DOE Joint Genome Institute 2008 Progress Report

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

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 imaginedmore » 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 dominated how sequencing was done in the last decade is being replaced by a variety of new processes and sequencing instruments. The JGI, with an increasing number of next-generation sequencers, whose throughput is 100- to 1,000-fold greater than the Sanger capillary-based sequencers, is increasingly focused in new directions on projects of scale and complexity not previously attempted. These new directions for the JGI come, in part, from the 2008 National Research Council report on the goals of the National Plant Genome Initiative as well as the 2007 National Research Council report on the New Science of Metagenomics. Both reports outline a crucial need for systematic large-scale surveys of the plant and microbial components of the biosphere as well as an increasing need for large-scale analysis capabilities to meet the challenge of converting sequence data into knowledge. The JGI is extensively discussed in both reports as vital to progress in these fields of major national interest. JGI's future plan for plants and microbes includes a systematic approach for investigation of these organisms at a scale requiring the special capabilities of the JGI to generate, manage, and analyze the datasets. JGI will generate and provide not only community access to these plant and microbial datasets, but also the tools for analyzing them. These activities will produce essential knowledge that will be needed if we are to be able to respond to the world's energy and environmental challenges. As the JGI Plant and Microbial programs advance, the JGI as a user facility is also evolving. The Institute has been highly successful in bending its technical and analytical skills to help users solve large complex problems of major importance, and that effort will continue unabated. The JGI will increasingly move from a central focus on 'one-off' user projects coming from small user communities to much larger scale projects driven by systematic and problem-focused approaches to selection of sequencing targets. Entire communities of scientists working in a particular field, such as feedstock improvement or biomass degradation, will be users of this information. Despite this new emphasis, an investigator-initiated user program will remain. This program in the future will replace small projects that increasingly can be accomplished without the involvement of JGI, with imaginative large-scale 'Grand Challenge' projects of foundational relevance to energy and the environment that require a new scale of sequencing and analysis capabilities. Close interactions with the DOE Bioenergy Research Centers, and with other DOE institutions that may follow, will also play a major role in shaping aspects of how the JGI operates as a user facility. Based on increased availability of high-throughput sequencing, the JGI will increasingly provide to users, in addition to DNA sequencing, an array of both pre- and post-sequencing value-added capabilities to accelerate their science.« less

Introduction to Metagenomics at DOE JGI (Opening Remarks for the Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Kyrpides, Nikos [DOE JGI

2018-05-30

After a quick introduction by DOE JGI Director Eddy Rubin, DOE JGI's Nikos Kyrpides delivers the opening remarks at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

DOE JGI Quality Metrics; Approaches to Scaling and Improving Metagenome Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

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

Copeland, Alex; Brown, C. Titus

2011-10-13

DOE JGI's Alex Copeland on "DOE JGI Quality Metrics" and Michigan State University's C. Titus Brown on "Approaches to Scaling and Improving Metagenome Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

DOE JGI Quality Metrics; Approaches to Scaling and Improving Metagenome Assembly (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Copeland, Alex; Brown, C. Titus

2018-04-27

DOE JGI's Alex Copeland on "DOE JGI Quality Metrics" and Michigan State University's C. Titus Brown on "Approaches to Scaling and Improving Metagenome Assembly" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Flash Updates of GSC projects (GSC8 Meeting)

ScienceCinema

Glockner, Frank Oliver; Markowitz, Victor; Kyrpides, Nikos; Meyer, Folker; Amaral-Zettler, Linda; Cole, James

2018-01-25

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. In quick succession Frank Oliver Glockner (MPI-Bremen), Victor Markowitz (LBNL), Nikos Kyripides (JGI), Folker Meyer (ANL), Linda Amaral-Zettler (Marine Biology Lab), and James Cole (Michigan State University) provide updates on a number of topics related to GSC projects at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Flash Updates of GSC projects (GSC8 Meeting)

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

Glockner, Frank Oliver; Markowitz, Victor; Kyrpides, Nikos

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. In quick succession Frank Oliver Glockner (MPI-Bremen), Victor Markowitz (LBNL), Nikos Kyripides (JGI), Folker Meyer (ANL), Linda Amaral-Zettler (Marine Biology Lab), and James Colemore » (Michigan State University) provide updates on a number of topics related to GSC projects at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.« less

Building Communities: The Community Sequencing Program at JGI (2011 JGI User Meeting)

ScienceCinema

Bristow, Jim

2018-01-22

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy Environment Meeting held March 22-24, 2011 in Walnut Creek, CA. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. DOE JGI Deputy Director Jim Bristow gives a presentation on the Community Sequencing Program at the 6th annual Genomics of Energy and Environment Meeting on March 23, 2011.

Metagenome Assembly at the DOE JGI (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Chain, Patrick

2018-01-25

Patrick Chain of DOE JGI at LANL, Co-Chair of the Metagenome-specific Assembly session, on Metagenome Assembly at the DOE JGIat the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Annotations in Refseq (GSC8 Meeting)

ScienceCinema

Tatusova, Tatiana

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 10, 2009.

Towards a Consensus Annotation System (GSC8 Meeting)

ScienceCinema

White, Owen

2018-02-01

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Towards Consensus Annotation at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 10, 2009.

CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-Scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

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

Shih, Patrick

2012-03-22

Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-Scale Genomics (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Shih, Patrick

2018-01-10

Patrick Shih, representing both the University of California, Berkeley and JGI, gives a talk titled "CyanoGEBA: A Better Understanding of Cynobacterial Diversity through Large-scale Genomics" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Systems Biology Knowledgebase (GSC8 Meeting)

ScienceCinema

Cottingham, Robert W.

2018-01-04

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Robert W. Cottingham of Oak Ridge National Laboratory discusses the DOE Knowledge Base at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Gene Calling Standards (GSC8 Meeting)

ScienceCinema

Kyrpides, Nikos

2018-04-27

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses gene calling standards at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 10, 2009.

Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

ScienceCinema

Jansson, Janet

2018-01-04

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

The Biocurator Society (GSC8 Meeting)

ScienceCinema

Gaudet, Pascal

2018-01-10

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Pascal Gaudet of Northwestern University talks about "The Biocurator Society" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 11, 2009.

Fueling the Future with Fungal Genomes

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

Grigoriev, Igor V.

2014-10-27

Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science 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 400 fungal genomes have beenmore » 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 will lead 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.« less

Fungal Genomics for Energy and Environment

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

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 usersmore » 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.« less

Standards and the INSDC: Submission of MIGS, MIMS, MIENS (GSC8 Meeting)

ScienceCinema

Mizrachi, Ilene

2017-12-21

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding. Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Ilene Mizrachi of the NCBI talks about submission of MIGS/MIMS/MIENS information at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

A GSC Global Genome Census (GSC8 Meeting)

ScienceCinema

Kyrpides, Nikos

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Nikos Kyrpides of the DOE Joint Genome Institute discusses the notion of a global genome census at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Oceanic Communities in a Changing Planet - The Tara Oceans Project (GSC8 Meeting)

ScienceCinema

Raes, Jeroen

2018-01-10

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Jeroen Raes of the University of Brussels discusses the Tara-Oceans expedition at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Terragenome: International Soil Metagenome Sequencing Consortium (GSC8 Meeting)

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

Jansson, Janet

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Janet Jansson of the Lawrence Berkeley National Laboratory discusses the Terragenome Initiative at the Genomic Standards Consortium's 8th meeting at the DOE JGI inmore » Walnut Creek, CA on Sept. 9, 2009.« less

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

Stacey, Gary

Gary Stacey, associate director of the National Center for Soybean Biotechnology at the University of Missouri, gives a talk simply titled "Soybean" on March 24, 2010 at the 5th Annual DOE JGI User Meeting.

JGI Fungal Genomics Program

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

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 functionalmore » 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« less

Illumina Production Sequencing at the DOE Joint Genome Institute - Workflow and Optimizations

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

Tarver, Angela; Fern, Alison; Diego, Matthew San

2010-06-18

The U.S. Department of Energy (DOE) Joint Genome Institute?s (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the DOE mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI?s Production Sequencing group, the Illumina Genome Analyzer pipeline has been established as one of three sequencing platforms, along with Roche/454 and ABI/Sanger. Optimization of the Illumina pipeline has been ongoing with the aim of continual process improvement of the laboratory workflow. These process improvement projects are being led by the JGI?s Process Optimization, Sequencing Technologies, Instrumentation&more » Engineering, and the New Technology Production groups. Primary focus has been on improving the procedural ergonomics and the technicians? operating environment, reducing manually intensive technician operations with different tools, reducing associated production costs, and improving the overall process and generated sequence quality. The U.S. DOE JGI was established in 1997 in Walnut Creek, CA, to unite the expertise and resources of five national laboratories? Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest ? along with HudsonAlpha Institute for Biotechnology. JGI is operated by the University of California for the U.S. DOE.« less

