutics and diagnostics.

  5. Genomics Portals: integrative web-platform for mining genomics data.

    Science.gov (United States)

    Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

    2010-01-13

    A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  6. Why size really matters when sequencing plant genomes

    Czech Academy of Sciences Publication Activity Database

    Kelly, L.J.; Leitch, A.R.; Fay, M. F.; Renny-Byfield, S.; Pellicer, J.; Macas, Jiří; Leitch, I.J.

    2012-01-01

    Roč. 5, č. 4 (2012), s. 415-425 ISSN 1755-0874 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : C-value * genome assembly * genome size evolution * genome sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.924, year: 2012

  7. POLICY AND INSTITUTIONS: POSSIBLE JOINT THEORY

    Directory of Open Access Journals (Sweden)

    Cristina Miyuki Hashizume

    2014-12-01

    Full Text Available This article will discuss theoretically the concept of politics and the importance of its redefinition, discussing the different political interests from Brazilian population, throughout our history. It proposes to rescue the original and ethical meaning of Politics and to review and redefine it inside a new Ethical-aesthetic-political paradigm. We have come from Greek Antiquity to our current Democracy, so as to raise reflections about possibilities for political actions despite of the lack of political past without participation. The concept of instituting process and micropolitical (for Institutional Analysis allow us to understand the possibilities for different and creative acting beyond the control in place.

  8. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  9. Genomics Portals: integrative web-platform for mining genomics data

    Directory of Open Access Journals (Sweden)

    Ghosh Krishnendu

    2010-01-01

    Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

  10. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  11. Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

    Directory of Open Access Journals (Sweden)

    Grigoriev Igor V

    2009-02-01

    Full Text Available Abstract Background Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR. Results 405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6% of these loci either had no preferred predicted gene model or the genome annotators' chosen "best" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models. Conclusion This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.

  12. Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger.

    Science.gov (United States)

    Wright, James C; Sugden, Deana; Francis-McIntyre, Sue; Riba-Garcia, Isabel; Gaskell, Simon J; Grigoriev, Igor V; Baker, Scott E; Beynon, Robert J; Hubbard, Simon J

    2009-02-04

    Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS) and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR). 405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6%) of these loci either had no preferred predicted gene model or the genome annotators' chosen "best" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models. This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST) data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.

  13. Guidelines for collecting vouchers and tissues intended for genomic work (Smithsonian Institution: Botany Best Practices

    Directory of Open Access Journals (Sweden)

    Vicki Funk

    2017-01-01

    Full Text Available The introduction of Next Generation Sequencing into the disciplines of plant systematics, ecology, and metagenomics, among others, has resulted in a phenomenal increase in the collecting and storing of tissue samples and their respective vouchers. This manual suggests standard practices that will insure the quality and preservation of the tissue and vouchers and their respective data. Although written for use by the Smithsonian Institution botanists it suggests a framework for collecting tissues and vouchers that other research programs can adapt to their own needs. It includes information on collecting voucher specimens, collecting plant tissue intended for genomic analysis, how to manage these collections, and how to incorporate the data into a database management system. It also includes many useful references for collecting and processing collections. We hope it will be useful for a variety of botanists but especially those who know how to collect plants and want to collect tissue samples that will be useful for genomic research, and those who are skilled in lab work and want to know how to properly voucher and record their tissue collections.

  14. Dana-Farber Cancer Institute: Identification of Therapeutic Targets in KRAS Driven Lung Cancer | Office of Cancer Genomics

    Science.gov (United States)

    The CTD2 Center at Dana Farber Cancer Institute focuses on the use of high-throughput genetic and bioinformatic approaches to identify and credential oncogenes and co-dependencies in cancers. This Center aims to provide the cancer research community with information that will facilitate the prioritization of targets based on both genomic and functional evidence, inform the most appropriate genetic context for downstream mechanistic and validation studies, and enable the translation of this information into therapeutics and diagnostics.

  15. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

    Science.gov (United States)

    Mavromatis, Konstantinos; Land, Miriam L; Brettin, Thomas S; Quest, Daniel J; Copeland, Alex; Clum, Alicia; Goodwin, Lynne; Woyke, Tanja; Lapidus, Alla; Klenk, Hans Peter; Cottingham, Robert W; Kyrpides, Nikos C

    2012-01-01

    The emergence of next generation sequencing (NGS) has provided the means for rapid and high throughput sequencing and data generation at low cost, while concomitantly creating a new set of challenges. The number of available assembled microbial genomes continues to grow rapidly and their quality reflects the quality of the sequencing technology used, but also of the analysis software employed for assembly and annotation. In this work, we have explored the quality of the microbial draft genomes across various sequencing technologies. We have compared the draft and finished assemblies of 133 microbial genomes sequenced at the Department of Energy-Joint Genome Institute and finished at the Los Alamos National Laboratory using a variety of combinations of sequencing technologies, reflecting the transition of the institute from Sanger-based sequencing platforms to NGS platforms. The quality of the public assemblies and of the associated gene annotations was evaluated using various metrics. Results obtained with the different sequencing technologies, as well as their effects on downstream processes, were analyzed. Our results demonstrate that the Illumina HiSeq 2000 sequencing system, the primary sequencing technology currently used for de novo genome sequencing and assembly at JGI, has various advantages in terms of total sequence throughput and cost, but it also introduces challenges for the downstream analyses. In all cases assembly results although on average are of high quality, need to be viewed critically and consider sources of errors in them prior to analysis. These data follow the evolution of microbial sequencing and downstream processing at the JGI from draft genome sequences with large gaps corresponding to missing genes of significant biological role to assemblies with multiple small gaps (Illumina) and finally to assemblies that generate almost complete genomes (Illumina+PacBio).

  16. Genome Variation Map: a data repository of genome variations in BIG Data Center

    OpenAIRE

    Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

    2017-01-01

    Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

  17. Genome sequence of Ensifer arboris strain LMG 14919T; a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan

    Science.gov (United States)

    Reeve, Wayne; Tian, Rui; Bräu, Lambert; Goodwin, Lynne; Munk, Christine; Detter, Chris; Tapia, Roxanne; Han, Cliff; Liolios, Konstantinos; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavrommatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Willems, Anne

    2013-01-01

    Ensifer arboris LMG 14919T is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of several species of legume trees. LMG 14919T was isolated in 1987 from a nodule recovered from the roots of the tree Prosopis chilensis growing in Kosti, Sudan. LMG 14919T is highly effective at fixing nitrogen with P. chilensis (Chilean mesquite) and Acacia senegal (gum Arabic tree or gum acacia). LMG 14919T does not nodulate the tree Leucena leucocephala, nor the herbaceous species Macroptilium atropurpureum, Trifolium pratense, Medicago sativa, Lotus corniculatus and Galega orientalis. Here we describe the features of E. arboris LMG 14919T, together with genome sequence information and its annotation. The 6,850,303 bp high-quality-draft genome is arranged into 7 scaffolds of 12 contigs containing 6,461 protein-coding genes and 84 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project. PMID:25197433

  18. Genome sequence of Ensifer arboris strain LMG 14919(T); a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan.

    Science.gov (United States)

    Reeve, Wayne; Tian, Rui; Bräu, Lambert; Goodwin, Lynne; Munk, Christine; Detter, Chris; Tapia, Roxanne; Han, Cliff; Liolios, Konstantinos; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavrommatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Willems, Anne

    2014-06-15

    Ensifer arboris LMG 14919(T) is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of several species of legume trees. LMG 14919(T) was isolated in 1987 from a nodule recovered from the roots of the tree Prosopis chilensis growing in Kosti, Sudan. LMG 14919(T) is highly effective at fixing nitrogen with P. chilensis (Chilean mesquite) and Acacia senegal (gum Arabic tree or gum acacia). LMG 14919(T) does not nodulate the tree Leucena leucocephala, nor the herbaceous species Macroptilium atropurpureum, Trifolium pratense, Medicago sativa, Lotus corniculatus and Galega orientalis. Here we describe the features of E. arboris LMG 14919(T), together with genome sequence information and its annotation. The 6,850,303 bp high-quality-draft genome is arranged into 7 scaffolds of 12 contigs containing 6,461 protein-coding genes and 84 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

  19. eGenomics: Cataloguing Our Complete Genome Collection III

    Directory of Open Access Journals (Sweden)

    Dawn Field

    2007-01-01

    Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

  20. Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach

    Directory of Open Access Journals (Sweden)

    Claudia Bartoli

    2017-05-01

    Full Text Available The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars. On the other hand, the prediction of pathogen's genetic determinants underlying disease emergence can help to identify plant resistance alleles. In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated with pathogenicity in microbes. Here, we reviewed GWA studies performed either in plants or in pathogenic microorganisms (bacteria, fungi and oomycetes. In addition, we highlighted the benefits and caveats of the emerging joint GWA mapping approach that allows for the simultaneous identification of genes interacting between genomes of both partners. Finally, based on co-evolutionary processes in wild populations, we highlighted a phenotyping-free joint GWA mapping approach as a promising tool for describing the molecular landscape underlying plant - microbe interactions.

  1. The Chlamydomonas genome project: a decade on

    Science.gov (United States)

    Blaby, Ian K.; Blaby-Haas, Crysten; Tourasse, Nicolas; Hom, Erik F. Y.; Lopez, David; Aksoy, Munevver; Grossman, Arthur; Umen, James; Dutcher, Susan; Porter, Mary; King, Stephen; Witman, George; Stanke, Mario; Harris, Elizabeth H.; Goodstein, David; Grimwood, Jane; Schmutz, Jeremy; Vallon, Olivier; Merchant, Sabeeha S.; Prochnik, Simon

    2014-01-01

    The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis and micronutrient homeostasis. Ten years since its genome project was initiated, an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the “omics” era. Housed at Phytozome, the Joint Genome Institute’s (JGI) plant genomics portal, the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of RNA-Seq data. Here, we present the past, present and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes. PMID:24950814

  2. Joint genome-wide prediction in several populations accounting for randomness of genotypes: A hierarchical Bayes approach. I: Multivariate Gaussian priors for marker effects and derivation of the joint probability mass function of genotypes.

    Science.gov (United States)

    Martínez, Carlos Alberto; Khare, Kshitij; Banerjee, Arunava; Elzo, Mauricio A

    2017-03-21

    It is important to consider heterogeneity of marker effects and allelic frequencies in across population genome-wide prediction studies. Moreover, all regression models used in genome-wide prediction overlook randomness of genotypes. In this study, a family of hierarchical Bayesian models to perform across population genome-wide prediction modeling genotypes as random variables and allowing population-specific effects for each marker was developed. Models shared a common structure and differed in the priors used and the assumption about residual variances (homogeneous or heterogeneous). Randomness of genotypes was accounted for by deriving the joint probability mass function of marker genotypes conditional on allelic frequencies and pedigree information. As a consequence, these models incorporated kinship and genotypic information that not only permitted to account for heterogeneity of allelic frequencies, but also to include individuals with missing genotypes at some or all loci without the need for previous imputation. This was possible because the non-observed fraction of the design matrix was treated as an unknown model parameter. For each model, a simpler version ignoring population structure, but still accounting for randomness of genotypes was proposed. Implementation of these models and computation of some criteria for model comparison were illustrated using two simulated datasets. Theoretical and computational issues along with possible applications, extensions and refinements were discussed. Some features of the models developed in this study make them promising for genome-wide prediction, the use of information contained in the probability distribution of genotypes is perhaps the most appealing. Further studies to assess the performance of the models proposed here and also to compare them with conventional models used in genome-wide prediction are needed. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Joint intentionality: from thin to thick

    Czech Academy of Sciences Publication Activity Database

    Koreň, Ladislav

    2016-01-01

    Roč. 2, č. 1 (2016), s. 75-85 ISSN 2196-9655 R&D Projects: GA ČR GA13-20785S Institutional support: RVO:67985955 Keywords : Tomasello * Cooperation * Joint intentionality * Joint action * Mindreading Subject RIV: AA - Philosophy ; Religion https://www.degruyter.com/view/j/jso.2016.2.issue-1/jso-2015-0047/jso-2015-0047.xml?format=INT

  4. IMPLEMENTATION OF ESG FOR INTERNATIONAL JOINT EDUCATION PROGRAMMES

    Directory of Open Access Journals (Sweden)

    Vera I. Zabotkina

    2016-12-01

    Full Text Available Introduction: joint international programmes stimulate staff and student mobility, provide joint studies, provide development of joint study programmes of excellence, and open up new possibilities for cooperation between countries. Promotion and development of joint international programmes depend on effective quality assurance system which is high on the universities` priority list. ESG provide solid basis for the quality assurance system development at both institutional and programme levels. The problems of ESG interpretation in compliance with national legislative systems and education traditions in the countries participating in Bologna process are paid much attention to. Our emphases are on the practical aspects of ESG (2015 version implementation. The article concentrates on one of the most acute problems facing Russian Higher Education Institutions in the field of development and promotion of joint international programs: the problem of setting up modern quality assurance systems compatible with those in European HEIs is closely correlating with the profile of the journal “Integration of Education”. The journal centers around the publications on the enhancement and dissemination of the best practices on integration of regional education in Russia and abroad. Materials and Methods: methodical and practical aspects of the implementation of the ESG provisions for international joint educational programs on the basis of the European approach to education quality are the materials of study. The descriptive method, analysis of documents about education quality, and synthesis were used as research methods. Results: the authors come up with concrete recommendations for the implementation of the ESG renewed version (2015 in Quality Assurance systems of joint international programmes. This approach enhances the practical value of ESG. Modern Quality Assurance system is one of the main prerequisites for the successful collaboration among higher

  5. COMPUTED TOMOGRAPHIC APPEARANCE OF THE TEMPOROMANDIBULAR JOINT IN 1018 ASYMPTOMATIC HORSES: A MULTI-INSTITUTION STUDY.

    Science.gov (United States)

    Carmalt, James L; Kneissl, Sibylle; Rawlinson, Jennifer E; Zwick, Timo; Zekas, Lisa; Ohlerth, Stefanie; Bienert-Zeit, Astrid

    2016-05-01

    Published descriptions of nonseptic arthritis of the equine temporomandibular joint (TMJ) are rare and large studies investigating variations in the TMJ for asymptomatic horses are lacking. The objectives of this cross-sectional, retrospective, multi-institutional study were to describe anatomical variations in the TMJ detected using computed tomography (CT) in an equid population asymptomatic for TMJ disease and determine whether these variations were associated with patient signalment, reason for CT examination, or CT slice width. Medical records at eight hospitals were searched for horses that had head/neck CT scans and no clinical signs of TMJ disease. Age, breed, sex, clinical presentation, and CT slice width data were recorded. Alterations in CT contour and density of the mandibular condyles, mandibular fossae, and TMJ intra-articular discs were described for each horse. Generalized logistic regression was used to test associations between anatomical variations and horse age. A total of 1018 horses were sampled. Anatomical variations were found in TMJ CT images for 40% of horses and 29% of joints. These were dichotomous with regard to age. Horses horses commonly had spherical hypodensities within the mandibular condyles consistent with bone cysts; and hyperdense regions of the intra-articular disc consistent with dystrophic mineralization. Findings indicated that TMJ anatomic variations were common in CT images of younger and older horses asymptomatic for TMJ disease. Future studies are needed to more definitively characterize these CT variations using gross pathology and histopathology. © 2016 American College of Veterinary Radiology.

  6. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  7. Radio- and magnetobiology program GENOM at Nuclear Institute

    Energy Technology Data Exchange (ETDEWEB)

    Molchanov, E

    1985-01-01

    The five-year program called GENOM was adopted at OIYAI five years ago. The main task of this program has been the study of mechanisms that determine differences in the biological effectiveness of ionizing radiations with different stopping powers, as well as regularities involved in the action of magnetic fields. A unit called GENOM, which is controlled by a computer, was built at OIYAI. With this unit, living cells have been irradiated with charged particles of various energies, using the U-200. Magnetic-field generators and a unit which makes it possible to weaken the strength of the earth's magnetic field by a million times have been developed for magnetobiology research. DNA molecules, bacteria, yeasts, plant cells, normal and tumor cells of animals, and nerve cells of mollusks have been objects of research.

  8. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

    Energy Technology Data Exchange (ETDEWEB)

    Bollmann, Annette [Miami University, Oxford, OH; Sedlacek, Christopher J [Miami University, Oxford, OH; Laanbroek, Hendrikus J [Netherlands Institute of Ecology (NIOO-KNAW); Suwa, Yuichi [Chuo University, Tokyo, Japan; Stein, Lisa Y [University of California, Riverside; Klotz, Martin G [University of Louisville, Louisville; Arp, D J [Oregon State University; Sayavedra-Soto, LA [Oregon State University; Lu, Megan [Los Alamos National Laboratory (LANL); Bruce, David [Los Alamos National Laboratory (LANL); Detter, J. Chris [U.S. Department of Energy, Joint Genome Institute; Tapia, Roxanne [Los Alamos National Laboratory (LANL); Han, James [U.S. Department of Energy, Joint Genome Institute; Woyke, Tanja [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Pennacchio, Len [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Land, Miriam L [ORNL; Huntemann, Marcel [U.S. Department of Energy, Joint Genome Institute; Deshpande, Shweta [U.S. Department of Energy, Joint Genome Institute; Han, Cliff [Los Alamos National Laboratory (LANL); Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Szeto, Ernest [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pagani, Ioanna [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Peters, Lin [U.S. Department of Energy, Joint Genome Institute; Ovchinnikova, Galina [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL)

    2013-01-01

    Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

  9. Genome sequence of Ensifer meliloti strain WSM1022; a highly effective microsymbiont of the model legume Medicago truncatula A17.

    Science.gov (United States)

    Terpolilli, Jason; Hill, Yvette; Tian, Rui; Howieson, John; Bräu, Lambert; Goodwin, Lynne; Han, James; Liolios, Konstantinos; Huntemann, Marcel; Pati, Amrita; Woyke, Tanja; Mavromatis, Konstantinos; Markowitz, Victor; Ivanova, Natalia; Kyrpides, Nikos; Reeve, Wayne

    2013-12-20

    Ensifer meliloti WSM1022 is an aerobic, motile, Gram-negative, non-spore-forming rod that can exist as a soil saprophyte or as a legume microsymbiont of Medicago. WSM1022 was isolated in 1987 from a nodule recovered from the roots of the annual Medicago orbicularis growing on the Cyclades Island of Naxos in Greece. WSM1022 is highly effective at fixing nitrogen with M. truncatula and other annual species such as M. tornata and M. littoralis and is also highly effective with the perennial M. sativa (alfalfa or lucerne). In common with other characterized E. meliloti strains, WSM1022 will nodulate but fixes poorly with M. polymorpha and M. sphaerocarpos and does not nodulate M. murex. Here we describe the features of E. meliloti WSM1022, together with genome sequence information and its annotation. The 6,649,661 bp high-quality-draft genome is arranged into 121 scaffolds of 125 contigs containing 6,323 protein-coding genes and 75 RNA-only encoding genes, and is one of 100 rhizobial genomes sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

  10. Frontotemporal dementia and its subtypes: a genome-wide association study.

    Science.gov (United States)

    Ferrari, Raffaele; Hernandez, Dena G; Nalls, Michael A; Rohrer, Jonathan D; Ramasamy, Adaikalavan; Kwok, John B J; Dobson-Stone, Carol; Brooks, William S; Schofield, Peter R; Halliday, Glenda M; Hodges, John R; Piguet, Olivier; Bartley, Lauren; Thompson, Elizabeth; Haan, Eric; Hernández, Isabel; Ruiz, Agustín; Boada, Mercè; Borroni, Barbara; Padovani, Alessandro; Cruchaga, Carlos; Cairns, Nigel J; Benussi, Luisa; Binetti, Giuliano; Ghidoni, Roberta; Forloni, Gianluigi; Galimberti, Daniela; Fenoglio, Chiara; Serpente, Maria; Scarpini, Elio; Clarimón, Jordi; Lleó, Alberto; Blesa, Rafael; Waldö, Maria Landqvist; Nilsson, Karin; Nilsson, Christer; Mackenzie, Ian R A; Hsiung, Ging-Yuek R; Mann, David M A; Grafman, Jordan; Morris, Christopher M; Attems, Johannes; Griffiths, Timothy D; McKeith, Ian G; Thomas, Alan J; Pietrini, P; Huey, Edward D; Wassermann, Eric M; Baborie, Atik; Jaros, Evelyn; Tierney, Michael C; Pastor, Pau; Razquin, Cristina; Ortega-Cubero, Sara; Alonso, Elena; Perneczky, Robert; Diehl-Schmid, Janine; Alexopoulos, Panagiotis; Kurz, Alexander; Rainero, Innocenzo; Rubino, Elisa; Pinessi, Lorenzo; Rogaeva, Ekaterina; St George-Hyslop, Peter; Rossi, Giacomina; Tagliavini, Fabrizio; Giaccone, Giorgio; Rowe, James B; Schlachetzki, Johannes C M; Uphill, James; Collinge, John; Mead, Simon; Danek, Adrian; Van Deerlin, Vivianna M; Grossman, Murray; Trojanowski, John Q; van der Zee, Julie; Deschamps, William; Van Langenhove, Tim; Cruts, Marc; Van Broeckhoven, Christine; Cappa, Stefano F; Le Ber, Isabelle; Hannequin, Didier; Golfier, Véronique; Vercelletto, Martine; Brice, Alexis; Nacmias, Benedetta; Sorbi, Sandro; Bagnoli, Silvia; Piaceri, Irene; Nielsen, Jørgen E; Hjermind, Lena E; Riemenschneider, Matthias; Mayhaus, Manuel; Ibach, Bernd; Gasparoni, Gilles; Pichler, Sabrina; Gu, Wei; Rossor, Martin N; Fox, Nick C; Warren, Jason D; Spillantini, Maria Grazia; Morris, Huw R; Rizzu, Patrizia; Heutink, Peter; Snowden, Julie S; Rollinson, Sara; Richardson, Anna; Gerhard, Alexander; Bruni, Amalia C; Maletta, Raffaele; Frangipane, Francesca; Cupidi, Chiara; Bernardi, Livia; Anfossi, Maria; Gallo, Maura; Conidi, Maria Elena; Smirne, Nicoletta; Rademakers, Rosa; Baker, Matt; Dickson, Dennis W; Graff-Radford, Neill R; Petersen, Ronald C; Knopman, David; Josephs, Keith A; Boeve, Bradley F; Parisi, Joseph E; Seeley, William W; Miller, Bruce L; Karydas, Anna M; Rosen, Howard; van Swieten, John C; Dopper, Elise G P; Seelaar, Harro; Pijnenburg, Yolande A L; Scheltens, Philip; Logroscino, Giancarlo; Capozzo, Rosa; Novelli, Valeria; Puca, Annibale A; Franceschi, Massimo; Postiglione, Alfredo; Milan, Graziella; Sorrentino, Paolo; Kristiansen, Mark; Chiang, Huei-Hsin; Graff, Caroline; Pasquier, Florence; Rollin, Adeline; Deramecourt, Vincent; Lebert, Florence; Kapogiannis, Dimitrios; Ferrucci, Luigi; Pickering-Brown, Stuart; Singleton, Andrew B; Hardy, John; Momeni, Parastoo

    2014-07-01

    Frontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three genes-MAPT, GRN, and C9orf72--have been associated with FTD. We sought to identify novel genetic risk loci associated with the disorder. We did a two-stage genome-wide association study on clinical FTD, analysing samples from 3526 patients with FTD and 9402 healthy controls. To reduce genetic heterogeneity, all participants were of European ancestry. In the discovery phase (samples from 2154 patients with FTD and 4308 controls), we did separate association analyses for each FTD subtype (behavioural variant FTD, semantic dementia, progressive non-fluent aphasia, and FTD overlapping with motor neuron disease [FTD-MND]), followed by a meta-analysis of the entire dataset. We carried forward replication of the novel suggestive loci in an independent sample series (samples from 1372 patients and 5094 controls) and then did joint phase and brain expression and methylation quantitative trait loci analyses for the associated (p<5 × 10(-8)) single-nucleotide polymorphisms. We identified novel associations exceeding the genome-wide significance threshold (p<5 × 10(-8)). Combined (joint) analyses of discovery and replication phases showed genome-wide significant association at 6p21.3, HLA locus (immune system), for rs9268877 (p=1·05 × 10(-8); odds ratio=1·204 [95% CI 1·11-1·30]), rs9268856 (p=5·51 × 10(-9); 0·809 [0·76-0·86]) and rs1980493 (p value=1·57 × 10(-8), 0·775 [0·69-0·86]) in the entire cohort. We also identified a potential novel locus at 11q14, encompassing RAB38/CTSC (the transcripts of which are related to lysosomal biology), for the behavioural FTD subtype for which joint analyses showed suggestive association for rs302668 (p=2·44 × 10(-7); 0·814 [0·71-0·92]). Analysis of expression and methylation quantitative trait loci data

  11. Organizational heterogeneity of vertebrate genomes.

    Science.gov (United States)

    Frenkel, Svetlana; Kirzhner, Valery; Korol, Abraham

    2012-01-01

    Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  12. Organizational heterogeneity of vertebrate genomes.

    Directory of Open Access Journals (Sweden)

    Svetlana Frenkel

    Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

  13. TCGA Workshop: Genomics and Biology of Glioblastoma Multiforme (GBM) - TCGA

    Science.gov (United States)

    The National Cancer Institute (NCI) and National Human Genome Research Institute (NHGRI) held a workshop entitled, “Genomics and Biology of Glioblastoma Multiforme (GBM),” to review the initial GBM data from the TCGA pilot project.

  14. Computer networks for financial activity management, control and statistics of databases of economic administration at the Joint Institute for Nuclear Research

    International Nuclear Information System (INIS)

    Tyupikova, T.V.; Samoilov, V.N.

    2003-01-01

    Modern information technologies urge natural sciences to further development. But it comes together with evaluation of infrastructures, to spotlight favorable conditions for the development of science and financial base in order to prove and protect legally new research. Any scientific development entails accounting and legal protection. In the report, we consider a new direction in software, organization and control of common databases on the example of the electronic document handling, which functions in some departments of the Joint Institute for Nuclear Research

  15. Genome Engineering for Personalized Arthritis Therapeutics.

    Science.gov (United States)

    Adkar, Shaunak S; Brunger, Jonathan M; Willard, Vincent P; Wu, Chia-Lung; Gersbach, Charles A; Guilak, Farshid

    2017-10-01

    Arthritis represents a family of complex joint pathologies responsible for the majority of musculoskeletal conditions. Nearly all diseases within this family, including osteoarthritis, rheumatoid arthritis, and juvenile idiopathic arthritis, are chronic conditions with few or no disease-modifying therapeutics available. Advances in genome engineering technology, most recently with CRISPR-Cas9, have revolutionized our ability to interrogate and validate genetic and epigenetic elements associated with chronic diseases such as arthritis. These technologies, together with cell reprogramming methods, including the use of induced pluripotent stem cells, provide a platform for human disease modeling. We summarize new evidence from genome-wide association studies and genomics that substantiates a genetic basis for arthritis pathogenesis. We also review the potential contributions of genome engineering in the development of new arthritis therapeutics. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Propionibacterium avidum as an Etiological Agent of Prosthetic Hip Joint Infection.

    Directory of Open Access Journals (Sweden)

    Peter Wildeman

    Full Text Available Propionibacterium acnes is well-established as a possible etiologic agent of prosthetic joint infections (PJIs. Other Propionibacterium spp. have occasionally been described as a cause of PJIs, but this has not previously been the case for P. avidum despite its capacity to form biofilm. We describe two patients with prosthetic hip joint infections caused by P. avidum. Both patients were primarily operated with an anteriorly curved skin incision close to the skin crease of the groin, and both were obese. Initial treatment was performed according to the DAIR procedure (debridement, antibiotics, and implant retention. In case 1, the outcome was successful, but in case 2, a loosening of the cup was present 18 months post debridement. The P. avidum isolate from case 1 and two isolates from case 2 (obtained 18 months apart were selected for whole genome sequencing. The genome of P. avidum obtained from case 1 was approximately 60 kb larger than the genomes of the two isolates of case 2. These latter isolates were clonal with the exception of SNPs in the genome. All three strains possessed the gene cluster encoding exopolysaccharide synthesis. P. avidum has a pathogenic potential and the ability to cause clinically relevant infections, including abscess formation, in the presence of foreign bodies such as prosthetic joint components. Skin incision in close proximity to the groin or deep skin crease, such as the anteriorly curved skin incision approach, might pose a risk of PJIs by P. avidum, especially in obese patients.

  17. Efficient strategy for detecting gene × gene joint action and its application in schizophrenia

    NARCIS (Netherlands)

    Won, Sungho; Kwon, Min-Seok; Mattheisen, Manuel; Park, Suyeon; Park, Changsoon; Kihara, Daisuke; Cichon, Sven; Ophoff, Roel; Nöthen, Markus M.; Rietschel, Marcella; Baur, Max; Uitterlinden, Andre G.; Hofmann, A.; Lange, Christoph; Kahn, René S.; Linszen, Don H.; van Os, Jim; Wiersma, Durk; Bruggeman, Richard; Cahn, Wiepke; de Haan, Lieuwe; Krabbendam, Lydia; Myin-Germeys, Inez

    2014-01-01

    We propose a new approach to detect gene × gene joint action in genome-wide association studies (GWASs) for case-control designs. This approach offers an exhaustive search for all two-way joint action (including, as a special case, single gene action) that is computationally feasible at the

  18. Web Apollo: a web-based genomic annotation editing platform.

    Science.gov (United States)

    Lee, Eduardo; Helt, Gregg A; Reese, Justin T; Munoz-Torres, Monica C; Childers, Chris P; Buels, Robert M; Stein, Lincoln; Holmes, Ian H; Elsik, Christine G; Lewis, Suzanna E

    2013-08-30

    Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current advances in sequencing technology is that there are more and more researchers sequencing new genomes. These researchers require tools to describe the functional features of their newly sequenced genomes. With Web Apollo researchers can use any of the common browsers (for example, Chrome or Firefox) to jointly analyze and precisely describe the features of a genome in real time, whether they are in the same room or working from opposite sides of the world.

  19. Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea ( Vigna unguiculata (L.) Walp).

    Science.gov (United States)

    Spriggs, Andrew; Henderson, Steven T; Hand, Melanie L; Johnson, Susan D; Taylor, Jennifer M; Koltunow, Anna

    2018-02-09

    Cowpea ( Vigna unguiculata (L.) Walp) is an important legume crop for food security in areas of low-input and smallholder farming throughout Africa and Asia. Genetic improvements are required to increase yield and resilience to biotic and abiotic stress and to enhance cowpea crop performance. An integrated cowpea genomic and gene expression data resource has the potential to greatly accelerate breeding and the delivery of novel genetic traits for cowpea. Extensive genomic resources for cowpea have been absent from the public domain; however, a recent early release reference genome for IT97K-499-35 ( Vigna unguiculata  v1.0, NSF, UCR, USAID, DOE-JGI, http://phytozome.jgi.doe.gov/) has now been established in a collaboration between the Joint Genome Institute (JGI) and University California (UC) Riverside. Here we release supporting genomic and transcriptomic data for IT97K-499-35 and a second transformable cowpea variety, IT86D-1010. The transcriptome resource includes six tissue-specific datasets for each variety, with particular emphasis on reproductive tissues that extend and support the V. unguiculata v1.0 reference. Annotations have been included in our resource to allow direct mapping to the v1.0 cowpea reference. Access to this resource provided here is supported by raw and assembled data downloads.

  20. Report on the project on the researcher dispatch type international joint research survey. International joint research for creation of new industries; Kenkyusha hakengata kokusai kyodo kenkyu chosa jigyo. Shinki sangyo soshutsu kokusai kyodo kenkyu hokokusho

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-03-01

    For the purpose of digging up themes of the joint research which develop the R and D in the industrial field in Japan to a new stage, researchers were dispatched to the world representing research institutes to make the research study. As to the survey of the trend of bio-informatics research, visits for survey were paid by 8 researchers to 19 research institutes in the U.S., Australia, France and Germany, and survey was made of the state of new researches such as the genetic network analysis by DNA chip data. Relating to the survey of the trend of the plan for ape genomic DNA sequence, visits for survey were paid by 6 researchers to 12 research institutes in Japan, Germany, France and the U.K. Concerning the research survey with aim of developing the selective reversible expression technology of target genes, researchers were dispatched to St. Jude Children's Research Hospital in the U.S. to conduct the following: construction of basic expression vectors, functional evaluation using cultured cells, making of the transgenic mice to which medicine dependent and cell peculiar expression control genes were introduced, analytical study of the situation of expression control, etc. (NEDO)

  1. ChickVD: a sequence variation database for the chicken genome

    DEFF Research Database (Denmark)

    Wang, Jing; He, Ximiao; Ruan, Jue

    2005-01-01

    Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DN...... on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.genomics.org.cn. Udgivelsesdato: 2005-Jan-1...

  2. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute’s genomic medicine portfolio

    Science.gov (United States)

    Manolio, Teri A.

    2016-01-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual’s genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of “Genomic Medicine Meetings,” under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and diffficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI’s genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. PMID:27612677

  3. Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park.

    Science.gov (United States)

    Brumm, Phillip; Land, Miriam L; Hauser, Loren J; Jeffries, Cynthia D; Chang, Yun-Juan; Mead, David A

    2015-01-01

    Geobacillus sp. Y412MC52 was isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2011 (CP002835). Based on 16S rRNA genes and average nucleotide identity, Geobacillus sp. Y412MC52 and the related Geobacillus sp. Y412MC61 appear to be members of a new species of Geobacillus. The genome of Geobacillus sp. Y412MC52 consists of one circular chromosome of 3,628,883 bp, an average G + C content of 52 % and one circular plasmid of 45,057 bp and an average G + C content of 45 %. Y412MC52 possesses arabinan, arabinoglucuronoxylan, and aromatic acid degradation clusters for degradation of hemicellulose from biomass. Transport and utilization clusters are also present for other carbohydrates including starch, cellobiose, and α- and β-galactooligosaccharides.

  4. Digital Preservation in the Context of Institutional Repositories

    Science.gov (United States)

    Hockx-Yu, Helen

    2006-01-01

    Purpose: To discuss the issues and challenges of digital preservation facing institutional repositories and to illustrate the Joint Information Systems Committee's (JISC) view on institutional repositories and its key initiatives in helping UK institutions address these issues. Design/methodology/approach: A combination of published work and JISC…

  5. Joint Attention and Anthropological Difference

    Czech Academy of Sciences Publication Activity Database

    Urban, Petr

    2014-01-01

    Roč. 11, č. 1 (2014), s. 59-70 ISSN 1718-0198 R&D Projects: GA ČR GAP401/10/1164 Institutional support: RVO:67985955 Keywords : joint attention * anthropological difference * phenomenology * great apes * shared intentionality Subject RIV: AA - Philosophy ; Religion

  6. A Blueprint for Genomic Nursing Science

    Science.gov (United States)

    Calzone, Kathleen A.; Jenkins, Jean; Bakos, Alexis D.; Cashion, Ann; Donaldson, Nancy; Feero, Greg; Feetham, Suzanne; Grady, Patricia A.; Hinshaw, Ada Sue; Knebel, Ann R.; Robinson, Nellie; Ropka, Mary E.; Seibert, Diane; Stevens, Kathleen R.; Tully, Lois A.; Webb, Jo Ann

    2012-01-01

    Purpose This article reports on recommendations arising from an invitational workshop series held at the National Institutes of Health for the purposes of identifying critical genomics problems important to the health of the public that can be addressed through nursing science. The overall purpose of the Genomic Nursing State of the Science Initiative is to establish a nursing research blueprint based on gaps in the evidence and expert evaluation of the current state of the science and through public comment. Organizing Constructs A Genomic Nursing State of the Science Advisory Panel was convened in 2012 to develop the nursing research blueprint. The Advisory Panel, which met via two webinars and two in-person meetings, considered existing evidence from evidence reviews, testimony from key stakeholder groups, presentations from experts in research synthesis, and public comment. Findings The genomic nursing science blueprint arising from the Genomic Nursing State of Science Advisory Panel focuses on biologic plausibility studies as well as interventions likely to improve a variety of outcomes (e.g., clinical, economic, environmental). It also includes all care settings and diverse populations. The focus is on (a) the client, defined as person, family, community, or population; (b) the context, targeting informatics support systems, capacity building, education, and environmental influences; and (c) cross-cutting themes. It was agreed that building capacity to measure the impact of nursing actions on costs, quality, and outcomes of patient care is a strategic and scientific priority if findings are to be synthesized and aggregated to inform practice and policy. Conclusions The genomic nursing science blueprint provides the framework for furthering genomic nursing science to improve health outcomes. This blueprint is an independent recommendation of the Advisory Panel with input from the public and is not a policy statement of the National Institutes of Health or the

  7. The Phaeodactylum genome reveals the evolutionary history of diatom genomes

    Czech Academy of Sciences Publication Activity Database

    Bowler, Ch.; Allen, A. E.; Badger, J. H.; Grimwood, J.; Jabbari, K.; Kuo, A.; Maheswari, U.; Martens, C.; Maumus, F.; Otillar, R. P.; Rayko, E.; Salamov, A.; Vandepoele, K.; Beszteri, B.; Gruber, A.; Heijde, M.; Katinka, M.; Mock, T.; Valentin, K.; Verret, F.; Berges, J. A.; Brownlee, C.; Cadoret, J.-P.; Chiovitti, A.; Choi, Ch. J.; Coesel, S.; De Martino, A.; Detter, J. Ch.; Durkin, C.; Falciatore, A.; Fournet, J.; Haruta, M.; Huysman, M. J. J.; Jenkins, B. D.; Jiroutová, Kateřina; Jorgensen, R. E.; Joubert, Y.; Kaplan, A.; Kröger, N.; Kroth, P. G.; La Roche, J.; Lindquist, E.; Lommer, M.; Martin–Jézéquel, V.; Lopez, P. J.; Lucas, S.; Mangogna, M.; McGinnis, K.; Medlin, L. K.; Montsant, A.; Oudot–Le Secq, M.-P.; Napoli, C.; Oborník, Miroslav; Schnitzler Parker, M.; Petit, J.-L.; Porcel, B. M.; Poulsen, N.; Robison, M.; Rychlewski, L.; Rynearson, T. A.; Schmutz, J.; Shapiro, H.; Siaut, M.; Stanley, M.; Sussman, M. R.; Taylor, A. R.; Vardi, A.; von Dassow, P.; Vyverman, W.; Willis, A.; Wyrwicz, L. S.; Rokhsar, D. S.; Weissenbach, J.; Armbrust, E. V.; Green, B. R.; Van de Peer, Y.; Grigoriev, I. V.