Phylogeonomics and Ecogenomics of the Mycorrhizal Symbiosis

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

Kuo, Alan; Grigoriev, Igor V.; Kohler, Annegret

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 2 dozen mycorrhizal genomes of numerous known mycorrhizal orders and several ecological types (ectomycorrhizal [ECM], ericoid, orchid, and arbuscular). JGI has developed and deployed high-throughput pipelines for genomic, transcriptomic, and re-sequencing, and platforms formore » assembly, annotation, and analysis. In the last 2 years we have sequenced 21 genomes of mycorrhizal fungi, and resequenced 6 additional strains of L. bicolor. Most of this data is publicly available on JGI MycoCosm?s Mycorrhizal Fungi Portal (http://jgi.doe.gov/Mycorrhizal_fungi/), which provides access to both the genome data and tools with which to analyze the data. These data allow us to address long-standing issues in mycorrhizal evolution and ecology. For example, a major observation of mycorrhizal evolution is that each of the major ecological types appears to have evolved independently in multiple fungal clades. Using an ecogenomic approach we provide preliminary evidence that 2 clades (Cantharellales and Sebacinales) of a single symbiotic ecotype (orchid) utilize some common regulatory (protein tyrosine kinase) and metabolic (lipase) paths, the latter of which may be the product of HGT. Using a phylogenomic approach we provide preliminary evidence that a particular ecotype (ericoid) may have evolved more than once within a major clade (Leotiomycetes).« less

Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

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

Goldberg, Robert

2012-03-21

Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Scalability of Comparative Analysis, Novel Algorithms and Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Mavrommatis, Kostas

2017-12-22

DOE JGI's Kostas Mavrommatis, chair of the Scalability of Comparative Analysis, Novel Algorithms and Tools panel, at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Using Genomics to Dissect Seed Development (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment Meeting)

ScienceCinema

Goldberg, Robert

2018-04-27

Robert Goldberg of UCLA presents "Using Genomics to Dissect Seed Development" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

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

ScienceCinema

Tringe, Susannah

2018-01-15

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.

Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Zimmer, Carl [New York Times, New York, NY (United States)

2018-05-23

Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Keynote Presentation: Genome Beat (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

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

Zimmer, Carl

Carl Zimmer, a reporter for the New York Times, speaks on "The Genome Beat," the opening keynote presentation at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

MIENS Minimum Information about an ENvironmental Sequence and The GSC's Not-for-Profit (GSC8 Meeting)

ScienceCinema

Yilmaz, Pelin; Kolker, Eugene

2018-01-24

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Pelin Yilmaz of the Max Planck Institute-Bremen talks about the MIENS specification and Eugene Kolker of Seattle Children's Hospital discusses the GSC's non-for-profit at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Harnessing the Flow of Data from Fungi at JGI

ScienceCinema

Grigoriev, Igor; Glass, N. Louise; Martin, Francis; Turgeon, Gillian; Spatafora, Joey; Berka, Randy

2018-06-12

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) managed by Lawrence Berkeley National Laboratory, is the only user facility in the world devoted to problems of energy and environment. With over one million species, fungi—which include mushrooms—represent one of the largest under-explored branches of the Tree of Life. Together with its community of more than 1,000 scientific collaborators, JGI helping to unlock the secrets encoded in the genomes of fungi to advance a better understanding of the global carbon cycle and to develop new biotechnology products, next-generation biofuels, and medicines.

Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

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

Gallivan, Justin

2012-03-21

Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, CA.

Reprogramming Bacteria to Seek and Destroy Small Molecules (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Gallivan, Justin

2018-05-01

Justin Gallivan, of Emory University presents a talk titled "Reprogramming Bacteria to Seek and Destroy Small Molecules" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, CA.

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

Karp, Peter D.

Pathway Tools is a systems-biology software package written by SRI International (SRI) that produces Pathway/Genome Databases (PGDBs) for organisms with a sequenced genome. Pathway Tools also provides a wide range of capabilities for analyzing predicted metabolic networks and user-generated omics data. More than 5,000 academic, industrial, and government groups have licensed Pathway Tools. This user community includes researchers at all three DOE bioenergy centers, as well as academic and industrial metabolic engineering (ME) groups. An integral part of the Pathway Tools software is MetaCyc, a large, multiorganism database of metabolic pathways and enzymes that SRI and its academic collaborators manuallymore » curate. This project included two main goals: I. Enhance the MetaCyc content of bioenergy-related enzymes and pathways. II. Develop computational tools for engineering metabolic pathways that satisfy specified design goals, in particular for bioenergy-related pathways. In part I, SRI proposed to significantly expand the coverage of bioenergy-related metabolic information in MetaCyc, followed by the generation of organism-specific PGDBs for all energy-relevant organisms sequenced at the DOE Joint Genome Institute (JGI). Part I objectives included: 1: Expand the content of MetaCyc to include bioenergy-related enzymes and pathways. 2: Enhance the Pathway Tools software to enable display of complex polymer degradation processes. 3: Create new PGDBs for the energy-related organisms sequenced by JGI, update existing PGDBs with new MetaCyc content, and make these data available to JBEI via the BioCyc website. In part II, SRI proposed to develop an efficient computational tool for the engineering of metabolic pathways. Part II objectives included: 4: Develop computational tools for generating metabolic pathways that satisfy specified design goals, enabling users to specify parameters such as starting and ending compounds, and preferred or disallowed intermediate compounds. The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.« less

Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

ScienceCinema

Shuster, Stephen

2018-02-13

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangered Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

ScienceCinema

Kolker, Eugene; Sansone, Susanna

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "The ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA. on Sept. 11, 2009.

The Genomes and Metagenomes (GEM) Catalogue (first presentation) and The ISA-GCDML Workshop (second presentation) (GSC8 Meeting)

ScienceCinema

Field, Dawn; Sansone, Susanna

2018-01-24

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding ''Research Coordination Network'' from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology & Hydrology briefly introduces the GEM Catalogue, followed by Susanna Sansone of the European Bioinformatics Institute who talks about the ISA-GCDML workshop at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Sayre, Richard; Kyrpides, Nikos

2018-05-03

Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Brady, Siobhan

2018-02-12

Siobhan Brady from University of California, Davis, gives a talk titled "Getting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Getting to the Root of Things: Spatiotemporal Regulatory Networks (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

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

Brady, Siobhan

2012-03-22

Siobhan Brady from University of California, Davis, gives a talk titled "Getting to the Root of things: Spatiotemporal Regulatory Networks" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Tapping the Molecular Potential of Microalgae to Produce Biomass (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

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

Sayre, Richard; Kyrpides, Nikos

2012-03-22

Richard Sayre, from Los Alamos National Laboratory, presents a talk titled "Tapping the Molecular Potential of Microalgae to Produce Biomass" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Genome-Scale Discovery of Cell Wall Biosynthesis Genes in Populus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Muchero, Wellington

2018-01-15

Wellington Muchero from Oak Ridge National Laboratory gives a talk titled "Discovery of Cell Wall Biosynthesis Genes in Populus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

JGI Plant Genomics Gene Annotation Pipeline

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

Shu, Shengqiang; Rokhsar, Dan; Goodstein, David

2014-07-14

Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward thismore » aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.« less

Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Benner, Steve

2018-05-08

Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Evaluation of the Cow Rumen Metagenome: Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Sczyrba, Alex

2018-02-13

DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Evaluation of the Cow Rumen Metagenome: Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

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

Sczyrba, Alex

2011-10-13

DOE JGI's Alex Sczyrba on "Evaluation of the Cow Rumen Metagenome" and "Assembly by Single Copy Gene Analysis and Single Cell Genome Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Closing Keynote Presentation on the Genomics of Energy and the Environment (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

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

Benner, Steve

2012-03-22

Steve Benner, a distinguished chemist at the Foundation for Applied Molecular Evolution, Westheimer Institute of Science and Technology, provides the closing keynote address for the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Genomics of Extinct and Endangered Species (2011 JGI User Meeting)

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

Shuster, Stephen

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Stephen Shuster of Penn State University gives a presentation on "Genomics of Extinct and Endangeredmore » Species" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.« less

Genomic Speciation and Adaptation in Aquilegia (2011 JGI User Meeting)

ScienceCinema

Hodges, Scott

2018-02-14

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Scott Hodges of the University of California, Santa Barbara gives a presentation on Genomic Speciation and Adaptation in Aquilegia at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

The Gulf Oil Spill: Ecogenomics and Ecoresilience (Keynote - 2011 JGI User Meeting)

ScienceCinema

Hazen, Terry [LBNL

2018-04-25

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Berkeley Lab microbial ecologist Terry Hazen delivers a keynote on "The Gulf Oil Spill: Ecogenomics and Ecoresilience" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011.

Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

ScienceCinema

Tuskan, Gerry

2018-02-13

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gerry Tuskan of Oak Ridge National Laboratory on Resequencing in Populus: Towards Genome Wide Association Genetics at the 6th annual Genomics of Energy Environment Meeting on March 23, 2011.