    2008-01-01

    Roč. 456, 13-11-2008 (2008), s. 239-244 ISSN 0028-0836 Institutional research plan: CEZ:AV0Z60220518 Keywords : Phaeodactylum * genome * evolution * diatom Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 31.434, year: 2008

  8. Genomic predictions across Nordic Holstein and Nordic Red using the genomic best linear unbiased prediction model with different genomic relationship matrices.

    Science.gov (United States)

    Zhou, L; Lund, M S; Wang, Y; Su, G

    2014-08-01

    This study investigated genomic predictions across Nordic Holstein and Nordic Red using various genomic relationship matrices. Different sources of information, such as consistencies of linkage disequilibrium (LD) phase and marker effects, were used to construct the genomic relationship matrices (G-matrices) across these two breeds. Single-trait genomic best linear unbiased prediction (GBLUP) model and two-trait GBLUP model were used for single-breed and two-breed genomic predictions. The data included 5215 Nordic Holstein bulls and 4361 Nordic Red bulls, which was composed of three populations: Danish Red, Swedish Red and Finnish Ayrshire. The bulls were genotyped with 50 000 SNP chip. Using the two-breed predictions with a joint Nordic Holstein and Nordic Red reference population, accuracies increased slightly for all traits in Nordic Red, but only for some traits in Nordic Holstein. Among the three subpopulations of Nordic Red, accuracies increased more for Danish Red than for Swedish Red and Finnish Ayrshire. This is because closer genetic relationships exist between Danish Red and Nordic Holstein. Among Danish Red, individuals with higher genomic relationship coefficients with Nordic Holstein showed more increased accuracies in the two-breed predictions. Weighting the two-breed G-matrices by LD phase consistencies, marker effects or both did not further improve accuracies of the two-breed predictions. © 2014 Blackwell Verlag GmbH.

  9. Joint MS Degree Program between the Korea University of Technology and Education and the University of Kansas

    Science.gov (United States)

    Dougherty, R. L.; Kim, Kwang Su

    This paper provides an overview of the Joint MS Degree Program between Korea University of Technology and Education’ s (KUT) Mechatronics Department and Kansas University’ s (KU) Mechanical Engineering Department. Discussions were initiated in early 2005 which resulted in a formal agreement being approved by both parties in mid-2007. The Joint MS Degree Program is composed of 30 semester credit hours, equally split between the two universities, with the actual degree being awarded by the institution at which the thesis work is performed. Issues addressed during the development of this Joint MS Program included: joint versus dual degrees, institutional acceptance of the transfer of fifteen hours of credit for an MS degree, different admissions requirements and procedures for the two institutions, financial support of the students, faculty advisors at each institution, Graduate Directors at each institution, transcript acknowledgement of the Joint Degree, residency requirements, English speaking requirements/abilities, thesis publication allowances/requirements, and time zone differences for virtual meetings. These issues have been addressed, and the Joint MS Degree Program is functioning with a small number of students having taken advantage of the opportunity since the Program’ s inception. Future considerations are: growing the number of students in the Program, expansion to other Departments besides KU-Mechanical Engineering and KUTMechatronics, including other universities in the Program, expansion to a Joint PhD Degree Program, and stronger funding resources.

  10. Stereosat: A proposed private sector/government joint venture in remote sensing from space

    Science.gov (United States)

    Anglin, R. L.

    1980-01-01

    Stereosat, a free flying Sun synchronous satellite whose purpose is to obtain worldwide cloud-free stereoscopic images of the Earth's land masses, is proposed as a joint private sector/government venture. A number of potential organization models are identified. The legal, economic, and institutional issues which could impact the continuum of potential joint private sector/government institutional structures are examined.

  11. Joint enterprise: righting a wrong turn?

    OpenAIRE

    Jacobson, Jessica; Kirby, Amy; Hunter, Gillian

    2016-01-01

    This report presents the findings of an exploratory study of joint enterprise, undertaken by the Institute for Criminal Policy Research, in partnership with the Prison Reform Trust, and within funding from the Nuffield Foundation. Joint enterprise is a doctrine of the criminal law which permits multiple defendants to be convicted of the same criminal offence even where they had different types or levels of involvement. It has been the source of great controversy in recent years.\\ud \\ud The st...

  12. Computation of the Likelihood of Joint Site Frequency Spectra Using Orthogonal Polynomials

    Directory of Open Access Journals (Sweden)

    Claus Vogl

    2016-02-01

    Full Text Available In population genetics, information about evolutionary forces, e.g., mutation, selection and genetic drift, is often inferred from DNA sequence information. Generally, DNA consists of two long strands of nucleotides or sites that pair via the complementary bases cytosine and guanine (C and G, on the one hand, and adenine and thymine (A and T, on the other. With whole genome sequencing, most genomic information stored in the DNA has become available for multiple individuals of one or more populations, at least in humans and model species, such as fruit flies of the genus Drosophila. In a genome-wide sample of L sites for M (haploid individuals, the state of each site may be made binary, by binning the complementary bases, e.g., C with G to C/G, and contrasting C/G to A/T, to obtain a “site frequency spectrum” (SFS. Two such samples of either a single population from different time-points or two related populations from a single time-point are called joint site frequency spectra (joint SFS. While mathematical models describing the interplay of mutation, drift and selection have been available for more than 80 years, calculation of exact likelihoods from joint SFS is difficult. Sufficient statistics for inference of, e.g., mutation or selection parameters that would make use of all the information in the genomic data are rarely available. Hence, often suites of crude summary statistics are combined in simulation-based computational approaches. In this article, we use a bi-allelic boundary-mutation and drift population genetic model to compute the transition probabilities of joint SFS using orthogonal polynomials. This allows inference of population genetic parameters, such as the mutation rate (scaled by the population size and the time separating the two samples. We apply this inference method to a population dataset of neutrally-evolving short intronic sites from six DNA sequences of the fruit fly Drosophila melanogaster and the reference

  13. Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.

    Science.gov (United States)

    Mead, David A; Lucas, Susan; Copeland, Alex; Lapidus, Alla; Cheng, Jan-Feng; Bruce, David C; Goodwin, Lynne A; Pitluck, Sam; Chertkov, Olga; Zhang, Xiaojing; Detter, John C; Han, Cliff S; Tapia, Roxanne; Land, Miriam; Hauser, Loren J; Chang, Yun-Juan; Kyrpides, Nikos C; Ivanova, Natalia N; Ovchinnikova, Galina; Woyke, Tanja; Brumm, Catherine; Hochstein, Rebecca; Schoenfeld, Thomas; Brumm, Phillip

    2012-07-30

    Paenibacillus sp.Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The isolate was initially classified as a Geobacillus sp. Y412MC10 based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species, and the organism was most closely related to Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome sequence was deposited at the NCBI in October 2009 (NC_013406). The genome of Paenibacillus sp. Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other paenibacilli. The Y412MC10 genome shows a high level of synteny and homology to the draft sequence of Paenibacillus sp. HGF5, an organism from the Human Microbiome Project (HMP) Reference Genomes. This, combined with genomic CAZyme analysis, suggests an intestinal, rather than environmental origin for Y412MC10.

  14. The Genomic Evolution of Prostate Cancer

    Science.gov (United States)

    2017-06-01

    the proposed project : 1. To continue to acquire a comprehensive understanding of prostate cancer genomics . 2. To develop an understanding of... Genetics I • ECEV 35901 Evolutionary Genomics • Fundamentals of Clinical Research • HGEN 47400 Introduction to Probability and Statistics for Geneticists...Marc Gillard,2 David M. Hatcher,5 Westin R. Tom,5 Walter M. Stadler2 and Kevin P. White1,2,3 1Institute for Genomics and Systems Biology , Departments of

  15. PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.

    Science.gov (United States)

    Spannagl, Manuel; Bader, Kai; Pfeifer, Matthias; Nussbaumer, Thomas; Mayer, Klaus F X

    2016-01-01

    PGSB (Plant Genome and Systems Biology; formerly MIPS-Munich Institute for Protein Sequences) has been involved in developing, implementing and maintaining plant genome databases for more than a decade. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable datasets for model plant genomes as a backbone against which experimental data, e.g., from high-throughput functional genomics, can be organized and analyzed. In addition, genomes from both model and crop plants form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny) between related species on macro- and micro-levels.The genomes of many economically important Triticeae plants such as wheat, barley, and rye present a great challenge for sequence assembly and bioinformatic analysis due to their enormous complexity and large genome size. Novel concepts and strategies have been developed to deal with these difficulties and have been applied to the genomes of wheat, barley, rye, and other cereals. This includes the GenomeZipper concept, reference-guided exome assembly, and "chromosome genomics" based on flow cytometry sorted chromosomes.

  16. The joint project for high-intensity proton accelerators

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-08-01

    Japan Atomic Energy Research Institute (JAERI) and the High Energy Accelerator Research Organization (KEK) agreed to promote the joint project integrating both the Neutron Science Project (NSP) of JAERI and the Japan Hadron Facility Project (JHF) of KEK for comprehensive studies on basic science and technology using high-intensity proton accelerator. This document describes the joint proposal prepared by the Joint Project Team of JAERI and KEK to construct accelerators and research facilities necessary both for the NSP and the JHF at the site of JAERI Tokai Establishment. (author)

  17. Second-site prosthetic joint infection in patients with multiple prosthetic joints.

    Science.gov (United States)

    Clesham, Kevin; Hughes, Andrew J; O' hEireamhoin, Sven; Fleming, Catherine; Murphy, Colin G

    2018-04-10

    Prosthetic joint infections (PJIs) are among the most serious complications in arthroplasty. A second-site PJI in patients with multiple prosthetic joints increases morbidity, with many requiring further revision procedures. We aimed to establish why some patients with multiple joints develop second-site infections. Our institution's arthroplasty database was reviewed from 2004 to 2017. All PJIs were identified, and all patients with more than one prosthetic joint in situ were included. We recorded risk factors, causative organisms, number of procedures and length of stay. Forty-four patients meeting the criteria were identified. Four patients (9.1%) developed second-site infection. Eight patients (18.2%) developed re-infection of the primary PJI. Positive MRSA carrier status and PJI of a total knee replacement were associated with an increased risk of a second episode of infection. Patients who developed further infection had more frequent admission and longer lengths of stay than isolated PJIs. Higher morbidity and use of hospital resources are associated with this cohort of patients. PJIs in total knee replacements and positive MRSA status are associated with higher rates of second infection. Identifying this vulnerable cohort of patients at an early stage is critical to ensure measures are taken to reduce the risks of further infection.

  18. Harnessing genomics to improve health in the Eastern Mediterranean Region – an executive course in genomics policy

    Directory of Open Access Journals (Sweden)

    Singer Peter A

    2005-01-01

    Full Text Available Abstract Background While innovations in medicine, science and technology have resulted in improved health and quality of life for many people, the benefits of modern medicine continue to elude millions of people in many parts of the world. To assess the potential of genomics to address health needs in EMR, the World Health Organization's Eastern Mediterranean Regional Office and the University of Toronto Joint Centre for Bioethics jointly organized a Genomics and Public Health Policy Executive Course, held September 20th–23rd, 2003, in Muscat, Oman. The 4-day course was sponsored by WHO-EMRO with additional support from the Canadian Program in Genomics and Global Health. The overall objective of the course was to collectively explore how to best harness genomics to improve health in the region. This article presents the course findings and recommendations for genomics policy in EMR. Methods The course brought together senior representatives from academia, biotechnology companies, regulatory bodies, media, voluntary, and legal organizations to engage in discussion. Topics covered included scientific advances in genomics, followed by innovations in business models, public sector perspectives, ethics, legal issues and national innovation systems. Results A set of recommendations, summarized below, was formulated for the Regional Office, the Member States and for individuals. • Advocacy for genomics and biotechnology for political leadership; • Networking between member states to share information, expertise, training, and regional cooperation in biotechnology; coordination of national surveys for assessment of health biotechnology innovation systems, science capacity, government policies, legislation and regulations, intellectual property policies, private sector activity; • Creation in each member country of an effective National Body on genomics, biotechnology and health to: - formulate national biotechnology strategies - raise

  19. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  20. Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

    Science.gov (United States)

    Anselmetti, Yoann; Duchemin, Wandrille; Tannier, Eric; Chauve, Cedric; Bérard, Sèverine

    2018-05-09

    Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADSEQ provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADSEQ to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes. We demonstrate the method's ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.

  1. MIT Experiments with Joint Venture Contract.

    Science.gov (United States)

    American School and University, 1981

    1981-01-01

    A new dormitory at Massachusetts Institute of Technology was constructed using a joint venture contract with safeguards and incentives that brought university, architect, and building contractor into a closer and more productive relationship than under conventional contract arrangements. (Author/MLF)

  2. Efficient strategy for detecting gene × gene joint action and its application in schizophrenia.

    Science.gov (United States)

    Won, Sungho; Kwon, Min-Seok; Mattheisen, Manuel; Park, Suyeon; Park, Changsoon; Kihara, Daisuke; Cichon, Sven; Ophoff, Roel; Nöthen, Markus M; Rietschel, Marcella; Baur, Max; Uitterlinden, Andre G; Hofmann, A; Lange, Christoph

    2014-01-01

    We propose a new approach to detect gene × gene joint action in genome-wide association studies (GWASs) for case-control designs. This approach offers an exhaustive search for all two-way joint action (including, as a special case, single gene action) that is computationally feasible at the genome-wide level and has reasonable statistical power under most genetic models. We found that the presence of any gene × gene joint action may imply differences in three types of genetic components: the minor allele frequencies and the amounts of Hardy-Weinberg disequilibrium may differ between cases and controls, and between the two genetic loci the degree of linkage disequilibrium may differ between cases and controls. Using Fisher's method, it is possible to combine the different sources of genetic information in an overall test for detecting gene × gene joint action. The proposed statistical analysis is efficient and its simplicity makes it applicable to GWASs. In the current study, we applied the proposed approach to a GWAS on schizophrenia and found several potential gene × gene interactions. Our application illustrates the practical advantage of the proposed method. © 2013 WILEY PERIODICALS, INC.

  3. RadGenomics project

    Energy Technology Data Exchange (ETDEWEB)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

    2002-06-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  4. RadGenomics project

    International Nuclear Information System (INIS)

    Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

    2002-01-01

    Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

  5. Annual report 1991. Environment Institute

    International Nuclear Information System (INIS)

    1992-01-01

    This is the annual report of the Environment Institute of the Joint Research Centre - Ispra Site - of the Commission of the European Communities. The report summarizes the progress accomplished in the course of 1991 - i.e. the last of the four year (1988-91) Specific Research Programme of the Joint Research Centre - in the projects tackled by the Institute. The activities were mainly focused on the areas of environmental chemicals, air pollution, water pollution, chemical waste and food and drug analysis, included in the programme Environmental Protection, and of safety assessment of nuclear waste disposal in geological formation as a part of the Radioactive Waste Management programme. The scientific support provided to different Commission Services is also described, proper emphasis being given to that provided to the Directorate General Xl (Environment, Nuclear Safety and Civil Protection) in the field of chemicals, air pollution, water pollution, chemical waste and radioactive environmental monitoring (REM). The above activities are aimed at the implementation of EC directives in the related fields. The work for third parties and the contribution of the Institute to various EUREKA and COST projects are also shortly described. Lastly the report provides essential data concerning the Institute structure and the human and financial resources

  6. JAERI-KEK joint project on high intensity proton accelerators

    International Nuclear Information System (INIS)

    Nagamiya, Shoji

    2000-01-01

    Japan Atomic Energy Research Institute (JAERI) and the High Energy Accelerator Organization (KEK) are promoting the joint project integrating both the Neutron Science Project (NSP) of JAERI and the Japan Hadron Facility Project (JHF) of KEK for comprehensive studies on basic science and technology using high-intensity proton accelerator. This paper describes the joint project prepared by the Joint Project Team of JAERI and KEK to construct accelerators and research facilities necessary both for the NSP and the JHF at the site of JAERI Tokai Establishment. (author)

  7. Genomics education for medical professionals - the current UK landscape.

    Science.gov (United States)

    Slade, Ingrid; Subramanian, Deepak N; Burton, Hilary

    2016-08-01

    Genomics education in the UK is at an early stage of development, and its pace of evolution has lagged behind that of the genomics research upon which it is based. As a result, knowledge of genomics and its applications remains limited among non-specialist clinicians. In this review article, we describe the complex landscape for genomics education within the UK, and highlight the large number and variety of organisations that can influence, direct and provide genomics training to medical professionals. Postgraduate genomics education is being shaped by the work of the Health Education England (HEE) Genomics Education Programme, working in conjunction with the Joint Committee on Genomics in Medicine. The success of their work will be greatly enhanced by the full cooperation and engagement of the many groups, societies and organisations involved with medical education and training (such as the royal colleges). Without this cooperation, there is a risk of poor coordination and unnecessary duplication of work. Leadership from an organisation such as the HEE Genomics Education Programme will have a key role in guiding the formulation and delivery of genomics education policy by various stakeholders among the different disciplines in medicine. © 2016 Royal College of Physicians.

  8. Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

    Energy Technology Data Exchange (ETDEWEB)

    Ditty, Jayna L.; Kvaal, Christopher A.; Goodner, Brad; Freyermuth, Sharyn K.; Bailey, Cheryl; Britton, Robert A.; Gordon, Stuart G.; Heinhorst, Sabine; Reed, Kelynne; Xu, Zhaohui; Sanders-Lorenz, Erin R.; Axen, Seth; Kim, Edwin; Johns, Mitrick; Scott, Kathleen; Kerfeld, Cheryl A.

    2011-08-01

    into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinformatics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG-ACT). It was developed by instructors from both research-intensive and predominately undergraduate institutions in collaboration with the Department of Energy-Joint Genome Institute (DOE-JGI) as a means to innovate and update undergraduate education and faculty development. The IMG-ACT program provides a cadre of tools, including access to a clearinghouse of genome sequences, bioinformatics databases, data storage, instructor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportunities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools ensures that all types of higher education institutions can utilize it. With the infrastructure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty members of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our development in terms of teaching and research with the hopes that it will inspire more faculty to get involved.

  9. Cambridge Healthtech Institute's 5th Annual Conference: impact of genomics on medicine.

    Science.gov (United States)

    Zanders, E D

    2001-08-01

    The recent publications in Nature and Science by the Human Genome Consortium and Celera Genomics, respectively, while being landmark achievements in themselves, have also given pause for thought. A definitive catalogue of human genes is still not available but the broad picture of how humans compare with lower organisms at the genomic level is becoming clearer. The full impact of these findings on the practice of medicine is hard to predict, but research being conducted now, in the early years of the 21st century, will form the basis of future advances in the diagnosis and treatment of disease. Exactly what this will entail is the subject of intense debate, but there are some common starting points that were discussed at this meeting in Munich. The main theme to emerge was the need to move beyond the human genome sequence towards an understanding of proteins and their interactions in complex biological pathways, thereby increasing opportunities for drug discovery through the identification of new targets. The majority of the talks were therefore devoted to the description of technological advances in the analysis of gene and protein expression (and interaction) and in the use of various methods of gene deletion in order to validate individual proteins as drug targets. Perhaps it will still be a few years before it will be possible to report on the application of genomic analyses to routine medical practice at the first point of care for patients but when that happens, the research efforts described here will have been worthwhile.

  10. Capturing prokaryotic dark matter genomes.

    Science.gov (United States)

    Gasc, Cyrielle; Ribière, Céline; Parisot, Nicolas; Beugnot, Réjane; Defois, Clémence; Petit-Biderre, Corinne; Boucher, Delphine; Peyretaillade, Eric; Peyret, Pierre

    2015-12-01

    Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  11. Joint implementation, clean development mechanism and Tradable Permits. International regulation of greenhouse gases

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, L.; Rose Olsen, K.

    2000-06-01

    A 'correct' accreditation is a key issue when evaluating Joint Implementation as a global environmental instrument. Problems mentioned in the literature on Joint Implementation - including the problem of additionality - are often relating to the problem of defining a correct accreditation. This paper lists some of these problems and lists some of the tools available to solve the reported problems of accreditation. The paper concludes that the institutional framework is crucial in defining what a correct accreditation is. It also concludes that different groups may have different interests in Joint Implementation, and that each of the reported problems may be a problem to some of the Joint Implementation interests groups but not to others. In designing the institutional framework for JI it is important to know the incentives and motivations of the different groups. The main part of the paper is an analysis of the basic incentives and motivations of the different Joint Implementation interest groups. This analysis can be used to weight the problems of Joint Implementation from an environmental perspective and from the perspective of cost effectiveness. (au)

  12. Joint implementation, clean development mechanism and Tradable Permits. International regulation of greenhouse gases

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, L; Rose Olsen, K

    2000-06-01

    A 'correct' accreditation is a key issue when evaluating Joint Implementation as a global environmental instrument. Problems mentioned in the literature on Joint Implementation - including the problem of additionality - are often relating to the problem of defining a correct accreditation. This paper lists some of these problems and lists some of the tools available to solve the reported problems of accreditation. The paper concludes that the institutional framework is crucial in defining what a correct accreditation is. It also concludes that different groups may have different interests in Joint Implementation, and that each of the reported problems may be a problem to some of the Joint Implementation interests groups but not to others. In designing the institutional framework for JI it is important to know the incentives and motivations of the different groups. The main part of the paper is an analysis of the basic incentives and motivations of the different Joint Implementation interest groups. This analysis can be used to weight the problems of Joint Implementation from an environmental perspective and from the perspective of cost effectiveness. (au)

  13. High participation rate among 25 721 patients with broad age range in a hospital-based research project involving whole-genome sequencing - the Lausanne Institutional Biobank.

    Science.gov (United States)

    Bochud, Murielle; Currat, Christine; Chapatte, Laurence; Roth, Cindy; Mooser, Vincent

    2017-10-24

    We aimed to evaluate the interest of adult inpatients and selected outpatients in engaging in a large, real-life, hospital-based, genomic medicine research project and in receiving clinically actionable incidental findings. Within the framework of the cross-sectional Institutional Biobank of Lausanne, Switzerland, a total of 25721 patients of the CHUV University Hospital were systematically invited to grant researchers access to their biomedical data and to donate blood for future analyses, including whole-genome sequencing. Multivariable logistic regression analysis was used to identify personal factors, including age, gender, religion, ethnicity, citizenship, education level and mode of admission, associated with willingness to participate in this genomic research project and with interest in receiving clinically actionable incidental findings. The overall participation rate was 79% (20343/25721). Participation rate declined progressively with age, averaging 83%, 75%, 67% and 62% in patients aged rate, but not with higher willingness to receive incidental findings within the population who had agreed to participate. A large proportion of adult patients, even among the elderly, are willing to actively participate and receive incidental findings in this systematic hospital-based precision and genomic medicine research program with broad consent.

  14. Genome medicine: gene therapy for the millennium, 30 September-3 October 2001, Rome, Italy.

    Science.gov (United States)

    Gruenert, D C; Novelli, G; Dallapiccola, B; Colosimo, A

    2002-06-01

    The recent surge of DNA sequence information resulting from the efforts of agencies interested in deciphering the human genetic code has facilitated technological developments that have been critical in the identification of genes associated with numerous disease pathologies. In addition, these efforts have opened the door to the opportunity to develop novel genetic therapies to treat a broad range of inherited disorders. Through a joint effort by the University of Vermont, the University of Rome, Tor Vergata, University of Rome, La Sapienza, and the CSS Mendel Institute, Rome, an international meeting, 'Genome Medicine: Gene Therapy for the Millennium' was organized. This meeting provided a forum for the discussion of scientific and clinical advances stimulated by the explosion of sequence information generated by the Human Genome Project and the implications these advances have for gene therapy. The meeting had six sessions that focused on the functional evaluation of specific genes via biochemical analysis and through animal models, the development of novel therapeutic strategies involving gene targeting, artificial chromsomes, DNA delivery systems and non-embryonic stem cells, and on the ethical and social implications of these advances.

  15. 12 CFR 573.13 - Exception to opt out requirements for service providers and joint marketing.

    Science.gov (United States)

    2010-01-01

    ... this section to a financial institution with which you perform joint marketing, your contractual... products or services or marketing of financial products or services offered pursuant to joint agreements... providers and joint marketing. 573.13 Section 573.13 Banks and Banking OFFICE OF THRIFT SUPERVISION...

  16. Characteristics of the joint mini-model high temperature superconducting cable

    International Nuclear Information System (INIS)

    Kim, H.; Sim, K.; Cho, J.; Kim, S.; Kim, J.H.; Jung, H.Y.

    2008-01-01

    To obtain realistic data on the high temperature superconducting (HTS) power cable, 3-phase 100 m long, 22.9 kV class HTS power transmission cable system have been developed by Korea Electrotechnology Research Institute (KERI) and LS cable Ltd. that is one of 21st Century Frontier Project in Korea. This cable was installed at Go-chang testing site of Korea Electric Power Corporation (KEPCO). For the application of the HTS power cable joint is very important to ensure the performance. Therefore, this paper gives some investigation of AC loss, critical current and joint resistance in jointed HTS tape. We experimentally showed that the influence of joint resistance on AC loss by using several joint methods. Finally, we are measured critical current, AC loss and jointed resistance for the manufactured mini-model cable

  17. Soviet efforts to attract foreign E and P investment through joint ventures

    International Nuclear Information System (INIS)

    Gochenour, D.T.

    1991-01-01

    This paper reports that since 1987, Soviet efforts to attract Western E and P investment have been evolving through the framework provided by the 1987 Joint-Venture Law. While this law and dozen or so regular acts, decrees, and amendments have sought to stimulate interest, they have failed to address significant failings in the Soviet Union's institutional organization of the petroleum industry. While we anticipate that institutional authority will continue to devolve away from the All-Union central control in Moscow to the republican authorities, many obstacles to investors still have not been addressed by the joint-venture laws. Among these are the export regime, fiscal regime (which we expect will get stiffer), and the rules for joint-venture capitalization and valuation

  18. 12 CFR 40.13 - Exception to opt out requirements for service providers and joint marketing.

    Science.gov (United States)

    2010-01-01

    ... providers and joint marketing. 40.13 Section 40.13 Banks and Banking COMPTROLLER OF THE CURRENCY, DEPARTMENT... performs joint marketing, the bank's contractual agreement with that institution meets the requirements of... include joint marketing. The services a nonaffiliated third party performs for a bank under paragraph (a...

  19. Comparative Genome Analysis Reveals Divergent Genome Size Evolution in a Carnivorous Plant Genus

    Czech Academy of Sciences Publication Activity Database

    Vu, G.T.H.; Schmutzer, T.; Bull, F.; Cao, H.X.; Fuchs, J.; Tran, T.D.; Jovtchev, G.; Pistrick, K.; Stein, N.; Pečinka, A.; Neumann, Pavel; Novák, Petr; Macas, Jiří; Dear, P.H.; Blattner, F.R.; Scholz, U.; Schubert, I.

    2015-01-01

    Roč. 8, č. 3 (2015) ISSN 1940-3372 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Genlisea * genome * repetitive sequences Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.509, year: 2015

  20. Description and Methods of the Automated Document Management System Usage in Scientific Organizational Activities of the Joint Institute for Nuclear Research (ADS SOA JINR)

    CERN Document Server

    Borisovsky, V F; Kekelidze, M G; Nikonov, E G; Senchenko, V A

    2005-01-01

    This paper presents the structure description and user guide for Information program system for automation of a document flow for support of scientific arrangement planning (ADS SOA) which can be used for planning and carrying out seminars, workshops, conferences and other arrangements of research management. This work is intended for automation of scientific research management in the Joint Institute for Nuclear Research. The complex of programs represents the CDS Agenda system used in the European Organization for Nuclear Research (CERN), which is adapted to the conditions of JINR.

  1. Development of Genomic and Genetic Tools for Foxtail Millet, and Use of These Tools in the Improvement of Biomass Production for Bioenergy Crops

    Energy Technology Data Exchange (ETDEWEB)

    Doust, Andrew, N.

    2011-11-11

    The overall aim of this research was to develop genomic and genetic tools in foxtail millet that will be useful in improving biomass production in bioenergy crops such as switchgrass, napier grass, and pearl millet. A variety of approaches have been implemented, and our lab has been primarily involved in genome analysis and quantitative genetic analysis. Our progress in these activities has been substantially helped by the genomic sequence of foxtail millet produced by the Joint Genome Institute (Bennetzen et al., in prep). In particular, the annotation and analysis of candidate genes for architecture, biomass production and flowering has led to new insights into the control of branching and flowering time, and has shown how closely related flowering time is to vegetative architectural development and biomass accumulation. The differences in genetic control identified at high and low density plantings have direct relevance to the breeding of bioenergy grasses that are tolerant of high planting densities. The developmental analyses have shown how plant architecture changes over time and may indicate which genes may best be manipulated at various times during development to obtain required biomass characteristics. This data contributes to the overall aim of significantly improving genetic and genomic tools in foxtail millet that can be directed to improvement of bioenergy grasses such as switchgrass, where it is important to maximize vegetative growth for greatest biomass production.

  2. Conceptual approaches to international cooperation between higher education institutions

    Directory of Open Access Journals (Sweden)

    Tetiana Obolenska

    2016-12-01

    Full Text Available The existing conceptual and technological approaches to the organization and implementation of international cooperation between higher education institutions with the performance of international accreditation based on education quality system have been characterized in complex, considering the key trends of internationalization of higher education. Priority strategies of higher education internationalization and types of international academic cooperation between universities regarding education services were defined. It has been substantiated that the most important manifestation of higher education internationalization is international cooperation between universities regarding rendering education services, while the highest level of internationalization of this service is joint educational programs. A complex analysis of international accreditation requirements to joint education programs was made on the basis of the system of education quality improvement, its advantages were proven and its distinct features that influence the choice and substantiation of international cooperation, marketing and branding of individual programs were characterized. Technology of international accreditation for joint programs was detailed. Special attention was paid to the practical component of launching joint degree programs between Ukrainian and foreign higher education institutions. The experience of joint master’s degree programs of Kyiv National Economic University named after Vadym Hetman and the University of Redlands Business School (California, USA was analyzed.

  3. 75 FR 54159 - National Institute on Aging; Notice of Closed Meetings

    Science.gov (United States)

    2010-09-03

    ...: National Institute on Aging Special Emphasis Panel, Stem Cells and Genomic Integrity Through Senescense.... 93.866, Aging Research, National Institutes of Health, HHS) Dated: August 26, 2010. Jennifer S...

  4. Remote transient Lactobacillus animalis bacteremia causing prosthetic hip joint infection: a case report.

    Science.gov (United States)

    Somayaji, R; Lynch, T; Powell, J N; Gregson, D

    2016-11-04

    Lactobacillus spp. are uncommon pathogens in immunocompetent hosts, and even rarer causes of prosthetic device infections. A case of chronic hip prosthetic joint infection (PJI) caused by L. animalis is described. This occurred 5 years after a transient bacteremia with the same organism. Whole genome sequencing of both isolates proved this PJI infection resulted from this remote bacteremia. We document that prosthetic joint infections may be a consequence of bacteremia as much as 3 years before the onset of symptoms.

  5. Genome Variation Map: a data repository of genome variations in BIG Data Center.

    Science.gov (United States)

    Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

    2018-01-04

    The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. Genome Variation Map: a data repository of genome variations in BIG Data Center

    Science.gov (United States)

    Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

    2018-01-01

    Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

  7. On joint numerical radius II

    Czech Academy of Sciences Publication Activity Database

    Drnovšek, R.; Müller, Vladimír

    2014-01-01

    Roč. 62, č. 9 (2014), s. 1197-1204 ISSN 0308-1087 R&D Projects: GA ČR GA201/09/0473; GA AV ČR IAA100190903 Institutional support: RVO:67985840 Keywords : joint numerical range * numerical radius Subject RIV: BA - General Mathematics Impact factor: 0.738, year: 2014 http://www.tandfonline.com/doi/abs/10.1080/03081087.2013.816303

  8. New Approaches and Technologies to Sequence de novo Plant reference Genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

    Energy Technology Data Exchange (ETDEWEB)

    Schmutz, Jeremy

    2013-03-01

    Jeremy Schmutz of the HudsonAlpha Institute for Biotechnology on New approaches and technologies to sequence de novo plant reference genomes at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 in Walnut Creek, CA.

  9. The joint FAO and IAEA programme

    International Nuclear Information System (INIS)

    Fried, M.; Lamm, C.G.

    1981-01-01

    In 1964 the FAO and IAEA decided to establish a joint programme for the specific purpose of assisting Member States in applying nuclear techniques to develop their food and agriculture. As a result, the Joint FAO/IAEA Division of Isotope and Radiation Applications of Atomic Energy and Agriculture Development was established. The objectives of this joint FAO/IAEA programme are to exploit the potential of isotopes and radiation applications in research and development to increase and stabilize agriculture production, to reduce production costs, to improve the quality of food, to protect agricultural products from spoilage and losses, and to minimize pollution of food and agricultural environment. The activities of the joint programme, which are briefly described, can be grouped under three main headings: co-ordination and support of research; technical assistance including training; and dissemination of information. Tables are shown giving a breakdown of 311 research contracts and agreements held with institutes in Member States and 86 technical assistance projects in 46 developing countries, providing training, expertise and specialized equipment

  10. The New Microbiology: a conference at the Institut de France.

    Science.gov (United States)

    Radoshevich, Lilliana; Bierne, Hélène; Ribet, David; Cossart, Pascale

    2012-08-01

    In May 2012, three European Academies held a conference on the present and future of microbiology. The conference, entitled "The New Microbiology", was a joint effort of the French Académie des sciences, of the German National Academy of Sciences Leopoldina and of the British Royal Society. The organizers - Pascale Cossart and Philippe Sansonetti from the "Académie des sciences", David Holden and Richard Moxon from the "Royal Society", and Jörg Hacker and Jürgen Hesseman from the "Leopoldina Nationale Akademie der Wissenschaften" - wanted to highlight the current renaissance in the field of microbiology mostly due to the advent of technological developments and allowing for single-cell analysis, rapid and inexpensive genome-wide comparisons, sophisticated microscopy and quantitative large-scale studies of RNA regulation and proteomics. The conference took place in the historical Palais de l'Institut de France in Paris with the strong support of Jean-François Bach, Secrétaire Perpétuel of the Académie des sciences. Copyright © 2012 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  11. Degenerative Joint Diseases and Neuroinflammation.

    Science.gov (United States)

    Fusco, Mariella; Skaper, Stephen D; Coaccioli, Stefano; Varrassi, Giustino; Paladini, Antonella

    2017-04-01

    Rheumatic and joint diseases, as exemplified by osteoarthritis and rheumatoid arthritis, are among the most widespread painful and disabling pathologies across the globe. Given the continuing rise in life expectancy, their prevalence is destined to grow. Osteoarthritis, a degenerative joint disease, is, in particular, on its way to becoming the fourth leading cause of disability worldwide by 2020, with the rising incidence of obesity in addition to age being important factors. It is estimated that 25% of osteoarthritic individuals are unable to perform daily activities. Accompanying osteoarthritis is rheumatoid arthritis, which is a chronic systemic disease that often causes pain and deformity. At least 50% of those affected are unable to remain gainfully employed within 10 years of disease onset. A growing body of evidence now points to inflammation, locally and more systemically, as a promoter of damage to joints and bones, as well as joint-related functional deficits. The pathogenesis underlying joint diseases remains unclear; however, it is currently believed that cross-talk between cartilage and subchondral bone-and loss of balance between these two structures in joint diseases-is a critical element. This view is amplified by the presence of mast cells, whose dysregulation is associated with alterations of junction structures (cartilage, bone, synovia, matrix, nerve endings, and blood vessels). In addition, persistent activation of mast cells facilitates the development of spinal neuroinflammation mediated through their interaction with microglia. Unfortunately, current treatment strategies for rheumatic and articular disease are symptomatic and do little to limit disease progression. Research now should be directed at therapeutic modalities that target osteoarticular structural elements and thereby delaying disease progression and joint replacement. © 2016 World Institute of Pain.

  12. First industrial application of MAG STT welding with auto adaptative joint control

    International Nuclear Information System (INIS)

    Tran Tien, Thong

    2006-01-01

    The Welding Institute has participated to an extraordinary plan: the manufacture of the new LHC (Large Hadron Collider) particles accelerator in a circular tunnel of 27 km of circumference, at the European laboratory for particles physics (CERN) located at the Franco-Swiss frontier. The LHC dipolar magnets wires constituted in semi-cylinders of 15 m length in 316 LN, thickness 10 mm, are assembled in horizontal-vertical position. The Welding Institute has developed a software allowing to implement the auto-adaptative welding with follow of laser joint, using the MAG STT (Surface Tension Transfer) process. The modeling of welding laws connected with the strategy of joints filling runs (in multi-passes), absorb the physical tolerances of the preparation (clearance, poor alignment, root of joint...) and this in welding dynamical condition. (O.M.)