Designing Biological Systems for Sustainability and Programmed Environmental Interface (2011 JGI User Meeting)

ScienceCinema

Silver, Pamela

2018-02-13

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Pam Silver of Harvard University gives a presentation on "Designing Biological Systems for Sustainability and Programmed Environmental Interface" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

Spatially and Temporally Resolved Studies of the Human Microbiome (2011 JGI User Meeting)

ScienceCinema

Knight, Rob

2018-04-26

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Rob Knight of the University of Colorado gives a presentation on "Spatially and Temporally Resolved Studies of the Human Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

MycoCosm, an Integrated Fungal Genomics Resource

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

Shabalov, Igor; Grigoriev, Igor

2012-03-16

MycoCosm is a web-based interactive fungal genomics resource, which was first released in March 2010, in response to an urgent call from the fungal community for integration of all fungal genomes and analytical tools in one place (Pan-fungal data resources meeting, Feb 21-22, 2010, Alexandria, VA). MycoCosm integrates genomics data and analysis tools to navigate through over 100 fungal genomes sequenced at JGI and elsewhere. This resource allows users to explore fungal genomes in the context of both genome-centric analysis and comparative genomics, and promotes user community participation in data submission, annotation and analysis. MycoCosm has over 4500 unique visitors/monthmore » or 35000+ visitors/year as well as hundreds of registered users contributing their data and expertise to this resource. Its scalable architecture allows significant expansion of the data expected from JGI Fungal Genomics Program, its users, and integration with external resources used by fungal community.« less

Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

ScienceCinema

Vaughan, Bob; Kaye, Jon

2018-01-24

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Betty Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) Portal to the HMP (GSC8 Meeting)

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

Weinstock, George; Wortman, Jennifer

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University ofmore » Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.« less

"A New Arm of the GSC: the RCN4GSC" and "Curation of MIGS-compliant Data" (GSC 8 Meeting)

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

Field, Dawn; Sterk, Peter

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology & Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology & Hydrologymore » follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.« less

A New Arm of the GSC: The RCN4GSC and Curation of MIGS-compliant Data (GSC8 Meeting)

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

Field, Dawn; Sterk, Peter

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology and Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology and Hydrologymore » follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.« less

Submitting MIGS, MIMS, MIENS Information to EMBL and Standards and the Sequencing Pipelines of the Gordon and Betty Moore Foundation (GSC8 Meeting)

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

Vaughan, Bob; Kaye, Jon

2009-09-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Bob Vaughan of EMBL on submitting MIGS/MIMS/MIENS information to EMBL-EBI's system, followed by a brief talk from Jon Kaye of the Gordon and Bettymore » Moore Foundation on standards and the foundation's sequencing pipelines at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.« less

The Human Microbiome Project (HMP) and the Data Analysis and Coordination Center (DAAC) Portal to the HMP (GSC8 Meeting)

ScienceCinema

Weinstock, George; Wortman, Jennifer

2018-01-22

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. George Weinstock from Washington University School of Medicine talks about the Human Microbiome Project (HMP) followed briefly by Jennifer Wortman from the University of Maryland School of Medicine on the Data Analysis and Coordination Center (DACC) portal to the HMP at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA on Sept. 9, 2009.

The Encyclopedia of Systems Biology and OMICS (first presentation) and The ISA Infrastructure for Multi-omics Data (second presentation) (GSC8 Meeting)

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

Kolker, Eugene; Sansone, Susanna

2011-09-11

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Eugene Kolker from Seattle Children's Hospital briefly discusses "The Encyclopedia of Systems Biology and OMICS," followed by Susanna Sansone from the EBI on "Themore » ISA Infrastructure for multi-omics data" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, CA. on Sept. 11, 2009.« less

A New Arm of the GSC: The RCN4GSC and Curation of MIGS-compliant Data (GSC8 Meeting)

ScienceCinema

Field, Dawn; Sterk, Peter

2018-01-09

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Dawn Field of the NERC Centre for Ecology and Hydrology briefly describes RCN4GSC and Peter Sterk of the NERC Centre for Ecology and Hydrology follows with a talk on curation of MIGS-compliant data at the Genomic Standards Consortium 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 9, 2009.

In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Mosier, Annika

2018-01-22

Annika Mosier, graduate student from Stanford University presents a talk titled "In Situ Expression of Acidic and Thermophilic Carbohydrate Active Enzymes by Filamentous Fungi" at the JGI User 7th Annual Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, CA.

Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Glass, N. Louise; Pennacchio, Len

2018-02-13

N. Louise Glass from the University of California, Berkeley, presents a talk titled "Systems Biology Approaches to Dissecting Plant Cell Wall Biosynthesis Genes in Poplus" at the JGI 7th Annual Users Meeting: Genomics of Energy & Environment Meeting on March 22, 2012 in Walnut Creek, California.

Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Stepanauskas, Ramunas

2018-02-06

DOE JGI's Tanja Woyke, chair of the Single Cells and Metagenomes session, delivers an introduction, followed by Bigelow Laboratory's Ramunas Stepanauskas on "Single Cell and Metagenomic Assemblies: Biology Drives Technical Choices and Goals" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

ScienceCinema

Robinson, Gene

2018-02-05

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, CA. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gene Robinson of the University of Illinois on Genomic and Systems Biology Analyses of Social Behavior at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011.

The Turn-on of LCLS: the X-Ray Free Electron Laser at SLAC ( Keynote - 2011 JGI User Meeting)

ScienceCinema

Drell, Persis [SLAC National Accelerator Lab., Menlo Park, CA (United States)

2018-06-15

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. SLAC National Laboratory Director Persis Drell gives a keynote talk on "The Turn-on of LCLS: the X-Ray Free-Electron Laser at SLAC" at the 6th Genomics of Energy & Environment Meeting on March 22, 2011

Regulatory Networks Controlling Plant Cold Acclimation or Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis (2011 JGI User Meeting)

ScienceCinema

Thomashow, Mike

2018-02-06

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Mike Thomashow of Michigan State University gives a presentation on on "Low Temperature Regulatory Networks Controlling Cold Acclimation in Arabidopsis" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011."

Association Genetics of Populus trichocarpa or Resequencing in Populus: Towards Genome Wide Association Genetics (2011 JGI User Meeting)

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

Tuskan, Gerry

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gerry Tuskan of Oak Ridge National Laboratory on Resequencing in Populus: Towards Genome Wide Association Geneticsmore » at the 6th annual Genomics of Energy Environment Meeting on March 23, 2011.« less

Host Genetic Control of the Microbiome in Humans and Maize or Relating Host Genetic Variation to the Microbiome (2011 JGI User Meeting)

ScienceCinema

Ley, Ruth E. [Cornell Univ., Ithaca, NY (United States). Cornell Center for Comparative and Population Genomics, Dept. of Microbiology and Dept. of Molecular Biology and Genetics

2018-06-27

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy and Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Ruth Ley of Cornell University gives a presentation on "Relating Host Genetic Variation to the Microbiome" at the 6th annual Genomics of Energy and Environment Meeting on March 23, 2011.

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

Harwood, Caroline S.

Rhodopseudomonas palustris is a common soil and water bacterium that makes its living by converting sunlight to cellular energy and by absorbing atmospheric carbon dioxide and converting it to biomass. This microbe can also degrade and recycle components of the woody tissues of plants, wood being the most abundant polymer on earth. Because of its intimate involvement in carbon management and recycling, R. palustris was selected by the DOE Carbon Management Program to have its genome sequenced by the Joint Genome Institute (JGI). This award provided funds for the preparation of R. palustris genomic DNA which was then supplied tomore » the JGI in sufficient amounts to enable the complete sequencing of the R. palustris genome. The PI also supplied the JGI with technical information about the molecular biology of R. palustris.« less

Host Genetic Control of the Microbiome in Humans and Maise or Relating Host Genetic Variation to the Microbiome (2011 JGI User Meeting)

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

Ley, Ruth

2011-03-23

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Ruth Ley of Cornell University gives a presentation on "Relating Host Genetic Variation to themore » Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.« less

Genomic and Systems Biology Analyses of Social Behavior or Evolutionary Genomic Analyses of Insect Society: Eat, Drink, and Be Scary (2011 JGI User Meeting)

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

Robinson, Gene

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, CA. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Gene Robinson of the University of Illinois on Genomic and Systems Biology Analyses of Socialmore » Behavior at the 6th Annual Genomics of Energy & Environment Meeting on March 23, 2011.« less

Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties (2011 JGI User Meeting)

ScienceCinema

Bork, Peer

2018-02-14

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Peer Bork of the European Molecular Biology Laboratory on Comparative Metagenomics of Gut and Ocean: Identification of Microbial Marker Genes for Complex Environmental Properties at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.

IMG 4 version of the integrated microbial genomes comparative analysis system

PubMed Central

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Woyke, Tanja; Huntemann, Marcel; Anderson, Iain; Billis, Konstantinos; Varghese, Neha; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N.; Kyrpides, Nikos C.

2014-01-01

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu). PMID:24165883

IMG 4 version of the integrated microbial genomes comparative analysis system

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

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Finally, different IMG datamarts providemore » support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).« less

IMG: the integrated microbial genomes database and comparative analysis system

PubMed Central

Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N.; Kyrpides, Nikos C.

2012-01-01

The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp). PMID:22194640

IMG: the Integrated Microbial Genomes database and comparative analysis system.

PubMed

Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Grechkin, Yuri; Ratner, Anna; Jacob, Biju; Huang, Jinghua; Williams, Peter; Huntemann, Marcel; Anderson, Iain; Mavromatis, Konstantinos; Ivanova, Natalia N; Kyrpides, Nikos C

2012-01-01

The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp).

IMG 4 version of the integrated microbial genomes comparative analysis system.

PubMed

Markowitz, Victor M; Chen, I-Min A; Palaniappan, Krishna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Ratner, Anna; Huang, Jinghua; Woyke, Tanja; Huntemann, Marcel; Anderson, Iain; Billis, Konstantinos; Varghese, Neha; Mavromatis, Konstantinos; Pati, Amrita; Ivanova, Natalia N; Kyrpides, Nikos C

2014-01-01

The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG's data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG's annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).