  13. Detection of periprosthetic joint infections in presumed aseptic patients

    DEFF Research Database (Denmark)

    Xu, Yijuan; Lorenzen, Jan; Thomsen, Trine Rolighed

    2016-01-01

    Title: Detection of periprosthetic joint infections in presumed aseptic patients Yijuan Xu1, Jan Lorenzen1, Trine Rolighed Thomsen1,2, Kathrin Kluba3, Kathrin Chamaon3, Christoph Lohmann3 1. Danish Technological Institute, Aarhus, Denmark 2. Center for Microbial Communities, Department of Biotech......Title: Detection of periprosthetic joint infections in presumed aseptic patients Yijuan Xu1, Jan Lorenzen1, Trine Rolighed Thomsen1,2, Kathrin Kluba3, Kathrin Chamaon3, Christoph Lohmann3 1. Danish Technological Institute, Aarhus, Denmark 2. Center for Microbial Communities, Department...... of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Denmark 3. Department of Orthopaedics, Otto-von-Guericke University of Magdeburg, Germany Aim: ”The HypOrth project (New approaches in the development of Hypoallergenic implant material in Orthopaedics: Steps to personalised medicine......) aims to investigate adverse immune reactions to implant materials. For this project, it is of utmost importance to exclude patients with periprosthetic joint infections (PJIs). The aim of this study was to rule out PJIs in included patients using prolonged culture and next generation sequencing (NGS...

  14. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

    Science.gov (United States)

    Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

    2017-06-01

    Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  15. Origins of the Human Genome Project.

    Science.gov (United States)

    Watson, J D; Cook-Deegan, R M

    1991-01-01

    The Human Genome Project has become a reality. Building on a debate that dates back to 1985, several genome projects are now in full stride around the world, and more are likely to form in the next several years. Italy began its genome program in 1987, and the United Kingdom and U.S.S.R. in 1988. The European communities mounted several genome projects on yeast, bacteria, Drosophila, and Arabidospis thaliana (a rapidly growing plant with a small genome) in 1988, and in 1990 commenced a new 2-year program on the human genome. In the United States, we have completed the first year of operation of the National Center for Human Genome Research at the National Institutes of Health (NIH), now the largest single funding source for genome research in the world. There have been dedicated budgets focused on genome-scale research at NIH, the U.S. Department of Energy, and the Howard Hughes Medical Institute for several years, and results are beginning to accumulate. There were three annual meetings on genome mapping and sequencing at Cold Spring Harbor, New York, in the spring of 1988, 1989, and 1990; the talks have shifted from a discussion about how to approach problems to presenting results from experiments already performed. We have finally begun to work rather than merely talk. The purpose of genome projects is to assemble data on the structure of DNA in human chromosomes and those of other organisms. A second goal is to develop new technologies to perform mapping and sequencing. There have been impressive technical advances in the past 5 years since the debate about the human genome project began. We are on the verge of beginning pilot projects to test several approaches to sequencing long stretches of DNA, using both automation and manual methods. Ordered sets of yeast artificial chromosome and cosmid clones have been assembled to span more than 2 million base pairs of several human chromosomes, and a region of 10 million base pairs has been assembled for

  16. Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park.

    Science.gov (United States)

    Brumm, Phillip J; Land, Miriam L; Mead, David A

    2015-01-01

    Geobacillus thermoglucosidasius C56-YS93 was one of several thermophilic organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. Comparison of 16 S rRNA sequences confirmed the classification of the strain as a G. thermoglucosidasius species. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2011 (CP002835). The genome of G. thermoglucosidasius C56-YS93 consists of one circular chromosome of 3,893,306 bp and two circular plasmids of 80,849 and 19,638 bp and an average G + C content of 43.93 %. G. thermoglucosidasius C56-YS93 possesses a xylan degradation cluster not found in the other G. thermoglucosidasius sequenced strains. This cluster appears to be related to the xylan degradation cluster found in G. stearothermophilus. G. thermoglucosidasius C56-YS93 possesses two plasmids not found in the other two strains. One plasmid contains a novel gene cluster coding for proteins involved in proline degradation and metabolism, the other contains a collection of mostly hypothetical proteins.

  17. An overview of wheat genome sequencing and its implications for ...

    Indian Academy of Sciences (India)

    National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110 067, India ... Wheat (Triticum aestivum L.) serves as the staple food for. 30% of the global .... bread wheat genome is a product of multiple rounds of hybrid.

  18. Joint Research on Scatterometry and AFM Wafer Metrology

    NARCIS (Netherlands)

    Bodermann, B.; Buhr, E.; Danzebrink, H.U.; Bär, M.; Scholze, F.; Krumrey, M.; Wurm, M.; Klapetek, P.; Hansen, P.E.; Korpelainen, V.; Van Veghel, M.; Yacoot, A.; Siitonen, S.; El Gawhary, O.; Burger, S.; Saastamoinen, T.

    2011-01-01

    Supported by the European Commission and EURAMET, a consortium of 10 participants from national metrology institutes, universities and companies has started a joint research project with the aim of overcoming current challenges in optical scatterometry for traceable linewidth metrology. Both

  19. Relaxation behaviour of gasketed joints during assembly using finite ...

    Indian Academy of Sciences (India)

    Faculty of Mechanical Engineering, Ghulam Ishaq Khan (GIK) Institute of ... Bolt scatter, bolt bending, joint relaxation and gasket stress variation are concluded the main .... In the present work, following two ..... American Society of Mech.

  20. Conceptual Dimension of Problems of Joint Activity of the State and Civil Society Institutes on Ensuring National Security of the Russian Federation

    Directory of Open Access Journals (Sweden)

    Gulyaikhin Vyacheslav N.

    2016-09-01

    Full Text Available In the article the main methodological approaches to the problem of interaction of institutes of the state and civil society in the context of ensuring national security of Russia are analyzed. Two main alternative concepts (liberal and etatist to which the Russian researchers adhere are allocated. Supporters of liberal approach suppose that domination of the interests of civil society and ensuring equal cooperation with government institutions at the solution of problems of ensuring national security is necessary. Adherents of the etatist concept defend an unconditional priority of government bodies in this sphere. The authors provide the conceptual analysis of estimates by domestic researchers of the main activities of associations of the citizens connected with the counteraction to threats of national security. In the article positive impact of institutes of civil society on political and social and economic processes in Russia is noted, their assistance in development of the state institutes of the state and the potential of constructive interaction with federal and regional authorities on ensuring national security is estimated. The detailed analysis of the politological concept according to which more active participation of public organizations and socially responsible citizens in ensuring national security is necessary, is carried out. Their influence on development of a security system has to become more and more considerable because of social and economic problems which are objectively demanding participation of civil society in their decision-making. It is connected also with the need of modernization breakthrough, not possible without civil initiatives. In the article the conclusion that the Russian researchers attach great value to interaction of institutes of the state and civil society in ensuring national security of the Russian Federation is drawn, conceptually proving the need of their joint activity for this direction, and

  1. Remote transient Lactobacillus animalis bacteremia causing prosthetic hip joint infection: a case report

    Directory of Open Access Journals (Sweden)

    R. Somayaji

    2016-11-01

    Full Text Available Abstract Background Lactobacillus spp. are uncommon pathogens in immunocompetent hosts, and even rarer causes of prosthetic device infections. Case presentation A case of chronic hip prosthetic joint infection (PJI caused by L. animalis is described. This occurred 5 years after a transient bacteremia with the same organism. Whole genome sequencing of both isolates proved this PJI infection resulted from this remote bacteremia. Conclusions We document that prosthetic joint infections may be a consequence of bacteremia as much as 3 years before the onset of symptoms.

  2. Correcting systematic inflation in genetic association tests that consider interaction effects: application to a genome-wide association study of posttraumatic stress disorder.

    Science.gov (United States)

    Almli, Lynn M; Duncan, Richard; Feng, Hao; Ghosh, Debashis; Binder, Elisabeth B; Bradley, Bekh; Ressler, Kerry J; Conneely, Karen N; Epstein, Michael P

    2014-12-01

    Genetic association studies of psychiatric outcomes often consider interactions with environmental exposures and, in particular, apply tests that jointly consider gene and gene-environment interaction effects for analysis. Using a genome-wide association study (GWAS) of posttraumatic stress disorder (PTSD), we report that heteroscedasticity (defined as variability in outcome that differs by the value of the environmental exposure) can invalidate traditional joint tests of gene and gene-environment interaction. To identify the cause of bias in traditional joint tests of gene and gene-environment interaction in a PTSD GWAS and determine whether proposed robust joint tests are insensitive to this problem. The PTSD GWAS data set consisted of 3359 individuals (978 men and 2381 women) from the Grady Trauma Project (GTP), a cohort study from Atlanta, Georgia. The GTP performed genome-wide genotyping of participants and collected environmental exposures using the Childhood Trauma Questionnaire and Trauma Experiences Inventory. We performed joint interaction testing of the Beck Depression Inventory and modified PTSD Symptom Scale in the GTP GWAS. We assessed systematic bias in our interaction analyses using quantile-quantile plots and genome-wide inflation factors. Application of the traditional joint interaction test to the GTP GWAS yielded systematic inflation across different outcomes and environmental exposures (inflation-factor estimates ranging from 1.07 to 1.21), whereas application of the robust joint test to the same data set yielded no such inflation (inflation-factor estimates ranging from 1.01 to 1.02). Simulated data further revealed that the robust joint test is valid in different heteroscedasticity models, whereas the traditional joint test is invalid. The robust joint test also has power similar to the traditional joint test when heteroscedasticity is not an issue. We believe the robust joint test should be used in candidate-gene studies and GWASs of

  3. Lubrication of the human ankle joint in running

    Czech Academy of Sciences Publication Activity Database

    Hlaváček, Miroslav

    2009-01-01

    Roč. 3, č. 5 (2009), s. 619-626 ISSN 1970-8734 R&D Projects: GA ČR(CZ) GA103/07/0043 Institutional research plan: CEZ:AV0Z20710524 Keywords : human ankle joint * lubrication * running Subject RIV: JJ - Other Materials

  4. Report of the research results with joint-use facilities in fiscal year 1977

    International Nuclear Information System (INIS)

    1978-01-01

    In the Nuclear Engineering Research Laboratory, the University of Tokyo, fast neutron source reactor 'Yayoi', linac and fusion-reactor blanket facility are jointly used by educational institutions. Research results from the joint uses of the facilities in fiscal 1977 are presented in individual summaries: (on-pile) irradiation, reactor physics and engineering, etc., (off-pile) equipment and component techniques, etc., (linac) operation, etc., with these joint uses, unique works are intended in resonable way. (Mori, K.)

  5. One Mission-Centered, Market-Smart Globalization Response: A Case Study of the Georgia Tech-Emory University Biomedical Engineering Curricular Joint Venture

    Science.gov (United States)

    Burriss, Annie Hunt

    2010-01-01

    One innovative, higher-education response to globalization and changing fiscal realities is the curricular joint venture (CJV), a formal collaboration between academic institutions that leverages missions through new joint degrees and research not previously offered by collaborating institutions (Eckel, 2003). In 1997, a pioneering biomedical…

  6. CONTACT SURFACES OF BIG JOINTS – SITES OF THE DEVELOPMENT OF LIMIT STATES AND OTHER CONSIDERATIONS

    Czech Academy of Sciences Publication Activity Database

    Fuis, Vladimír; Janíček, P.; Hlavoň, Pavel

    2008-01-01

    Roč. 15, č. 5 (2008), s. 381-388 ISSN 1802-1484 Institutional research plan: CEZ:AV0Z20760514 Keywords : biomechanics * big joints * contact pressure * pathological joints * system approach Subject RIV: BO - Biophysics

  7. Genome position and gene amplification

    Czech Academy of Sciences Publication Activity Database

    Jirsová, Pavla; Snijders, A.M.; Kwek, S.; Roydasgupta, R.; Fridlyand, J.; Tokuyasu, T.; Pinkel, D.; Albertson, D. G.

    2007-01-01

    Roč. 8, č. 6 (2007), r120 ISSN 1474-760X Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : gene amplification * array comparative genomic hybridization * oncogene Subject RIV: BO - Biophysics Impact factor: 6.589, year: 2007

  8. Genome-wide study of correlations between genomic features and their relationship with the regulation of gene expression.

    Science.gov (United States)

    Kravatsky, Yuri V; Chechetkin, Vladimir R; Tchurikov, Nikolai A; Kravatskaya, Galina I

    2015-02-01

    The broad class of tasks in genetics and epigenetics can be reduced to the study of various features that are distributed over the genome (genome tracks). The rapid and efficient processing of the huge amount of data stored in the genome-scale databases cannot be achieved without the software packages based on the analytical criteria. However, strong inhomogeneity of genome tracks hampers the development of relevant statistics. We developed the criteria for the assessment of genome track inhomogeneity and correlations between two genome tracks. We also developed a software package, Genome Track Analyzer, based on this theory. The theory and software were tested on simulated data and were applied to the study of correlations between CpG islands and transcription start sites in the Homo sapiens genome, between profiles of protein-binding sites in chromosomes of Drosophila melanogaster, and between DNA double-strand breaks and histone marks in the H. sapiens genome. Significant correlations between transcription start sites on the forward and the reverse strands were observed in genomes of D. melanogaster, Caenorhabditis elegans, Mus musculus, H. sapiens, and Danio rerio. The observed correlations may be related to the regulation of gene expression in eukaryotes. Genome Track Analyzer is freely available at http://ancorr.eimb.ru/. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  9. Helminth genome projects: all or nothing

    Czech Academy of Sciences Publication Activity Database

    Lukeš, Julius; Horák, Aleš; Scholz, Tomáš

    2005-01-01

    Roč. 21, č. 6 (2005), s. 265-266 ISSN 1471-4922 Institutional research plan: CEZ:AV0Z60220518 Keywords : genome project * helminth * Dracunculus Subject RIV: EG - Zoology Impact factor: 4.526, year: 2005

  10. A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China.

    Science.gov (United States)

    Yu, Jun; Wong, Gane Ka-Shu; Liu, Siqi; Wang, Jian; Yang, Huanming

    2007-06-29

    In May 2000, the Beijing Institute of Genomics formally announced the launch of a comprehensive crop genome research project on rice genomics, the Chinese Superhybrid Rice Genome Project. SRGP is not simply a sequencing project targeted to a single rice (Oryza sativa L.) genome, but a full-swing research effort with an ultimate goal of providing inclusive basic genomic information and molecular tools not only to understand biology of the rice, both as an important crop species and a model organism of cereals, but also to focus on a popular superhybrid rice landrace, LYP9. We have completed the first phase of SRGP and provide the rice research community with a finished genome sequence of an indica variety, 93-11 (the paternal cultivar of LYP9), together with ample data on subspecific (between subspecies) polymorphisms, transcriptomes and proteomes, useful for within-species comparative studies. In the second phase, we have acquired the genome sequence of the maternal cultivar, PA64S, together with the detailed catalogues of genes uniquely expressed in the parental cultivars and the hybrid as well as allele-specific markers that distinguish parental alleles. Although SRGP in China is not an open-ended research programme, it has been designed to pave a way for future plant genomics research and application, such as to interrogate fundamentals of plant biology, including genome duplication, polyploidy and hybrid vigour, as well as to provide genetic tools for crop breeding and to carry along a social burden-leading a fight against the world's hunger. It began with genomics, the newly developed and industry-scale research field, and from the world's most populous country. In this review, we summarize our scientific goals and noteworthy discoveries that exploit new territories of systematic investigations on basic and applied biology of rice and other major cereal crops.

  11. "Harnessing genomics to improve health in India" – an executive course to support genomics policy

    Directory of Open Access Journals (Sweden)

    Acharya Tara

    2004-05-01

    Full Text Available Abstract Background The benefits of scientific medicine have eluded millions in developing countries and the genomics revolution threatens to increase health inequities between North and South. India, as a developing yet also industrialized country, is uniquely positioned to pioneer science policy innovations to narrow the genomics divide. Recognizing this, the Indian Council of Medical Research and the University of Toronto Joint Centre for Bioethics conducted a Genomics Policy Executive Course in January 2003 in Kerala, India. The course provided a forum for stakeholders to discuss the relevance of genomics for health in India. This article presents the course findings and recommendations formulated by the participants for genomics policy in India. Methods The course goals were to familiarize participants with the implications of genomics for health in India; analyze and debate policy and ethical issues; and develop a multi-sectoral opinion leaders' network to share perspectives. To achieve these goals, the course brought together representatives of academic research centres, biotechnology companies, regulatory bodies, media, voluntary, and legal organizations to engage in discussion. Topics included scientific advances in genomics, followed by innovations in business models, public sector perspectives, ethics, legal issues and national innovation systems. Results Seven main recommendations emerged: increase funding for healthcare research with appropriate emphasis on genomics; leverage India's assets such as traditional knowledge and genomic diversity in consultation with knowledge-holders; prioritize strategic entry points for India; improve industry-academic interface with appropriate incentives to improve public health and the nation's wealth; develop independent, accountable, transparent regulatory systems to ensure that ethical, legal and social issues are addressed for a single entry, smart and effective system; engage the public and

  12. Electronic Health Record for Temporomandibular Joint Disorders – Support in Therapeutic Process

    Czech Academy of Sciences Publication Activity Database

    Hippmann, R.; Nagy, Miroslav; Dostálová, T.; Zvárová, Jana; Seydlová, M.; Feltlová, E.

    2010-01-01

    Roč. 6, č. 1 (2010), s. 27-32 ISSN 1801-5603 R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : electronic health record * automatic speech recognition * dental cross * temporomandibular joint * temporomandibular joint disorders * structured data entry * dentistry * data model * text-to-speech system * Research Diagnostic Criteria for TMD Subject RIV: IN - Informatics, Computer Science http://www.ejbi.org/en/ejbi/article/25-en- electronic - health - record -for-temporomandibular-joint-disorders-support-in-therapeutic-process.html

  13. Genomics, transcriptomics and proteomics to elucidate the pathogenesis of rheumatoid arthritis.

    Science.gov (United States)

    Song, Xinqiang; Lin, Qingsong

    2017-08-01

    Rheumatoid arthritis is an autoimmune disease that affects several organs and tissues, predominantly the synovial joints. The pathogenesis of this disease is not completely understood, which maybe involved in the genomic variations, gene expression, protein translation and post-translational modifications. These system variations in genomics, transcriptomics and proteomics are dynamic in nature and their crosstalk is overwhelmingly complex, thus analyzing them separately may not be very informative. However, various '-omics' techniques developed in recent years have opened up new possibilities for clarifying disease pathways and thereby facilitating early diagnosis and specific therapies. This review examines how recent advances in the fields of genomics, transcriptomics and proteomics have contributed to our understanding of rheumatoid arthritis.

  14. Managing Resources and Relations in Higher Education Institutions: A Framework for Understanding Performance Improvement

    Science.gov (United States)

    Ho, Sophia Shi-Huei; Peng, Michael Yao-Ping

    2016-01-01

    Changes in social systems demonstrate that various structural disadvantages have jointly led to increasing competition among higher education institutions (HEIs) in many countries, especially Taiwan. Institutional administrators must recognize the need to understand how to improve performance and consistently outperform other institutions.…

  15. Proceedings of 2012 JAEA/KAERI joint seminar on advanced irradiation and PIE technologies

    International Nuclear Information System (INIS)

    Ishihara, Masahiro; Ishitsuka, Etsuo; Suzuki, Masahide

    2012-12-01

    Under the 'Arrangement for Corporation in the field of peaceful uses of Nuclear Energy between the Japan Atomic Energy Agency (JAEA) and the Korean Atomic Energy Research Institute (KAERI)', the 2012 JAEA/KAERI Joint Seminar on Advanced Irradiation and PIE (post-irradiation examination) Technologies has been held at Mito, Japan from March 28 to 30, 2012. This triennial seminar is the seventh in series of bilateral exchange of irradiation and PIE technologies and research reactor management. Since the first joint seminar on the PIE Technology between JAERI (Japan Atomic Energy Research Institute, former agency of JAEA) and KAERI was held at JAERI Oarai Research Institute, Japan in 1992, the international cooperation program between JAEA and KAERI has been actively carried out in the field of neutron irradiation. At the fifth seminar in 2005 and sixth in 2008, the irradiation technology and the research reactor management fields were included, respectively, to the joint seminar, and it covers whole areas of irradiation using research reactors. In this seminar total 37 presentations were made in three technical sessions, which are 'research reactor management', 'advanced irradiation technology' and 'post-irradiation examination technology', and active information exchange was done among participants. Papers or manuscripts presented in the 2012 JAEA/KAERI Joint Seminar on Advanced Irradiation and PIE Technologies are contained in the proceedings. (author)

  16. HGVA: the Human Genome Variation Archive.

    Science.gov (United States)

    Lopez, Javier; Coll, Jacobo; Haimel, Matthias; Kandasamy, Swaathi; Tarraga, Joaquin; Furio-Tari, Pedro; Bari, Wasim; Bleda, Marta; Rueda, Antonio; Gräf, Stefan; Rendon, Augusto; Dopazo, Joaquin; Medina, Ignacio

    2017-07-03

    High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK's 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. The joint essential numerical range, compact perturbations, and the Olsen problem

    Czech Academy of Sciences Publication Activity Database

    Müller, Vladimír

    2010-01-01

    Roč. 197, č. 3 (2010), s. 275-290 ISSN 0039-3223 R&D Projects: GA ČR GA201/09/0473; GA AV ČR IAA100190903 Institutional research plan: CEZ:AV0Z10190503 Keywords : joint essential numerical range * joint numerical range * compact perturbation * Olsen's problem Subject RIV: BA - General Mathematics Impact factor: 0.567, year: 2010 http://journals.impan.pl/cgi-bin/doi?sm197-3-5

  18. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  19. 76 FR 77315 - Agency Information Collection Activities: Submission for OMB Review; Joint Comment Request

    Science.gov (United States)

    2011-12-12

    ... clearance, the agencies, under the auspices of the Federal Financial Institutions Examination Council (FFIEC... CAMELS ratings and certain forward-looking financial measures to assess the risk such institutions pose... House, and the Financial Services Roundtable jointly commented. The Risk Management Association...

  20. Relations with the Joint Institute for Nuclear Research (JINR) and draft agreement between UNESCO and that body. Executive Board 151. session. Item 9.11 of the provisional agenda

    International Nuclear Information System (INIS)

    Mayor, F.; Kadyshevsky, V.G.

    1997-01-01

    This document contains a proposal for the conclusion of an agreement between UNESCO and the Joint Institute for Nuclear Research (JINR) in Dubna (Russian Federation) in order to promote international co-operation for research on the fundamental properties of matter. The proposal made was initiated by JINR which is an international intergovernmental organization with 18 Member States. In accordance with Article XI.1 of UNESCO's Constitution, the Director-General requests the Executive Board's approval of the draft agreement with JINR

  1. Health behavior change: can genomics improve behavioral adherence?

    Science.gov (United States)

    McBride, Colleen M; Bryan, Angela D; Bray, Molly S; Swan, Gary E; Green, Eric D

    2012-03-01

    The National Human Genome Research Institute recommends pursuing "genomic information to improve behavior change interventions" as part of its strategic vision for genomics. The limited effectiveness of current behavior change strategies may be explained, in part, by their insensitivity to individual variation in adherence responses. The first step in evaluating whether genomics can inform customization of behavioral recommendations is evidence reviews to identify adherence macrophenotypes common across behaviors and individuals that have genetic underpinnings. Conceptual models of how biological, psychological, and environmental factors influence adherence also are needed. Researchers could routinely collect biospecimens and standardized adherence measurements of intervention participants to enable understanding of genetic and environmental influences on adherence, to guide intervention customization and prospective comparative effectiveness studies.

  2. Joint Matrices Decompositions and Blind Source Separation

    Czech Academy of Sciences Publication Activity Database

    Chabriel, G.; Kleinsteuber, M.; Moreau, E.; Shen, H.; Tichavský, Petr; Yeredor, A.

    2014-01-01

    Roč. 31, č. 3 (2014), s. 34-43 ISSN 1053-5888 R&D Projects: GA ČR GA102/09/1278 Institutional support: RVO:67985556 Keywords : joint matrices decomposition * tensor decomposition * blind source separation Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 5.852, year: 2014 http://library.utia.cas.cz/separaty/2014/SI/tichavsky-0427607.pdf

  3. Radiographic evaluation of degenerative joint disease in horses: interpretive principles

    International Nuclear Information System (INIS)

    Widmer, W.R.; Blevins, W.E.

    1994-01-01

    Degenerative joint disease in horses is characterized by the progressive deterioration of articular cartilage of synovial joints. The morbidity associated with degenerative joint disease, particularly the loss of function in pleasure and performance horses, costs horse owners millions of dollars each year. Although new drugs, such as polysulfated glycosaminoglycans and hyaluronic acid, are available for the treatment of patients with degenerative joint disease, the success of therapy depends on early diagnosis. Diagnostic imaging strategies, therefore, should focus on accurate and timely diagnosis of degenerative joint disease to provide prompt therapy. Early identification of degenerative joint disease is also beneficial because the use and/or training methods of affected patients may be altered, possibly limiting the progression of the disease. The pathogenesis of degenerative joint disease is complex and multifactorial. Current evidence suggests that initiating factors lead to a final common pathway-breakdown of articular cartilage. There are many diagnostic tests that aid practitioners in detecting degenerative joint disease; however, the most important imaging technique is radiography. During the early stages of the disease, radiographic changes may be slight; therefore, it is essential that practitioners have adequate equipment to obtain high-quality radiographs. Thinning of the joint space, osteophytosis, enthesopathy, changes in subchondral bone, and increased synovium and synovia provide radiographic evidence of degenerative joint disease. By understanding the pathophysiology of the disease and how technical alterations affect the subtle radiographic changes, practitioners can more accurately diagnose degenerative joint disease during its early stages and institute proper therapy

  4. Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae)

    Czech Academy of Sciences Publication Activity Database

    Krahulcová, Anna; Trávníček, Pavel; Krahulec, František; Rejmánek, M.

    2017-01-01

    Roč. 119, č. 6 (2017), s. 957-964 ISSN 0305-7364 Institutional support: RVO:67985939 Keywords : Aesculus * chromosome number * genome size * phylogeny * seed mass Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 4.041, year: 2016

  5. The NCI Genomic Data Commons as an engine for precision medicine.

    Science.gov (United States)

    Jensen, Mark A; Ferretti, Vincent; Grossman, Robert L; Staudt, Louis M

    2017-07-27

    The National Cancer Institute Genomic Data Commons (GDC) is an information system for storing, analyzing, and sharing genomic and clinical data from patients with cancer. The recent high-throughput sequencing of cancer genomes and transcriptomes has produced a big data problem that precludes many cancer biologists and oncologists from gleaning knowledge from these data regarding the nature of malignant processes and the relationship between tumor genomic profiles and treatment response. The GDC aims to democratize access to cancer genomic data and to foster the sharing of these data to promote precision medicine approaches to the diagnosis and treatment of cancer.

  6. Passage relevance models for genomics search

    Directory of Open Access Journals (Sweden)

    Frieder Ophir

    2009-03-01

    Full Text Available Abstract We present a passage relevance model for integrating syntactic and semantic evidence of biomedical concepts and topics using a probabilistic graphical model. Component models of topics, concepts, terms, and document are represented as potential functions within a Markov Random Field. The probability of a passage being relevant to a biologist's information need is represented as the joint distribution across all potential functions. Relevance model feedback of top ranked passages is used to improve distributional estimates of query concepts and topics in context, and a dimensional indexing strategy is used for efficient aggregation of concept and term statistics. By integrating multiple sources of evidence including dependencies between topics, concepts, and terms, we seek to improve genomics literature passage retrieval precision. Using this model, we are able to demonstrate statistically significant improvements in retrieval precision using a large genomics literature corpus.

  7. Lubrication of the Human Ankle Joint in Walking

    Czech Academy of Sciences Publication Activity Database

    Hlaváček, Miroslav

    2010-01-01

    Roč. 132, č. 1 (2010), s. 1-8 ISSN 0742-4787 R&D Projects: GA ČR(CZ) GA103/07/0043 Institutional research plan: CEZ:AV0Z20710524 Keywords : articular cartilage * human ankle joint * lubrication * walking Subject RIV: JJ - Other Materials Impact factor: 0.449, year: 2010

  8. Freedom and Responsibility in Synthetic Genomics: The Synthetic Yeast Project

    OpenAIRE

    Sliva, Anna; Yang, Huanming; Boeke, Jef D.; Mathews, Debra J. H.

    2015-01-01

    First introduced in 2011, the Synthetic Yeast Genome (Sc2.0) Project is a large international synthetic genomics project that will culminate in the first eukaryotic cell (Saccharomyces cerevisiae) with a fully synthetic genome. With collaborators from across the globe and from a range of institutions spanning from do-it-yourself biology (DIYbio) to commercial enterprises, it is important that all scientists working on this project are cognizant of the ethical and policy issues associated with...

  9. US/Brazil joint pilot project objectives

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-01

    This paper describes a joint US/Brazil pilot project for rural electrification, whose major goals are: to establish technical, institutional, and economic confidence in using renewable energy (PV and wind) to meet the needs of the citizens of rural Brazil; to establish on-going institutional, individual and business relationships necessary to implement sustainable programs and commitments; to lay the groundwork for larger scale rural electrification through the use of distributed renewable technologies. The projects have supported low power home lighting systems, lighting and refrigeration for schools and medical centers, and water pumping systems. This is viewed as a long term project, where much of the equipment will come from the US, but Brazil will be responsible for program management, and sharing data gained from the program. The paper describes in detail the Brazilian program which was instituted to support this phased project.

  10. Annual report 90 Environment Institute

    International Nuclear Information System (INIS)

    1991-01-01

    This is the second annual report of the Environment Institute of the Joint Research Centre, Ispra Site, of the Commission of the European Communities. The report summarizes the progress accomplished in the course of 1990 in the various projects included in the multiannual (1988-91) Specific Research Programmes tackled by the Institute i.e. Environment Protection and Radioactive Waste Management, the former being focused on environmental chemicals, air pollution and pollutant transport, water pollution, chemical waste, food and drug analysis, the latter on safety assessment for waste disposal in geological formations. The scientific support given to the Commission Services for the implementation of EC directives dealing with chemicals, air pollution, water pollution, chemical waste and radioactive environmental monitoring (REM) is also described. Lastly the outcome of various activities related to work for third parties and to the participation of the Institute in EUREKA and COST projects is shortly outlined. The report includes data on the Institute Structure, human and budget resources and large installations operated by the Institute

  11. Integrated Genome-Based Studies of Shewanella Ecophysiology

    Energy Technology Data Exchange (ETDEWEB)

    Andrei L. Osterman, Ph.D.

    2012-12-17

    Integration of bioinformatics and experimental techniques was applied to mapping and characterization of the key components (pathways, enzymes, transporters, regulators) of the core metabolic machinery in Shewanella oneidensis and related species with main focus was on metabolic and regulatory pathways involved in utilization of various carbon and energy sources. Among the main accomplishments reflected in ten joint publications with other participants of Shewanella Federation are: (i) A systems-level reconstruction of carbohydrate utilization pathways in the genus of Shewanella (19 species). This analysis yielded reconstruction of 18 sugar utilization pathways including 10 novel pathway variants and prediction of > 60 novel protein families of enzymes, transporters and regulators involved in these pathways. Selected functional predictions were verified by focused biochemical and genetic experiments. Observed growth phenotypes were consistent with bioinformatic predictions providing strong validation of the technology and (ii) Global genomic reconstruction of transcriptional regulons in 16 Shewanella genomes. The inferred regulatory network includes 82 transcription factors, 8 riboswitches and 6 translational attenuators. Of those, 45 regulons were inferred directly from the genome context analysis, whereas others were propagated from previously characterized regulons in other species. Selected regulatory predictions were experimentally tested. Integration of this analysis with microarray data revealed overall consistency and provided additional layer of interactions between regulons. All the results were captured in the new database RegPrecise, which is a joint development with the LBNL team. A more detailed analysis of the individual subsystems, pathways and regulons in Shewanella spp included bioinfiormatics-based prediction and experimental characterization of: (i) N-Acetylglucosamine catabolic pathway; (ii)Lactate utilization machinery; (iii) Novel Nrt

  12. Frontotemporal dementia and its subtypes: a genome-wide association study

    Science.gov (United States)

    Ferrari, Raffaele; Hernandez, Dena G; Nalls, Michael A; Rohrer, Jonathan D; Ramasamy, Adaikalavan; Kwok, John B J; Dobson-Stone, Carol; Brooks, William S; Schofield, Peter R; Halliday, Glenda M; Hodges, John R; Piguet, Olivier; Bartley, Lauren; Thompson, Elizabeth; Haan, Eric; Hernández, Isabel; Ruiz, Agustín; Boada, Mercè; Borroni, Barbara; Padovani, Alessandro; Cruchaga, Carlos; Cairns, Nigel J; Benussi, Luisa; Binetti, Giuliano; Ghidoni, Roberta; Forloni, Gianluigi; Galimberti, Daniela; Fenoglio, Chiara; Serpente, Maria; Scarpini, Elio; Clarimón, Jordi; Lleó, Alberto; Blesa, Rafael; Waldö, Maria Landqvist; Nilsson, Karin; Nilsson, Christer; Mackenzie, Ian R A; Hsiung, Ging-Yuek R; Mann, David M A; Grafman, Jordan; Morris, Christopher M; Attems, Johannes; Griffiths, Timothy D; McKeith, Ian G; Thomas, Alan J; Pietrini, P; Huey, Edward D; Wassermann, Eric M; Baborie, Atik; Jaros, Evelyn; Tierney, Michael C; Pastor, Pau; Razquin, Cristina; Ortega-Cubero, Sara; Alonso, Elena; Perneczky, Robert; Diehl-Schmid, Janine; Alexopoulos, Panagiotis; Kurz, Alexander; Rainero, Innocenzo; Rubino, Elisa; Pinessi, Lorenzo; Rogaeva, Ekaterina; George-Hyslop, Peter St; Rossi, Giacomina; Tagliavini, Fabrizio; Giaccone, Giorgio; Rowe, James B; Schlachetzki, J C M; Uphill, James; Collinge, John; Mead, S; Danek, Adrian; Van Deerlin, Vivianna M; Grossman, Murray; Trojanowsk, John Q; van der Zee, Julie; Deschamps, William; Van Langenhove, Tim; Cruts, Marc; Van Broeckhoven, Christine; Cappa, Stefano F; Le Ber, Isabelle; Hannequin, Didier; Golfier, Véronique; Vercelletto, Martine; Brice, Alexis; Nacmias, Benedetta; Sorbi, Sandro; Bagnoli, Silvia; Piaceri, Irene; Nielsen, Jørgen E; Hjermind, Lena E; Riemenschneider, Matthias; Mayhaus, Manuel; Ibach, Bernd; Gasparoni, Gilles; Pichler, Sabrina; Gu, Wei; Rossor, Martin N; Fox, Nick C; Warren, Jason D; Spillantini, Maria Grazia; Morris, Huw R; Rizzu, Patrizia; Heutink, Peter; Snowden, Julie S; Rollinson, Sara; Richardson, Anna; Gerhard, Alexander; Bruni, Amalia C; Maletta, Raffaele; Frangipane, Francesca; Cupidi, Chiara; Bernardi, Livia; Anfossi, Maria; Gallo, Maura; Conidi, Maria Elena; Smirne, Nicoletta; Rademakers, Rosa; Baker, Matt; Dickson, Dennis W; Graff-Radford, Neill R; Petersen, Ronald C; Knopman, David; Josephs, Keith A; Boeve, Bradley F; Parisi, Joseph E; Seeley, William W; Miller, Bruce L; Karydas, Anna M; Rosen, Howard; van Swieten, John C; Dopper, Elise G P; Seelaar, Harro; Pijnenburg, Yolande AL; Scheltens, Philip; Logroscino, Giancarlo; Capozzo, Rosa; Novelli, Valeria; Puca, Annibale A; Franceschi, M; Postiglione, Alfredo; Milan, Graziella; Sorrentino, Paolo; Kristiansen, Mark; Chiang, Huei-Hsin; Graff, Caroline; Pasquier, Florence; Rollin, Adeline; Deramecourt, Vincent; Lebert, Florence; Kapogiannis, Dimitrios; Ferrucci, Luigi; Pickering-Brown, Stuart; Singleton, Andrew B; Hardy, John; Momeni, Parastoo

    2014-01-01

    Summary Background Frontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three genes—MAPT, GRN, and C9orf72—have been associated with FTD. We sought to identify novel genetic risk loci associated with the disorder. Methods We did a two-stage genome-wide association study on clinical FTD, analysing samples from 3526 patients with FTD and 9402 healthy controls. All participants had European ancestry. In the discovery phase (samples from 2154 patients with FTD and 4308 controls), we did separate association analyses for each FTD subtype (behavioural variant FTD, semantic dementia, progressive non-fluent aphasia, and FTD overlapping with motor neuron disease [FTD-MND]), followed by a meta-analysis of the entire dataset. We carried forward replication of the novel suggestive loci in an independent sample series (samples from 1372 patients and 5094 controls) and then did joint phase and brain expression and methylation quantitative trait loci analyses for the associated (p<5 × 10−8) and suggestive single-nucleotide polymorphisms. Findings We identified novel associations exceeding the genome-wide significance threshold (p<5 × 10−8) that encompassed the HLA locus at 6p21.3 in the entire cohort. We also identified a potential novel locus at 11q14, encompassing RAB38/CTSC, for the behavioural FTD subtype. Analysis of expression and methylation quantitative trait loci data suggested that these loci might affect expression and methylation incis. Interpretation Our findings suggest that immune system processes (link to 6p21.3) and possibly lysosomal and autophagy pathways (link to 11q14) are potentially involved in FTD. Our findings need to be replicated to better define the association of the newly identified loci with disease and possibly to shed light on the pathomechanisms contributing to FTD. Funding The National Institute of

  13. Transarticular invasion of bone tumours across the sacroiliac joint

    International Nuclear Information System (INIS)

    Chhaya, S.; White, L.M.; Kandel, R.; Wunder, J.S.; Ferguson, P.; Agur, A.

    2005-01-01

    The purpose of this study was to evaluate the pattern of tumour spread across the SI articulation, correlating with cadaveric anatomic observations, in order to better understand the local spread of tumour and to assist in the assessment of local staging. Twenty-four consecutive patients (14 male, 10 female; age range 22-89 years, mean 52 years) with primary bone tumours of the iliac bone or sacrum abutting the SI joint, in whom surgical resection of the SI joint was performed, were studied following institutional ethics approval. In all patients, preoperative magnetic resonance (MR) imaging studies of the pelvis and SI joint were reviewed for imaging evidence of transarticular extension across the SI joint. Gross pathologic and histologic assessment of possible transarticular SI joint tumour extension was performed in all patients. Nine cadaveric pelvic specimens without pelvic neoplastic disease (4 male, 5 female; age range 20-84 years, mean 59 years, median 58 years) were anatomically dissected and the articular anatomy of the SI joint examined macroscopically. Twelve of the twenty-four patients demonstrated imaging and histological evidence of transarticular SI joint invasion. Eight tumours infiltrated only the interosseous ligamentous aspect of the SI joint. In the remaining four cases, extensive tumour infiltrated both the cartilaginous and ligamentous aspects of the joint. No case showed tumour involvement isolated to the cartilaginous aspect of the joint. Among the cadaveric specimens studied, degenerative changes were found involving the majority of cases (6/9), with cartilage thinning and fibrillation and antero-superior marginal osteophytes seen involving the cartilaginous portion of the SI joint articulation. Four of the nine specimens demonstrated central ossification bridging the iliac and sacral aspects of the ligamentous (interosseous) SI joint. (orig.)

  14. Transarticular invasion of bone tumours across the sacroiliac joint

    Energy Technology Data Exchange (ETDEWEB)

    Chhaya, S. [University of Toronto, Department of Medical Imaging, Mount Sinai Hospital and the University Health Network, Toronto (Canada); University of Texas Health Science Centre, Department of Radiology, San Antonio, TX (United States); White, L.M. [University of Toronto, Department of Medical Imaging, Mount Sinai Hospital and the University Health Network, Toronto (Canada); Kandel, R. [University of Toronto, Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto (Canada); Wunder, J.S.; Ferguson, P. [Univeristy of Toronto, University Musculoskeletal Oncology Unit, Department of Orthopedic Surgery, Mount Sinai Hospital, Toronto (Canada); Agur, A. [University of Toronto, Division of Anatomy, Department of Surgery, Toronto (Canada)

    2005-12-01

    The purpose of this study was to evaluate the pattern of tumour spread across the SI articulation, correlating with cadaveric anatomic observations, in order to better understand the local spread of tumour and to assist in the assessment of local staging. Twenty-four consecutive patients (14 male, 10 female; age range 22-89 years, mean 52 years) with primary bone tumours of the iliac bone or sacrum abutting the SI joint, in whom surgical resection of the SI joint was performed, were studied following institutional ethics approval. In all patients, preoperative magnetic resonance (MR) imaging studies of the pelvis and SI joint were reviewed for imaging evidence of transarticular extension across the SI joint. Gross pathologic and histologic assessment of possible transarticular SI joint tumour extension was performed in all patients. Nine cadaveric pelvic specimens without pelvic neoplastic disease (4 male, 5 female; age range 20-84 years, mean 59 years, median 58 years) were anatomically dissected and the articular anatomy of the SI joint examined macroscopically. Twelve of the twenty-four patients demonstrated imaging and histological evidence of transarticular SI joint invasion. Eight tumours infiltrated only the interosseous ligamentous aspect of the SI joint. In the remaining four cases, extensive tumour infiltrated both the cartilaginous and ligamentous aspects of the joint. No case showed tumour involvement isolated to the cartilaginous aspect of the joint. Among the cadaveric specimens studied, degenerative changes were found involving the majority of cases (6/9), with cartilage thinning and fibrillation and antero-superior marginal osteophytes seen involving the cartilaginous portion of the SI joint articulation. Four of the nine specimens demonstrated central ossification bridging the iliac and sacral aspects of the ligamentous (interosseous) SI joint. (orig.)

  15. Prediction in medicine – genome contra envirome

    Czech Academy of Sciences Publication Activity Database

    Brdička, Radim

    2012-01-01

    Roč. 151, č. 1 (2012), s. 22-25 ISSN 0008-7335 R&D Projects: GA MZd NS9804 Institutional research plan: CEZ:AV0Z50390703 Keywords : genome * genotype * phenotype Subject RIV: FP - Other Medical Disciplines

  16. Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data.

    Science.gov (United States)

    Dunn, Joshua G; Weissman, Jonathan S

    2016-11-22

    Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments - for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length - analytical tools are often required to extract the biological meaning from the alignments before analysis. Many assay-specific pipelines exist for this purpose, but there remains a need for user-friendly, generalized, nucleotide-resolution tools that are not limited to specific experimental regimes or analytical workflows. Plastid is a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data. As such, Plastid is designed to extract assay-specific information from read alignments while retaining generality and extensibility to novel NGS assays. Plastid represents NGS and other biological data as arrays of values associated with genomic or transcriptomic positions, and contains configurable tools to convert data from a variety of sources to such arrays. Plastid also includes numerous tools to manipulate even discontinuous genomic features, such as spliced transcripts, with nucleotide precision. Plastid automatically handles conversion between genomic and feature-centric coordinates, accounting for splicing and strand, freeing users of burdensome accounting. Finally, Plastid's data models use consistent and familiar biological idioms, enabling even beginners to develop sophisticated analytical workflows with minimal effort. Plastid is a versatile toolkit that has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of our ORF annotation tool, ORF-RATER, and is readily

  17. Electronic System for Data Record and Automatic Diagnosis Assessment in the Temporomandibular Joint Disorders

    Czech Academy of Sciences Publication Activity Database

    Hippmann, R.; Nagy, Miroslav; Dostálová, T.; Zvárová, Jana; Seydlová, M.

    2011-01-01

    Roč. 7, č. 1 (2011), s. 11-16 ISSN 1801-5603 R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : temporomandibular joint * temporomandibular joint disorders * DentCross * electronic health record * AAOP classification Subject RIV: IN - Informatics, Computer Science http://www.ejbi.eu/images/2011-1/Hippmann_en.pdf

  18. Septic arthritis of the sacroiliac joint

    Science.gov (United States)

    Sebastian, Agata; Błach, Katarzyna; Silicki, Jurand; Wiland, Piotr

    2018-01-01

    Septic arthritis is an inflammation of a joint caused directly by various microorganisms. It is often characterized by many unspecific symptoms. Bacteria is the most often etiological factor. We present a case report of a 76-years old woman with a unilateral septic arthritis of the sacroiliac joint. Bacterial sacroiliitis should be taken into account in patients with sacroiliitis and fever onset. Proper diagnosis can be very often difficult and delayed but fast implementation of antibiotic therapy is extremely important in the treatment process. Diagnostic imaging is crucial to the diagnosis and monitoring of septic arthritis. Magnetic resonance imaging is the most relevant tool for the detection of sacroiliitis, allowing the institution of therapeutic strategies to impede the progression of the disease. PMID:29686444

  19. CAS at the Cockcroft Institute

    CERN Multimedia

    2007-01-01

    The CERN Accelerator School (CAS) and the UK’s new centre for accelerator science, the Cockcroft Institute, jointly organised a course on General Accelerator Physics, at intermediate level, at the Cockcroft Institute, Daresbury, UK, from 16 to 28 September 2007. The venue took advantage of the excellent new facilities in the Institute and the existing infrastructure of the adjacent Daresbury Laboratory. The intermediate level course followed established practice, with lectures on core topics in the mornings and specialised courses in the afternoons. The latter provided "hands-on" education and experience in the three selected topics: "RF Measurements Techniques", "Beam Instrumentation and Diagnostics" and "Optics Design and Correction". These proved to be highly successful, with participants choosing one course and following the topic throughout the school. Guided studies, tutorials, seminars and a poster session completed the prog...

  20. Developing institutional collaboration between Wageningen University and the Chinese Academy of Agricultural Sciences

    OpenAIRE

    Bonnema, A.B.; Lin, Zhai; Qu, Liang; Jacobsen, E.

    2006-01-01

    Scientific co-operation between the Chinese Academy of Agricultural Sciences (CAAS) and Wageningen University (WU) has been underway since 1990, especially in the field of plant sciences. In 2001, CAAS and WU initiated a formal joint PhD training programme to further structure their co-operation. The goals of this co-operation are to: (1) initiate long-term institutional collaboration through capacity building; (2) jointly establish a modern laboratory; (3) jointly develop a cross-cultural sc...

  1. Stakeholder engagement: a key component of integrating genomic information into electronic health records.

    Science.gov (United States)

    Hartzler, Andrea; McCarty, Catherine A; Rasmussen, Luke V; Williams, Marc S; Brilliant, Murray; Bowton, Erica A; Clayton, Ellen Wright; Faucett, William A; Ferryman, Kadija; Field, Julie R; Fullerton, Stephanie M; Horowitz, Carol R; Koenig, Barbara A; McCormick, Jennifer B; Ralston, James D; Sanderson, Saskia C; Smith, Maureen E; Trinidad, Susan Brown

    2013-10-01

    Integrating genomic information into clinical care and the electronic health record can facilitate personalized medicine through genetically guided clinical decision support. Stakeholder involvement is critical to the success of these implementation efforts. Prior work on implementation of clinical information systems provides broad guidance to inform effective engagement strategies. We add to this evidence-based recommendations that are specific to issues at the intersection of genomics and the electronic health record. We describe stakeholder engagement strategies employed by the Electronic Medical Records and Genomics Network, a national consortium of US research institutions funded by the National Human Genome Research Institute to develop, disseminate, and apply approaches that combine genomic and electronic health record data. Through select examples drawn from sites of the Electronic Medical Records and Genomics Network, we illustrate a continuum of engagement strategies to inform genomic integration into commercial and homegrown electronic health records across a range of health-care settings. We frame engagement as activities to consult, involve, and partner with key stakeholder groups throughout specific phases of health information technology implementation. Our aim is to provide insights into engagement strategies to guide genomic integration based on our unique network experiences and lessons learned within the broader context of implementation research in biomedical informatics. On the basis of our collective experience, we describe key stakeholder practices, challenges, and considerations for successful genomic integration to support personalized medicine.

  2. BGI-RIS: an integrated information resource and comparative analysis workbench for rice genomics

    DEFF Research Database (Denmark)

    Zhao, Wenming; Wang, Jing; He, Ximiao

    2004-01-01

    Rice is a major food staple for the world's population and serves as a model species in cereal genome research. The Beijing Genomics Institute (BGI) has long been devoting itself to sequencing, information analysis and biological research of the rice and other crop genomes. In order to facilitate....... Designed as a basic platform, BGI-RIS presents the sequenced genomes and related information in systematic and graphical ways for the convenience of in-depth comparative studies (http://rise.genomics.org.cn/). Udgivelsesdato: 2004-Jan-1...

  3. 10KP: A phylodiverse genome sequencing plan.

    Science.gov (United States)

    Cheng, Shifeng; Melkonian, Michael; Smith, Stephen A; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Li, Fay-Wei; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun; Wong, Gane Ka-Shu

    2018-03-01

    Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here.

  4. 10KP: A phylodiverse genome sequencing plan

    Science.gov (United States)

    Cheng, Shifeng; Melkonian, Michael; Brockington, Samuel; Archibald, John M; Delaux, Pierre-Marc; Melkonian, Barbara; Mavrodiev, Evgeny V; Sun, Wenjing; Fu, Yuan; Yang, Huanming; Soltis, Douglas E; Graham, Sean W; Soltis, Pamela S; Liu, Xin; Xu, Xun

    2018-01-01

    Abstract Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here. PMID:29618049

  5. Synergy between Medical Informatics and Bioinformatics: Facilitating Genomic Medicine for Future Health Care

    Czech Academy of Sciences Publication Activity Database

    Martin-Sanchez, F.; Iakovidis, I.; Norager, S.; Maojo, V.; de Groen, P.; Van der Lei, J.; Jones, T.; Abraham-Fuchs, K.; Apweiler, R.; Babic, A.; Baud, R.; Breton, V.; Cinquin, P.; Doupi, P.; Dugas, M.; Eils, R.; Engelbrecht, R.; Ghazal, P.; Jehenson, P.; Kulikowski, C.; Lampe, K.; De Moor, G.; Orphanoudakis, S.; Rossing, N.; Sarachan, B.; Sousa, A.; Spekowius, G.; Thireos, G.; Zahlmann, G.; Zvárová, Jana; Hermosilla, I.; Vicente, F. J.

    2004-01-01

    Roč. 37, - (2004), s. 30-42 ISSN 1532-0464 Institutional research plan: CEZ:AV0Z1030915 Keywords : bioinformatics * medical informatics * genomics * genomic medicine * biomedical informatics Subject RIV: BD - Theory of Information Impact factor: 1.013, year: 2004

  6. Exploration of Metagenome Assemblies with an Interactive Visualization Tool

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Michael; Nordberg, Henrik; Smirnova, Tatyana; Andersen, Evan; Tringe, Susannah; Hess, Matthias; Dubchak, Inna

    2014-07-09

    Metagenomics, one of the fastest growing areas of modern genomic science, is the genetic profiling of the entire community of microbial organisms present in an environmental sample. Elviz is a web-based tool for the interactive exploration of metagenome assemblies. Elviz can be used with publicly available data sets from the Joint Genome Institute or with custom user-loaded assemblies. Elviz is available at genome.jgi.doe.gov/viz

  7. The improvement of the methods of radial diagnosis and surgical treatment of patients with rheumatoid arthritis of knee and elbow joints

    International Nuclear Information System (INIS)

    Karimov, M.Yu.

    2005-05-01

    of knee and elbow joints and more objective estimation of the stage of process and effectiveness of surgical treatment. The surgical approaches and methods of operative treatment of knee and elbow joints, deformity and methods of early postoperational rehabilitation of patients with RA have been worked out. Degree of embedi: The worked out methods of radial study (equipment for polypositional roentgenography of knee joint, RD, DSA, MRI) of knee joint and elbow joint of the patients with RA are in use in the department of radiology diagnosis of the First and Second Tashkent State Medical Institutes. Developed operative methods of surgical treatment of knee joint and elbow joint deformity of patients with RA are used in the clinics of the Second Tashkent State Medical Institutes, Scientific Research Institute of Traumatology and Orthopedics of the Ministry of Public Health of the Republic of Uzbekistan, the clinic of traumatology and orthopedics of South Kazakhstan State Medical Academy, and also in the departments of traumatology and orthopedics, topographic anatomy of the Second Medical Institute and Radiology Diagnostics Department of Tashkent Institute of advanced medical studies. (author)

  8. An analysis of a joint shear model for jointed media with orthogonal joint sets

    International Nuclear Information System (INIS)

    Koteras, J.R.

    1991-10-01

    This report describes a joint shear model used in conjunction with a computational model for jointed media with orthogonal joint sets. The joint shear model allows nonlinear behavior for both joint sets. Because nonlinear behavior is allowed for both joint sets, a great many cases must be considered to fully describe the joint shear behavior of the jointed medium. An extensive set of equations is required to describe the joint shear stress and slip displacements that can occur for all the various cases. This report examines possible methods for simplifying this set of equations so that the model can be implemented efficiently form a computational standpoint. The shear model must be examined carefully to obtain a computationally efficient implementation that does not lead to numerical problems. The application to fractures in rock is discussed. 5 refs., 4 figs

  9. Temporomandibular joint formation requires two distinct hedgehog-dependent steps.

    Science.gov (United States)

    Purcell, Patricia; Joo, Brian W; Hu, Jimmy K; Tran, Pamela V; Calicchio, Monica L; O'Connell, Daniel J; Maas, Richard L; Tabin, Clifford J

    2009-10-27

    We conducted a genetic analysis of the developing temporo-mandibular or temporomandi-bular joint (TMJ), a highly specialized synovial joint that permits movement and function of the mammalian jaw. First, we used laser capture microdissection to perform a genome-wide expression analysis of each of its developing components. The expression patterns of genes identified in this screen were examined in the TMJ and compared with those of other synovial joints, including the shoulder and the hip joints. Striking differences were noted, indicating that the TMJ forms via a distinct molecular program. Several components of the hedgehog (Hh) signaling pathway are among the genes identified in the screen, including Gli2, which is expressed specifically in the condyle and in the disk of the developing TMJ. We found that mice deficient in Gli2 display aberrant TMJ development such that the condyle loses its growth-plate-like cellular organization and no disk is formed. In addition, we used a conditional strategy to remove Smo, a positive effector of the Hh signaling pathway, from chondrocyte progenitors. This cell autonomous loss of Hh signaling allows for disk formation, but the resulting structure fails to separate from the condyle. Thus, these experiments establish that Hh signaling acts at two distinct steps in disk morphogenesis, condyle initiation, and disk-condyle separation and provide a molecular framework for future studies of the TMJ.

  10. The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

    Science.gov (United States)

    Shaffer, Christopher D.; Alvarez, Consuelo; Bailey, Cheryl; Barnard, Daron; Bhalla, Satish; Chandrasekaran, Chitra; Chandrasekaran, Vidya; Chung, Hui-Min; Dorer, Douglas R.; Du, Chunguang; Eckdahl, Todd T.; Poet, Jeff L.; Frohlich, Donald; Goodman, Anya L.; Gosser, Yuying; Hauser, Charles; Hoopes, Laura L.M.; Johnson, Diana; Jones, Christopher J.; Kaehler, Marian; Kokan, Nighat; Kopp, Olga R.; Kuleck, Gary A.; McNeil, Gerard; Moss, Robert; Myka, Jennifer L.; Nagengast, Alexis; Morris, Robert; Overvoorde, Paul J.; Shoop, Elizabeth; Parrish, Susan; Reed, Kelynne; Regisford, E. Gloria; Revie, Dennis; Rosenwald, Anne G.; Saville, Ken; Schroeder, Stephanie; Shaw, Mary; Skuse, Gary; Smith, Christopher; Smith, Mary; Spana, Eric P.; Spratt, Mary; Stamm, Joyce; Thompson, Jeff S.; Wawersik, Matthew; Wilson, Barbara A.; Youngblom, Jim; Leung, Wilson; Buhler, Jeremy; Mardis, Elaine R.; Lopatto, David

    2010-01-01

    Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students. PMID:20194808

  11. A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies

    Czech Academy of Sciences Publication Activity Database

    Ruperao, P.; Chan, C.K.K.; Azam, S.; Karafiátová, Miroslava; Hayashi, S.; Čížková, Jana; Šimková, Hana; Vrána, Jan; Doležel, Jaroslav; Varshney, R.K.; Edwards, D.

    2014-01-01

    Roč. 12, č. 6 (2014), s. 778-786 ISSN 1467-7644 R&D Projects: GA ČR GBP501/12/G090; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : chickpea * genome assembly * cytogenetics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.752, year: 2014

  12. A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules

    Directory of Open Access Journals (Sweden)

    Queiroux Clothilde

    2012-05-01

    Full Text Available Abstract Background We have used the genomic data in the Integrated Microbial Genomes system of the Department of Energy’s Joint Genome Institute to make predictions about rhizobial open reading frames that play a role in nodulation of host plants. The genomic data was screened by searching for ORFs conserved in α-proteobacterial rhizobia, but not conserved in closely-related non-nitrogen-fixing α-proteobacteria. Results Using this approach, we identified many genes known to be involved in nodulation or nitrogen fixation, as well as several new candidate genes. We knocked out selected new genes and assayed for the presence of nodulation phenotypes and/or nodule-specific expression. One of these genes, SMc00911, is strongly expressed by bacterial cells within host plant nodules, but is expressed minimally by free-living bacterial cells. A strain carrying an insertion mutation in SMc00911 is not defective in the symbiosis with host plants, but in contrast to expectations, this mutant strain is able to out-compete the S. meliloti 1021 wild type strain for nodule occupancy in co-inoculation experiments. The SMc00911 ORF is predicted to encode a “SodM-like” (superoxide dismutase-like protein containing a rhodanese sulfurtransferase domain at the N-terminus and a chromate-resistance superfamily domain at the C-terminus. Several other ORFs (SMb20360, SMc01562, SMc01266, SMc03964, and the SMc01424-22 operon identified in the screen are expressed at a moderate level by bacteria within nodules, but not by free-living bacteria. Conclusions Based on the analysis of ORFs identified in this study, we conclude that this comparative genomics approach can identify rhizobial genes involved in the nitrogen-fixing symbiosis with host plants, although none of the newly identified genes were found to be essential for this process.

  13. Summer Institute in Biomedical Engineering for College Teachers

    Science.gov (United States)

    Cleaver, T. G.; And Others

    1973-01-01

    Discusses the objectives, curricula, and accomplishments of an interdisciplinary summer institute designed to prepare college teachers qualified in both the life sciences and engineering. Indicates that joint educational programs between engineering, science, and medical faculties are completely feasible if each group is interested in the other…

  14. A 'joint venture' model of recontacting in clinical genomics : Challenges for responsible implementation

    NARCIS (Netherlands)

    Dheensa, Sandi; Carrieri, Daniele; Kelly, Susan; Clarke, Angus; Doheny, Shane; Turnpenny, Peter; Lucassen, Anneke

    Advances in genomics often lead healthcare professionals (HCPs) to learn new information, e.g., about reinterpreted variants that could have clinical significance for patients seen previously. A question arises of whether HCPs should recontact these former patients. We present some findings

  15. Applications of Support Vector Machine (SVM) Learning in Cancer Genomics.

    Science.gov (United States)

    Huang, Shujun; Cai, Nianguang; Pacheco, Pedro Penzuti; Narrandes, Shavira; Wang, Yang; Xu, Wayne

    2018-01-01

    Machine learning with maximization (support) of separating margin (vector), called support vector machine (SVM) learning, is a powerful classification tool that has been used for cancer genomic classification or subtyping. Today, as advancements in high-throughput technologies lead to production of large amounts of genomic and epigenomic data, the classification feature of SVMs is expanding its use in cancer genomics, leading to the discovery of new biomarkers, new drug targets, and a better understanding of cancer driver genes. Herein we reviewed the recent progress of SVMs in cancer genomic studies. We intend to comprehend the strength of the SVM learning and its future perspective in cancer genomic applications. Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

  16. Genomic repeat abundances contain phylogenetic signal

    Czech Academy of Sciences Publication Activity Database

    Dodsworth, S.; Chase, M.W.; Kelly, L.J.; Leitch, I.J.; Macas, Jiří; Novák, Petr; Piednoël, M.; Weiß-Schneeweiss, H.; Leitch, A.R.

    2015-01-01

    Roč. 64, č. 1 (2015), s. 112-126 ISSN 1063-5157 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : Repetitive DNA * continuous characters * genomics * next-generation sequencing * phylogenetics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.225, year: 2015

  17. Molecular Mechanisms Underlying Genomic Instability in Brca-Deficient Cells

    Science.gov (United States)

    2014-11-01

    increased by hydroxyurea, ATR inhibition, deregulated c-Myc expression and by PARPi treatment of BRCA1 deficient cells. This work was recently published...Genome Stability." 6: May 27, 2013-Collaborative Research Center 655 from Cells to Tissues seminar series at the Max-Planck-Institute in Dresden, Germany ...Eisenach, Germany -“Genome Stability during DNA Replication” 8: May 3, 2013- Chemical and Systems Biology Department Seminar Series at Stanford

  18. Analysis of TCRAD gene recombination: radio-induct rearrangement and signal joint structure

    International Nuclear Information System (INIS)

    Touvrey, C.

    2005-09-01

    We have shown that irradiation of pre-TCR-deficient CD3ε -/- mice restores thymocyte differentiation, by a p53-dependent and by a p53-independent pathway. Events normally associated during normal thymocyte development are dissociated in response to radiation exposure. Both of these pathways require LAT expression. Therefore, radiation exposure activates pre-TCR-like signals. TCRA gene rearrangement is induced following radiation exposure. The signal joints resulting from TCRA gene rearrangement have the same structure than those found in wild type mice. All signal joint analyzed in un-manipulated wild type mice do exhibit junctional diversity. This diversity results mainly from TdT activity. We present evidences that proteins involved in DNA repair and genomic stability participated in SJ formation. We propose that signal joint diversity is not an aberrant process but is a key feature of V(D)J recombination. All our work increases our understanding of molecular events associated with V(D)J recombination. (author)

  19. Proceedings of the joint meeting of ultrafast pulse high intensity laser research collaboration and JAEA-KPSI 7th symposium on advanced photon research

    International Nuclear Information System (INIS)

    2007-03-01

    The Joint Meeting of Ultrafast Pulse High Intensity Laser Research Collaboration and JAEA-KPSI 7th Symposium on Advanced Photon Research was jointly held at Kansai Photon Research Institute, Japan Atomic Energy Agency (JAEA-KPSI) in Kizu, Kyoto on May 10-12, 2006. This report consists of contributed papers for the speeches and poster presentations including joint research and cooperative research performed in FY2004 and FY2005 with Japan Atomic Energy Research Institute (JAERI). The 47 of the presented papers are indexed individually. (J.P.N.)

  20. 28 November 2013 - N. N. Kudryavtsev, Russian Rector of the Moscow Institute of Physics and Technology signing an Agreement and the Guest Book with CERN Director-General R. Heuer; visiting the ATLAS cavern with ATLAS Deputy Spokesperson B. Heinemann and visiting the LHC tunnel at Point 1 with AGH University of Science and Technology A. Erokhin. M. Savino, Physics Department, Joint Institute for Nuclear Research also present.

    CERN Multimedia

    Jean-Claude Gadmer

    2013-01-01

    28 November 2013 - N. N. Kudryavtsev, Russian Rector of the Moscow Institute of Physics and Technology signing an Agreement and the Guest Book with CERN Director-General R. Heuer; visiting the ATLAS cavern with ATLAS Deputy Spokesperson B. Heinemann and visiting the LHC tunnel at Point 1 with AGH University of Science and Technology A. Erokhin. M. Savino, Physics Department, Joint Institute for Nuclear Research also present.

  1. 76 FR 8357 - Biological and Environmental Research Advisory Committee

    Science.gov (United States)

    2011-02-14

    ..., 2011, 9 a.m. to 12 p.m. ADDRESSES: Omni Shoreham Hotel, 2500 Calvert Street, NW., Washington, DC 20008... Response Joint Genome Institute Update and ARM review outbrief 2012 Budget briefing New Business Public...

  2. Proceedings of the relevance of mass spectrometry to DNA sequence determination: Research needs for the Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    Edmonds, C.G.; Smith, R.D. (Pacific Northwest Lab., Richland, WA (USA)); Smith, L.M. (Wisconsin Univ., Madison, WI (USA))

    1990-11-01

    A workshop was sponsored for the US Department of Energy (DOE), Office of Health and Environmental Research by Pacific Northwest Laboratory, April 4--5, 1990, in Seattle, Washington, to examine the potential role of mass spectrometry in the joint DOE/National Institutes of Health (NIH) Human Genome Program. The workshop was occasioned by recent developments in mass spectrometry that are providing new levels for selectivity, sensitivity, and, in particular, new methods of ionization appropriate for large biopolymers such as DNA. During discussions, three general mass spectrometric approaches to the determination of DNA sequence were considered: (1) the mass spectrometric detection of isotopic labels from DNA sequencing mixtures separated using gel electrophoresis, (2) the direct mass spectrometric analysis from direct ionization of unfractionated sequencing mixtures where the measured mass of the constituents functions to identify and order the base sequence (replacing separation by gel electrophoresis), and (3) an approach in which a single highly charged molecular ion of a large DNA segment produced is rapidly sequenced in an ion cyclotron resonance ion trap. The consensus of the workshop was that, on the basis of the new developments, mass spectrometry has the potential to provide the substantial increases in sequencing speed required for the Human Genome Program. 66 refs., 3 tabs.

  3. Beyond the human genome: Microbes, methaphors and what it means to be human in an interconnected post-genomic world

    NARCIS (Netherlands)

    Nerlich, B.; Hellsten, I.R.

    2009-01-01

    Four years after the completion of the Human Genome Project, the US National Institutes for Health launched the Human Microbiome Project on 19 December 2007. Using metaphor analysis, this article investigates reporting in English-language newspapers on advances in microbiomics from 2003 onwards,

  4. Current Activities of the Joint Council on Economic Education.

    Science.gov (United States)

    Highsmith, Robert J.

    1987-01-01

    Reviews current activities of the Joint Council, among them, a researcher training institute, a new K-12 economic education scope and sequence document, a junior high level test of economic knowledge, an instructional package for advanced placement classes, a textbook conference, a project to help teachers of students who work with at-risk…

  5. Voice-supported Electronic Health Record for Temporomandibular Joint Disorders

    Czech Academy of Sciences Publication Activity Database

    Hippmann, R.; Dostálová, T.; Zvárová, Jana; Nagy, Miroslav; Seydlová, M.; Hanzlíček, Petr; Kříž, P.; Šmídl, L.; Trmal, J.

    2010-01-01

    Roč. 49, č. 2 (2010), s. 168-172 ISSN 0026-1270 R&D Projects: GA MŠk(CZ) 1M06014 Institutional research plan: CEZ:AV0Z10300504 Keywords : electronic health record * structured data entry * dentistry * temporomandibular joint disorder Subject RIV: IN - Informatics, Computer Science Impact factor: 1.472, year: 2010

  6. Annual report of the research works with joint-use JAERI facilities for fiscal 1974

    International Nuclear Information System (INIS)

    1975-01-01

    Results of the research works by national universities with JAERI's (Japan Atomic Energy Research Institute) joint-use facilities for fiscal 1974 are described. Facilities are research reactors, Co-60, Linac, etc. Research results are presented in individual summaries, covering radiation damage and solid state physics, activation analysis and nuclear chemistry, irradiation effects, etc. Results of the joint works with JAERI are also presented similarly. (Mori, K.)

  7. Analytical modeling of mixed-Mode bending behavior of asymmetric adhesively bonded pultruded GFRP joints

    Czech Academy of Sciences Publication Activity Database

    Ševčík, Martin; Shahverdi, M.; Hutař, Pavel; Vassilopoulos, Anastasios P.

    2015-01-01

    Roč. 147, OCT (2015), s. 228-242 ISSN 0013-7944 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0068; GA MŠk(CZ) EE2.3.30.0063 Institutional support: RVO:68081723 Keywords : Mixed-Mode delamination * Asymmetric joint * Adhesively bonded joint * Failure criterion * Analytical prediction * GFRP Subject RIV: JL - Materials Fatigue, Friction Mechanics Impact factor: 2.024, year: 2015

  8. A chromosome conformation capture ordered sequence of the barley genome

    Czech Academy of Sciences Publication Activity Database

    Mascher, M.; Gundlach, H.; Himmelbach, A.; Beier, S.; Twardziok, S. O.; Wicker, T.; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, S.; Munoz-Amatrian, M.; Houben, A.; Doležel, Jaroslav; Ayling, S.; Lonardi, S.; Mayer, K.F.X.; Zhang, G.; Braumann, I.; Spannagl, M.; Li, C.; Waugh, R.; Stein, N.

    2017-01-01

    Roč. 544, č. 7651 (2017), s. 427-433 ISSN 0028-0836 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : bacterial artificial chromosomes * inverted-repeat elements * complex-plant genomes * hi-c * environmental adaptation * ltr retrotransposons * structural variation * maize genome * software * database Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 40.137, year: 2016

  9. Nuclear genome size and genomic distribution of ribosomal DNA in Musa and Ensete (Musaceae): taxonomic implications

    Czech Academy of Sciences Publication Activity Database

    Bartoš, Jan; Alkhimova, Olena; Kubaláková, Marie; De Langhe, E.; Doležel, Jaroslav

    2005-01-01

    Roč. 109, - (2005), s. 50-57 ISSN 1424-8581 R&D Projects: GA AV ČR IAA6038204 Grant - others:IAEA Research Contract 12230/RBF Institutional research plan: CEZ:AV0Z50380511 Keywords : Musa and Ensete * nuclear genome size * FISH Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.076, year: 2005

  10. MR diagnosis of temporomandibular joint. A study of joint effusion

    International Nuclear Information System (INIS)

    Kaneda, Takashi; Yamashiro, Mitsuaki; Ozawa, Kaoru; Suzuki, Hiromi; Okada, Hiroyuki; Yamamoto, Hirotsugu

    1998-01-01

    The purposes of this study were to evaluate the relationship between correlation of MR joint effusion of the temporomandibular joint and disk position, to evaluate the relationship between joint effusion and aging, and to assess the frequency of MR joint effusion of bilateral temporomandibular joints. The temporomandibular joints of 192 patients with clinical symptoms of temporomandibular joint disorders were imaged bilaterally using high field, surface-coil MR imaging. Oblique sagittal and coronal proton density-weighted and T2-weighted images were obtained. Imaging findings of joint effusion were correlated with disk position, aging, and bilateral temporomandibular joints. MR showed effusion in 4% of the joints with normal superior disk position, 36% of the joints with disk displacement with reduction, and 45% of the joints with disk displacement without reduction. There were significant differences in the incidence of joint effusion between normal disk position and anterior disk displacement with or without reduction. Younger patients less than 40 years were significant higher the incidence of joint effusion than those of older patients. A significant association was seen between joint effusion and aging. MR showed effusion in 17% of the unilateral temporomandibular joint, 24% of the bilateral temporomandibular joints. There was no significant difference between unilateral and bilateral case. These results indicated that joint effusion using MR imaging was associated with varied temporomandibular joint pathologic states. (author)

  11. Prospects for genomic selection in cassava breeding

    Science.gov (United States)

    Cassava (Manihot esculenta Crantz) is a clonally propagated staple food crop in the tropics. Genomic selection (GS) has been implemented at three breeding institutions in Africa in order to reduce cycle times. Initial studies provided promising estimates of predictive abilities. Here, we expand on p...

  12. Fast Approximate Joint Diagonalization Incorporating Weight Matrices

    Czech Academy of Sciences Publication Activity Database

    Tichavský, Petr; Yeredor, A.

    2009-01-01

    Roč. 57, č. 3 (2009), s. 878-891 ISSN 1053-587X R&D Projects: GA MŠk 1M0572 Institutional research plan: CEZ:AV0Z10750506 Keywords : autoregressive processes * blind source separation * nonstationary random processes Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 2.212, year: 2009 http://library.utia.cas.cz/separaty/2009/SI/tichavsky-fast approximate joint diagonalization incorporating weight matrices.pdf

  13. Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens

    Czech Academy of Sciences Publication Activity Database

    Sharaf, Abdoallah; Mercati, F.; Elmaghraby, I.; Elbaz, R. M.; Marei, E. M.

    2017-01-01

    Roč. 17, 3 March (2017), č. článku 51. ISSN 1471-2180 Institutional support: RVO:60077344 Keywords : bacteriophage * biological stability * whole genome sequence * ngs * comparative genomics Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 2.644, year: 2016

  14. Factors of formation of the dividend policy of joint stock companies

    Directory of Open Access Journals (Sweden)

    Rohov Heorhii K.

    2014-01-01

    Full Text Available The article is devoted to justification of factors of formation of the dividend policy of Ukrainian public joint stock companies (PJSC at the modern stage of development of corporate relations. It analyses specific features of the dividend policy of Ukrainian PJSC, which, in particular, shows that their financial results practically do not influence the practice of net profit distribution. It identifies main factors of formation of the corporate dividend policy and provides theoretical justification of the governing practice of net profit distribution by Ukrainian PJSC under the modern state of the stock market. It justifies that the unrepresentative listing of stock exchanges, extremely high concentration of capital and rather limited influence of institutes of joint investment are key factors that cause a very weak reaction of the Ukrainian securities market on payment of dividends, which, in its turn, is the main reason of rejection of expediency of development and realisation of the consistent dividend policy by overwhelming majority of joint stock companies. The article draws a conclusion that the basis of evolution changes in the corporate vision of the dividend policy should be creation of the institutional environment, which would be adequate to the needs of sustainable development. The article offers to fix, at the legislative level and while being at the transitional stage, the right of minor shareholders to get income from owning ordinary shares of companies, which aggregate joint participation of co-owners is more than 75%.

  15. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

    Energy Technology Data Exchange (ETDEWEB)

    Catfish Genome Consortium; Wang, Shaolin; Peatman, Eric; Abernathy, Jason; Waldbieser, Geoff; Lindquist, Erika; Richardson, Paul; Lucas, Susan; Wang, Mei; Li, Ping; Thimmapuram, Jyothi; Liu, Lei; Vullaganti, Deepika; Kucuktas, Huseyin; Murdock, Christopher; Small, Brian C; Wilson, Melanie; Liu, Hong; Jiang, Yanliang; Lee, Yoona; Chen, Fei; Lu, Jianguo; Wang, Wenqi; Xu, Peng; Somridhivej, Benjaporn; Baoprasertkul, Puttharat; Quilang, Jonas; Sha, Zhenxia; Bao, Baolong; Wang, Yaping; Wang, Qun; Takano, Tomokazu; Nandi, Samiran; Liu, Shikai; Wong, Lilian; Kaltenboeck, Ludmilla; Quiniou, Sylvie; Bengten, Eva; Miller, Norman; Trant, John; Rokhsar, Daniel; Liu, Zhanjiang

    2010-03-23

    Background-Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results-A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35percent of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions-This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.