A Taste of Algal Genomes from the Joint Genome Institute

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

Kuo, Alan; Grigoriev, Igor

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 basicmore » 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.« less

Genomic Encyclopedia of Fungi

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

Grigoriev, Igor

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 supportedmore » 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.« less

Assembly, Annotation, and Analysis of Multiple Mycorrhizal Fungal Genomes

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

Initiative Consortium, Mycorrhizal Genomics; Kuo, Alan; Grigoriev, Igor

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 2012more » 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.« less

SPRUCE Deep Peat Heating (DPH) to Whole Ecosystem Warming (WEW) Metagenomes for Peat Samples Collected June 2016

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

Kluber, Laurel A; Yip, Daniel Z; Yang, Zamin K

This data set provides links to the results of metagenomic analyses of 44 peat samples collected on 13 June 2016 from SPRUCE experiment treatment and ambient plots. Experimental plots had received approximately 24 months of belowground warming (deep peat heating (DPH), Hanson et al. 2015) with the last 9 of those months including air warming for implementation of whole ecosystems warming (WEW – Hanson et al. 2016). WEW Metagenomes: Data from these metagenomes are archived in the U.S. Department of Energy Joint Genome Institute (DOE JGI) Integrated Microbial Genomes (IMG) system (http://img.jgi.doe.gov/) and are available at the accession numbers providedmore » below (Table 2) and in the accompanying inventory file. The easiest way to find results on IMG is at this link, https://img.jgi.doe.gov/cgi-bin/m/main.cgi, and then enter “June2016WEW” as a search term in the “Quick Genome Search:” box at the top of the page.« less

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

Grigoriev, Igor; Glass, N. Louise; Martin, Francis

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) managed by Lawrence Berkeley National Laboratory, is the only user facility in the world devoted to problems of energy and environment. With over one million species, fungi—which include mushrooms—represent one of the largest under-explored branches of the Tree of Life. Together with its community of more than 1,000 scientific collaborators, JGI helping to unlock the secrets encoded in the genomes of fungi to advance a better understanding of the global carbon cycle and to develop new biotechnology products, next-generation biofuels, and medicines.

SPRUCE Deep Peat Heat (DPH) Metagenomes for Peat Samples Collected June 2015

DOE Data Explorer

Klumber, Laurel A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Yang, Zamin K. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Schadt, Christopher W. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.

2015-01-01

This data set provides links to the results of metagenomic analyses of 38 peat core samples collected on 16 June 2015 from SPRUCE experiment treatment plots after approximately one year of belowground heating. These metagenomes are archived in the U.S. Department of Energy Joint Genome Institute (DOE JGI) Integrated Microbial Genomes (IMG) system and are available at the accession numbers provided in the accompanying inventory file.

Fungal Genomics Program

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

Grigoriev, Igor

The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scalemore » genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.« less

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

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

Gilbert, David

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.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

PubMed

Huntemann, Marcel; Ivanova, Natalia N; Mavromatis, Konstantinos; Tripp, H James; Paez-Espino, David; Palaniappan, Krishnaveni; Szeto, Ernest; Pillay, Manoj; Chen, I-Min A; Pati, Amrita; Nielsen, Torben; Markowitz, Victor M; Kyrpides, Nikos C

2015-01-01

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. Structural annotation is followed by assignment of protein product names and functions.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

DOE PAGES

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; ...

2015-10-26

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

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

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos

The DOE-JGI Microbial Genome Annotation Pipeline performs structural and functional annotation of microbial genomes that are further included into the Integrated Microbial Genome comparative analysis system. MGAP is applied to assembled nucleotide sequence datasets that are provided via the IMG submission site. Dataset submission for annotation first requires project and associated metadata description in GOLD. The MGAP sequence data processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements. In conclusion, structural annotation is followed by assignment of protein product names and functions.

Defining Genome Project Standards in a New Era of Sequencing (GSC8 Meeting)

ScienceCinema

Chain, Patrick

2018-01-15

The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding Research Coordination Network from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego.

Hope or Hype? What is Next for Biofuels? (LBNL Science at the Theater)

ScienceCinema

Keasling, Jay; Bristow, Jim; Tringe, Susannah Green

2017-12-09

Science at the Theater: From the sun to your gas tank: A new breed of biofuels may help solve the global energy challenge and reduce the impact of fossil fuels on global warming. KTVU Channel 2 health and science editor John Fowler will moderate a panel of Lawrence Berkeley National Laboratory scientists who are developing ways to convert the solar energy stored in plants into liquid fuels. Jay Keasling is one of the foremost authorities in the field of synthetic biology. He is applying this research toward the production of advanced carbon-neutral biofuels that can replace gasoline on a gallon-for-gallon basis. Keasling is Berkeley Labs Acting Deputy Director and the Chief Executive Officer of the U.S. Department of Energys Joint BioEnergy Institute. Jim Bristow is deputy director of programs for the U.S. Department of Energy Joint Genome Institute (JGI), a national user facility in Walnut Creek, CA. He developed and implemented JGIs Community Sequencing Program, which provides large-scale DNA sequencing and analysis to advance genomics related to bioenergy and environmental characterization and cleanup. Susanna Green Tringe is a computational biologist with the U.S. Department of Energy Joint Genome Institute (JGI). She helped pioneer the field of metagenomics, a new strategy for isolating, sequencing, and characterizing DNA extracted directly from environmental samples, such as the contents of the termite gut, which yielded enzymes responsible for breakdown of wood into fuel.

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

Knight, Rob

The U.S. Department of Energy Joint Genome Institute (JGI) invited scientists interested in the application of genomics to bioenergy and environmental issues, as well as all current and prospective users and collaborators, to attend the annual DOE JGI Genomics of Energy & Environment Meeting held March 22-24, 2011 in Walnut Creek, Calif. The emphasis of this meeting was on the genomics of renewable energy strategies, carbon cycling, environmental gene discovery, and engineering of fuel-producing organisms. The meeting features presentations by leading scientists advancing these topics. Rob Knight of the University of Colorado gives a presentation on "Spatially and Temporally Resolvedmore » Studies of the Human Microbiome" at the 6th annual Genomics of Energy & Environment Meeting on March 23, 2011.« less

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

PubMed Central

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

2018-01-01

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. PMID:29528046

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

PubMed

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.

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

DOE PAGES

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; ...

2016-02-24

The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provide d via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation ismore » followed by functional annotation including assignment of protein product names and connection to various protein family databases.« less

The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)

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

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos

The DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provide d via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation ismore » followed by functional annotation including assignment of protein product names and connection to various protein family databases.« less

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

Tuskan, Gerald

Jerry Tuskan of Oak Ridge National Laboratory and the DOE JGI talks about poplar trees as models for selective adaptation to an environment. This video complements a study published ahead online August 24, 2014 in Nature Genetics.

Gene context analysis in the Integrated Microbial Genomes (IMG) data management system.

PubMed

Mavromatis, Konstantinos; Chu, Ken; Ivanova, Natalia; Hooper, Sean D; Markowitz, Victor M; Kyrpides, Nikos C

2009-11-24

Computational methods for determining the function of genes in newly sequenced genomes have been traditionally based on sequence similarity to genes whose function has been identified experimentally. Function prediction methods can be extended using gene context analysis approaches such as examining the conservation of chromosomal gene clusters, gene fusion events and co-occurrence profiles across genomes. Context analysis is based on the observation that functionally related genes are often having similar gene context and relies on the identification of such events across phylogenetically diverse collection of genomes. We have used the data management system of the Integrated Microbial Genomes (IMG) as the framework to implement and explore the power of gene context analysis methods because it provides one of the largest available genome integrations. Visualization and search tools to facilitate gene context analysis have been developed and applied across all publicly available archaeal and bacterial genomes in IMG. These computations are now maintained as part of IMG's regular genome content update cycle. IMG is available at: http://img.jgi.doe.gov.

IMG-ABC: An Atlas of Biosynthetic Gene Clusters to Fuel the Discovery of Novel Secondary Metabolites

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

Chen, I-Min; Chu, Ken; Ratner, Anna

2014-10-28

In the discovery of secondary metabolites (SMs), large-scale analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of relevant computational resources. We present IMG-ABC (https://img.jgi.doe.gov/abc/) -- An Atlas of Biosynthetic gene Clusters within the Integrated Microbial Genomes (IMG) system1. IMG-ABC is a rich repository of both validated and predicted biosynthetic clusters (BCs) in cultured isolates, single-cells and metagenomes linked with the SM chemicals they produce and enhanced with focused analysis tools within IMG. The underlying scalable framework enables traversal of phylogenetic dark matter and chemical structure space -- serving as a doorwaymore » to a new era in the discovery of novel molecules.« less

Finding Fingerprints of Selection in Poplar Genomes

ScienceCinema

Tuskan, Gerald

2018-05-30

Jerry Tuskan of Oak Ridge National Laboratory and the DOE JGI talks about poplar trees as models for selective adaptation to an environment. This video complements a study published ahead online August 24, 2014 in Nature Genetics.