  16. Firms’ corporate social responsibility behavior: An integration of institutional and profit maximization approaches

    OpenAIRE

    Susan L Young; Mona V Makhija

    2014-01-01

    Understanding firms’ behavior across countries – a key concern in the international business literature – requires the joint consideration of both institutional influences and firms’ profit maximization goals. In the corporate social responsibility (CSR) area, however, researchers have utilized theories that take into account only one or the other – institutional theory, which explains CSR as legitimacy-seeking activities in line with national-level institutions, or economic-based approaches ...

  17. Use of Comparative Genomics To Characterize the Diversity of Acinetobacter baumannii Surveillance Isolates in a Health Care Institution

    Science.gov (United States)

    Wallace, Lalena; Daugherty, Sean C.; Nagaraj, Sushma; Johnson, J. Kristie; Harris, Anthony D.

    2016-01-01

    Despite the increasing prevalence of the nosocomial pathogen Acinetobacter baumannii, little is known about which genomic components contribute to clinical presentation of this important pathogen. Most whole-genome comparisons of A. baumannii have focused on specific genomic regions associated with phenotypes in a limited number of genomes. In this work, we describe the results of a whole-genome comparative analysis of 254 surveillance isolates of Acinetobacter species, 203 of which were A. baumannii, isolated from perianal swabs and sputum samples collected as part of an infection control active surveillance program at the University of Maryland Medical Center. The collection of surveillance isolates includes both carbapenem-susceptible and -resistant isolates. Based on the whole-genome phylogeny, the A. baumannii isolates collected belong to two major phylogenomic lineages. Results from multilocus sequence typing indicated that one of the major phylogenetic groups of A. baumannii was comprised solely of strains from the international clonal lineage 2. The genomic content of the A. baumannii isolates was examined using large-scale BLAST score ratio analysis to identify genes that are associated with carbapenem-susceptible and -resistant isolates, as well as genes potentially associated with the source of isolation. This analysis revealed a number of genes that were exclusive or at greater frequency in each of these classifications. This study is the most comprehensive genomic comparison of Acinetobacter isolates from a surveillance study to date and provides important information that will contribute to our understanding of the success of A. baumannii as a human pathogen. PMID:27458211

  18. Integrating cancer genomic data into electronic health records

    Directory of Open Access Journals (Sweden)

    Jeremy L. Warner

    2016-10-01

    Full Text Available Abstract The rise of genomically targeted therapies and immunotherapy has revolutionized the practice of oncology in the last 10–15 years. At the same time, new technologies and the electronic health record (EHR in particular have permeated the oncology clinic. Initially designed as billing and clinical documentation systems, EHR systems have not anticipated the complexity and variety of genomic information that needs to be reviewed, interpreted, and acted upon on a daily basis. Improved integration of cancer genomic data with EHR systems will help guide clinician decision making, support secondary uses, and ultimately improve patient care within oncology clinics. Some of the key factors relating to the challenge of integrating cancer genomic data into EHRs include: the bioinformatics pipelines that translate raw genomic data into meaningful, actionable results; the role of human curation in the interpretation of variant calls; and the need for consistent standards with regard to genomic and clinical data. Several emerging paradigms for integration are discussed in this review, including: non-standardized efforts between individual institutions and genomic testing laboratories; “middleware” products that portray genomic information, albeit outside of the clinical workflow; and application programming interfaces that have the potential to work within clinical workflow. The critical need for clinical-genomic knowledge bases, which can be independent or integrated into the aforementioned solutions, is also discussed.

  19. Nuclear Genome Size: Are We Getting Closer?

    Czech Academy of Sciences Publication Activity Database

    Doležel, Jaroslav; Greilhuber, J.

    77A, č. 7 (2010), s. 635-642 ISSN 1552-4922 R&D Projects : GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50380511 Keywords : cytometric techniques * reference standards * genome sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.749, year: 2010

  20. Concepts for institutional arrangements for the nuclear fuel cycle

    International Nuclear Information System (INIS)

    1979-02-01

    These concepts deal with establishing a framework for the analysis of institutional arrangements, with institutional arrangements under consideration in the working groups on fuel and heavy water availability, enrichment availability, assurances of long-term supply, reprocessing-plutonium handling-recycling, fast breeder reactors, spent fuel management, waste management and disposal, and advanced reactor concepts. The standardization of nuclear practices, joint commercial and development undertakings, nuclear supply assurances, developing a consensus in international nuclear co-operation, and settlements of disputes are treated

  1. Annual report of National Institute for Fusion Science. April 2013 - March 2014

    International Nuclear Information System (INIS)

    2014-01-01

    This annual report summarizes achievements from research activities at the National Institute for Fusion Science (NIFS) between April 2013 and March 2014. NIFS is an inter-university research organization and conducts open collaboration research under three frameworks which are the General Collaboration Research, the Large Helical Device Collaboration Research and the Bilateral Collaboration Research. More than 500 collaborating studies were implemented during the covered period. About 2,400 collaborators studies were implemented during the covered period. About 2,400 collaborators participated in joint research from 220 external institutions. Many intensively advanced results in plasma physics, fusion science and related fields have been obtained from these studies. Not only NIFS, but also 6 university centers serve as joint research laboratories/centers under bilateral collaboration research. NIFS also organizes diversified frameworks for international collaboration through 6 bilateral agreements, 3 multi-lateral agreements and academic exchange agreements with 18 institutes abroad for the global development of the function of inter-university research organization. (J.P.N.)

  2. Nature-inspired novel Cuckoo Search Algorithm for genome

    Indian Academy of Sciences (India)

    This study aims to produce a novel optimization algorithm, called the Cuckoo Search Algorithm (CS), for solving the genome sequence assembly problem. ... Department of Electronics and Communication Engineering, Coimbatore Institute of Technology, Coimbatore 641 014, India; Department of Information Technology, ...

  3. A broadly implementable research course in phage discovery and genomics for first-year undergraduate students.

    Science.gov (United States)

    Jordan, Tuajuanda C; Burnett, Sandra H; Carson, Susan; Caruso, Steven M; Clase, Kari; DeJong, Randall J; Dennehy, John J; Denver, Dee R; Dunbar, David; Elgin, Sarah C R; Findley, Ann M; Gissendanner, Chris R; Golebiewska, Urszula P; Guild, Nancy; Hartzog, Grant A; Grillo, Wendy H; Hollowell, Gail P; Hughes, Lee E; Johnson, Allison; King, Rodney A; Lewis, Lynn O; Li, Wei; Rosenzweig, Frank; Rubin, Michael R; Saha, Margaret S; Sandoz, James; Shaffer, Christopher D; Taylor, Barbara; Temple, Louise; Vazquez, Edwin; Ware, Vassie C; Barker, Lucia P; Bradley, Kevin W; Jacobs-Sera, Deborah; Pope, Welkin H; Russell, Daniel A; Cresawn, Steven G; Lopatto, David; Bailey, Cheryl P; Hatfull, Graham F

    2014-02-04

    Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training. Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome

  4. Institute annual report 2004

    International Nuclear Information System (INIS)

    2005-01-01

    The mission of the ITU (Institute for Transuranium Elements) is to protect the European citizen against risk associated with the handling and storage of highly radioactive elements. The JRC (Joint Research Center) provide customer-driven scientific and technical support for the conception, development, implementation and monitoring of EU policies. In this framework this annual report presents the TU actions in: basic actinide research, spent fuel characterization, safety of nuclear fuels, partitioning and transmutation, alpha-immunotherapy/radiobiology, measurement of radioactivity in the environment, safeguards research and development. (A.L.B.)

  5. Institute annual report 2004

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2005-07-01

    The mission of the ITU (Institute for Transuranium Elements) is to protect the European citizen against risk associated with the handling and storage of highly radioactive elements. The JRC (Joint Research Center) provide customer-driven scientific and technical support for the conception, development, implementation and monitoring of EU policies. In this framework this annual report presents the TU actions in: basic actinide research, spent fuel characterization, safety of nuclear fuels, partitioning and transmutation, alpha-immunotherapy/radiobiology, measurement of radioactivity in the environment, safeguards research and development. (A.L.B.)

  6. Quality Assurance of Joint Degree Programs from the Perspective of Quality Assurance Agencies: Experience in East Asia

    Science.gov (United States)

    Hou, Yung-Chi; Ince, Martin; Tsai, Sandy; Wang, Wayne; Hung, Vicky; Lin Jiang, Chung; Chen, Karen Hui-Jung

    2016-01-01

    Joint degree programs have gained popularity in East Asia, due to the growth of transnational higher education in the region since 2000. However, the external quality assurance (QA) and accreditation of joint degree programs is a challenge for QA agencies, as it normally involves the engagement of several institutions and multiple national…

  7. Annual report 1991. Institute for Advanced Materials

    International Nuclear Information System (INIS)

    1992-01-01

    The Institute executed in 1991 the R and D programme on advanced materials of the Joint Research Centre and contributed to the programmes: reactor safety, radio-active waste management, fusion technology and safety, nuclear fuel and actinide research. The supplementary programme: Operation of the High Flux Reactor is presented in condensed form. A full report is published separately. (Author). refs., figs., tabs

  8. Empowering Mayo Clinic Individualized Medicine with Genomic Data Warehousing

    Directory of Open Access Journals (Sweden)

    Iain Horton

    2017-08-01

    Full Text Available Individualized medicine enables better diagnoses and treatment decisions for patients and promotes research in understanding the molecular underpinnings of disease. Linking individual patient’s genomic and molecular information with their clinical phenotypes is crucial to these efforts. To address this need, the Center for Individualized Medicine at Mayo Clinic has implemented a genomic data warehouse and a workflow management system to bring data from institutional electronic health records and genomic sequencing data from both clinical and research bioinformatics sources into the warehouse. The system is the foundation for Mayo Clinic to build a suite of tools and interfaces to support various clinical and research use cases. The genomic data warehouse is positioned to play a key role in enhancing the research capabilities and advancing individualized patient care at Mayo Clinic.

  9. Empowering Mayo Clinic Individualized Medicine with Genomic Data Warehousing.

    Science.gov (United States)

    Horton, Iain; Lin, Yaxiong; Reed, Gay; Wiepert, Mathieu; Hart, Steven

    2017-08-22

    Individualized medicine enables better diagnoses and treatment decisions for patients and promotes research in understanding the molecular underpinnings of disease. Linking individual patient's genomic and molecular information with their clinical phenotypes is crucial to these efforts. To address this need, the Center for Individualized Medicine at Mayo Clinic has implemented a genomic data warehouse and a workflow management system to bring data from institutional electronic health records and genomic sequencing data from both clinical and research bioinformatics sources into the warehouse. The system is the foundation for Mayo Clinic to build a suite of tools and interfaces to support various clinical and research use cases. The genomic data warehouse is positioned to play a key role in enhancing the research capabilities and advancing individualized patient care at Mayo Clinic.

  10. Strain-stress analysis of surface prosthesis of hip joint

    Czech Academy of Sciences Publication Activity Database

    Návrat, Tomáš; Fuis, Vladimír; Florian, Z.; Hlavoň, Pavel

    2007-01-01

    Roč. 40, č. 2 (2007), S559-S559 ISSN 0021-9290. [ISB 2007. Taipei, 01.07.2007-05.07.2007] R&D Projects: GA ČR GA101/05/0136 Institutional research plan: CEZ:AV0Z20760514 Keywords : surface prosthesis * hip joint * FEM Subject RIV: BO - Biophysics Impact factor: 2.897, year: 2007

  11. Genomes-based phylogeny of the genus Xanthomonas

    Directory of Open Access Journals (Sweden)

    Rodriguez-R Luis M

    2012-03-01

    Full Text Available Abstract Background The genus Xanthomonas comprises several plant pathogenic bacteria affecting a wide range of hosts. Despite the economic, industrial and biological importance of Xanthomonas, the classification and phylogenetic relationships within the genus are still under active debate. Some of the relationships between pathovars and species have not been thoroughly clarified, with old pathovars becoming new species. A change in the genus name has been recently suggested for Xanthomonas albilineans, an early branching species currently located in this genus, but a thorough phylogenomic reconstruction would aid in solving these and other discrepancies in this genus. Results Here we report the results of the genome-wide analysis of DNA sequences from 989 orthologous groups from 17 Xanthomonas spp. genomes available to date, representing all major lineages within the genus. The phylogenetic and computational analyses used in this study have been automated in a Perl package designated Unus, which provides a framework for phylogenomic analyses which can be applied to other datasets at the genomic level. Unus can also be easily incorporated into other phylogenomic pipelines. Conclusions Our phylogeny agrees with previous phylogenetic topologies on the genus, but revealed that the genomes of Xanthomonas citri and Xanthomonas fuscans belong to the same species, and that of Xanthomonas albilineans is basal to the joint clade of Xanthomonas and Xylella fastidiosa. Genome reduction was identified in the species Xanthomonas vasicola in addition to the previously identified reduction in Xanthomonas albilineans. Lateral gene transfer was also observed in two gene clusters.

  12. Joint Universities as a Tool for Promoting the National Interests of Russia and China

    Directory of Open Access Journals (Sweden)

    Elena Medyanik

    2017-03-01

    Full Text Available At present, the opening of joint educational institutions is one of the leading educational trends. It allows states to improve the quality of national human resources and the national education system. Thus, it is particularly important for transition economies in the context of an innovative model of development. Russia and China turned to this practice in 2010 after the launch of the SCO University, established by the Shanghai Cooperation Organisation. Today joint educational institutions function not only multilaterally but also bilaterally. This article examines the Shenzhen MSU-BIT University, a joint Russian-Chinese university, as a tool to promote the national interests of the two countries. The author presents the basic history of Russian-Chinese cooperation in education in the second half of the 20th century. She argues that the Cultural Revolution and period the subsequent of difficult relations between the two countries had a negative impact on educational ties. Russia lost 17 years in China’s educational market, which was filled by other countries, primarily the United States. At the beginning of the 20th century, Russian-Chinese humanitarian cooperation was positive. The author relates the increase in the volume of Russian-Chinese educational exchange to the success of several events, including the large-scale projects of the Year of Russia in China and the Year of China in Russia, the Year of Chinese Language in Russia and Russian Language in China, the opening of the Russian Cultural Centre and the Chinese Cultural Centre, Russian centres and cabinets of the “Russian World” in China, and Confucius Institutes and classes in Russia. After analyzing the current situation, the author describes the new forms of cooperation, which include the opening of joint institutions. She assesses the interests and prospects of Russian and Chinese participation in the creation of the Shenzhen MSU-BIT University through the prism of national

  13. The Joint Lessons Learned System and Interoperability

    Science.gov (United States)

    1989-06-02

    Learned: 1988-1989 As mentioned in the introduction to this chaoter, the Organizacion of the JcinC Chiefs cf Staff .OJCS) ueren significant transformatioi...Organization and Functions Manual . Washington, D.C.: HQDA, Office of the Deputy Chief 0f Staff for Operations and Plans, June 1984. ’..S. Army. Concept...U.S. Department of Defense. Joint Universal Lessons Learned System (JULLS) User’s Manual . Orlando, Florida: University of Central Florida, Institute

  14. Joint Force Quarterly. Number 2, Autumn 1993

    Science.gov (United States)

    1993-09-01

    Typography and Design Division Government Printing Office Joint Force Quarterly is published by the Institute for National Strategic Studies, National...Decisions regard- ing the key force will affect many factors in the new environment. It determines reaction time, how much and what type of force to...shelters destroyed? Only indirectly. Attacks on shel- ters had forced a reaction by the Iraqis, one that caused the loss of their air arm as a force in

  15. Building local capacity for genomics research in Africa: recommendations from analysis of publications in Sub-Saharan Africa from 2004 to 2013.

    Science.gov (United States)

    Adedokun, Babatunde O; Olopade, Christopher O; Olopade, Olufunmilayo I

    2016-01-01

    The poor genomics research capacity of Sub-Saharan Africa (SSA) could prevent maximal benefits from the applications of genomics in the practice of medicine and research. The objective of this study is to examine the author affiliations of genomic epidemiology publications in order to make recommendations for building local genomics research capacity in SSA. SSA genomic epidemiology articles published between 2004 and 2013 were extracted from the Human Genome Epidemiology (HuGE) database. Data on authorship details, country of population studied, and phenotype or disease were extracted. Factors associated with the first author, who has an SSA institution affiliation (AIAFA), were determined using a Chi-square test and multiple logistic regression analysis. The most commonly studied population was South Africa, accounting for 31.1%, followed by Ghana (10.6%) and Kenya (7.5%). About one-tenth of the papers were related to non-communicable diseases (NCDs) such as cancer (6.1%) and cardiovascular diseases (CVDs) (4.3%). Fewer than half of the first authors (46.9%) were affiliated with an African institution. Among the 238 articles with an African first author, over three-quarters (79.8%) belonged to a university or medical school, 16.8% were affiliated with a research institute, and 3.4% had affiliations with other institutions. Significant disparities currently exist among SSA countries in genomics research capacity. South Africa has the highest genomics research output, which is reflected in the investments made in its genomics and biotechnology sector. These findings underscore the need to focus on developing local capacity, especially among those affiliated with SSA universities where there are more opportunities for teaching and research.

  16. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

    Science.gov (United States)

    Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor M.; Kyrpides, Nikos C.

    2010-01-01

    The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/ PMID:19914934

  17. Sino-American Joint Partnerships: Why Some Succeed and Others Fail. Research & Occasional Paper Series: CSHE.1.14

    Science.gov (United States)

    Julius, Daniel J.; Leventhal, Mitch

    2014-01-01

    This article examines institutional and demographic variables associated with successful joint partnerships between US and Chinese institutions of higher education. Understanding those variables requires an appreciation of overarching issues or catalysts bringing both nations together and, as well, how postsecondary environments differ and the…

  18. First industrial application of the auto-adaptative MAG STT welding technique with laser joint tracking

    International Nuclear Information System (INIS)

    Tran Tien, Th.

    2007-01-01

    The Welding Institute has participated to the plan of construction of the Large Hadron Collider. The hoops of the dipolar magnets are composed of two half cylinders 15 m in length in 10 mm 316LN austenitic stainless steel and are assembled around the magnet in a horizontal-vertical position. The Welding Institute has developed a software for carrying out the auto-adaptative welding technique with laser joint tracking, in using the MAG STT (Surface Tension Transfer) process. The modelling of the welding laws and the strategy of filling the joints in multi-paths absorb the physical tolerances of the preparation (clearance, poor alignment, root..) in dynamic welding condition too. (O.M.)

  19. Improving biological understanding and complex trait prediction by integrating prior information in genomic feature models

    DEFF Research Database (Denmark)

    Edwards, Stefan McKinnon

    externally founded information, such as KEGG pathways, Gene Ontology gene sets, or genomic features, and estimate the joint contribution of the genetic variants within these sets to complex trait phenotypes. The analysis of complex trait phenotypes is hampered by the myriad of genes that control the trait...

  20. Concepts for institutional arrangements for the nuclear fuel cycle

    International Nuclear Information System (INIS)

    1979-01-01

    The paper focuses on the role of institutional arrangements in developing a consensus in international nuclear cooperation. Institutional arrangements are defined as undertakings and activities by governments or private entities to facilitate the efficient and secure functioning of the nuclear fuel cycle. The first two sections of the paper explore the historical role of cooperative arrangements, suggest criteria for evaluating the usefulness of institutional arrangements, and review the status of the discussion of institutional arrangements in INFCE Working Groups as of December 1978. The final section of the paper, explores potential relationships between various institutional arrangements and suggests that certain areas such as, the standardization of nuclear practices, joint commercial and development undertakings, nuclear supply assurances, and the settlement of disputes may have broad application for several stages of the fuel cycle and merit further study

  1. Remembrance of things past retrieved from the Paramecium genome.

    Science.gov (United States)

    Sperling, Linda

    2011-01-01

    Paramecium and other ciliates are the only unicellular eukaryotes that separate germinal and somatic functions. A germline micronucleus transmits the genetic information to sexual progeny, while a somatic macronucleus expresses the genetic information during vegetative growth to determine the phenotype. At each sexual generation, a new macronucleus develops from the zygotic nucleus through programmed rearrangements of the germline genome. Paramecium tetraurelia somatic genome sequencing, reviewed here, has provided insight into the organization and evolution of the genome. A series of at least 3 whole genome duplications was detected in the Paramecium lineage and selective pressures that determine the fate of the gene duplicates analyzed. Variability in the somatic DNA was characterized and could be attributed to the genome rearrangement processes. Since, in Paramecium, alternative genome rearrangement patterns can be inherited across sexual generations by homology-dependent epigenetic mechanisms and can affect phenotype, I discuss the possibility that ciliate nuclear dimorphism buffers genetic variation hidden in the germline. Copyright © 2011 Institut Pasteur. Published by Elsevier SAS. All rights reserved.

  2. Chromosome-specific sequencing reveals an extensive dispensable genome component in wheat

    Czech Academy of Sciences Publication Activity Database

    Liu, M.; Stiller, J.; Holušová, Kateřina; Vrána, Jan; Liu, D.; Doležel, Jaroslav; Liu, C.

    2016-01-01

    Roč. 6, NOV 8 (2016), č. článku 36398. ISSN 2045-2322 R&D Projects: GA MŠk(CZ) LO1204; GA ČR GBP501/12/G090 Institutional support: RVO:61389030 Keywords : triticum-aestivum l. * fusarium crown rot * pan-genome * hexaploid wheat * bread wheat * draft genome * rna-seq * maize * transcriptome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.259, year: 2016

  3. MIPS: a database for protein sequences and complete genomes.

    Science.gov (United States)

    Mewes, H W; Hani, J; Pfeiffer, F; Frishman, D

    1998-01-01

    The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database of the yeast genome, a database reflecting the progress in sequencing the Arabidopsis thaliana genome, the systematic analysis of other small genomes and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). Through its WWW server (http://www.mips.biochem.mpg.de ) MIPS provides access to a variety of generic databases, including a database of protein families as well as automatically generated data by the systematic application of sequence analysis algorithms. The yeast genome sequence and its related information was also compiled on CD-ROM to provide dynamic interactive access to the 16 chromosomes of the first eukaryotic genome unraveled. PMID:9399795

  4. Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family

    Czech Academy of Sciences Publication Activity Database

    Lugli, G. A.; Milani, C.; Turroni, F.; Duranti, S.; Mancabelli, L.; Mangifesta, M.; Ferrario, C.; Modesto, M.; Mattarelli, P.; Killer, Jiří; van Sinderen, D.

    2017-01-01

    Roč. 18, č. 1 (2017), č. článku 568. ISSN 1471-2164 Institutional support: RVO:67985904 Keywords : Bifidobacteriaceae * genomics * phlogenomics Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.729, year: 2016

  5. Social and behavioral science priorities for genomic translation.

    Science.gov (United States)

    Koehly, Laura M; Persky, Susan; Spotts, Erica; Acca, Gillian

    2018-01-29

    This commentary highlights the essential role of the social and behavioral sciences for genomic translation, and discusses some priority research areas in this regard. The first area encompasses genetics of behavioral, social, and neurocognitive factors, and how integration of these relationships might impact the development of treatments and interventions. The second area includes the contributions that social and behavioral sciences make toward the informed translation of genomic developments. Further, there is a need for behavioral and social sciences to inform biomedical research for effective implementation. The third area speaks to the need for increased outreach and education efforts to improve the public's genomic literacy such that individuals and communities can make informed health-related and societal (e.g., in legal or consumer settings) decisions. Finally, there is a need to prioritize representation of diverse communities in genomics research and equity of access to genomic technologies. Examples from National Institutes of Health-based intramural and extramural research programs and initiatives are used to discuss these points. © Society of Behavioral Medicine 2018.

  6. Heads, Shoulders, Elbows, Knees, and Toes: Modular Gdf5 Enhancers Control Different Joints in the Vertebrate Skeleton.

    Science.gov (United States)

    Chen, Hao; Capellini, Terence D; Schoor, Michael; Mortlock, Doug P; Reddi, A Hari; Kingsley, David M

    2016-11-01

    Synovial joints are crucial for support and locomotion in vertebrates, and are the frequent site of serious skeletal defects and degenerative diseases in humans. Growth and differentiation factor 5 (Gdf5) is one of the earliest markers of joint formation, is required for normal joint development in both mice and humans, and has been genetically linked to risk of common osteoarthritis in Eurasian populations. Here, we systematically survey the mouse Gdf5 gene for regulatory elements controlling expression in synovial joints. We identify separate regions of the locus that control expression in axial tissues, in proximal versus distal joints in the limbs, and in remarkably specific sub-sets of composite joints like the elbow. Predicted transcription factor binding sites within Gdf5 regulatory enhancers are required for expression in particular joints. The multiple enhancers that control Gdf5 expression in different joints are distributed over a hundred kilobases of DNA, including regions both upstream and downstream of Gdf5 coding exons. Functional rescue tests in mice confirm that the large flanking regions are required to restore normal joint formation and patterning. Orthologs of these enhancers are located throughout the large genomic region previously associated with common osteoarthritis risk in humans. The large array of modular enhancers for Gdf5 provide a new foundation for studying the spatial specificity of joint patterning in vertebrates, as well as new candidates for regulatory regions that may also influence osteoarthritis risk in human populations.

  7. Reoperations following proximal interphalangeal joint nonconstrained arthroplasties.

    Science.gov (United States)

    Pritsch, Tamir; Rizzo, Marco

    2011-09-01

    To retrospectively analyze the reasons for reoperations following primary nonconstrained proximal interphalangeal (PIP) joint arthroplasty and review clinical outcomes in this group of patients with 1 or more reoperations. Between 2001 and 2009, 294 nonconstrained (203 pyrocarbon and 91 metal-plastic) PIP joint replacements were performed in our institution. A total of 76 fingers (59 patients) required reoperation (50 pyrocarbon and 26 metal-plastic). There were 40 women and 19 men with an average age of 51 years (range, 19-83 y). Primary diagnoses included osteoarthritis in 35, posttraumatic arthritis in 24, and inflammatory arthritis in 17 patients. There were 21 index, 27 middle, 18 ring, and 10 small fingers. The average number of reoperations per PIP joint was 1.6 (range, 1-4). A total of 45 joints had 1 reoperation, 19 had 2, 11 had 3, and 1 had 4. Extensor mechanism dysfunction was the most common reason for reoperation; it involved 51 of 76 fingers and was associated with Chamay or tendon-reflecting surgical approaches. Additional etiologies included component loosening in 17, collateral ligament failure in 10, and volar plate contracture in 8 cases. Inflammatory arthritis was associated with collateral ligament failure. Six fingers were eventually amputated, 9 had PIP joint arthrodeses, and 2 had resection arthroplasties. The arthrodesis and amputation rates correlated with the increased number of reoperations per finger. Clinically, most patients had no or mild pain at the most recent follow-up, and the PIP joint range-of-motion was not significantly different from preoperative values. Pain levels improved with longer follow-up. Reoperations following primary nonconstrained PIP joint arthroplasties are common. Extensor mechanism dysfunction was the most common reason for reoperation. The average reoperation rate was 1.6, and arthrodesis and amputation are associated with an increasing number of operations. Overall clinical outcomes demonstrated no

  8. 75 FR 29386 - Consumer Protections for Depository Institution Sales of Insurance

    Science.gov (United States)

    2010-05-25

    ... DEPARTMENT OF THE TREASURY Office of Thrift Supervision Consumer Protections for Depository...: Consumer Protection for Depository Institution Sales of Insurance. OMB Number: 1550-0106. Regulation..., Federal Deposit Insurance Corporation, and Office of Thrift Supervision to prescribe joint consumer...

  9. The genomic applications in practice and prevention network.

    Science.gov (United States)

    Khoury, Muin J; Feero, W Gregory; Reyes, Michele; Citrin, Toby; Freedman, Andrew; Leonard, Debra; Burke, Wylie; Coates, Ralph; Croyle, Robert T; Edwards, Karen; Kardia, Sharon; McBride, Colleen; Manolio, Teri; Randhawa, Gurvaneet; Rasooly, Rebekah; St Pierre, Jeannette; Terry, Sharon

    2009-07-01

    The authors describe the rationale and initial development of a new collaborative initiative, the Genomic Applications in Practice and Prevention Network. The network convened by the Centers for Disease Control and Prevention and the National Institutes of Health includes multiple stakeholders from academia, government, health care, public health, industry and consumers. The premise of Genomic Applications in Practice and Prevention Network is that there is an unaddressed chasm between gene discoveries and demonstration of their clinical validity and utility. This chasm is due to the lack of readily accessible information about the utility of most genomic applications and the lack of necessary knowledge by consumers and providers to implement what is known. The mission of Genomic Applications in Practice and Prevention Network is to accelerate and streamline the effective integration of validated genomic knowledge into the practice of medicine and public health, by empowering and sponsoring research, evaluating research findings, and disseminating high quality information on candidate genomic applications in practice and prevention. Genomic Applications in Practice and Prevention Network will develop a process that links ongoing collection of information on candidate genomic applications to four crucial domains: (1) knowledge synthesis and dissemination for new and existing technologies, and the identification of knowledge gaps, (2) a robust evidence-based recommendation development process, (3) translation research to evaluate validity, utility and impact in the real world and how to disseminate and implement recommended genomic applications, and (4) programs to enhance practice, education, and surveillance.

  10. International joint research of the Danube radioactivity

    International Nuclear Information System (INIS)

    Szerbin, P.; Szabo, G.; Guczi, J.; Koblinger-Bokori, E.; Kurtacs, E.; Dovlete, C.; Ruzsa, G.; Major, V.; Maringer, F.J.

    1998-01-01

    A PHARE (Poland Hungary Aid for Reconstruction of Economy) subsidized study was initiated in 1995 with coordination of Vituki Innosystem (Hungary) and with participation of Austrian, Romanian, and Hungarian research institutes to reveal and investigate in detail hot spots of radioactivity and sources of contamination in the Danube catchment area. The general objective of the project was to assess whether or not potential upstream radionuclide sources in the countries in the upper part of the Danube basin have resulted in evidential downstream accumulation of radionuclides and have a potential impact into the Black sea contamination. The presentation summarizes the results of the international joint research study, and some other data obtained in the framework of cooperation between monitoring institutes of the riparian states

  11. Building a Science Software Institute: Synthesizing the Lessons Learned from the ISEES and WSSI Software Institute Conceptualization Efforts

    Science.gov (United States)

    Idaszak, R.; Lenhardt, W. C.; Jones, M. B.; Ahalt, S.; Schildhauer, M.; Hampton, S. E.

    2014-12-01

    The NSF, in an effort to support the creation of sustainable science software, funded 16 science software institute conceptualization efforts. The goal of these conceptualization efforts is to explore approaches to creating the institutional, sociological, and physical infrastructures to support sustainable science software. This paper will present the lessons learned from two of these conceptualization efforts, the Institute for Sustainable Earth and Environmental Software (ISEES - http://isees.nceas.ucsb.edu) and the Water Science Software Institute (WSSI - http://waters2i2.org). ISEES is a multi-partner effort led by National Center for Ecological Analysis and Synthesis (NCEAS). WSSI, also a multi-partner effort, is led by the Renaissance Computing Institute (RENCI). The two conceptualization efforts have been collaborating due to the complementarity of their approaches and given the potential synergies of their science focus. ISEES and WSSI have engaged in a number of activities to address the challenges of science software such as workshops, hackathons, and coding efforts. More recently, the two institutes have also collaborated on joint activities including training, proposals, and papers. In addition to presenting lessons learned, this paper will synthesize across the two efforts to project a unified vision for a science software institute.

  12. Scientific information exchange in the field of humanities between academic institutions of Ukraine and Poland (1955-1960

    Directory of Open Access Journals (Sweden)

    Indychenko H.

    2015-01-01

    Full Text Available The article presents a historical reconstruction of Ukrainian-Polish scientific relations in the field of humanities in 1955-1960, conducted on the basis of archival sources study. Scientific information exchange of humanitarian institutions of the AS of the Ukrainian SSR with Polish research institutions was quite diversified. It included mutual visits of the scientists from research institutes as delegations members, individual scientific missions to research institutions in order to acquaint with scientific developments, participation in international workshops, congresses and conferences, international book exchange, joint publishing, mutual reviewing of scientific publications. From the second half of the 50s of the 20th century there was an intensification of joint research projects conducted for the development of certain scientific issues, which were of interest for both Ukrainian and Polish scientists, who endeavored to solve them

  13. Behaviour of Frictional Joints in Steel Arch Yielding Supports

    Czech Academy of Sciences Publication Activity Database

    Horyl, P.; Šňupárek, Richard; Maršálek, P.

    2014-01-01

    Roč. 59, č. 3 (2014), s. 723-734 ISSN 0860-7001 R&D Projects: GA MŠk ED2.1.00/03.0082; GA MŠk ED1.1.00/02.0070 Institutional support: RVO:68145535 Keywords : steel arch yielding support * friction al joints * bolt connection * slip support * fem Subject RIV: DH - Mining, incl. Coal Mining Impact factor: 0.608, year: 2013

  14. Perspectives of joint implementation projects in Lithuania

    OpenAIRE

    Štreimikienė, Dalia; Mikalauskienė, Asta

    2004-01-01

    The paper deals with the perspectives of joint implementation (JI) projects in Lithuania. The analysis of flexible mechanisms under the Kyoto protocol including Jl benefits is presented in the paper. The main aim of the article is to analyze current macroeconomic environment which has impact on the JI perspectives in Lithuania and based on this analysis to define activities, measures and institutions necessary for the implementation of these projects. A very important issue in this context is...

  15. PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data.

    Science.gov (United States)

    Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai; Gundlach, Heidrun; Mayer, Klaus F X

    2017-01-01

    Plant Genome and Systems Biology (PGSB), formerly Munich Institute for Protein Sequences (MIPS) PlantsDB, is a database framework for the integration and analysis of plant genome data, developed and maintained for more than a decade now. Major components of that framework are genome databases and analysis resources focusing on individual (reference) genomes providing flexible and intuitive access to data. Another main focus is the integration of genomes from both model and crop plants to form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny). Data exchange and integrated search functionality with/over many plant genome databases is provided within the transPLANT project.

  16. Framework for development of physician competencies in genomic medicine: report of the Competencies Working Group of the Inter-Society Coordinating Committee for Physician Education in Genomics.

    Science.gov (United States)

    Korf, Bruce R; Berry, Anna B; Limson, Melvin; Marian, Ali J; Murray, Michael F; O'Rourke, P Pearl; Passamani, Eugene R; Relling, Mary V; Tooker, John; Tsongalis, Gregory J; Rodriguez, Laura L

    2014-11-01

    Completion of the Human Genome Project, in conjunction with dramatic reductions in the cost of DNA sequencing and advances in translational research, is gradually ushering genomic discoveries and technologies into the practice of medicine. The rapid pace of these advances is opening up a gap between the knowledge available about the clinical relevance of genomic information and the ability of clinicians to include such information in their medical practices. This educational gap threatens to be rate limiting to the clinical adoption of genomics in medicine. Solutions will require not only a better understanding of the clinical implications of genetic discoveries but also training in genomics at all levels of professional development, including for individuals in formal training and others who long ago completed such training. The National Human Genome Research Institute has convened the Inter-Society Coordinating Committee for Physician Education in Genomics (ISCC) to develop and share best practices in the use of genomics in medicine. The ISCC has developed a framework for development of genomics practice competencies that may serve as a starting point for formulation of competencies for physicians in various medical disciplines.

  17. Joint Research on Scatterometry and AFM Wafer Metrology

    OpenAIRE

    Bodermann, B.; Buhr, E.; Danzebrink, H.U.; Bär, M.; Scholze, F.; Krumrey, M.; Wurm, M.; Klapetek, P.; Hansen, P.E.; Korpelainen, V.; Van Veghel, M.; Yacoot, A.; Siitonen, S.; El Gawhary, O.; Burger, S.

    2011-01-01

    Supported by the European Commission and EURAMET, a consortium of 10 participants from national metrology institutes, universities and companies has started a joint research project with the aim of overcoming current challenges in optical scatterometry for traceable linewidth metrology. Both experimental and modelling methods will be enhanced and different methods will be compared with each other and with specially adapted atomic force microscopy (AFM) and scanning electron microscopy (SEM) m...

  18. Temporomandibular Joint and its Two-Dimensional and Three-Dimensional Modelling

    Czech Academy of Sciences Publication Activity Database

    Hliňáková, P.; Dostálová, T.; Daněk, Josef; Nedoma, Jiří; Hlaváček, Ivan

    2010-01-01

    Roč. 80, č. 6 (2010), s. 1256-1268 ISSN 0378-4754 Grant - others:GA MZd(CZ) NS9902 Institutional research plan: CEZ:AV0Z10300504; CEZ:AV0Z10190503 Keywords : dentistry * temporomandibular joint * mathematical modelling * contact problem * finite element method Subject RIV: FF - HEENT, Dentistry Impact factor: 0.812, year: 2010

  19. Genomic impact of eukaryotic transposable elements.

    Science.gov (United States)

    Arkhipova, Irina R; Batzer, Mark A; Brosius, Juergen; Feschotte, Cédric; Moran, John V; Schmitz, Jürgen; Jurka, Jerzy

    2012-11-21

    The third international conference on the genomic impact of eukaryotic transposable elements (TEs) was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.

  20. Annual Report 1991. Institute for systems engineering and informatics

    International Nuclear Information System (INIS)

    1992-01-01

    The report presents the achievements of the Institute for Systems Engineering and Informatics (ISEI) of the Joint Research Centre (JRC) of the Commission of the European Communities (CEC) for 1991. The JRC is a European scientific and technical research centre established by the member states of the CEC. Its four sites in Belgium (Geel), Germany (Karlsruhe), the Netherland (Petten) and Italy (Ispra) house 8 institutes, each with its own focus of expertise. ISEI, based at Ispra, was created in 1990 by the merger of the Institute for Systems Engineering (ISE) and the Centre for Information Technologies and Electronics (CITE). The main areas of activity of the Institute are: - Industrial and Environmental Risk, - Nuclear Safeguards, -Fusion Reactor Systems Integration and Safety, - Solar Energy Systems and Energy Management, - Advanced Computing, - Informatic services

  1. International team with Virginia Tech participation maps genome of dengue and yellow fever mosquito

    OpenAIRE

    Trulove, Susan

    2007-01-01

    Developing new strategies to prevent and control yellow fever and dengue fever has become more possible with the completion of the first draft of the genome sequence of Aedes aegypti mosquito by scientists led by Vishvanath Nene at The Institute for Genomic Research (TIGR) and David Severson at the University of Notre Dame. The genome is the complete set of genetic material including genes and other segments of DNA in an organism.

  2. Unexplored therapeutic opportunities in the human genome.

    Science.gov (United States)

    Oprea, Tudor I; Bologa, Cristian G; Brunak, Søren; Campbell, Allen; Gan, Gregory N; Gaulton, Anna; Gomez, Shawn M; Guha, Rajarshi; Hersey, Anne; Holmes, Jayme; Jadhav, Ajit; Jensen, Lars Juhl; Johnson, Gary L; Karlson, Anneli; Leach, Andrew R; Ma'ayan, Avi; Malovannaya, Anna; Mani, Subramani; Mathias, Stephen L; McManus, Michael T; Meehan, Terrence F; von Mering, Christian; Muthas, Daniel; Nguyen, Dac-Trung; Overington, John P; Papadatos, George; Qin, Jun; Reich, Christian; Roth, Bryan L; Schürer, Stephan C; Simeonov, Anton; Sklar, Larry A; Southall, Noel; Tomita, Susumu; Tudose, Ilinca; Ursu, Oleg; Vidovic, Dušica; Waller, Anna; Westergaard, David; Yang, Jeremy J; Zahoránszky-Köhalmi, Gergely

    2018-05-01

    A large proportion of biomedical research and the development of therapeutics is focused on a small fraction of the human genome. In a strategic effort to map the knowledge gaps around proteins encoded by the human genome and to promote the exploration of currently understudied, but potentially druggable, proteins, the US National Institutes of Health launched the Illuminating the Druggable Genome (IDG) initiative in 2014. In this article, we discuss how the systematic collection and processing of a wide array of genomic, proteomic, chemical and disease-related resource data by the IDG Knowledge Management Center have enabled the development of evidence-based criteria for tracking the target development level (TDL) of human proteins, which indicates a substantial knowledge deficit for approximately one out of three proteins in the human proteome. We then present spotlights on the TDL categories as well as key drug target classes, including G protein-coupled receptors, protein kinases and ion channels, which illustrate the nature of the unexplored opportunities for biomedical research and therapeutic development.

  3. Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm.

    Science.gov (United States)

    Jin, Jingjing; Lee, May; Bai, Bin; Sun, Yanwei; Qu, Jing; Rahmadsyah; Alfiko, Yuzer; Lim, Chin Huat; Suwanto, Antonius; Sugiharti, Maria; Wong, Limsoon; Ye, Jian; Chua, Nam-Hai; Yue, Gen Hua

    2016-12-01

    Oil palm is the world's leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  4. From simple to supercomplex: mitochondrial genomes of euglenozoan protists

    Czech Academy of Sciences Publication Activity Database

    Faktorová, Drahomíra; Dobáková, Eva; Peña-Diaz, Priscila; Lukeš, Julius

    2016-01-01

    Roč. 5, 15 NOV (2016), č. článku 392. ISSN 2046-1402 R&D Projects: GA ČR GA15-21974S Institutional support: RVO:60077344 Keywords : euglenozoa * mitochondria * mitochondrial genome Subject RIV: EB - Genetics ; Molecular Biology

  5. Theories on the beginnings and structure of joint-families ("zadruga"

    Directory of Open Access Journals (Sweden)

    Novaković Nada

    2005-01-01

    Full Text Available In this paper the author has a critical standpoint toward the most known theories on joint family communities. The works of the up-to-now called Yugoslav authors were put in the foreground. The works of foreign authors were placed after. They were classified by a general criterion, by how the authors saw the origins of this form of family. The comprehension of the basic characteristics depends, as a rule, on that, as well as the elements structure, changing processes, adjustment to new conditions and extinction of the joint family community. The first part of this article is devoted to theories about family communities as an institution of the Slavs. In this way its origin is connected with elements of a certain ethnic community. The range and consequences of such beliefs are suggested. The second part is reserved to explaining the family community as an institution which appeared in feudalism. It is a consequence of the tax system role. With its termination, the communities fell apart. This kind of social development determination and this type of family is proven to be ahistorical. It is predominantly stressed that the authors neglected that feudalism was a class society and overemphasized the force factor significance. The third part deals with theories which believe joint-family communities as an institution which arose in the transition from tribal to class society. These researchers stress that it is a general, historically determined conditioned form, which originated before class society and terminated with its development. Elements of its structure are especially important, as well as methods of its transformation in new conditions and termination processes. The essence of this belief is the following: a joint-family is a general historical form of family organization which arose in the transition from tribal to class society. The most important characteristics are: 1 blood relationship among men members; 2 common property; 3

  6. GGRaSP: A R-package for selecting representative genomes using Gaussian mixture models.

    Science.gov (United States)

    Clarke, Thomas H; Brinkac, Lauren M; Sutton, Granger; Fouts, Derrick E

    2018-04-14

    The vast number of available sequenced bacterial genomes occasionally exceeds the facilities of comparative genomic methods or is dominated by a single outbreak strain, and thus a diverse and representative subset is required. Generation of the reduced subset currently requires a priori supervised clustering and sequence-only selection of medoid genomic sequences, independent of any additional genome metrics or strain attributes. The GGRaSP R-package described below generates a reduced subset of genomes that prioritizes maintaining genomes of interest to the user as well as minimizing the loss of genetic variation. The package also allows for unsupervised clustering by modeling the genomic relationships using a Gaussian Mixture Model to select an appropriate cluster threshold. We demonstrate the capabilities of GGRaSP by generating a reduced list of 315 genomes from a genomic dataset of 4600 Escherichia coli genomes, prioritizing selection by type strain and by genome completeness. GGRaSP is available at https://github.com/JCVenterInstitute/ggrasp/. tclarke@jcvi.org. Supplementary data are available at the GitHub site.

  7. Determination of Parachute Joint Factors using Seam and Joint Testing

    Science.gov (United States)

    Mollmann, Catherine

    2015-01-01

    This paper details the methodology for determining the joint factor for all parachute components. This method has been successfully implemented on the Capsule Parachute Assembly System (CPAS) for the NASA Orion crew module for use in determining the margin of safety for each component under peak loads. Also discussed are concepts behind the joint factor and what drives the loss of material strength at joints. The joint factor is defined as a "loss in joint strength...relative to the basic material strength" that occurs when "textiles are connected to each other or to metals." During the CPAS engineering development phase, a conservative joint factor of 0.80 was assumed for each parachute component. In order to refine this factor and eliminate excess conservatism, a seam and joint testing program was implemented as part of the structural validation. This method split each of the parachute structural joints into discrete tensile tests designed to duplicate the loading of each joint. Breaking strength data collected from destructive pull testing was then used to calculate the joint factor in the form of an efficiency. Joint efficiency is the percentage of the base material strength that remains after degradation due to sewing or interaction with other components; it is used interchangeably with joint factor in this paper. Parachute materials vary in type-mainly cord, tape, webbing, and cloth -which require different test fixtures and joint sample construction methods. This paper defines guidelines for designing and testing samples based on materials and test goals. Using the test methodology and analysis approach detailed in this paper, the minimum joint factor for each parachute component can be formulated. The joint factors can then be used to calculate the design factor and margin of safety for that component, a critical part of the design verification process.

  8. CRISPR-Cas9; an efficient tool for precise plant genome editing.

    Science.gov (United States)

    Islam, Waqar

    2018-04-03

    Efficient plant genome editing is dependent upon induction of double stranded DNA breaks (DSBs) through site specified nucleases. These DSBs initiate the process of DNA repair which can either base upon homologous recombination (HR) or non-homologous end jointing (NHEJ). Recently, CRISPR-Cas9 mechanism got highlighted as revolutionizing genetic tool due to its simpler frame work along with the broad range of adaptability and applications. So, in this review, I have tried to sum up the application of this biotechnological tool in plant genome editing. Furthermore, I have tried to explain successful adaptation of CRISPR in various plant species where it is used for the successful generation of stable mutations in a steadily growing number of species through NHEJ. The review also sheds light upon other biotechnological approaches relying upon single DNA lesion induction such as genomic deletion or pair wise nickases for evasion of offsite effects. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Temporomandibular joint space in children without joint disease

    International Nuclear Information System (INIS)

    Larheim, T.A.

    1981-01-01

    Bilateral assessment of the temporomandibular joint space in children without joint disease is reported. Twenty-eight children were examined with conventional radiography and 23 with tomography. High prevalence of asymmetric joint spaces with both techniques indicated that great care should be taken when using narrowing or widening of the joint space as a diagnostic criterion in children with juvenile rheumatoid arthritis. Other signs, such as restricted translation of the mandibular head, and clinical symptoms should be evaluated. (Auth.)

  10. Following the Path of the Teacher´s Development: Joint Reflection

    Czech Academy of Sciences Publication Activity Database

    Hošpesová, A.; Tichá, Marie

    2009-01-01

    Roč. 17, č. 1 (2009), s. 212-232 ISSN 1732-6729 R&D Projects: GA ČR(CZ) GA406/08/0710 Institutional research plan: CEZ:AV0Z10190503 Keywords : primary school teachers * teachers´competences * qualified joint reflection Subject RIV: AM - Education Impact factor: 0.064, year: 2009

  11. Temporomandibular Joint Prosthesis - 3D-CT Reconstruction before and after Treatment

    Czech Academy of Sciences Publication Activity Database

    Feltlová, E.; Dostálová, T.; Kašparová, M.; Daněk, J.; Hliňáková, P.; Hubáček, M.; Nedoma, Jiří

    2010-01-01

    Roč. 6, č. 1 (2010), s. 15-19 ISSN 1801-5603 Institutional research plan: CEZ:AV0Z10300504 Keywords : dentistry * maxillofacial surgery * partial TMJ prosthesis * three-dimensional computed tomography * magnetic resonance imaging * temporomandibular joint Subject RIV: BA - General Mathematics http://www.ejbi.cz/articles/201012/50/1.html

  12. 77 FR 9273 - WORKSHOP Sponsored by the Nuclear Regulatory Commission and the Electric Power Research Institute...

    Science.gov (United States)

    2012-02-16

    ... Commission and the Electric Power Research Institute on the Treatment of Probabilistic Risk Assessment.... SUMMARY: The U.S. Nuclear Regulatory Commission (NRC), Office of Nuclear Regulatory Research (RES), in cooperation with the Electric Power Research Institute (EPRI), will hold a joint workshop on the Treatment of...

  13. Analysis of radiation-induced genome alterations in Vigna unguiculata

    Directory of Open Access Journals (Sweden)

    van der Vyver C

    2011-09-01

    Full Text Available Christell van der Vyver1, B Juan Vorster2, Karl J Kunert3, Christopher A Cullis41Institute for Plant Biotechnology, Department of Genetics, University of Stellenbosch, Stellenbosch, South Africa; 2Department of Plant Production and Soil Science, and 3Department of Plant Science, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa; 4Case Western Reserve University, Department of Biology, Cleveland, OH, USAAbstract: Seeds from an inbred Vigna unguiculata (cowpea cultivar were gamma-irradiated with a dose of 180 Gy in order to identify and characterize possible mutations. Three techniques, ie, random amplified polymorphic DNA, microsatellites, and representational difference analysis, were used to characterize possible DNA variation among the mutants and nonirradiated control plants both immediately after irradiation and in subsequent generations. A large portion of putative radiation-induced genome changes had significant similarities to chloroplast sequences. The frequency of mutation at three of these isolated polymorphic regions with chloroplast similarity was further determined by polymerase chain reaction screening using a large number of individual parental, M1, and M2 plants. Analysis of these sequences indicated that the rate at which various regions of the genome is mutated in irradiation experiments differs significantly and also that mutations have variable “repair” rates. Furthermore, regions of the nuclear DNA derived from the chloroplast genome are highly susceptible to modification by radiation treatment. Overall, data have provided detailed information on the effects of gamma irradiation on the cowpea genome and about the ability of the plant to repair these genome changes in subsequent plant generations.Keywords: mutation breeding, gamma radiation, genetic mutations, cowpea, representational difference analysis

  14. A computational genomics pipeline for prokaryotic sequencing projects.

    Science.gov (United States)

    Kislyuk, Andrey O; Katz, Lee S; Agrawal, Sonia; Hagen, Matthew S; Conley, Andrew B; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C; Sammons, Scott A; Govil, Dhwani; Mair, Raydel D; Tatti, Kathleen M; Tondella, Maria L; Harcourt, Brian H; Mayer, Leonard W; Jordan, I King

    2010-08-01

    New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.

  15. Nuclear genome size analysis of Agave tequilana Weber

    Czech Academy of Sciences Publication Activity Database

    Palomino, G.; Doležel, Jaroslav; Méndez, I.; Rubluo, A.

    2003-01-01

    Roč. 56, č. 1 (2003), s. 37-46 ISSN 0008-7114 Grant - others:Itálie(IT) Z5038910 Institutional research plan: CEZ:AV0Z5038910 Keywords : Flow cytometry * nuclear genome size * Agave tequilana Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.337, year: 2003

  16. Contrasting evolutionary dynamics between angiosperm and mammalian genomes

    Czech Academy of Sciences Publication Activity Database

    Kejnovský, Eduard; Leitch, I.J.; Leitch, A.R.

    2009-01-01

    Roč. 24, č. 10 (2009), s. 572-582 ISSN 0169-5347 R&D Projects: GA MŠk(CZ) LC06004 Institutional research plan: CEZ:AV0Z50040507; CEZ:AV0Z50040702 Keywords : genomes * evolutionary dynamics * recombination Subject RIV: BO - Biophysics Impact factor: 11.564, year: 2009

  17. Proceedings of the third JAERI-KAERI joint seminar on post irradiation examination technology

    International Nuclear Information System (INIS)

    1999-09-01

    Between the Department of JMTR of the Japan Atomic Energy Research Institute (JAERI) and the Nuclear Fuel Cycle Research Group of the Korea Atomic Energy Research Institute (KAERI), it has been periodically carried out the collaboration on technical information exchange by specialists and scientists, under the Arrangement of the Implementation of Cooperative Research Program in the Field of Peaceful Uses of Nuclear between JAERI and KAERI. And JAERI-KAERI joint seminar has been held every three years. The 1st and 2nd JAERI-KAERI Joint Seminars were held in November 1992 at JAERI and in September 1995 at KAERI, respectively. The 3rd JAERI-KAERI Joint Seminar was held on 25 and 26 March, 1999 at the Oarai Research Establishment of JAERI. In this seminar, total participants of 84 were joined from JAERI, KAERI, Hanyang University, Japan Nuclear Cycle Development Institute, Oarai Branch of Institute for Materials Research (IMR) of Tohoku University, Nippon Nuclear Fuel Development Co., Ltd., Nuclear Development Corporation and others. Contributed presentations were in three sessions; Current status and future perspectives on PIE, PIE techniques and Evaluation of PIE data. Re-assembling technique for JOYO fuel, Nd-YAG laser welding technique, grain boundary analysis using FEG-TEM, lift time estimation of PWR Rod Cluster Control Assembly (RCCA) rodlet and failure analysis of Korea Nuclear Power Plant (KNP) fuel have been widely noticed as topic items on PIE. And some comments from PIE user, were pointed out that the nano-PIE technique, the flexibility to ad-hoc demands on testing space or utilization, and the international collaboration were very important for the next generation's PIE. The 34 of the present papers are indexed individually. (J.P.N.)

  18. Proceedings of the third JAERI-KAERI joint seminar on post irradiation examination technology

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-09-01

    Between the Department of JMTR of the Japan Atomic Energy Research Institute (JAERI) and the Nuclear Fuel Cycle Research Group of the Korea Atomic Energy Research Institute (KAERI), it has been periodically carried out the collaboration on technical information exchange by specialists and scientists, under the Arrangement of the Implementation of Cooperative Research Program in the Field of Peaceful Uses of Nuclear between JAERI and KAERI. And JAERI-KAERI joint seminar has been held every three years. The 1st and 2nd JAERI-KAERI Joint Seminars were held in November 1992 at JAERI and in September 1995 at KAERI, respectively. The 3rd JAERI-KAERI Joint Seminar was held on 25 and 26 March, 1999 at the Oarai Research Establishment of JAERI. In this seminar, total participants of 84 were joined from JAERI, KAERI, Hanyang University, Japan Nuclear Cycle Development Institute, Oarai Branch of Institute for Materials Research (IMR) of Tohoku University, Nippon Nuclear Fuel Development Co., Ltd., Nuclear Development Corporation and others. Contributed presentations were in three sessions; Current status and future perspectives on PIE, PIE techniques and Evaluation of PIE data. Re-assembling technique for JOYO fuel, Nd-YAG laser welding technique, grain boundary analysis using FEG-TEM, lift time estimation of PWR Rod Cluster Control Assembly (RCCA) rodlet and failure analysis of Korea Nuclear Power Plant (KNP) fuel have been widely noticed as topic items on PIE. And some comments from PIE user, were pointed out that the nano-PIE technique, the flexibility to ad-hoc demands on testing space or utilization, and the international collaboration were very important for the next generation's PIE. The 34 of the present papers are indexed individually. (J.P.N.)

  19. FAA/NASA Joint University Program for Air Transportation Research 1994-1995

    Science.gov (United States)

    Remer, J. H.

    1998-01-01

    The Joint University Program for Air Transportation Research (JUP) is a coordinated set of three grants co-sponsored by the Federal Aviation Administration (FAA) and the National Aeronautics and Space Administration (NASA). Under JUP, three institutions: the Massachusetts Institute of Technology, Princeton, and Ohio Universities receive research grants and collaborate with FAA and NASA in defining and performing civil aeronautics research in a multitude of areas. Some of these disciplines are artificial intelligence, control theory, atmospheric hazards, navigation, avionics, human factors, flight dynamics, air traffic management, and electronic communications.

  20. Software Technologies - 8th International Joint Conference, ICSOFT 2013 : Revised Selected Papers

    NARCIS (Netherlands)

    Cordeiro, José; van Sinderen, Marten J.

    2014-01-01

    The present book includes extended and revised versions of a set of selected papers from the 8th International Joint Conference on Software Technologies (ICSOFT 2013), which was co-organized by the Reykjavik University (RU) and sponsored by the Institute for Systems and Technologies of Information,

  1. An evaluation of the carrying angle of the elbow joint in adolescents

    African Journals Online (AJOL)

    McRoy

    Department of Anatomy and Orthopedics, Sri Lakshmi Narayana Institute of Medical Sciences,. Pondicherry - 605 502 ... forearm deviates laterally from the long axis of the humerus, with the arm extended and the palm ... for elbow reconstruction. Key words: Carrying angle, elbow joint, adolescent, forearm, humerus, ulna ...

  2. Protecting and Evaluating Genomic Privacy in Medical Tests and Personalized Medicine

    OpenAIRE

    Ayday, Erman; Raisaro, Jean Louis; Rougemont, Jacques; Hubaux, Jean-Pierre

    2013-01-01

    In this paper, we propose privacy-enhancing technologies for medical tests and personalized medicine methods that use patients' genomic data. Focusing on genetic disease-susceptibility tests, we develop a new architecture (between the patient and the medical unit) and propose a "privacy-preserving disease susceptibility test" (PDS) by using homomorphic encryption and proxy re-encryption. Assuming the whole genome sequencing to be done by a certified institution, we propose to store patients' ...

  3. The genome of the model beetle and pest Tribolium castaneum

    Czech Academy of Sciences Publication Activity Database

    Richards, S.; Jindra, Marek

    2008-01-01

    Roč. 452, č. 7190 (2008), s. 949-955 ISSN 0028-0836 Institutional research plan: CEZ:AV0Z50070508 Keywords : Tribolium castaneum * genome * sequencing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 31.434, year: 2008

  4. Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size

    Czech Academy of Sciences Publication Activity Database

    Kelly, L.J.; Renny-Byfield, S.; Macas, Jiří; Novák, Petr; Neumann, Pavel; Lysák, M.; Day, P.D.; Berger, M.; Fay, M. F.; Nichols, R. A.; Leitch, A. R.; Leitch, I. J.

    2015-01-01

    Roč. 208, č. 2 (2015), s. 596-607 ISSN 0028-646X R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:60077344 Keywords : DNA deletion * Fritillaria * Liliaceae * genome size evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.210, year: 2015

  5. Magneto-therapy of human joint cartilage.

    Science.gov (United States)

    Wierzcholski, Krzysztof; Miszczak, Andrzej

    2017-01-01

    The topic of the present paper concerns the human joint cartilage therapy performed by the magnetic induction field. There is proved the thesis that the applied magnetic field for concrete cartilage illness should depend on the proper relative and concrete values of applied magnetic induction, intensity as well the time of treatment duration. Additionally, very important are frequencies and amplitudes of magnetic field as well as magnetic permeability of the synovial fluid. The research methods used in this paper include: magnetic induction field produced by a new Polish and German magneto electronic devices for the therapy of human joint cartilage diseases, stationary and movable magnetic applicators, magnetic bandage, ferrofluid injections, author's experience gained in Germany research institutes and practical results after measurements and information from patients. The results of this paper concern concrete parameters of time dependent electro-magnetic field administration during the joint cartilage therapy duration and additionally concern the corollaries which are implied from reading values gained on the magnetic induction devices. The main conclusions obtained in this paper are as follows: Time dependent magnetic induction field increases the dynamic viscosity of movable synovial fluid and decreases symptoms of cartilage illness for concrete intensity of magnetic field and concrete field line architecture. The ferrofluid therapy and phospholipids bilayer simultaneously with the administrated external electromagnetic field, increases the dynamic viscosity of movable synovial fluid.

  6. Validation of rice genome sequence by optical mapping

    Directory of Open Access Journals (Sweden)

    Pape Louise

    2007-08-01

    Full Text Available Abstract Background Rice feeds much of the world, and possesses the simplest genome analyzed to date within the grass family, making it an economically relevant model system for other cereal crops. Although the rice genome is sequenced, validation and gap closing efforts require purely independent means for accurate finishing of sequence build data. Results To facilitate ongoing sequencing finishing and validation efforts, we have constructed a whole-genome SwaI optical restriction map of the rice genome. The physical map consists of 14 contigs, covering 12 chromosomes, with a total genome size of 382.17 Mb; this value is about 11% smaller than original estimates. 9 of the 14 optical map contigs are without gaps, covering chromosomes 1, 2, 3, 4, 5, 7, 8 10, and 12 in their entirety – including centromeres and telomeres. Alignments between optical and in silico restriction maps constructed from IRGSP (International Rice Genome Sequencing Project and TIGR (The Institute for Genomic Research genome sequence sources are comprehensive and informative, evidenced by map coverage across virtually all published gaps, discovery of new ones, and characterization of sequence misassemblies; all totalling ~14 Mb. Furthermore, since optical maps are ordered restriction maps, identified discordances are pinpointed on a reliable physical scaffold providing an independent resource for closure of gaps and rectification of misassemblies. Conclusion Analysis of sequence and optical mapping data effectively validates genome sequence assemblies constructed from large, repeat-rich genomes. Given this conclusion we envision new applications of such single molecule analysis that will merge advantages offered by high-resolution optical maps with inexpensive, but short sequence reads generated by emerging sequencing platforms. Lastly, map construction techniques presented here points the way to new types of comparative genome analysis that would focus on discernment of

  7. Inspection of welded joints and cords using industrial x-ray and gamma radiography

    International Nuclear Information System (INIS)

    Escobar R, E.J.

    2000-01-01

    The first part of this work contains five chapters related to theoretical aspects and basic knowledge of welding metallurgy, welding, welded joint discontinuity, non-destructive testing (NDT) and industrial x-rays. The second part contains experimental works applied and carried out by the Peruvian Institute of Nuclear Energy (IPEN). Due to the importance of identifying and applying the different methods of NDT in the industry's quality control, more emphasis is placed on industrial x-ray and gamma radiography, a method that involves the radiographic inspection of welded joints and cords

  8. Moth sex chromatin probed by comparative genomic hybridization (CGH)

    Czech Academy of Sciences Publication Activity Database

    Sahara, K.; Marec, František; Eickhoff, U.; Traut, W.

    2003-01-01

    Roč. 46, - (2003), s. 339-342 ISSN 0831-2796 R&D Projects: GA AV ČR IAA6007307 Institutional research plan: CEZ:AV0Z5007907 Keywords : Lepidoptera * comparative genomic hybridization Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.861, year: 2003

  9. Joint Replacement (Finger and Wrist Joints)

    Science.gov (United States)

    ... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is a Hand Surgeon? What is a Hand Therapist? Media Find a Hand Surgeon Home Anatomy Joint Replacement Email to a friend * required fields ...

  10. Joint Operation Planning

    National Research Council Canada - National Science Library

    2006-01-01

    .... It sets forth joint doctrine to govern the joint operation planning activities and performance of the Armed Forces of the United States in joint operations, and provides the joint doctrinal basis...

  11. Site acceptability and power availability: needed institutional changes

    International Nuclear Information System (INIS)

    Haggard, J.E.

    1975-01-01

    Timely assurance of power plant site availability is threatened by institutional inabilities to resolve often competing environmental/energy requirements. Institutional changes are needed. The issue of site approval should be separated from that of plant approval. A ''one-stop'' forum for site approval, modeled after Washington State's Thermal Power Plant Siting Act, is needed. The one-stop process utilizes one forum composed of officials drawn from all agencies involved in site related issues. A joint Federal/State Siting Council, with sole jurisdiction over site approval, is recommended. The State Council would have a determinative vote on all issues not otherwise preempted by federal legislation. 21 references. (U.S.)

  12. Jointness for the Rest of Us: Reforming Joint Professional Development

    Science.gov (United States)

    2016-06-10

    transferred to the Joint Staff. 13 DOD’s instinct to “overly centralize planning, organization, and management.”20 The authors contend that this...2. 3 John F. Schank and others, Who is Joint? Reevaluating the Joint Duty Assignment List : A Study Prepared for the Joint Staff, by the RAND...and code those billets as such. Once identified, DOD must expand the Joint Duty Assignment List (JDAL) to include billets that offer enlisted personnel

  13. KAIKObase: An integrated silkworm genome database and data mining tool

    Directory of Open Access Journals (Sweden)

    Nagaraju Javaregowda

    2009-10-01

    Full Text Available Abstract Background The silkworm, Bombyx mori, is one of the most economically important insects in many developing countries owing to its large-scale cultivation for silk production. With the development of genomic and biotechnological tools, B. mori has also become an important bioreactor for production of various recombinant proteins of biomedical interest. In 2004, two genome sequencing projects for B. mori were reported independently by Chinese and Japanese teams; however, the datasets were insufficient for building long genomic scaffolds which are essential for unambiguous annotation of the genome. Now, both the datasets have been merged and assembled through a joint collaboration between the two groups. Description Integration of the two data sets of silkworm whole-genome-shotgun sequencing by the Japanese and Chinese groups together with newly obtained fosmid- and BAC-end sequences produced the best continuity (~3.7 Mb in N50 scaffold size among the sequenced insect genomes and provided a high degree of nucleotide coverage (88% of all 28 chromosomes. In addition, a physical map of BAC contigs constructed by fingerprinting BAC clones and a SNP linkage map constructed using BAC-end sequences were available. In parallel, proteomic data from two-dimensional polyacrylamide gel electrophoresis in various tissues and developmental stages were compiled into a silkworm proteome database. Finally, a Bombyx trap database was constructed for documenting insertion positions and expression data of transposon insertion lines. Conclusion For efficient usage of genome information for functional studies, genomic sequences, physical and genetic map information and EST data were compiled into KAIKObase, an integrated silkworm genome database which consists of 4 map viewers, a gene viewer, and sequence, keyword and position search systems to display results and data at the level of nucleotide sequence, gene, scaffold and chromosome. Integration of the

  14. Periprosthetic joint infection: are patients with multiple prosthetic joints at risk?

    Science.gov (United States)

    Jafari, S Mehdi; Casper, David S; Restrepo, Camilo; Zmistowski, Benjamin; Parvizi, Javad; Sharkey, Peter F

    2012-06-01

    Patients who present with a periprosthetic joint infection in a single joint may have multiple prosthetic joints. The risk of these patients developing a subsequent infection in another prosthetic joint is unknown. Our purposes were (1) to identify the risk of developing a subsequent infection in another prosthetic joint and (2) to describe the time span and organism profile to the second prosthetic infection. We retrospectively identified 55 patients with periprosthetic joint infection who had another prosthetic joint in place at the time of presentation. Of the 55 patients, 11 (20%) developed a periprosthetic joint infection in a second joint. The type of organism was the same as the first infection in 4 (36%) of 11 patients. The time to developing a second infection averaged 2.0 years (range, 0-6.9 years). Copyright © 2012 Elsevier Inc. All rights reserved.

  15. Stress analysis of the hip joint endoprosthesis with shape deflections

    Czech Academy of Sciences Publication Activity Database

    Fuis, Vladimír; Návrat, Tomáš

    2005-01-01

    Roč. 12, č. 5 (2005), s. 323-330 ISSN 1802-1484. [Mechatronics, Robotics and Biomechanics 2005. Třešť, 26.09.2005-29.09.2005] R&D Projects: GA ČR(CZ) GA101/05/0136 Institutional research plan: CEZ:AV0Z20760514 Keywords : hip joint endoprosthesis * weibul weakest link Subject RIV: JH - Ceramics, Fire-Resistant Materials and Glass

  16. Joint utility task group CGI data-base procurement history module

    International Nuclear Information System (INIS)

    Rosch, F.

    1993-01-01

    The purpose of the procurement history record module of the Joint Utility Task Group's (JUTG's) commercial-grade item (CGI) data base is to assist utilities to cost effectively implement the dedication methodology provided in the Electric Power Research Institute's (EPRI's) report NP-5652, open-quotes Guidelines for the Utilization of Commercial Grade Items in Nuclear Safety-Related Applications.close quotes

  17. Data analysis in the post-genome-wide association study era

    Directory of Open Access Journals (Sweden)

    Qiao-Ling Wang

    2016-12-01

    Full Text Available Since the first report of a genome-wide association study (GWAS on human age-related macular degeneration, GWAS has successfully been used to discover genetic variants for a variety of complex human diseases and/or traits, and thousands of associated loci have been identified. However, the underlying mechanisms for these loci remain largely unknown. To make these GWAS findings more useful, it is necessary to perform in-depth data mining. The data analysis in the post-GWAS era will include the following aspects: fine-mapping of susceptibility regions to identify susceptibility genes for elucidating the biological mechanism of action; joint analysis of susceptibility genes in different diseases; integration of GWAS, transcriptome, and epigenetic data to analyze expression and methylation quantitative trait loci at the whole-genome level, and find single-nucleotide polymorphisms that influence gene expression and DNA methylation; genome-wide association analysis of disease-related DNA copy number variations. Applying these strategies and methods will serve to strengthen GWAS data to enhance the utility and significance of GWAS in improving understanding of the genetics of complex diseases or traits and translate these findings for clinical applications. Keywords: Genome-wide association study, Data mining, Integrative data analysis, Polymorphism, Copy number variation

  18. Rare and common regulatory variation in population-scale sequenced human genomes.

    Directory of Open Access Journals (Sweden)

    Stephen B Montgomery

    2011-07-01

    Full Text Available Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.

  19. Coracoclavicular joint

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kun Sang; Park, Chan Il; Ahn, Jae Doo; Lim, Chong Won [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    1970-10-15

    The coracoclvicular joint, a rear abnormality which may be the cause of pain in the shoulder and limitation of motion of the shoulder joint, is discussed. A case of coracoclvicular joint with shoulder pain was observed in 65 yrs old Korean male.

  20. A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data.

    Science.gov (United States)

    Lu, Qiongshi; Hu, Yiming; Sun, Jiehuan; Cheng, Yuwei; Cheung, Kei-Hoi; Zhao, Hongyu

    2015-05-27

    Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu.

  1. Somatic DNA recombination yielding circular DNA and deletion of a genomic region in embryonic brain

    International Nuclear Information System (INIS)

    Maeda, Toyoki; Chijiiwa, Yoshiharu; Tsuji, Hideo; Sakoda, Saburo; Tani, Kenzaburo; Suzuki, Tomokazu

    2004-01-01

    In this study, a mouse genomic region is identified that undergoes DNA rearrangement and yields circular DNA in brain during embryogenesis. External region-directed inverse polymerase chain reaction on circular DNA extracted from late embryonic brain tissue repeatedly detected DNA of this region containing recombination joints. Wide-range genomic PCR and digestion-circularization PCR analysis showed this region underwent recombination accompanied with deletion of intervening sequences, including the circularized regions. This region was mapped by fluorescence in situ hybridization to C1 on mouse chromosome 16, where no gene and no physiological DNA rearrangement had been identified. DNA sequence in the region has segmental homology to an orthologous region on human chromosome 3q.13. These observations demonstrated somatic DNA recombination yielding genomic deletions in brain during embryogenesis

  2. Temporomandibular joint

    International Nuclear Information System (INIS)

    Westesson, P.L.; Hatala, M.; Tallents, R.H.; Katzberg, R.W.; Musgrave, M.; Levitt, S.

    1990-01-01

    This paper determines the frequency of MR signs of abnormal temporomandibular joints (TMJs) in asymptomatic volunteers. Forty-two volunteers with 84 clinically normal TMJs were imaged in the sagittal and coronal planes with surface coil MR imaging. Sagittal closed and open and coronal closed views were obtained bilaterally in all volunteers. The images were classified as normal (superior disk position) or abnormal (disk displacement of degenerative joint disease). Eighteen joints in 11 volunteers were abnormal; 12 had disk displacement with reduction and six had disk displacement without reduction, with associated degenerative joint disease in three of the six. Asymptomatic internal derangement and degenerative joint disease occur in about one-fourth of asymptomatic volunteers

  3. Digital image correlation in analysis of striffness in local zones of welded joints

    Czech Academy of Sciences Publication Activity Database

    Milosevic, M.; Milosevic, N.J.; Sedmak, S.; Tatic, U.; Mitrovic, N.; Hloch, Sergej; Jovicic, R.

    2016-01-01

    Roč. 23, č. 1 (2016), s. 19-24 ISSN 1330-3651 Institutional support: RVO:68145535 Keywords : Aramis software * digital image correlation * strain analysis * stiffness * welded joints Subject RIV: JQ - Machines ; Tools Impact factor: 0.723, year: 2016 http://hrcak.srce.hr/file/225545

  4. Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa?

    Czech Academy of Sciences Publication Activity Database

    Flegontov, Pavel; Gray, M.W.; Burger, G.; Lukeš, Julius

    2011-01-01

    Roč. 57, č. 4 (2011), 225-232 ISSN 0172-8083 Institutional research plan: CEZ:AV0Z60220518 Keywords : Euglena * Diplonema * Mitochondrial genome * RNA editing * Constructive neutral evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.556, year: 2011

  5. Emerging technologies advancing forage and turf grass genomics

    Czech Academy of Sciences Publication Activity Database

    Kopecký, David; Studer, B.

    2014-01-01

    Roč. 32, č. 1 (2014), s. 190-199 ISSN 0734-9750 R&D Projects: GA ČR(CZ) GAP501/11/0504; GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Cytogenetics * Epigenetics * Genome-wide association studies (GWAS) Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 9.015, year: 2014

  6. Genome-wide association study identifies five new schizophrenia loci.

    LENUS (Irish Health Repository)

    Ripke, Stephan

    2011-10-01

    We examined the role of common genetic variation in schizophrenia in a genome-wide association study of substantial size: a stage 1 discovery sample of 21,856 individuals of European ancestry and a stage 2 replication sample of 29,839 independent subjects. The combined stage 1 and 2 analysis yielded genome-wide significant associations with schizophrenia for seven loci, five of which are new (1p21.3, 2q32.3, 8p23.2, 8q21.3 and 10q24.32-q24.33) and two of which have been previously implicated (6p21.32-p22.1 and 18q21.2). The strongest new finding (P = 1.6 × 10(-11)) was with rs1625579 within an intron of a putative primary transcript for MIR137 (microRNA 137), a known regulator of neuronal development. Four other schizophrenia loci achieving genome-wide significance contain predicted targets of MIR137, suggesting MIR137-mediated dysregulation as a previously unknown etiologic mechanism in schizophrenia. In a joint analysis with a bipolar disorder sample (16,374 affected individuals and 14,044 controls), three loci reached genome-wide significance: CACNA1C (rs4765905, P = 7.0 × 10(-9)), ANK3 (rs10994359, P = 2.5 × 10(-8)) and the ITIH3-ITIH4 region (rs2239547, P = 7.8 × 10(-9)).