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

Daum, Chris

Chris Daum of the DOE Joint Genome Institute discusses how the DOE JGI's Production Sequencing group optimizes the sequencer pipelines and assesses quality on the Production line on June 2, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

Illumina GA IIx& HiSeq 2000 Production Sequenccing and QC Analysis Pipelines at the DOE Joint Genome Institute

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

Daum, Christopher; Zane, Matthew; Han, James

2011-01-31

The U.S. Department of Energy (DOE) Joint Genome Institute's (JGI) Production Sequencing group is committed to the generation of high-quality genomic DNA sequence to support the mission areas of renewable energy generation, global carbon management, and environmental characterization and clean-up. Within the JGI's Production Sequencing group, a robust Illumina Genome Analyzer and HiSeq pipeline has been established. Optimization of the sesequencer pipelines has been ongoing with the aim of continual process improvement of the laboratory workflow, reducing operational costs and project cycle times to increases ample throughput, and improving the overall quality of the sequence generated. A sequence QC analysismore » pipeline has been implemented to automatically generate read and assembly level quality metrics. The foremost of these optimization projects, along with sequencing and operational strategies, throughput numbers, and sequencing quality results will be presented.« less

Complete genome sequence of Serratia plymuthica strain AS12

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

Neupane, Saraswoti; Finlay, Roger D.; Alstrom, Sadhna

2012-01-01

A plant associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest due to its plant growth promoting and plant pathogen inhibiting ability. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled 'Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens'.

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

DOE PAGES

Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna; ...

2016-10-30

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs aremore » grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.« less

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

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

Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from > 6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs aremore » grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparingwith external sequences, thus serving as an essential resource in the viral genomics community.« less

Genomics of Climate Resilience (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Bermingham, Eldredge

2013-03-27

Eldredge Bermingham of the Smithsonian Tropical Research Institute-Panama on "Genomics of climate resilience" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

A Novel Method for Producing Transgenic Enzymes and Peptides

DTIC Science & Technology

2004-03-04

eutropha”. Biotechnol. Bioeng. 84(1): 114-120. Wieczorek, R., A. Steinbuchel, et al. (1996). “Occurrence of polyhydroxyalkanoic acid granule... polyhydroxyalkanoate (PHA), a biodegradable polymer, by ICI/Zeneca and later Monsanto. The genome has been sequenced (http://jgi.doe * Corresponding

Genomics of Climate Resilience (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

ScienceCinema

Bermingham, Eldredge

2018-02-13

Eldredge Bermingham of the Smithsonian Tropical Research Institute-Panama on "Genomics of climate resilience" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Genome Assembly Forensics: Metrics for Assessing Assembly Correctness (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Pop, Mihai

2018-04-27

University of Maryland's Mihai Pop on Genome Assembly Forensics: Metrics for Assessing Assembly Correctness at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Memory Efficient Sequence Analysis Using Compressed Data Structures (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Simpson, Jared

2018-01-24

Wellcome Trust Sanger Institute's Jared Simpson on Memory efficient sequence analysis using compressed data structures at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

New Technology Drafts: Production and Improvements

ScienceCinema

Lapidus, Alla

2018-01-22

Alla Lapidus, head of the DOE Joint Genome Institute's Finishing group, gives a talk on how the DOE JGI's microbial genome sequencing pipeline has been adapted to accommodate next generation sequencing platforms at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM.

Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Quake, Steve

2018-02-02

Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

The Sunflower Genome and its Evolution (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Rieseberg, Loren

2018-02-06

Loren Rieseberg from the University of British Columbia on "The Sunflower Genome and its Evolution" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

Sequencing Single Cell Microbial Genomes with Microfluidic Amplifications Tools (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

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

Quake, Steve

2011-10-12

Stanford University's Steve Quake on "Sequencing Single Cell Microbial Genomes with Microfluidic Amplification Tools" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Regulation of Flowering in Brachypodium distachyon (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Amasino, Rick

2013-03-01

Rick Amasino of the University of Wisconsin on "Regulation of Flowering in Brachypodium distachyon" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

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

ScienceCinema

Gilbert, Tom

2018-02-06

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

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

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

Gilbert, Tom

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

PMI: Plant-Microbe Interfaces (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Schadt, Christopher

2013-03-01

Christopher Schadt of Oak Ridge National Laboratory on Plant-Microbe Interactions in the context of poplar trees at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 held in Walnut Creek, CA.

Comparison of Normalized and Unnormalized Single Cell and Population Assemblies (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Hugenholtz, Phil

2018-02-12

University of Queensland's Phil Hugenholtz on "Comparison of Normalized and Unnormalized Single Cell and Population Assemblies" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Complete genome sequence of the plant-associated Serratia plymuthica strain AS13

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

Neupane, Saraswoti; Finlay, Roger D.; Kyrpides, Nikos C

2012-01-01

Serratia plymuthica AS13 is a plant-associated Gammaproteobacteria, isolated from rapeseed roots. It is of special interest because of its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The complete genome of S. plymuthica AS13 consists of a 5,442,549 bp circular chromosome. The chromosome contains 4,951 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced as part of the project enti- tled Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens within the 2010 DOE-JGI Community Sequencing Program (CSP2010).

Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidionycetes (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Hibbett, David

2018-05-18

David Hibbett from Clark University on "Evolutionary Perspectives on Diversity of Lignocellulose Decay Mechanisms in Basidiomycetes" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

Metagenomics, metaMicrobesOnline and Kbase Data Integration (MICW - Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Dehal, Paramvir

2018-02-06

Berkeley Lab's Paramvir Dehal on "Managing and Storing large Datasets in MicrobesOnline, metaMicrobesOnline and the DOE Knowledgebase" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Succession of Phylogeny and Function During Plant Litter Decomposition (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

ScienceCinema

Brodie, Eoin

2018-04-26

Eoin Brodie of Berkeley Lab on "Succession of phylogeny and function during plant litter decomposition" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, CA.

Succession of Phylogeny and Function During Plant Litter Decomposition (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Brodie, Eoin

2013-03-01

Eoin Brodie of Berkeley Lab on "Succession of phylogeny and function during plant litter decomposition" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, CA.

Improving Biofuel Feedstocks by Modifying Xylan Biosynthesis (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Lau, Jane

2013-03-01

Jane Lau of the Joint BioEnergy Institute on Improving biofuel feedstocks by modifying xylan biosynthesis at the 8th Annual Genomics of Energy Environment Meeting on March 28, 2013 in Walnut Creek, CA.

The DOE Bioenergy Research Centers: History, Operations, and Scientific Output

DOE PAGES

Slater, Steven C.; Simmons, Blake A.; Rogers, Tamara S.; ...

2015-08-20

Over the past 7 years, the US Department of Energy's Office of Biological and Environmental Research has funded three Bioenergy Research Centers (BRCs). These centers have developed complementary and collaborative research portfolios that address the key technical and economic challenges in biofuel production from lignocellulosic biomass. All three centers have established a close, productive relationship with DOE's Joint Genome Institute (JGI). This special issue of Bioenergy Research samples the breadth of basic science and engineering work required to underpin a diverse, sustainable, and robust biofuel industry. In this report, which was collaboratively produced by all three BRCs, we discuss themore » BRC contributions over their first 7 years to the development of renewable transportation fuels. In additon, we also highlight the BRC research published in the current issue and discuss technical challenges in light of recent progress.« less

IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses.

PubMed

Paez-Espino, David; Chen, I-Min A; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Huang, Jinghua; Markowitz, Victor M; Nielsen, Torben; Huntemann, Marcel; K Reddy, T B; Pavlopoulos, Georgios A; Sullivan, Matthew B; Campbell, Barbara J; Chen, Feng; McMahon, Katherine; Hallam, Steve J; Denef, Vincent; Cavicchioli, Ricardo; Caffrey, Sean M; Streit, Wolfgang R; Webster, John; Handley, Kim M; Salekdeh, Ghasem H; Tsesmetzis, Nicolas; Setubal, Joao C; Pope, Phillip B; Liu, Wen-Tso; Rivers, Adam R; Ivanova, Natalia N; Kyrpides, Nikos C

2017-01-04

Viruses represent the most abundant life forms on the planet. Recent experimental and computational improvements have led to a dramatic increase in the number of viral genome sequences identified primarily from metagenomic samples. As a result of the expanding catalog of metagenomic viral sequences, there exists a need for a comprehensive computational platform integrating all these sequences with associated metadata and analytical tools. Here we present IMG/VR (https://img.jgi.doe.gov/vr/), the largest publicly available database of 3908 isolate reference DNA viruses with 264 413 computationally identified viral contigs from >6000 ecologically diverse metagenomic samples. Approximately half of the viral contigs are grouped into genetically distinct quasi-species clusters. Microbial hosts are predicted for 20 000 viral sequences, revealing nine microbial phyla previously unreported to be infected by viruses. Viral sequences can be queried using a variety of associated metadata, including habitat type and geographic location of the samples, or taxonomic classification according to hallmark viral genes. IMG/VR has a user-friendly interface that allows users to interrogate all integrated data and interact by comparing with external sequences, thus serving as an essential resource in the viral genomics community. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Challenges and Opportunities for Extending Plant Genomics to Climate (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Weston, David

2013-03-01

David Weston of Oak Ridge National Laboratory on "The challenges and opportunities for extending plant genomics to climate" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, CA.

TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Karsenti, Eric

2013-03-01

Eric Karsenti of EMBL delivers the closing keynote on "TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, California.

TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

ScienceCinema

Karsenti, Eric [European Molecular Biology Lab. (EMBL), Heidelberg (Germany)

2018-05-23

Eric Karsenti of EMBL delivers the closing keynote on "TARA OCEANS: A Global Analysis of Oceanic Plankton Ecosystems" at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, California.