  7. FUNCTIONS OF THE HEAD OF SPECIAL (CORRECTIONAL) EDUCATIONAL INSTITUTION ON PERFECTION OF ESTIMATION OF EDUCATIONAL SYSTEM

    OpenAIRE

    Voynelenko Natalya Vaselyevna

    2012-01-01

    In article the maintenance of activity of the head of special (correctional) educational institution on the organization of estimation of quality of educational system is discussed. The model of joint activity of participants of educational process on estimation of educational objects, as component of system of quality management in Educational institution is presented. Functions of estimation of educational system in activity of the head of educational institution are formulated.

  8. Unexpectedly Streamlined Mitochondrial Genome of the Euglenozoan Euglena gracilis

    Czech Academy of Sciences Publication Activity Database

    Dobáková, Eva; Flegontov, Pavel; Skalický, Tomáš; Lukeš, Julius

    2015-01-01

    Roč. 7, č. 12 (2015), s. 3358-3367 ISSN 1759-6653 R&D Projects: GA ČR GA15-21974S Institutional support: RVO:60077344 Keywords : Euglena gracilis * mitochondrial genome * transcription * RNA editing Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.098, year: 2015

  9. The amphioxus genome illuminates vertebrate origins and cephalochordate biology

    Czech Academy of Sciences Publication Activity Database

    Holland, L. Z.; Albalat, R.; Azumi, K.; Gutierrez, E.B.; Blow, M.J.; Bronner-Fraser, M.; Brunet, F.; Butts, T.; Candiani, S.; Dishaw, L. J.; Ferrier, D.E.K.; Garcia-Fernandez, J.; Gibson-Brown, J.J.; Gissi, C.; Godzik, A.; Hallbook, F.; Hirose, D.; Hosomichi, K.; Ikuta, T.; Inoko, H.; Kasahara, M.; Kasamatsu, J.; Kawashima, T.; Kimura, A.; Kobayashi, M.; Kozmik, Zbyněk; Kubokawa, K.; Laudet, V.; Litman, G.W.; McHardy, A.; Meulemans, D.; Nonaka, M.; Olinski, R.P.; Pancer, Z.; Pennacchio, L.A.; Pestarino, M.; Rast, J.P.; Rigoutsos, I.; Robinson-Rechavi, M.; Roch, G.; Saiga, H.; Sasakura, Y.; Satake, M.; Satou, Y.; Schubert, M.; Sherwood, N.; Shiina, T.; Takatori, N.; Tello, J.; Vopálenský, Pavel; Wada, S.; Xu, A.; Ye, Y.; Yoshida, K.; Yoshizaki, F.; Yu, J.K.; Zhang, Q.; Zmasek, C.M.; De Jong, P.J.; Osoegawa, K.; Putnam, N. H.; Rokhsar, D. S.; Satoh, N.; Holland, P.W.H.

    2008-01-01

    Roč. 18, č. 7 (2008), s. 1100-1111 ISSN 1088-9051 R&D Projects: GA MŠk(CZ) 1M0520 Institutional research plan: CEZ:AV0Z50520514 Keywords : evolution * amphioxus genome * opsin Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 10.176, year: 2008

  10. "Harnessing genomics to improve health in Africa" – an executive course to support genomics policy

    Directory of Open Access Journals (Sweden)

    Singer Peter A

    2005-01-01

    Full Text Available Abstract Background Africa in the twenty-first century is faced with a heavy burden of disease, combined with ill-equipped medical systems and underdeveloped technological capacity. A major challenge for the international community is to bring scientific and technological advances like genomics to bear on the health priorities of poorer countries. The New Partnership for Africa's Development has identified science and technology as a key platform for Africa's renewal. Recognizing the timeliness of this issue, the African Centre for Technology Studies and the University of Toronto Joint Centre for Bioethics co-organized a course on Genomics and Public Health Policy in Nairobi, Kenya, the first of a series of similar courses to take place in the developing world. This article presents the findings and recommendations that emerged from this process, recommendations which suggest that a regional approach to developing sound science and technology policies is the key to harnessing genome-related biotechnology to improve health and contribute to human development in Africa. Methods The objectives of the course were to familiarize participants with the current status and implications of genomics for health in Africa; to provide frameworks for analyzing and debating the policy and ethical questions; and to begin developing a network across different sectors by sharing perspectives and building relationships. To achieve these goals the course brought together a diverse group of stakeholders from academic research centres, the media, non-governmental, voluntary and legal organizations to stimulate multi-sectoral debate around issues of policy. Topics included scientific advances in genomics innovation systems and business models, international regulatory frameworks, as well as ethical and legal issues. Results Seven main recommendations emerged: establish a network for sustained dialogue among participants; identify champions among politicians; use the

  11. The founding charter of the Genomic Observatories Network.

    Science.gov (United States)

    Davies, Neil; Field, Dawn; Amaral-Zettler, Linda; Clark, Melody S; Deck, John; Drummond, Alexei; Faith, Daniel P; Geller, Jonathan; Gilbert, Jack; Glöckner, Frank Oliver; Hirsch, Penny R; Leong, Jo-Ann; Meyer, Chris; Obst, Matthias; Planes, Serge; Scholin, Chris; Vogler, Alfried P; Gates, Ruth D; Toonen, Rob; Berteaux-Lecellier, Véronique; Barbier, Michèle; Barker, Katherine; Bertilsson, Stefan; Bicak, Mesude; Bietz, Matthew J; Bobe, Jason; Bodrossy, Levente; Borja, Angel; Coddington, Jonathan; Fuhrman, Jed; Gerdts, Gunnar; Gillespie, Rosemary; Goodwin, Kelly; Hanson, Paul C; Hero, Jean-Marc; Hoekman, David; Jansson, Janet; Jeanthon, Christian; Kao, Rebecca; Klindworth, Anna; Knight, Rob; Kottmann, Renzo; Koo, Michelle S; Kotoulas, Georgios; Lowe, Andrew J; Marteinsson, Viggó Thór; Meyer, Folker; Morrison, Norman; Myrold, David D; Pafilis, Evangelos; Parker, Stephanie; Parnell, John Jacob; Polymenakou, Paraskevi N; Ratnasingham, Sujeevan; Roderick, George K; Rodriguez-Ezpeleta, Naiara; Schonrogge, Karsten; Simon, Nathalie; Valette-Silver, Nathalie J; Springer, Yuri P; Stone, Graham N; Stones-Havas, Steve; Sansone, Susanna-Assunta; Thibault, Kate M; Wecker, Patricia; Wichels, Antje; Wooley, John C; Yahara, Tetsukazu; Zingone, Adriana

    2014-03-07

    The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington (DC, USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.

  12. Canine urothelial carcinoma: genomically aberrant and comparatively relevant.

    Science.gov (United States)

    Shapiro, S G; Raghunath, S; Williams, C; Motsinger-Reif, A A; Cullen, J M; Liu, T; Albertson, D; Ruvolo, M; Bergstrom Lucas, A; Jin, J; Knapp, D W; Schiffman, J D; Breen, M

    2015-06-01

    Urothelial carcinoma (UC), also referred to as transitional cell carcinoma (TCC), is the most common bladder malignancy in both human and canine populations. In human UC, numerous studies have demonstrated the prevalence of chromosomal imbalances. Although the histopathology of the disease is similar in both species, studies evaluating the genomic profile of canine UC are lacking, limiting the discovery of key comparative molecular markers associated with driving UC pathogenesis. In the present study, we evaluated 31 primary canine UC biopsies by oligonucleotide array comparative genomic hybridization (oaCGH). Results highlighted the presence of three highly recurrent numerical aberrations: gain of dog chromosome (CFA) 13 and 36 and loss of CFA 19. Regional gains of CFA 13 and 36 were present in 97 % and 84 % of cases, respectively, and losses on CFA 19 were present in 77 % of cases. Fluorescence in situ hybridization (FISH), using targeted bacterial artificial chromosome (BAC) clones and custom Agilent SureFISH probes, was performed to detect and quantify these regions in paraffin-embedded biopsy sections and urine-derived urothelial cells. The data indicate that these three aberrations are potentially diagnostic of UC. Comparison of our canine oaCGH data with that of 285 human cases identified a series of shared copy number aberrations. Using an informatics approach to interrogate the frequency of copy number aberrations across both species, we identified those that had the highest joint probability of association with UC. The most significant joint region contained the gene PABPC1, which should be considered further for its role in UC progression. In addition, cross-species filtering of genome-wide copy number data highlighted several genes as high-profile candidates for further analysis, including CDKN2A, S100A8/9, and LRP1B. We propose that these common aberrations are indicative of an evolutionarily conserved mechanism of pathogenesis and harbor genes

  13. Genomic impact of eukaryotic transposable elements

    Directory of Open Access Journals (Sweden)

    Arkhipova Irina R

    2012-11-01

    Full Text Available Abstract The third international conference on the genomic impact of eukaryotic transposable elements (TEs was held 24 to 28 February 2012 at the Asilomar Conference Center, Pacific Grove, CA, USA. Sponsored in part by the National Institutes of Health grant 5 P41 LM006252, the goal of the conference was to bring together researchers from around the world who study the impact and mechanisms of TEs using multiple computational and experimental approaches. The meeting drew close to 170 attendees and included invited floor presentations on the biology of TEs and their genomic impact, as well as numerous talks contributed by young scientists. The workshop talks were devoted to computational analysis of TEs with additional time for discussion of unresolved issues. Also, there was ample opportunity for poster presentations and informal evening discussions. The success of the meeting reflects the important role of Repbase in comparative genomic studies, and emphasizes the need for close interactions between experimental and computational biologists in the years to come.

  14. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism

    Czech Academy of Sciences Publication Activity Database

    Armbrust, E. V.; Berges, J. A.; Bowler, C.; Green, B. R.; Martinez, D.; Putnam, N. H.; Zhou, S.; Allen, A. E.; Apt, K. E.; Bechner, M.; Brzezinski, M. A.; Chaal, B. K.; Chiovitti, A.; Davis, A. K.; Demarest, M. S.; Detter, J. C.; Glavina, T.; Goodstein, D.; Hadi, M. Z.; Hellsten, U.; Hildebrand, M.; Jenkins, B. D.; Jurka, J.; Kapitonov, V. V.; Kröger, N.; Lau, W. W. Y.; Lane, T. W.; Larimer, F. W.; Lippmeier, J. C.; Lucas, S.; Medina, M.; Montsant, A.; Oborník, Miroslav; Schnitzler Parker, M.; Palenik, B.; Pazour, G. J.; Richardson, P. M.; Rynearson, T. A.; Saito, M. A.; Schwartz, D. C.; Thamatrakoln, K.; Valentin, K.; Vardi, A.; Wilkerson, F. P.; Rokhsar, D. S.

    2004-01-01

    Roč. 306, č. 5693 (2004), s. 79-86 ISSN 0036-8075 Institutional research plan: CEZ:AV0Z6022909 Keywords : diatom * genome * Thalassiosira Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 31.853, year: 2004

  15. Complete genome sequence of currant latent virus (genus Cheravirus, family Secoviridae)

    Czech Academy of Sciences Publication Activity Database

    Petrzik, Karel; Koloniuk, Igor; Přibylová, Jaroslava; Špak, Josef

    2016-01-01

    Roč. 161, č. 2 (2016), s. 491-493 ISSN 0304-8608 Institutional support: RVO:60077344 Keywords : Stranded-RNA * complete genome sequence * Currant latent virus Subject RIV: EE - Microbiology, Virology Impact factor: 2.058, year: 2016

  16. Hospital nursing leadership-led interventions increased genomic awareness and educational intent in Magnet settings.

    Science.gov (United States)

    Calzone, Kathleen A; Jenkins, Jean; Culp, Stacey; Badzek, Laurie

    2017-11-13

    The Precision Medicine Initiative will accelerate genomic discoveries that improve health care, necessitating a genomic competent workforce. This study assessed leadership team (administrator/educator) year-long interventions to improve registered nurses' (RNs) capacity to integrate genomics into practice. We examined genomic competency outcomes in 8,150 RNs. Awareness and intention to learn more increased compared with controls. Findings suggest achieving genomic competency requires a longer intervention and support strategies such as infrastructure and policies. Leadership played a role in mobilizing staff, resources, and supporting infrastructure to sustain a large-scale competency effort on an institutional basis. Results demonstrate genomic workforce competency can be attained with leadership support and sufficient time. Our study provides evidence of the critical role health-care leaders play in facilitating genomic integration into health care to improve patient outcomes. Genomics' impact on quality, safety, and cost indicate a leader-initiated national competency effort is achievable and warranted. Published by Elsevier Inc.

  17. Joint resistance measurements of pancake and terminal joints for JT-60SA EF coils

    Energy Technology Data Exchange (ETDEWEB)

    Obana, Tetsuhiro, E-mail: obana.tetsuhiro@LHD.nifs.ac.jp [National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292 (Japan); Takahata, Kazuya; Hamaguchi, Shinji; Mito, Toshiyuki; Imagawa, Shinsaku [National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292 (Japan); Kizu, Kaname; Murakami, Haruyuki; Yoshida, Kiyoshi [Japan Atomic Energy Agency, 801-1 Mukoyama, Naka, Ibaraki 311-0193 (Japan)

    2013-11-15

    Highlights: • To evaluate the joint fabrication technology for the JT-60SA EF coils, joint resistance measurements were conducted with a joint sample. • The joint sample was composed of pancake and terminal joints. • The measurements demonstrated that both joints fulfilled the design requirement. • Considering the measurements, the characteristics of both joints were investigated using an analytical model that represents the joints. -- Abstract: To evaluate the joint fabrication technology for the JT-60SA EF coils, joint resistance measurements were conducted using a sample consisting of pancake and terminal joints. Both joints are shake-hands lap joints composed of cable-in-conduit conductors and a pure copper saddle-shaped spacer. The measurements demonstrated that both joints fulfilled the design requirement. Considering these measurements, the characteristics of both joints were investigated using analytical models that represent the joints. The analyses indicated that the characteristics of the conductors used in the joints affect the characteristics of the joints.

  18. Evidence for Integrity of Parental Genomes in the Diploid Hybridogenetic Water Frog Pelophylax esculentus by Genomic in situ Hybridization

    Czech Academy of Sciences Publication Activity Database

    Zalésna, A.; Choleva, Lukáš; Ogielska, M.; Rábová, Marie; Marec, František; Ráb, Petr

    2011-01-01

    Roč. 134, č. 3 (2011), s. 206-212 ISSN 1424-8581 R&D Projects: GA MŠk LC06073; GA ČR GA523/09/2106 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50070508 Keywords : Amphibia * Chromosomes * Genomic in situ hybridization (GISH) Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.533, year: 2011

  19. Revisiting the classification of curtoviruses based on genome-wide pairwise identity

    KAUST Repository

    Varsani, Arvind; Martin, Darren Patrick; Navas-Castillo, Jesú s; Moriones, Enrique; Herná ndez-Zepeda, Cecilia; Idris, Ali; Murilo Zerbini, F.; Brown, Judith K.

    2014-01-01

    Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV). © 2014 Springer-Verlag Wien.

  20. Revisiting the classification of curtoviruses based on genome-wide pairwise identity

    KAUST Repository

    Varsani, Arvind

    2014-01-25

    Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV). © 2014 Springer-Verlag Wien.

  1. Joint Identification of Genetic Variants for Physical Activity in Korean Population

    Directory of Open Access Journals (Sweden)

    Jayoun Kim

    2014-07-01

    Full Text Available There has been limited research on genome-wide association with physical activity (PA. This study ascertained genetic associations between PA and 344,893 single nucleotide polymorphism (SNP markers in 8842 Korean samples. PA data were obtained from a validated questionnaire that included information on PA intensity and duration. Metabolic equivalent of tasks were calculated to estimate the total daily PA level for each individual. In addition to single- and multiple-SNP association tests, a pathway enrichment analysis was performed to identify the biological significance of SNP markers. Although no significant SNP was found at genome-wide significance level via single-SNP association tests, 59 genetic variants mapped to 76 genes were identified via a multiple SNP approach using a bootstrap selection stability measure. Pathway analysis for these 59 variants showed that maturity onset diabetes of the young (MODY was enriched. Joint identification of SNPs could enable the identification of multiple SNPs with good predictive power for PA and a pathway enriched for PA.

  2. Prosthetic joint infection, dental treatment and antibiotic prophylaxis

    Directory of Open Access Journals (Sweden)

    Marthinus J. Kotzé

    2009-06-01

    Full Text Available Current international and national prophylactic antibiotic regimens have been analyzed in respect of the prevention of bacteremia after dental and surgical procedures and, therefore, of joint prosthesis infection. This information was used to formulate guidelines for the Department of Maxillofacial and Oral Surgery. Publications since 2003 were used in this research. In addition, recommendations of accredited institutions and associations were examined. These included the guidelines of the American Dental Association in association with the American Academy of Orthopaedic Surgeons (2003, the American Heart Association (2007, the Working Party of the British Society for Antimicrobial Chemotherapy (2006 and the Australian Dental Guidelines (2005. No guidelines published by any institution in South Africa were found. The general rationale for the use of antibiotic prophylaxis for surgical (including dental interventions is that those procedures may result in a bacteremia that may cause infection in joint prostheses. Antibiotics, however, should therefore be administered to susceptible patients, e.g. immunocompromised patients, prior to the development of bacteremia. The guidelines recommended for use in South Africa are based solely on those used outside South Africa. South Africa is regarded as a developing country with its own population and demographic characteristics. Eleven percent of our population is infected with HIV, and a specific guideline for prophylactic antibiotic treatment is, therefore, essential.

  3. Joint instability and osteoarthritis.

    Science.gov (United States)

    Blalock, Darryl; Miller, Andrew; Tilley, Michael; Wang, Jinxi

    2015-01-01

    Joint instability creates a clinical and economic burden in the health care system. Injuries and disorders that directly damage the joint structure or lead to joint instability are highly associated with osteoarthritis (OA). Thus, understanding the physiology of joint stability and the mechanisms of joint instability-induced OA is of clinical significance. The first section of this review discusses the structure and function of major joint tissues, including periarticular muscles, which play a significant role in joint stability. Because the knee, ankle, and shoulder joints demonstrate a high incidence of ligament injury and joint instability, the second section summarizes the mechanisms of ligament injury-associated joint instability of these joints. The final section highlights the recent advances in the understanding of the mechanical and biological mechanisms of joint instability-induced OA. These advances may lead to new opportunities for clinical intervention in the prevention and early treatment of OA.

  4. A revised timescale for human evolution based on ancient mitochondrial genomes

    Czech Academy of Sciences Publication Activity Database

    Fu, Q.; Mittnik, A.; Johnson, P. L. F.; Bos, K.; Lari, M.; Bollongino, R.; Sun, Ch.; Giemsch, L.; Schmitz, R.; Burger, J.; Ronchitelli, A. M.; Martini, F.; Cremonesi, R. G.; Svoboda, Jiří; Bauer, P.; Caramelli, D.; Castellano, S.; Reich, D.; Pääbo, S.; Krause, J.

    2013-01-01

    Roč. 23, April 8 (2013), s. 553-559 ISSN 0960-9822 Institutional support: RVO:68081758 Keywords : mitochondrial genome * human evolution * calibration Subject RIV: AC - Archeology, Anthropology, Ethnology OBOR OECD: Archaeology Impact factor: 9.916, year: 2013

  5. A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia.

    LENUS (Irish Health Repository)

    Jia, Peilin

    2012-02-01

    After the recent successes of genome-wide association studies (GWAS), one key challenge is to identify genetic variants that might have a significant joint effect on complex diseases but have failed to be identified individually due to weak to moderate marginal effect. One popular and effective approach is gene set based analysis, which investigates the joint effect of multiple functionally related genes (eg, pathways). However, a typical gene set analysis method is biased towards long genes, a problem that is especially severe in psychiatric diseases.

  6. Informal Institutional Responses to Government Interventions: Lessons from Madhupur National Park, Bangladesh

    Science.gov (United States)

    Rahman, H. M. Tuihedur; Sarker, Swapan Kumar; Hickey, Gordon M.; Mohasinul Haque, M.; Das, Niamjit

    2014-11-01

    Madhupur National Park is renowned for severe resource ownership conflicts between ethnic communities and government authorities in Bangladesh. In this study, we applied the Institutional Analysis and Development framework to identify: (i) past and present informal institutional structures within the ethnic Garo community for land resource management; (ii) the origin of the land ownership dispute; (iii) interaction mechanisms between formal and informal institutions; and (iv) change in land management authority and informal governance structures. We identify that the informal institutions of the traditional community have undergone radical change due to government interventions with implications for the regulation of land use, informal institutional functions, and joint-decision-making. Importantly, the government's persistent denial of the role of existing informal institutions is widening the gap between government and community actors, and driving land ownership conflicts in a cyclic way with associated natural resource degradation.

  7. Research Institute for Technical Careers

    Science.gov (United States)

    Glenn, Ronald L.

    1996-01-01

    The NASA research grant to Wilberforce University enabled us to establish the Research Institute for Technical Careers (RITC) in order to improve the teaching of science and engineering at Wilberforce. The major components of the research grant are infrastructure development, establishment of the Wilberforce Intensive Summer Experience (WISE), and Joint Research Collaborations with NASA Scientists. (A) Infrastructure Development. The NASA grant has enabled us to improve the standard of our chemistry laboratory and establish the electronics, design, and robotics laboratories. These laboratories have significantly improved the level of instruction at Wilberforce University. (B) Wilberforce Intensive Summer Experience (WISE). The WISE program is a science and engineering bridge program for prefreshman students. It is an intensive academic experience designed to strengthen students' knowledge in mathematics, science, engineering, computing skills, and writing. (C) Joint Collaboration. Another feature of the grant is research collaborations between NASA Scientists and Wilberforce University Scientists. These collaborations have enabled our faculty and students to conduct research at NASA Lewis during the summer and publish research findings in various journals and scientific proceedings.

  8. Joint Instability and Osteoarthritis

    Directory of Open Access Journals (Sweden)

    Darryl Blalock

    2015-01-01

    Full Text Available Joint instability creates a clinical and economic burden in the health care system. Injuries and disorders that directly damage the joint structure or lead to joint instability are highly associated with osteoarthritis (OA. Thus, understanding the physiology of joint stability and the mechanisms of joint instability-induced OA is of clinical significance. The first section of this review discusses the structure and function of major joint tissues, including periarticular muscles, which play a significant role in joint stability. Because the knee, ankle, and shoulder joints demonstrate a high incidence of ligament injury and joint instability, the second section summarizes the mechanisms of ligament injury-associated joint instability of these joints. The final section highlights the recent advances in the understanding of the mechanical and biological mechanisms of joint instability-induced OA. These advances may lead to new opportunities for clinical intervention in the prevention and early treatment of OA.

  9. International joint ventures

    DEFF Research Database (Denmark)

    Sørensen, Karsten Engsig

    2001-01-01

    The article analysis problems connected with corporate joint ventures. Among others the possible conflicts between the joint venture agreement and the statutes of the companies is examined, as well as certain problems connected to the fact that the joint venture partners have created commen control...... over their joint company....

  10. Stability of Genome Composition and Recombination between Homoeologous Chromosomes in Festulolium (Festuca × Lolium) Cultivars

    Czech Academy of Sciences Publication Activity Database

    Kopecký, David; Šimoníková, Denisa; Ghesquière, M.; Doležel, Jaroslav

    2017-01-01

    Roč. 151, č. 2 (2017), s. 106-114 ISSN 1424-8581 R&D Projects: GA MŠk(CZ) LO1204 Institutional support: RVO:61389030 Keywords : Festulolium * Genome composition * Genomic in situ hybridization * Grass hybrids * Homoeologous recombination * Lolium × Festuca Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany Impact factor: 1.354, year: 2016

  11. FAA/NASA Joint University Program for Air Transportation Research, 1992-1993

    Science.gov (United States)

    Morrell, Frederick R. (Compiler)

    1994-01-01

    The research conducted during the academic year 1992-1993 under the FAA/NASA sponsored Joint University Program for Air Transportation Research is summarized. The year end review was held at Ohio University, Athens, Ohio, 17-18 June 1993. The Joint University Program is a coordinated set of three grants sponsored by the Federal Aviation Administration and NASA Langley Research Center, one each with the Massachusetts Institute of Technology, Ohio University, and Princeton University. Completed works, status reports, and annotated bibliographies are presented for research topics, which include navigation, guidance, and control theory and practice, aircraft performance, human factors and air traffic management. An overview of the year's activities for each university is also presented.

  12. Differences between the genomes of lymphoblastoid cell lines and blood-derived samples

    Directory of Open Access Journals (Sweden)

    Joesch-Cohen LM

    2017-02-01

    Full Text Available Lena M Joesch-Cohen, Gustavo Glusman Institute for Systems Biology, Seattle, WA, USA Abstract: Lymphoblastoid cell lines (LCLs represent a convenient research tool for expanding the amount of biologic material available from an individual. LCLs are commonly used as reference materials, most notably from the Genome in a Bottle Consortium. However, the question remains how faithfully LCL-derived genome assemblies represent the germline genome of the donor individual as compared to the genome assemblies derived from peripheral blood mononuclear cells. We present an in-depth comparison of a large collection of LCL- and peripheral blood mononuclear cell-derived genomes in terms of distributions of coverage and copy number alterations. We found significant differences in the depth of coverage and copy number calls, which may be driven by differential replication timing. Importantly, these copy number changes preferentially affect regions closer to genes and with higher GC content. This suggests that genomic studies based on LCLs may display locus-specific biases, and that conclusions based on analysis of depth of coverage and copy number variation may require further scrutiny. Keywords: genomics, whole-genome sequencing, viral transformation, copy number changes, bioinformatics

  13. Two New Loci for Body-Weight Regulation Identified in a Joint Analysis of Genome-Wide Association Studies for Early-Onset Extreme Obesity in French and German Study Groups

    Science.gov (United States)

    Scherag, André; Dina, Christian; Hinney, Anke; Vatin, Vincent; Scherag, Susann; Vogel, Carla I. G.; Müller, Timo D.; Grallert, Harald; Wichmann, H.-Erich; Balkau, Beverley; Heude, Barbara; Jarvelin, Marjo-Riitta; Hartikainen, Anna-Liisa; Levy-Marchal, Claire; Weill, Jacques; Delplanque, Jérôme; Körner, Antje; Kiess, Wieland; Kovacs, Peter; Rayner, Nigel W.; Prokopenko, Inga; McCarthy, Mark I.; Schäfer, Helmut; Jarick, Ivonne; Boeing, Heiner; Fisher, Eva; Reinehr, Thomas; Heinrich, Joachim; Rzehak, Peter; Berdel, Dietrich; Borte, Michael; Biebermann, Heike; Krude, Heiko; Rosskopf, Dieter; Rimmbach, Christian; Rief, Winfried; Fromme, Tobias; Klingenspor, Martin; Schürmann, Annette; Schulz, Nadja; Nöthen, Markus M.; Mühleisen, Thomas W.; Erbel, Raimund; Jöckel, Karl-Heinz; Moebus, Susanne; Boes, Tanja; Illig, Thomas; Froguel, Philippe; Hebebrand, Johannes; Meyre, David

    2010-01-01

    Meta-analyses of population-based genome-wide association studies (GWAS) in adults have recently led to the detection of new genetic loci for obesity. Here we aimed to discover additional obesity loci in extremely obese children and adolescents. We also investigated if these results generalize by estimating the effects of these obesity loci in adults and in population-based samples including both children and adults. We jointly analysed two GWAS of 2,258 individuals and followed-up the best, according to lowest p-values, 44 single nucleotide polymorphisms (SNP) from 21 genomic regions in 3,141 individuals. After this DISCOVERY step, we explored if the findings derived from the extremely obese children and adolescents (10 SNPs from 5 genomic regions) generalized to (i) the population level and (ii) to adults by genotyping another 31,182 individuals (GENERALIZATION step). Apart from previously identified FTO, MC4R, and TMEM18, we detected two new loci for obesity: one in SDCCAG8 (serologically defined colon cancer antigen 8 gene; p = 1.85×10−8 in the DISCOVERY step) and one between TNKS (tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase gene) and MSRA (methionine sulfoxide reductase A gene; p = 4.84×10−7), the latter finding being limited to children and adolescents as demonstrated in the GENERALIZATION step. The odds ratios for early-onset obesity were estimated at ∼1.10 per risk allele for both loci. Interestingly, the TNKS/MSRA locus has recently been found to be associated with adult waist circumference. In summary, we have completed a meta-analysis of two GWAS which both focus on extremely obese children and adolescents and replicated our findings in a large followed-up data set. We observed that genetic variants in or near FTO, MC4R, TMEM18, SDCCAG8, and TNKS/MSRA were robustly associated with early-onset obesity. We conclude that the currently known major common variants related to obesity overlap to a substantial degree between

  14. Two new Loci for body-weight regulation identified in a joint analysis of genome-wide association studies for early-onset extreme obesity in French and german study groups.

    Directory of Open Access Journals (Sweden)

    André Scherag

    2010-04-01

    Full Text Available Meta-analyses of population-based genome-wide association studies (GWAS in adults have recently led to the detection of new genetic loci for obesity. Here we aimed to discover additional obesity loci in extremely obese children and adolescents. We also investigated if these results generalize by estimating the effects of these obesity loci in adults and in population-based samples including both children and adults. We jointly analysed two GWAS of 2,258 individuals and followed-up the best, according to lowest p-values, 44 single nucleotide polymorphisms (SNP from 21 genomic regions in 3,141 individuals. After this DISCOVERY step, we explored if the findings derived from the extremely obese children and adolescents (10 SNPs from 5 genomic regions generalized to (i the population level and (ii to adults by genotyping another 31,182 individuals (GENERALIZATION step. Apart from previously identified FTO, MC4R, and TMEM18, we detected two new loci for obesity: one in SDCCAG8 (serologically defined colon cancer antigen 8 gene; p = 1.85x10(-8 in the DISCOVERY step and one between TNKS (tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase gene and MSRA (methionine sulfoxide reductase A gene; p = 4.84x10(-7, the latter finding being limited to children and adolescents as demonstrated in the GENERALIZATION step. The odds ratios for early-onset obesity were estimated at approximately 1.10 per risk allele for both loci. Interestingly, the TNKS/MSRA locus has recently been found to be associated with adult waist circumference. In summary, we have completed a meta-analysis of two GWAS which both focus on extremely obese children and adolescents and replicated our findings in a large followed-up data set. We observed that genetic variants in or near FTO, MC4R, TMEM18, SDCCAG8, and TNKS/MSRA were robustly associated with early-onset obesity. We conclude that the currently known major common variants related to obesity overlap to a substantial

  15. Tumor Genomic Profiling in Breast Cancer Patients Using Targeted Massively Parallel Sequencing

    Science.gov (United States)

    2016-03-01

    2015 “Cancer Care as a Model for Precision Medicine” MIT Collaborative Series Massachusetts Institute of Technology Invited Talk 2016 “Cancer...Precision Medicine” MIT -CHIEF Series Massachusetts Institute of Technology Invited Talk National 2013 “CanSeq: The Use of Whole Exome Sequencing To...Pennsylvania Philadelphia, PA Invited Talk 2014 “Clinical Genomics and Precision Cancer Medicine” Center for Molecular Oncology Memorial Sloan

  16. New developments of RNAi in Paracoccidioides brasiliensis: prospects for high-throughput, genome-wide, functional genomics.

    Directory of Open Access Journals (Sweden)

    Tercio Goes

    2014-10-01

    Full Text Available The Fungal Genome Initiative of the Broad Institute, in partnership with the Paracoccidioides research community, has recently sequenced the genome of representative isolates of this human-pathogen dimorphic fungus: Pb18 (S1, Pb03 (PS2 and Pb01. The accomplishment of future high-throughput, genome-wide, functional genomics will rely upon appropriate molecular tools and straightforward techniques to streamline the generation of stable loss-of-function phenotypes. In the past decades, RNAi has emerged as the most robust genetic technique to modulate or to suppress gene expression in diverse eukaryotes, including fungi. These molecular tools and techniques, adapted for RNAi, were up until now unavailable for P. brasiliensis.In this paper, we report Agrobacterium tumefaciens mediated transformation of yeast cells for high-throughput applications with which higher transformation frequencies of 150±24 yeast cell transformants per 1×106 viable yeast cells were obtained. Our approach is based on a bifunctional selective marker fusion protein consisted of the Streptoalloteichus hindustanus bleomycin-resistance gene (Shble and the intrinsically fluorescent monomeric protein mCherry which was codon-optimized for heterologous expression in P. brasiliensis. We also report successful GP43 gene knock-down through the expression of intron-containing hairpin RNA (ihpRNA from a Gateway-adapted cassette (cALf which was purpose-built for gene silencing in a high-throughput manner. Gp43 transcript levels were reduced by 73.1±22.9% with this approach.We have a firm conviction that the genetic transformation technique and the molecular tools herein described will have a relevant contribution in future Paracoccidioides spp. functional genomics research.

  17. Joint Chiefs of Staff > About > The Joint Staff > Senior Enlisted Advisor

    Science.gov (United States)

    Skip to main content (Press Enter). Toggle navigation Joint Chiefs of Staff Joint Chiefs of Staff Joint Chiefs of Staff Facebook Twitter YouTube Flickr Blog Instagram Search JCS: Search Search Search JCS: Search Home Media News Photos Videos Publications About The Joint Staff Chairman Vice Chairman

  18. A joint-constraint model for human joints using signed distance-fields

    DEFF Research Database (Denmark)

    Engell-Nørregård, Morten Pol; Abel, Sarah Maria Niebe; Erleben, Kenny

    2012-01-01

    We present a local joint-constraint model for a single joint which is based on distance fields. Our model is fast, general, and well suited for modeling human joints. In this work, we take a geometric approach and model the geometry of the boundary of the feasible region, i.e., the boundary of all...... allowed poses. A region of feasible poses can be built by embedding motion captured data points in a signed distance field. The only assumption is that the feasible poses form a single connected set of angular values. We show how signed distance fields can be used to generate fast and general joint......-joint dependencies, or joints with more than three degrees of freedom. The resolution of the joint-constraints can be tweaked individually for each degree of freedom, which can be used to optimize memory usage. We perform a comparative study of the key-properties of various joint-constraint models, as well...

  19. Guidelines for the Institutional Implementation of Developmental Neuroprotective Care in the NICU. Part B: Recommendations and Justification. A Joint Position Statement From the CANN, CAPWHN, NANN, and COINN.

    Science.gov (United States)

    Milette, Isabelle; Martel, Marie-Josée; da Silva, Margarida Ribeiro; Coughlin McNeil, Mary

    2017-06-01

    The use of age-appropriate care as an organized framework for care delivery in the NICU is founded on the work of Heidelise Als, PhD, and her synactive theory of development. This theoretical construct has recently been advanced by the work of Gibbins and colleagues with the "universe of developmental care" conceptual model and developmental care core measures which were endorsed by the National Association of Neonatal Nurses in their age-appropriate care of premature infant guidelines as best-practice standards for the provision of high-quality care in the NICU. These guidelines were recently revised and expanded. In alignment with the Joint Commission's requirement for healthcare professionals to provide age-specific care across the lifespan, the core measures for developmental care suggest the necessary competencies for those caring for the premature and critically ill hospitalized infant. Further supported by the Primer Standards of Accreditation and Health Canada, the institutional implementation of these core measures require a strong framework for institutional operationalization presented in these guidelines. Part B will present the recommendations and justification of each steps behind the present guidelines to facilitate their implementation.

  20. Estimation of Joint types and Joint Limits from Motion capture data

    DEFF Research Database (Denmark)

    Engell-Nørregård, Morten Pol; Erleben, Kenny

    2009-01-01

    It is time-consuming for an animator to explicitly model joint types and joint limits of articulated figures. In this paper we describe a simple and fast approach to automated joint estimation from motion capture data of articulated figures. Our method will make the joint modeling more efficient ...

  1. Seeds as emerging hotspot for maintenance of genome stability

    Czech Academy of Sciences Publication Activity Database

    Diaz, Mariana; Pečinka, Aleš

    2017-01-01

    Roč. 82, č. 5 (2017), s. 467-470 ISSN 0011-4545 Institutional support: RVO:61389030 Keywords : Chromatin * Chromosome * DNA damage repair * Genome stability * Seed * Structural maintenance of chromosome Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 0.913, year: 2016

  2. Low Level Laser Therapy for chronic knee joint pain patients.

    Science.gov (United States)

    Nakamura, Takashi; Ebihara, Satoru; Ohkuni, Ikuko; Izukura, Hideaki; Harada, Takashi; Ushigome, Nobuyuki; Ohshiro, Toshio; Musha, Yoshiro; Takahashi, Hiroshi; Tsuchiya, Kazuaki; Kubota, Ayako

    2014-12-27

    Chronic knee joint pain is one of the most frequent complaints which is seen in the outpatient clinic in our medical institute. In previous studies we have reported the benefits of low level laser therapy (LLLT) for chronic pain in the shoulder joints, elbow, hand, finger and the lower back. The present study is a report on the effects of LLLT for chronic knee joint pain. Over the past 5 years, 35 subjects visited the outpatient clinic with complaints of chronic knee joint pain caused by the knee osteoarthritis-induced degenerative meniscal tear. They received low level laser therapy. A 1000 mW semi-conductor laser device was used to deliver 20.1 J/cm(2) per point in continuous wave at 830nm, and four points were irradiated per session (1 treatment) twice a week for 4 weeks. A visual analogue scale (VAS) was used to determine the effects of LLLT for the chronic pain and after the end of the treatment regimen a significant improvement was observed (pknee joint range of motion. Discussions with the patients revealed that it was important for them to learn how to avoid postures that would cause them knee pain in everyday life in order to have continuous benefits from the treatment. The present study demonstrated that 830 nm LLLT was an effective form of treatment for chronic knee pain caused by knee osteoarthritis. Patients were advised to undertake training involving gentle flexion and extension of the knee.

  3. ROLE OF FINANCIAL INSTITUTIONS IN THE PUBLIC-PRIVATE PARTNERSHIPS DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    Ion POTLOG

    2015-12-01

    Full Text Available Public-Private Partnership represents institutional and organizational alliance of the state and business, consisting of financial actors interaction, legal, social and policy oriented joint public and private resources from different sources into a single complex to solve strategic socio-economic problems of country. The aim of the research is to demonstrate the importance of financial institutions in publicprivate partnership projects implementation. Research methodology – in order to achieve the expected results, author applied recognized methods and techniques applied as economic investigations: comparative method, statistical method, logical analysis method. The research results, expressed by knowledge through mentioned field can be applied to improve the process of attracting local and international financial institutions to ensure success in public-private partnerships projects in Republic of Moldova.

  4. Haplotype assembly in polyploid genomes and identical by descent shared tracts.

    Science.gov (United States)

    Aguiar, Derek; Istrail, Sorin

    2013-07-01

    Genome-wide haplotype reconstruction from sequence data, or haplotype assembly, is at the center of major challenges in molecular biology and life sciences. For complex eukaryotic organisms like humans, the genome is vast and the population samples are growing so rapidly that algorithms processing high-throughput sequencing data must scale favorably in terms of both accuracy and computational efficiency. Furthermore, current models and methodologies for haplotype assembly (i) do not consider individuals sharing haplotypes jointly, which reduces the size and accuracy of assembled haplotypes, and (ii) are unable to model genomes having more than two sets of homologous chromosomes (polyploidy). Polyploid organisms are increasingly becoming the target of many research groups interested in the genomics of disease, phylogenetics, botany and evolution but there is an absence of theory and methods for polyploid haplotype reconstruction. In this work, we present a number of results, extensions and generalizations of compass graphs and our HapCompass framework. We prove the theoretical complexity of two haplotype assembly optimizations, thereby motivating the use of heuristics. Furthermore, we present graph theory-based algorithms for the problem of haplotype assembly using our previously developed HapCompass framework for (i) novel implementations of haplotype assembly optimizations (minimum error correction), (ii) assembly of a pair of individuals sharing a haplotype tract identical by descent and (iii) assembly of polyploid genomes. We evaluate our methods on 1000 Genomes Project, Pacific Biosciences and simulated sequence data. HapCompass is available for download at http://www.brown.edu/Research/Istrail_Lab/. Supplementary data are available at Bioinformatics online.

  5. Factors influencing success of clinical genome sequencing across a broad spectrum of disorders

    OpenAIRE

    Taylor, Jenny C; Martin, Hilary C; Lise, Stefano; Broxholme, John; Cazier, Jean-Baptiste; Rimmer, Andy; Kanapin, Alexander; Lunter, Gerton; Fiddy, Simon; Allan, Chris; Aricescu, A. Radu; Attar, Moustafa; Babbs, Christian; Becq, Jennifer; Beeson, David

    2015-01-01

    To assess factors influencing the success of whole genome sequencing for mainstream clinical diagnosis, we sequenced 217 individuals from 156 independent cases across a broad spectrum of disorders in whom prior screening had identified no pathogenic variants. We quantified the number of candidate variants identified using different strategies for variant calling, filtering, annotation and prioritisation. We found that jointly calling variants across samples, filtering against both local and e...

  6. Embracing the Future: Embedding Digital Repositories in Higher Education Institutions. Research Brief

    Science.gov (United States)

    Hoorens, Stijn; van Dijk, Lidia Villalba; van Stolk, Christian

    2009-01-01

    This briefing paper captures the key findings and recommendations of a study commissioned by the Joint Information Systems Committee on aspects of the strategic commitment of institutions to repository sustainability. This project, labelled EMBRACE (EMBedding Repositories And Consortial Enhancement), is aimed at enhancing the functionality,…

  7. Organization and Evolution of Subtelomeric Satellite Repeats in the Potato Genome

    Czech Academy of Sciences Publication Activity Database

    Torres, A.T.; Gong, Z.; Iovene, M.; Hirsch, C.D.; Buell, C.R.; Bryan, G.J.; Novák, Petr; Macas, Jiří; Jiang, J.

    2011-01-01

    Roč. 1, July 2011 (2011), s. 85-92 ISSN 2160-1836 R&D Projects: GA MŠk(CZ) LH11058 Institutional research plan: CEZ:AV0Z50510513 Keywords : Satellite sequences * Potato genome * Repeats Subject RIV: EB - Genetics ; Molecular Biology

  8. Ensembl Genomes 2016: more genomes, more complexity.

    Science.gov (United States)

    Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

    2016-01-04

    Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. The central gamma spectrometry laboratory of the GSF Institute of Radiation Protection

    International Nuclear Information System (INIS)

    Ruckerbauer, F.; Dietl, F.; Winkler, R.

    1997-01-01

    Since the middle of 1995 the WG Radioecology is operating the central gamma spectrometry laboratory of the GSF-Institute of Radiation Protection. The main scope of the laboratory is the gamma spectrometric analysis of samples within the research program of the institute and within joint programs with other institutes of the GSF research center. In the present report set-up and technical data of the measuring equipment, the central operating and data evaluation system and measures for quality assurance are described. At that time 18 semiconductor detectors are available for gamma spectrometric sample analysis which is standardized with respect to operation, evaluation algorithms, nuclide data, data safety and documentation. (orig.) [de

  10. Cubozoan genome illuminates functional diversification of opsins and photoreceptor evolution

    Czech Academy of Sciences Publication Activity Database

    Liegertová, Michaela; Pergner, Jiří; Kozmiková, Iryna; Fabian, Peter; Pombinho, António R.; Strnad, Hynek; Pačes, Jan; Vlček, Čestmír; Bartůněk, Petr; Kozmik, Zbyněk

    2015-01-01

    Roč. 5, Jul 8 (2015) ISSN 2045-2322 R&D Projects: GA ČR GAP305/10/2141; GA MŠk LO1220 Institutional support: RVO:68378050 Keywords : Cubozoan genome * opsins * photoreceptor * evolution Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.228, year: 2015

  11. Global Implementation of Genomic Medicine: We Are Not Alone

    Science.gov (United States)

    Manolio, Teri A.; Abramowicz, Marc; Al-Mulla, Fahd; Anderson, Warwick; Balling, Rudi; Berger, Adam C.; Bleyl, Steven; Chakravarti, Aravinda; Chantratita, Wasun; Chisholm, Rex L.; Dissanayake, Vajira H. W.; Dunn, Michael; Dzau, Victor J.; Han, Bok-Ghee; Hubbard, Tim; Kolbe, Anne; Korf, Bruce; Kubo, Michiaki; Lasko, Paul; Leego, Erkki; Mahasirimongkol, Surakameth; Majumdar, Partha P.; Matthijs, Gert; McLeod, Howard L.; Metspalu, Andres; Meulien, Pierre; Miyano, Satoru; Naparstek, Yaakov; O’Rourke, P. Pearl; Patrinos, George P.; Rehm, Heidi L.; Relling, Mary V.; Rennert, Gad; Rodriguez, Laura Lyman; Roden, Dan M.; Shuldiner, Alan R.; Sinha, Sukdev; Tan, Patrick; Ulfendahl, Mats; Ward, Robyn; Williams, Marc S.; Wong, John E.L.; Green, Eric D.; Ginsburg, Geoffrey S.

    2016-01-01

    Advances in high-throughput genomic technologies coupled with a growing number of genomic results potentially useful in clinical care have led to ground-breaking genomic medicine implementation programs in various nations. Many of these innovative programs capitalize on unique local capabilities arising from the structure of their health care systems or their cultural or political milieu, as well as from unusual burdens of disease or risk alleles. Many such programs are being conducted in relative isolation and might benefit from sharing of approaches and lessons learned in other nations. The National Human Genome Research Institute recently brought together 25 of these groups from around the world to describe and compare projects, examine the current state of implementation and desired near-term capabilities, and identify opportunities for collaboration to promote the responsible implementation of genomic medicine. The wide variety of nascent programs in diverse settings demonstrates that implementation of genomic medicine is expanding globally in varied and highly innovative ways. Opportunities for collaboration abound in the areas of evidence generation, health information technology, education, workforce development, pharmacogenomics, and policy and regulatory issues. Several international organizations that are already facilitating effective research collaborations should engage to ensure implementation proceeds collaboratively without potentially wasteful duplication. Efforts to coalesce these groups around concrete but compelling signature projects, such as global eradication of genetically-mediated drug reactions or developing a truly global genomic variant data resource across a wide number of ethnicities, would accelerate appropriate implementation of genomics to improve clinical care world-wide. PMID:26041702

  12. Iron and genome stability: An update

    International Nuclear Information System (INIS)

    Prá, Daniel; Franke, Silvia Isabel Rech; Henriques, João Antonio Pêgas; Fenech, Michael

    2012-01-01

    Iron is an essential micronutrient which is required in a relatively narrow range for maintaining metabolic homeostasis and genome stability. Iron participates in oxygen transport and mitochondrial respiration as well as in antioxidant and nucleic acid metabolism. Iron deficiency impairs these biological pathways, leading to oxidative stress and possibly carcinogenesis. Iron overload has been linked to genome instability as well as to cancer risk increase, as seen in hereditary hemochromatosis. Iron is an extremely reactive transition metal that can interact with hydrogen peroxide to generate hydroxyl radicals that form the 8-hydroxy-guanine adduct, cause point mutations as well as DNA single and double strand breaks. Iron overload also induces DNA hypermethylation and can reduce telomere length. The current Recommended Dietary Allowances (RDA) for iron, according with Institute of Medicine Dietary Reference Intake (DRI), is based in the concept of preventing anemia, and ranges from 7 mg/day to 18 mg/day depending on life stage and gender. Pregnant women need 27 mg/day. The maximum safety level for iron intake, the Upper Level (UL), is 40–45 mg/day, based on the prevention of gastrointestinal distress associated to high iron intakes. Preliminary evidence indicates that 20 mg/day iron, an intake slightly higher than the RDA, may reduce the risk of gastrointestinal cancer in the elderly as well as increasing genome stability in lymphocytes of children and adolescents. Current dietary recommendations do not consider the concept of genome stability which is of concern because damage to the genome has been linked to the origin and progression of many diseases and is the most fundamental pathology. Given the importance of iron for homeostasis and its potential influence over genome stability and cancer it is recommended to conduct further studies that conclusively define these relationships.

  13. Iron and genome stability: An update

    Energy Technology Data Exchange (ETDEWEB)

    Pra, Daniel, E-mail: daniel_pra@yahoo.com [PPG em Promocao da Saude, Universidade de Santa Cruz do Sul (UNISC), Santa Cruz do Sul, RS (Brazil); PPG em Saude e Comportamento, Universidade Catolica de Pelotas, Pelotas, RS (Brazil); Franke, Silvia Isabel Rech [PPG em Promocao da Saude, Universidade de Santa Cruz do Sul (UNISC), Santa Cruz do Sul, RS (Brazil); Henriques, Joao Antonio Pegas [Instituto de Biotecnologia, Universidade de Caxias do Sul, Caxias do Sul, RS (Brazil); Fenech, Michael [CSIRO Food and Nutritional Sciences, Adelaide, SA (Australia)

    2012-05-01

    Iron is an essential micronutrient which is required in a relatively narrow range for maintaining metabolic homeostasis and genome stability. Iron participates in oxygen transport and mitochondrial respiration as well as in antioxidant and nucleic acid metabolism. Iron deficiency impairs these biological pathways, leading to oxidative stress and possibly carcinogenesis. Iron overload has been linked to genome instability as well as to cancer risk increase, as seen in hereditary hemochromatosis. Iron is an extremely reactive transition metal that can interact with hydrogen peroxide to generate hydroxyl radicals that form the 8-hydroxy-guanine adduct, cause point mutations as well as DNA single and double strand breaks. Iron overload also induces DNA hypermethylation and can reduce telomere length. The current Recommended Dietary Allowances (RDA) for iron, according with Institute of Medicine Dietary Reference Intake (DRI), is based in the concept of preventing anemia, and ranges from 7 mg/day to 18 mg/day depending on life stage and gender. Pregnant women need 27 mg/day. The maximum safety level for iron intake, the Upper Level (UL), is 40-45 mg/day, based on the prevention of gastrointestinal distress associated to high iron intakes. Preliminary evidence indicates that 20 mg/day iron, an intake slightly higher than the RDA, may reduce the risk of gastrointestinal cancer in the elderly as well as increasing genome stability in lymphocytes of children and adolescents. Current dietary recommendations do not consider the concept of genome stability which is of concern because damage to the genome has been linked to the origin and progression of many diseases and is the most fundamental pathology. Given the importance of iron for homeostasis and its potential influence over genome stability and cancer it is recommended to conduct further studies that conclusively define these relationships.

  14. Effectiveness of Low-Level Laser Therapy in Temporomandibular Joint Disorders: A Placebo-Controlled Study

    Czech Academy of Sciences Publication Activity Database

    Fikáčková, H.; Dostálová, T.; Navrátil, L.; Klaschka, Jan

    2007-01-01

    Roč. 25, č. 4 (2007), s. 297-303 ISSN 1549-5418 Grant - others:GA MZd(CZ) NR8112 Institutional research plan: CEZ:AV0Z10300504 Keywords : temporomandibular joint disorder * laser therapy Subject RIV: BB - Applied Statistics, Operational Research Impact factor: 1.230, year: 2007

  15. phiGENOME: an integrative navigation throughout bacteriophage genomes.

    Science.gov (United States)

    Stano, Matej; Klucar, Lubos

    2011-11-01

    phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

  16. Reliability of Tubular Joints

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Thoft-Christensen, Palle

    In this paper the preliminary results obtained by tests on tubular joints are presented. The joints are T-joints and the loading is static. It is the intention in continuation of these tests to perform tests on other types of joints (e.g. Y-joints) and also with dynamic loading. The purpose...... of the test is partly to obtain empirical data for the ultimate load-carrying capacity of tubular T-joints and partly to obtain some experience in performing tests with tubular joints. It is well known that tubular joints are usually designed in offshore engineering on the basis of empirical formulas obtained...... by experimental test results. Therefore, there is a need for performing experimental tests in this area....

  17. Joint Quantum Institute |

    Science.gov (United States)

    is eligible for exemplary seniors who have been nominated by their faculty advisors. Fenton earned -light interactions. His thesis work was nominated by the...Continue Reading READ MORE Latest nanowire

  18. On the Application of Joint-Domain Dictionary Mapping for Multiple Power Disturbance Assessment

    Directory of Open Access Journals (Sweden)

    Delong Cai

    2018-02-01

    Full Text Available This paper proposes a joint-domain dictionary mapping method to obtain high assessment accuracy of multiple power disturbances. Firstly, in order to achieve resolutions in both the time and frequency domains, a joint-domain dictionary is proposed which consists of a discrete Hartley base and an identity matrix. Due to the low correlation between the discrete Hartley base and the identity matrix, the joint-domain dictionary mapping can separately capture the approximations of the sinusoidal components and transients. Since the mapping coefficients contain the physical quantities, the eigenvalues of each component can be effectively estimated. A quantified eigenvalue classifier was designed for identifying power disturbances using the estimated eigenvalues. The proposed method was compared with several advanced methods through simulated power disturbances under different noise conditions, and actual data from the Institute of Electrical and Electronics Engineers Power and Energy Society database. The results reveal that the joint-domain dictionary mapping technique shows good performance on parameter estimation and recognition precision, even dealing with complicated multiple power disturbances.

  19. Investigation of an autologous blood treatment strategy for temporomandibular joint hypermobility in a pig model

    Czech Academy of Sciences Publication Activity Database

    Štembírek, Jan; Matalová, Eva; Buchtová, Marcela; Machoň, V.; Míšek, Ivan

    2013-01-01

    Roč. 42, č. 3 (2013), s. 369-375 ISSN 0901-5027 Grant - others:GA MŠk(CZ) 1M0528 Institutional support: RVO:67985904 Keywords : temporomandibular joint * pig * autologous blood * hypermobility Subject RIV: FF - HEENT, Dentistry Impact factor: 1.359, year: 2013

  20. Computational modeling of the probability of destructions in total joint endoprosthesis ceramic heads using Weibull's theory

    Czech Academy of Sciences Publication Activity Database

    Janíček, P.; Fuis, Vladimír; Málek, M.

    2010-01-01

    Roč. 14, č. 4 (2010), s. 42-51 ISSN 1335-2393 Institutional research plan: CEZ:AV0Z20760514 Keywords : computational modeling * ceramic head * in vivo destructions * hip joint endoprosthesis * probabily of rupture Subject RIV: BO - Biophysics

  1. The Virtual Institute for Integrative Biology (VIIB)

    International Nuclear Information System (INIS)

    Rivera, G.; Gonzalez-Nieto, F.; Perez-Acle, T.; Isea, R.; Holmes, D. S.

    2007-01-01

    The Virtual Institute for Integrative Biology (VII B) is a Latin American initiative for achieving global collaborative e-Science in the areas of bioinformatics, genome biology, systems biology, Metagenomic, medical applications and nanobiotechnolgy. The scientific agenda of VIIB includes: construction of databases for comparative genomic, the AlterORF database for alternate open reading frames discovery in genomes, bioinformatics services and protein simulations for biotechnological and medical applications. Human resource development has been promoted through co-sponsored students and shared teaching and seminars via video conferencing. E-Science challenges include: inter operability and connectivity concerns, high performance computing limitations, and the development of customized computational frameworks and flexible work flows to efficiently exploit shared resources without causing impediments to the user. Outreach programs include training workshops and classes for high school teachers and students and the new Adopt-a-Gene initiative. The VIIB has proved an effective way for small teams to transcend the critical mass problem, to overcome geographic limitations, to harness the power of large scale, collaborative science and improve the visibility of Latin American science It may provide a useful paradigm for developing further e-Science initiatives in Latin America and other emerging regions. (Author)

  2. Genomic-Enabled Prediction Based on Molecular Markers and Pedigree Using the Bayesian Linear Regression Package in R

    Directory of Open Access Journals (Sweden)

    Paulino Pérez

    2010-09-01

    Full Text Available The availability of dense molecular markers has made possible the use of genomic selection in plant and animal breeding. However, models for genomic selection pose several computational and statistical challenges and require specialized computer programs, not always available to the end user and not implemented in standard statistical software yet. The R-package BLR (Bayesian Linear Regression implements several statistical procedures (e.g., Bayesian Ridge Regression, Bayesian LASSO in a unified framework that allows including marker genotypes and pedigree data jointly. This article describes the classes of models implemented in the BLR package and illustrates their use through examples. Some challenges faced when applying genomic-enabled selection, such as model choice, evaluation of predictive ability through cross-validation, and choice of hyper-parameters, are also addressed.

  3. 10. international mouse genome conference

    Energy Technology Data Exchange (ETDEWEB)

    Meisler, M.H.

    1996-12-31

    Ten years after hosting the First International Mammalian Genome Conference in Paris in 1986, Dr. Jean-Louis Guenet presided over the Tenth Conference at the Pasteur Institute, October 7--10, 1996. The 1986 conference was a satellite to the Human Gene Mapping Workshop and had approximately 50 attendees. The 1996 meeting was attended by 300 scientists from around the world. In the interim, the number of mapped loci in the mouse increased from 1,000 to over 20,000. This report contains a listing of the program and its participants, and two articles that review the meeting and the role of the laboratory mouse in the Human Genome project. More than 200 papers were presented at the conference covering the following topics: International mouse chromosome committee meetings; Mutant generation and identification; Physical and genetic maps; New technology and resources; Chromatin structure and gene regulation; Rate and hamster genetic maps; Informatics and databases; and Quantitative trait analysis.

  4. An information-theoretic approach to the modeling and analysis of whole-genome bisulfite sequencing data.

    Science.gov (United States)

    Jenkinson, Garrett; Abante, Jordi; Feinberg, Andrew P; Goutsias, John

    2018-03-07

    DNA methylation is a stable form of epigenetic memory used by cells to control gene expression. Whole genome bisulfite sequencing (WGBS) has emerged as a gold-standard experimental technique for studying DNA methylation by producing high resolution genome-wide methylation profiles. Statistical modeling and analysis is employed to computationally extract and quantify information from these profiles in an effort to identify regions of the genome that demonstrate crucial or aberrant epigenetic behavior. However, the performance of most currently available methods for methylation analysis is hampered by their inability to directly account for statistical dependencies between neighboring methylation sites, thus ignoring significant information available in WGBS reads. We present a powerful information-theoretic approach for genome-wide modeling and analysis of WGBS data based on the 1D Ising model of statistical physics. This approach takes into account correlations in methylation by utilizing a joint probability model that encapsulates all information available in WGBS methylation reads and produces accurate results even when applied on single WGBS samples with low coverage. Using the Shannon entropy, our approach provides a rigorous quantification of methylation stochasticity in individual WGBS samples genome-wide. Furthermore, it utilizes the Jensen-Shannon distance to evaluate differences in methylation distributions between a test and a reference sample. Differential performance assessment using simulated and real human lung normal/cancer data demonstrate a clear superiority of our approach over DSS, a recently proposed method for WGBS data analysis. Critically, these results demonstrate that marginal methods become statistically invalid when correlations are present in the data. This contribution demonstrates clear benefits and the necessity of modeling joint probability distributions of methylation using the 1D Ising model of statistical physics and of

  5. Next-Generation Sequencing Reveals the Impact of Repetitive DNA Across Phylogenetically Closely Related Genomes of Orobanchaceae

    Czech Academy of Sciences Publication Activity Database

    Piednoël, M.; Aberer, A.J.; Schneeweiss, G. M.; Macas, Jiří; Novák, Petr; Gundlach, H.; Temsch, E.M.; Renner, S.S.

    2012-01-01

    Roč. 29, č. 11 (2012), s. 3601-3611 ISSN 0737-4038 Institutional research plan: CEZ:AV0Z50510513 Institutional support: RVO:60077344 Keywords : next-generation sequencing * polyploidy * genome size * Ty3/Gypsy * transposable elements Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 10.353, year: 2012

  6. Meeting Report: Minutes from EMBO: Ten Years of Comparative Genomics of Eukaryotic Microorganisms

    Czech Academy of Sciences Publication Activity Database

    Lukeš, Julius; López-García, P.; Louis, E.; Boekhout, T.

    2016-01-01

    Roč. 167, č. 3 (2016), s. 217-221 ISSN 1434-4610 Institutional support: RVO:60077344 Keywords : protist * eukaryotic microorganisms * genomics Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.794, year: 2016

  7. A 5-year profile of the incidence of total joint replacement in South ...

    African Journals Online (AJOL)

    During this period there was a 28% increase in the number of TJRs performed annually with an average increase of 20% in total hip replacements and 40% in total knee replacements. The number of surgeons involved in joint replacement during the survey period decreased by 7% in state-subsidised institutions but ...

  8. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  9. PREFACE: Joint IPPP Durham/Cockcroft Institute/ICFA Workshop on Advanced QED methods for Future Accelerators

    Science.gov (United States)

    Bailey, I. R.; Barber, D. P.; Chattopadhyay, S.; Hartin, A.; Heinzl, T.; Hesselbach, S.; Moortgat-Pick, G. A.

    2009-11-01

    The joint IPPP Durham/Cockcroft Institute/ICFA workshop on advanced QED methods for future accelerators took place at the Cockcroft Institute in early March 2009. The motivation for the workshop was the need for a detailed consideration of the physics processes associated with beam-beam effects at the interaction points of future high-energy electron-positron colliders. There is a broad consensus within the particle physics community that the next international facility for experimental high-energy physics research beyond the Large Hadron Collider at CERN should be a high-luminosity electron-positron collider working at the TeV energy scale. One important feature of such a collider will be its ability to deliver polarised beams to the interaction point and to provide accurate measurements of the polarisation state during physics collisions. The physics collisions take place in very dense charge bunches in the presence of extremely strong electromagnetic fields of field strength of order of the Schwinger critical field strength of 4.4×1013 Gauss. These intense fields lead to depolarisation processes which need to be thoroughly understood in order to reduce uncertainty in the polarisation state at collision. To that end, this workshop reviewed the formalisms for describing radiative processes and the methods of calculation in the future strong-field environments. These calculations are based on the Furry picture of organising the interaction term of the Lagrangian. The means of deriving the transition probability of the most important of the beam-beam processes - Beamsstrahlung - was reviewed. The workshop was honoured by the presentations of one of the founders, V N Baier, of the 'Operator method' - one means for performing these calculations. Other theoretical methods of performing calculations in the Furry picture, namely those due to A I Nikishov, V I Ritus et al, were reviewed and intense field quantum processes in fields of different form - namely those

  10. ReMixT: clone-specific genomic structure estimation in cancer.

    Science.gov (United States)

    McPherson, Andrew W; Roth, Andrew; Ha, Gavin; Chauve, Cedric; Steif, Adi; de Souza, Camila P E; Eirew, Peter; Bouchard-Côté, Alexandre; Aparicio, Sam; Sahinalp, S Cenk; Shah, Sohrab P

    2017-07-27

    Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complicating estimation of clone-specific genotypes. We introduce ReMixT, a method to unmix tumor and contaminating normal signals and jointly predict mixture proportions, clone-specific segment copy number, and clone specificity of breakpoints. ReMixT is free, open-source software and is available at http://bitbucket.org/dranew/remixt .

  11. Long-term reinfection of the human genome by endogenous retroviruses

    Czech Academy of Sciences Publication Activity Database

    Belshaw, R.; Pereira, V.; Katzourakis, A.; Talbot, G.; Pačes, Jan; Burt, A.

    2004-01-01

    Roč. 101, č. 14 (2004), s. 4894-4899 ISSN 0027-8424 R&D Projects: GA MŠk LN00A079 Institutional research plan: CEZ:AV0Z5052915 Keywords : endogenous retroviruses * human genome * HERV Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 10.452, year: 2004

  12. Post-acute care disparities in total joint arthroplasty.

    Science.gov (United States)

    Lan, Roy H; Kamath, Atul F

    2017-09-01

    Understanding the socioeconomic factors that influence hospitalization and post-discharge metrics after joint replacement is important for identifying key areas of improvement in the delivery of orthopaedic care. An institutional administrative data set of 2869 patients from an academic arthroplasty referral center was analyzed to quantify the relationship between socioeconomic factors and post-acute rehabilitation care received, length of stay, and cost of care. The study used International Classification of Disease, ninth edition coding in order to identify cohorts of patients who received joint arthroplasty of the knee and hip between January 2007 and May 2015. The study found that females (odds ratio [OR], 2.07; 95% confidence interval [CI], 1.74-2.46), minorities (OR, 2.11; 95% CI, 1.78-2.51), and non-private insurance holders (OR, 1.56; 95% CI, 1.26-1.94) were more likely to be assigned to institutional care after discharge. The study also found that minorities (OR, 1.45; 95% CI, 1.24-1.70) and non-private insurance holders (OR, 1.43; 95% CI, 1.16-1.77) are more likely to exhibit longer length of stay. Mean charges were higher for males when compared to females ($80,010 vs $74,855; P total costs ($19,910 vs $18,613; P  = .001). Socioeconomic factors such as gender, race, and insurance status should be further explored with respect to healthcare policies seeking to influence quality of care and health outcomes.

  13. Efficient Server-Aided Secure Two-Party Function Evaluation with Applications to Genomic Computation

    Directory of Open Access Journals (Sweden)

    Blanton Marina

    2016-10-01

    Full Text Available Computation based on genomic data is becoming increasingly popular today, be it for medical or other purposes. Non-medical uses of genomic data in a computation often take place in a server-mediated setting where the server offers the ability for joint genomic testing between the users. Undeniably, genomic data is highly sensitive, which in contrast to other biometry types, discloses a plethora of information not only about the data owner, but also about his or her relatives. Thus, there is an urgent need to protect genomic data. This is particularly true when the data is used in computation for what we call recreational non-health-related purposes. Towards this goal, in this work we put forward a framework for server-aided secure two-party computation with the security model motivated by genomic applications. One particular security setting that we treat in this work provides stronger security guarantees with respect to malicious users than the traditional malicious model. In particular, we incorporate certified inputs into secure computation based on garbled circuit evaluation to guarantee that a malicious user is unable to modify her inputs in order to learn unauthorized information about the other user’s data. Our solutions are general in the sense that they can be used to securely evaluate arbitrary functions and offer attractive performance compared to the state of the art. We apply the general constructions to three specific types of genomic tests: paternity, genetic compatibility, and ancestry testing and implement the constructions. The results show that all such private tests can be executed within a matter of seconds or less despite the large size of one’s genomic data.

  14. Institute for transuranium elements Karlsruhe Annual Report 1988

    International Nuclear Information System (INIS)

    1989-01-01

    The present report summarizes the results of the work which has been performed in 1988 at the Institute for Transuranium Elements of the Joint Research Centre of the Commission of the European Communities. While, as in the past, major efforts were devoted to the Programme on Nuclear Fuels and Actinide Research, important contributions were made to other JRC Specific Programmes, i.e. Reactor Safety, Radioactive Waste Management, and Safeguards and Fissile Materials Control. In addition, The Institute has carried out analytical work for the EURATOM Safeguards Directorate and executed research tasks in the safeguards context, both, for the Commission of the European Communities and for the International Atomic Energy Agency in Vienna. Exploratory Research, finally, dealt with an investigation of possibilities of acoustic aerosol scavenging

  15. Institutional arrangements for a multinational reprocessing plant

    International Nuclear Information System (INIS)

    Smith, C.B.; Chayes, A.

    1977-01-01

    The paper lists some of the major issues that would have to be faced in negotiating the institutional structure of a multinational nuclear-fuel center. None of the organization problems is inherently insoluble. Difficulties are exacerbated by the large number of questions, their interrelations, and the complexity of the assumed structure. However, the assumptions posed the most difficult case. A reduction in membership and in the ambitious scope of the enterprise, at least at the outset, would greatly reduce the complexity of the organizational structure and the difficulty of negotiations. The analysis suggests that multinational fuel-cycle activities should start out more modestly, perhaps only with joint appraisal by a relatively few countries with existing geographic or economic connections. If operations are contemplated it would seem that the first step should be joint arrangements for spent-fuel storage, with the decision to go forward to more elaborate activities deferred. This approach would not only be simpler and permit the parties to gain experience working together, but it would have the virtue of delaying reprocessing until it was clear that there was a real need for it. Even on this reduced basis, the negotiating task would not be easy. The key, of course, to overcoming difficult technical problems of institutional structure is politial will--the genuine commitment of the participants to the aims and values of the enterprise. This suggests that any effort to cajole--not to say coerce--participation in a multinational fuel-cycle enterprise would be wholly misplaced. A reluctant partner would have available an infinitude of points and issues to create plausible, irritating, and ultimately defeating delay and complication in the negotiating process. Only assent freely given in the perception that the enterprise really serves the interest of the countries involved will be able to surmount the many institutional problems that will inevitably arise

  16. Parallel computing in genomic research: advances and applications

    Directory of Open Access Journals (Sweden)

    Ocaña K

    2015-11-01

    Full Text Available Kary Ocaña,1 Daniel de Oliveira2 1National Laboratory of Scientific Computing, Petrópolis, Rio de Janeiro, 2Institute of Computing, Fluminense Federal University, Niterói, Brazil Abstract: Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own workstations. Parallelism techniques and high-performance computing (HPC environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data. However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological, and mathematical techniques and technologies. Several solutions have already been proposed to allow scientists for processing their genomic experiments using HPC capabilities and parallelism techniques. This article brings a systematic review of literature that surveys the most recently published research involving genomics and parallel computing. Our objective is to gather the main characteristics, benefits, and challenges that can be considered by scientists when running their genomic experiments to benefit from parallelism techniques and HPC capabilities. Keywords: high-performance computing, genomic research, cloud computing, grid computing, cluster computing, parallel computing

  17. Clinical Presentation, Risk Factors, and Outcomes of Hematogenous Prosthetic Joint Infection in Patients with Staphylococcus aureus Bacteremia.

    Science.gov (United States)

    Tande, Aaron J; Palraj, Bharath Raj; Osmon, Douglas R; Berbari, Elie F; Baddour, Larry M; Lohse, Christine M; Steckelberg, James M; Wilson, Walter R; Sohail, M Rizwan

    2016-02-01

    Staphylococcus aureus bacteremia is a life-threatening condition that may lead to metastatic infection, including prosthetic joint infection. To assess clinical factors associated with hematogenous prosthetic joint infection, we retrospectively reviewed all patients with a joint arthroplasty in place at the time of a first episode of S. aureus bacteremia over a 5-year period at our institution. Patients with postsurgical prosthetic joint infection without hematogenous prosthetic joint infection were excluded. There were 85 patients (143 arthroplasties) with either no prosthetic joint infection (n = 50; 58.8%) or hematogenous prosthetic joint infection in at least one arthroplasty (n = 35; 41.2%). The odds of hematogenous prosthetic joint infection was significantly increased among patients with community-acquired S. aureus bacteremia (odds ratio [OR] 18.07; 95% confidence interval [CI] 2.64-infinity; P = .001), as compared with nosocomial S. aureus bacteremia, in which there were no patients with hematogenous prosthetic joint infection. After adjusting for S. aureus bacteremia classification, the presence of ≥3 joint arthroplasties in place was associated with a nearly ninefold increased odds of hematogenous prosthetic joint infection as compared with those with 1-2 joint arthroplasties in place (OR 8.55; 95% CI 1.44-95.71; P = .012). All but one joint with prosthetic joint infection demonstrated at least one clinical feature suggestive of infection. There were 4 additional S. aureus prosthetic joint infections diagnosed during a median of 3.4 years of follow-up post hospitalization for S. aureus bacteremia. Prosthetic joint infection is frequent in patients with existing arthroplasties and concomitant S. aureus bacteremia, particularly with community-acquired S. aureus bacteremia and multiple prostheses. In contrast, occult S. aureus prosthetic joint infection without clinical features suggestive of prosthetic joint infection at the time of S. aureus bacteremia

  18. Infants' Early Visual Attention and Social Engagement as Developmental Precursors to Joint Attention

    Science.gov (United States)

    Salley, Brenda; Sheinkopf, Stephen J.; Neal-Beevers, A. Rebecca; Tenenbaum, Elena J.; Miller-Loncar, Cynthia L.; Tronick, Ed; Lagasse, Linda L.; Shankaran, Seetha; Bada, Henrietta; Bauer, Charles; Whitaker, Toni; Hammond, Jane; Lester, Barry M.

    2016-01-01

    This study examined infants' early visual attention (at 1 month of age) and social engagement (4 months) as predictors of their later joint attention (12 and 18 months). The sample (n = 325), drawn from the Maternal Lifestyle Study, a longitudinal multicenter project conducted at 4 centers of the National Institute of Child Health and Human…

  19. Comparative effectiveness of open versus minimally invasive sacroiliac joint fusion.

    Science.gov (United States)

    Ledonio, Charles Gt; Polly, David W; Swiontkowski, Marc F; Cummings, John T

    2014-01-01

    The mainstay of sacroiliac joint disruption/degenerative sacroiliitis therapy has been nonoperative management. This nonoperative management often includes a regimen of physical therapy, chiropractic treatment, therapeutic injections, and possibly radiofrequency ablation at the discretion of the treating physician. When these clinical treatments fail, sacroiliac joint fusion has been recommended as the standard treatment. Open and minimally invasive (MIS) surgical techniques are typical procedures. This study aims to compare the perioperative measures and Oswestry Disability Index (ODI) outcomes associated with each of these techniques. A comparative retrospective chart review of patients with sacroiliac joint fusion and a minimum of 1 year of follow-up was performed. Perioperative measures and ODI scores were compared using the Fisher's exact test and two nonparametric tests, ie, the Mann-Whitney U test and the Wilcoxon signed-rank test. The results are presented as percent or median with range, as appropriate. Forty-nine patients from two institutions underwent sacroiliac joint fusion between 2006 and 2012. Ten patients were excluded because of incomplete data, leaving 39 evaluable patients, of whom 22 underwent open and 17 underwent MIS sacroiliac joint fusion. The MIS group was significantly older (median age 66 [39-82] years) than the open group (median age 51 [34-74] years). Surgical time and hospital stay were significantly shorter in the MIS group than in the open group. Preoperative ODI was significantly greater in the open group (median 64 [44-78]) than in the MIS group (median 53 [14-84]). Postoperative improvement in ODI was statistically significant within and between groups, with MIS resulting in greater improvement. The open and MIS sacroiliac joint fusion techniques resulted in statistically and clinically significant improvement for patients with degenerative sacroiliitis refractory to nonoperative management. However, the number of patients

  20. Health care joint ventures between tax-exempt organizations and for-profit entities.

    Science.gov (United States)

    Sanders, Michael I

    2005-01-01

    Health care exempt organizations have many options regarding their structure and affiliations with for-profit entities. As long as any joint ventures are carefully structured and the nonprofit retains control over the exempt health care activities, the Internal Revenue Service should not question the structure. However, as outlined above, if the for-profit entity effectively gains control over the activities of the venture, the structure is not likely to be upheld by the IRS or the courts, and either the exempt status of the nonprofit will be denied or revoked, or health care income will be subject to the unrelated business income tax. In summary, the health care industry has been severely impacted by many economic forces, including uncertainty in the area of joint ventures between nonprofits and for-profit health care systems. The uncertainty as to whether the joint venture would negatively impact the nonprofit's tax-exempt status undoubtedly caused many nonprofits to form for-profit subsidiaries and otherwise expanded operations in a for-profit marketplace. Fortunately, with the guidance that is currently available in the form of Revenue Ruling 98-15, Redlands, St. David's, and now Revenue Ruling 2004-51, health care institutions can move forward with properly structured joint ventures with greater confidence that the joint venture will not endanger the tax-exempt status of the nonprofit.

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