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

ScienceCinema

Li, Weizhong

2018-02-12

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

The Genome of Selaginella: A Remnant of an Ancient Vascular Plant Lineage (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

ScienceCinema

Banks, Jody

2018-02-12

Jody Banks from Purdue University on "The Genome of Selaginella, a Remnant of an Ancient Vascular Plant Lineage" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, Calif.

Delineating Molecular Interaction Mechanisms in an In Vitro Microbial-Plant Community (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Larsen, Peter

2013-03-01

Peter Larsen of Argonne National Lab on "Delineating molecular interaction mechanisms in an in vitro microbial-plant community" at the 8th Annual Genomics of Energy & Environment Meeting in Walnut Creek, CA.

Genomic Analysis of Natural Variation for Seed and Plant Size in Maize (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Kaeppler, Shawn

2018-02-01

Shawn Kaeppler from the University of Wisconsin-Madison on "Genomic Analysis of Biofuel Traits in Maize and Switchgrass" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, CA.

JGI's Carbon Cycling Studies on Restored Marshes

ScienceCinema

Tringe, Susannah; Theroux, Susanna

2018-02-14

DOE Joint Genome Institute Metagenome Program Head, Susannah Tringe, and postdoc, Susie Theroux, discuss the lessons to be learned from studying the microbial diversity of marshes that have been converted to other uses, and are now being restored, as well as the potential impacts on the global carbon cycle.

Assembly-Driven Metagenomics of a Hypersaline Microbial Ecosystem (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

ScienceCinema

Allen, Eric

2018-02-05

Eric Allen of Scripps and UC San Diego on Assembly-driven metagenomics of a hypersaline microbial ecosystem at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, CA.

Erratum to: The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)

DOE PAGES

Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos; ...

2016-03-21

After publication of this study [1], we noticed that the Strain ID summary was not removed from the PDF due to a copyediting error. The original version of this article was corrected. The publisher apologizes for any inconvenience caused.

Metabolic Engineering of Clostridium thermocellum for Biofuel Production (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Guess, Adam

2013-03-01

Adam Guss of Oak Ridge National Lab presents on Metabolic engineering of Clostridium thermocellum for biofuel production at the 8th Annual Genomics of Energy & Environment Meeting on March 28, 2013 in Walnut Creek, CA.

Assembly-Driven Metagenomics of a Hypersaline Microbial Ecosystem (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Allen, Eric

2013-03-01

Eric Allen of Scripps and UC San Diego on Assembly-driven metagenomics of a hypersaline microbial ecosystem at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, CA.

Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Hazen, Sam

2013-03-01

Sam Hazen of the University of Massachusetts on "Genetic Regulation of Grass Biomass Accumulation and Biological Conversion Quality" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, CA.

MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

ScienceCinema

Sakakibara, Yasumbumi

2018-02-13

Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Understanding Historical Human Migration Patterns and Interbreeding (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Willerslev, Eske

2018-02-14

Eske Willerslev from the University of Copenhagen on Understanding Historical Human Migration Patterns and Interbreeding Using the Ancient Genomes of a Palaeo-Eskimo and an Aboriginal Australian at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

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

ScienceCinema

Schmutz, Jeremy

2018-02-01

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.

MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads (Metagenomics Informatics Challenges Workshop: 10K Genomes at a Time)

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

Sakakibara, Yasumbumi

2011-10-13

Keio University's Yasumbumi Sakakibara on "MetaVelvet: An Extension of Velvet Assembler to de novo Metagenome Assembly from Short Sequence Reads" at the Metagenomics Informatics Challenges Workshop held at the DOE JGI on October 12-13, 2011.

Sequencing and functional validation of the JGI Brachypodium distachyon T-DNA collection

USDA-ARS?s Scientific Manuscript database

Brachypodium distachyon is a powerful experimental model for the grasses with a large and growing collection of genomic and experimental resources. We have added to these resources by greatly expanding the number of sequence-indexed T-DNA lines. We sequenced 21,165 T-DNA lines, 15,569 of which were ...

Modulation of Root Microbiome Community Assembly by the Plant Immune Response (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Lebeis, Sarah

2013-03-01

Sarah Lebeis of University of North Carolina on Modulation of root microbiome community assembly by the plant immune response at the 8th Annual Genomics of Energy Environment Meeting on March 28, 2013 in Walnut Creek, CA.

Applications of Genome-based Science in Shaping Citrus Industries of the World (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

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

Gmitter, Jr., Fred; Rokhsar, Dan

Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

Applications of Genome-based Science in Shaping Citrus Industries of the World (JGI Seventh Annual User Meeting, 2012: Genomics of Energy and Environment)

ScienceCinema

Gmitter, Jr., Fred; Rokhsar, Dan

2018-02-16

Fred Gmitter from the University of Florida on "Applications of Genome-based Science in Shaping the Future of the World's Citrus Industries" at the 7th Annual Genomics of Energy & Environment Meeting on March 21, 2012 in Walnut Creek, California.

Natural Variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Gordon, Sean

2013-03-01

Sean Gordon of the USDA on Natural variation in Brachypodium disctachyon: Deep Sequencing of Highly Diverse Natural Accessions at the 8th Annual Genomics of Energy Environment Meeting on March 27, 2013 in Walnut Creek, CA.

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

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

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.

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

Goudeau, Danielle; Nath, Nandita; Ciobanu, Doina

Our approach to prokaryotic single-cell Whole Genome Amplification at the JGI continues to evolve. To increase both the quality and number of single-cell genomes produced, we explore all aspects of the process from cell sorting to sequencing. For example, we now utilize specialized reagents, acoustic liquid handling, and reduced reaction volumes eliminate non-target DNA contamination in WGA reactions. More specifically, we use a cleaner commercial WGA kit from Qiagen that employs a UV decontamination procedure initially developed at the JGI, and we use the Labcyte Echo for tip-less liquid transfer to set up 2uL reactions. Acoustic liquid handling also dramaticallymore » reduces reagent costs. In addition, we are exploring new cell lysis methods including treatment with Proteinase K, lysozyme, and other detergents, in order to complement standard alkaline lysis and allow for more efficient disruption of a wider range of cells. Incomplete lysis represents a major hurdle for WGA on some environmental samples, especially rhizosphere, peatland, and other soils. Finding effective lysis strategies that are also compatible with WGA is challenging, and we are currently assessing the impact of various strategies on genome recovery.« less

Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems (JGI Seventh Annual User Meeting 2012: Genomics of Energy and Environment)

ScienceCinema

Wullschleger, Stan

2018-02-13

Stan Wullschleger of Oak Ridge National Laboratory on "Omics in the Arctic: Genome-enabled Contributions to Carbon Cycle Research in High-Latitude Ecosystems" on March 22, 2012 at the 7th Annual Genomics of Energy & Environment Meeting in Walnut Creek, California.

PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

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

Lukjancenko, Oksana

2012-06-01

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

PanFunPro: Bacterial Pan-Genome Analysis Based on the Functional Profiles (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Lukjancenko, Oksana

2018-01-10

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes (2013 DOE JGI Genomics of Energy and Environment 8th Annual User Meeting)

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

Reeve, Wayne

2013-03-01

Wayne Reeve of Murdoch University on "Genomics Encyclopedia of Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB): a resource for microsymbiont genomes" at the 8th Annual Genomics of Energy & Environment Meeting on March 27, 2013 in Walnut Creek, Calif.

Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Tremblay, Julien

2018-01-22

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

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

Tremblay, Julien

2012-06-01

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Fueling Future with Algal Genomics

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

Grigoriev, Igor

Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils ofmore » secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.« less

MEETING: Chlamydomonas Annotation Jamboree - October 2003

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

Grossman, Arthur R

2007-04-13

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

The Chlamydomonas genome project: a decade on

PubMed Central

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

Complete genome sequence of the rapeseed plant-growth promoting Serratia plymuthica strain AS9

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

Neupane, Saraswoti; Hogberg, Nils; Alstrom, Sadhna

2012-01-01

Serratia plymuthica are plant-associated, plant beneficial species belonging to the family Enterobacteriaceae. The members of the genus Serratia are ubiquitous in nature and their life style varies from endophytic to free-living. S. plymuthica AS9 is of special interest for its ability to inhibit fungal pathogens of rapeseed and to promote plant growth. The genome of S. plymuthica AS9 comprises a 5,442,880 bp long circular chromosome that consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome is part of the project entitled Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogensmore » awarded through the 2010 DOE-JGI Community Sequencing Program (CSP2010).« less

Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

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

Peng, Ze

2012-06-01

Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Peng, Ze

2018-01-24

Ze Peng from DOE JGI presents "Fosmid Cre-LoxP Inverse PCR Paired-End (Fosmid CLIP-PE), a Novel Method for Constructing Fosmid Pair-End Library" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Acidovorax citrulli: generating basic and applied knowledge to tackle a global threat to the cucurbit industry.

PubMed

Burdman, Saul; Walcott, Ron

2012-10-01

Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB) of cucurbit plants. In recent years, the disease has spread to many parts of the world, mainly via the inadvertent distribution of contaminated commercial seeds. Because of the costly lawsuits filed by growers against seed companies and the lack of efficient management methods, BFB represents a serious threat to the cucurbit industry, and primarily to watermelons and melons. Despite the economic importance of the disease, little is known about the basic aspects of A. citrulli pathogenesis. Nevertheless, the release of the genome of one A. citrulli strain, as well as the optimization of molecular manipulation and inoculation methods, has prompted basic studies and allowed advances towards an understanding of A. citrulli pathogenicity. In this article, we summarize the current knowledge about this important pathogen, with emphasis on its epidemiology and the factors involved in its pathogenicity and virulence. Bacteria; Betaproteobacteria; order Burkholderiales; family C omamonadaceae; genus Acidovorax; species citrulli. Gram-negative, strictly aerobic, rod-shaped; average dimensions of 0.5 μm × 1.7 μm; motile by means of an ~5.0-μm-long polar flagellum; colonies on King's medium B are round, smooth, transparent and nonpigmented; optimal temperatures for growth around 27-30 °C; induces a hypersensitive response on nonhost tobacco and tomato leaves. Acidovorax citrulli strains are pathogenic to various species of the Cucurbitaceae family, including watermelon, melon, squash, pumpkin and cucumber. Significant economic losses have been reported in watermelon and melon. Watermelon and melon seedlings and fruits are highly susceptible to A. citrulli. Typical seedling symptoms include water-soaked lesions on cotyledons that are often adjacent to the veins and later become necrotic, lesions on the hypocotyl, and seedling collapse and death. On watermelon fruits, symptoms begin as small, irregular, water-soaked lesions which later extend through the rind, turn brown and crack. On melon fruits, symptoms are characterized by small, often sunken rind lesions and internal fruit decay. Symptoms on the leaves of mature plants are difficult to diagnose because they are often inconspicuous or similar to those caused by other biotic or abiotic stresses. When they occur, leaf lesions can spread along the midrib and main veins. Lesions appear dark-brown to black on watermelon and light to reddish-brown on melon. Bacterial fruit blotch of cucurbits at APSnet, http://www.apsnet.org/edcenter/intropp/lessons/prokaryotes/Pages/BacterialBlotch.aspx; bacterial fruit blotch guide from ASTA, http://www.amseed.com/pdfs/DiseaseGuide-BFB-English.pdf; Acidovorax citrulli AAC00-1 genome at JGI, http://genome.jgi-psf.org/aciav/aciav.info.html. © 2012 THE AUTHORS. MOLECULAR PLANT PATHOLOGY © 2012 BSPP AND BLACKWELL PUBLISHING LTD.

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

DOE PAGES

Whitman, William B.; Woyke, Tanja; Klenk, Hans-Peter; ...

2015-05-17

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Here in this paper, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while theymore » are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity« less

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

PubMed Central

2015-01-01

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Herein, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity. PMID:26203337

The Chlamydomonas genome project: a decade on.

PubMed

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

2014-10-01

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 plant genomics portal of the Joint Genome Institute (JGI), 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 whole transcriptome sequencing (RNA-Seq) data. We present here 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains

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

Whitman, William B.; Woyke, Tanja; Klenk, Hans-Peter

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Here in this paper, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while theymore » are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity« less

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

Klenk, Hans-Peter; Lu, Megan; Lucas, Susan

Saccharomonospora marina Liu et al. 2010 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they might play a role in the primary degradation of plant material by attacking hemicellulose. Organisms belonging to the genus are usually Gram-positive staining, non-acid fast, and classify among the actinomycetes. Next to S. viridis and S. azurea, S. marina is the third member in the genus Saccharomonosporamore » for with a completely sequenced (permanent draft status) type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 5,965,593 bp long chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).« less

Wetlands, Microbes, and the Carbon Cycle: Behind the Scenes @ Berkeley Lab

ScienceCinema

Tringe, Susannah

2018-02-14

Susannah Tringe, who leads the Metagenome Program at the Department of Energy's Joint Genome Institute (JGI), a collaboration in which Berkeley Lab plays a leading role, takes us behind the scenes to show how DNA from unknown wild microbes is extracted and analyzed to see what role they play in the carbon cycle. Tringe collects samples of microbial communities living in the wetland muck of the Sacramento-San Joaquin River Delta, organisms that can determine how these wetlands store or release carbon.

Streamlining the Design-to-Build Transition with Build-Optimization Software Tools.

PubMed

Oberortner, Ernst; Cheng, Jan-Fang; Hillson, Nathan J; Deutsch, Samuel

2017-03-17

Scaling-up capabilities for the design, build, and test of synthetic biology constructs holds great promise for the development of new applications in fuels, chemical production, or cellular-behavior engineering. Construct design is an essential component in this process; however, not every designed DNA sequence can be readily manufactured, even using state-of-the-art DNA synthesis methods. Current biological computer-aided design and manufacture tools (bioCAD/CAM) do not adequately consider the limitations of DNA synthesis technologies when generating their outputs. Designed sequences that violate DNA synthesis constraints may require substantial sequence redesign or lead to price-premiums and temporal delays, which adversely impact the efficiency of the DNA manufacturing process. We have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows. BOOST incorporates knowledge of DNA synthesis success determinants into the design process to output ready-to-build sequences, preempting the need for sequence redesign. The BOOST web application is available at https://boost.jgi.doe.gov and its Application Program Interfaces (API) enable integration into automated, customized DNA design processes. The herein presented results highlight the effectiveness of BOOST in reducing DNA synthesis costs and timelines.

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

PubMed

May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

2009-05-04

The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

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

Meier-Kolthoff, Jan P.; Lu, Megan; Huntemann, Marcel

Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyanmore » blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).« less

Subsurface Microbes Expanding the Tree of Life

ScienceCinema

Banfield, Jillian

2018-02-14

Jillian Banfield, Ph.D., UC Berkeley Professor and Berkeley Lab Earth Sciences Division staff scientist and long-time user of the DOE Joint Genome Institute’s resources shares her perspective on how the DOE JGI helps advance her research addressing knowledge gaps related to the roles of subsurface microbial communities in biogeochemical cycling. The video was filmed near the town of Rifle, Colorado at the primary field site for Phase I of the Subsurface Systems Scientific Focus Area 2.0 sponsored by the DOE Office of Biological and Environmental Research.

The integrated microbial genome resource of analysis.

PubMed

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.

Models of Hematopoietic Dynamics Following Burn for Use in Combined Injury Simulations

DTIC Science & Technology

2015-04-28

distribution is unlimited. 13. SUPPLEMENTARY NOTES 14. ABSTRACT The effects of thermal injury were incorporated into previously developed models that...per kilogram (C kg–1) absorbed dose (rad) 1 × 10–2 joule per kilogram (J kg–1§) equivalent and effective dose (rem) 1 × 10–2 joule per kilogram (J...Gy = 1 J kg–1). **The special name for the SI unit of equivalent and effective dose is the sievert (Sv). (1 Sv = 1 J kg–1). Table of Contents Table

Comparative biochemistry and physiology of iron-respiring bacteria from acidic and neutral-pH environments: Final Technical Report

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

Magnuson, T S

2009-04-07

Acidophilic dissimilatory iron-reducing bacteria (DIRB) are now being detected in a variety of ‘extreme’ low-pH, radionuclide- and heavy-metal contaminated habitats where Fe(III) reduction is taking place, and may represent a significant proportion of metal-transforming organisms in these environments. Acidiphilium cryptum is our model organism, a facultative iron-respiring Alphaproteobacterium. Major findings of this project have been 1) Discovery of novel outer-membrane and periplasmic cytochromes c in acidophiles that are reactive with Fe and Cr, 2) Discovery of Cr(VI) reduction mechanisms in acidophiles, mediated by c-type cytochromes and other reductase activity, 3) Development of enzyme detection methods specific for Cr-reducing enzymes, 4)more » Characterization of biofilm formation in A. cryptum, and 5) Annotation of the Acidiphilium cryptum genome (Magnuson, Kusel, and Cummings, DOE-JGI 2005-2006). Two manuscripts and one book chapter have been published, and several more mauscripts are prepared for submission.« less

Sorbitol dehydrogenase of Aspergillus niger, SdhA, is part of the oxido-reductive D-galactose pathway and essential for D-sorbitol catabolism.

PubMed

Koivistoinen, Outi M; Richard, Peter; Penttilä, Merja; Ruohonen, Laura; Mojzita, Dominik

2012-02-17

In filamentous fungi D-galactose can be catabolised through the oxido-reductive and/or the Leloir pathway. In the oxido-reductive pathway D-galactose is converted to d-fructose in a series of steps where the last step is the oxidation of d-sorbitol by an NAD-dependent dehydrogenase. We identified a sorbitol dehydrogenase gene, sdhA (JGI53356), in Aspergillus niger encoding a medium chain dehydrogenase which is involved in D-galactose and D-sorbitol catabolism. The gene is upregulated in the presence of D-galactose, galactitol and D-sorbitol. An sdhA deletion strain showed reduced growth on galactitol and growth on D-sorbitol was completely abolished. The purified enzyme converted D-sorbitol to D-fructose with K(m) of 50±5 mM and v(max) of 80±10 U/mg. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

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

Kuo, Alan; Grigoriev, Igor

2009-04-17

Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentousmore » ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.« less

Complete genome sequence of Staphylothermus hellenicus P8T

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

Anderson, Iain; Wirth, Reinhard; Lucas, Susan

2011-01-01

Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phy- lum Crenarchaeota. Strain P8T is the type strain of the species and was isolated from a shal- low hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the com- plete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein- coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) La- boratory Sequencing Program (LSP) project.

Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

DOE PAGES

Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex; ...

2017-09-21

Dethiobacter alkaliphilus strain AHT1 T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is thus a Gram-positive bacterium with low GC content, within the phylum Firmicutes. We report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1 T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.

Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile

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

Melton, Emily Denise; Sorokin, Dimitry Y.; Overmars, Lex

Dethiobacter alkaliphilus strain AHT1 T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is thus a Gram-positive bacterium with low GC content, within the phylum Firmicutes. We report its draft genome sequence, which consists of 34 contigs with a total sequence length of 3.12 Mbp. D. alkaliphilus strain AHT1 T was sequenced by the Joint Genome Institute (JGI) as part of the Community Science Program due to its relevance to bioremediation and biotechnological applications.

Utility of screening computed tomography of chest, abdomen and pelvis in patients after heart transplantation.

PubMed

Dasari, Tarun W; Pavlovic-Surjancev, Biljana; Dusek, Linda; Patel, Nilamkumar; Heroux, Alain L

2011-12-01

Malignancy is a late cause of mortality in heart transplant recipients. It is unknown if screening computed tomography scan would lead to early detection of such malignancies or serious vascular anomalies post heart transplantation. This is a single center observational study of patients undergoing surveillance computed tomography of chest, abdomen and pelvis at least 5 years after transplantation. Abnormal findings, included pulmonary nodules, lymphadenopathy and intra-thoracic and intra-abdominal masses and vascular anomalies such as abdominal aortic aneurysm. The clinical follow up of each of these major abnormal findings is summarized. A total of 63 patients underwent computed tomography scan of chest, abdomen and pelvis at least 5 years after transplantation. Of these, 54 (86%) were male and 9 (14%) were female. Mean age was 52±9.2 years. Computed tomography revealed 1 lung cancer (squamous cell) only. Non specific pulmonary nodules were seen in 6 patients (9.5%). The most common incidental finding was abdominal aortic aneurysms (N=6 (9.5%)), which necessitated follow up computed tomography (N=5) or surgery (N=1). Mean time to detection of abdominal aortic aneurysms from transplantation was 14.6±4.2 years. Mean age at the time of detection of abdominal aortic aneurysms was 74.5±3.2 years. Screening computed tomography scan in patients 5 years from transplantation revealed only one malignancy but lead to increased detection of abdominal aortic aneurysms. Thus the utility is low in terms of detection of malignancy. Based on this study we do not recommend routine computed tomography post heart transplantation. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

PubMed Central

Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon; Ovchinnikova, Galina; Verezemska, Olena; Isbandi, Michelle; Thomas, Alex D.; Ali, Rida; Sharma, Kaushal; Kyrpides, Nikos C.; Reddy, T. B. K.

2017-01-01

The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects. These are integrated with over 312 metadata fields from which 58 are controlled vocabularies with 2067 terms. The web interface facilitates submission of a diverse range of Sequencing Projects (such as isolate genome, single-cell genome, metagenome, metatranscriptome) and complex Analysis Projects (such as genome from metagenome, or combined assembly from multiple Sequencing Projects). GOLD provides a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes the Genomic Standards Consortium (GSC) Minimum Information standards. This paper describes the data updates and additional features added during the last two years. PMID:27794040

5 CFR 630.310 - Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion...

Code of Federal Regulations, 2014 CFR

2014-01-01

... determined necessary for Year 2000 computer conversion efforts. 630.310 Section 630.310 Administrative... Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion efforts. (a) Year 2000 computer conversion efforts are deemed to be an exigency of the public business for the...

5 CFR 630.310 - Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion...

Code of Federal Regulations, 2012 CFR

2012-01-01

... determined necessary for Year 2000 computer conversion efforts. 630.310 Section 630.310 Administrative... Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion efforts. (a) Year 2000 computer conversion efforts are deemed to be an exigency of the public business for the...

5 CFR 630.310 - Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion...

Code of Federal Regulations, 2013 CFR

2013-01-01

... determined necessary for Year 2000 computer conversion efforts. 630.310 Section 630.310 Administrative... Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion efforts. (a) Year 2000 computer conversion efforts are deemed to be an exigency of the public business for the...

5 CFR 630.310 - Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion...

Code of Federal Regulations, 2011 CFR

2011-01-01

... determined necessary for Year 2000 computer conversion efforts. 630.310 Section 630.310 Administrative... Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion efforts. (a) Year 2000 computer conversion efforts are deemed to be an exigency of the public business for the...

5 CFR 630.310 - Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion...

Code of Federal Regulations, 2010 CFR

2010-01-01

... determined necessary for Year 2000 computer conversion efforts. 630.310 Section 630.310 Administrative... Scheduling of annual leave by employees determined necessary for Year 2000 computer conversion efforts. (a) Year 2000 computer conversion efforts are deemed to be an exigency of the public business for the...

A homologue of the defender against the apoptotic death gene (dad1 )in UV-exposed Chlamydomonas cells is downregulated with the onset of programmed cell death.

PubMed

Moharikar, Swati; D'Souza, Jacinta S; Rao, Basuthkar J

2007-03-01

We report here the isolation of a homologue of the potential anti-apoptotic gene, defender against apoptotic death (dad1 )from Chlamydomonas reinhardtii cells.Using polymerase chain reaction (PCR),we investigated its expression in the execution process of programmed cell death (PCD)in UV-C exposed dying C.reinhardtii cells.Reverse- transcriptase (RT)-PCR showed that C.reinhardtii dad1 amplification was drastically reduced in UV-C exposed dying C.reinhardtii cells.We connect the downregulation of dad1 with the upregulation of apoptosis protease activating factor-1 (APAF-1)and the physiological changes that occur in C.reinhardtii cells upon exposure to 12 J/m 2 UV-C in order to show a reciprocal relationship between proapoptotic and inhibitor of apoptosis factors.The temporal changes indicate a correlation between the onset of cell death and dad1 downregulation.The sequence of the PCR product of the cDNA encoding the dad1 homologue was aligned with the annotated dad1 (C_20215)from the Chlamydomonas database (http://genome.jgi-psf.org:8080/annotator/servlet/jgi.annotation.Annotation?pDb=chlre2); Annotation?pDb=chlre2 );this sequence was found to show 100% identity,both at the nucleotide and amino acid level. The 327 bp transcript showed an open reading frame of 87 amino acid residues.The deduced amino acid sequence of the putative C.reinhardtii DAD1 homologue showed 54% identity with Oryza sativa, 56 identity with Drosophila melanogaster, 66% identity with Xenopus laevis, and 64% identity with Homo sapiens,Sus scrofa,Gallus gallus,Rattus norvegicus and Mus musculus.

Genome Sequencing and Comparative Analysis of the Biocontrol Agent Trichoderma harzianum sensu stricto TR274

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

Steindorff, Andrei S.; Noronha, Elilane F.; Ulhoa, Cirano J.

2015-03-17

Biological control is a complex process which requires many mechanisms and a high diversity of biochemical pathways. The species of Trichoderma harzianum are well known for their biocontrol activity against many plant pathogens. To gain new insights into the biocontrol mechanism used by T. harzianum, we sequenced the isolate TR274 genome using Illumina. The assembly was performed using AllPaths-LG with a maximum coverage of 100x. The assembly resulted in 2282 contigs with a N50 of 37033bp. The genome size generated was 40.8 Mb and the GC content was 47.7%, similar to other Trichoderma genomes. Using the JGI Annotation Pipeline wemore » predicted 13,932 genes with a high transcriptome support. CEGMA tests suggested 100% genome completeness and 97.9% of RNA-SEQ reads were mapped to the genome. The phylogenetic comparison using orthologous proteins with all Trichoderma genomes sequenced at JGI, corroborates the Trichoderma (T. asperellum and T. atroviride), Longibrachiatum (T. reesei and T. longibrachiatum) and Pachibasium (T. harzianum and T. virens) section division described previously. The comparison between two Trichoderma harzianum species suggests a high genome similarity but some strain-specific expansions. Analyses of the secondary metabolites, CAZymes, transporters, proteases, transcription factors were performed. The Pachybasium section expanded virtually all categories analyzed compared with the other sections, specially Longibrachiatum section, that shows a clear contraction. These results suggests that these proteins families have an important role in their respective phenotypes. Future analysis will improve the understanding of this complex genus and give some insights about its lifestyle and the interactions with the environment.« less

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

PubMed

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).

IMG-ABC: A Knowledge Base To Fuel Discovery of Biosynthetic Gene Clusters and Novel Secondary Metabolites.

PubMed

Hadjithomas, Michalis; Chen, I-Min Amy; Chu, Ken; Ratner, Anna; Palaniappan, Krishna; Szeto, Ernest; Huang, Jinghua; Reddy, T B K; Cimermančič, Peter; Fischbach, Michael A; Ivanova, Natalia N; Markowitz, Victor M; Kyrpides, Nikos C; Pati, Amrita

2015-07-14

In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In this work, we present IMG-ABC (https://img.jgi.doe.gov/abc), an atlas of biosynthetic gene clusters within the Integrated Microbial Genomes (IMG) system, which is aimed at harnessing the power of "big" genomic data for discovering small molecules. IMG-ABC relies on IMG's comprehensive integrated structural and functional genomic data for the analysis of biosynthetic gene clusters (BCs) and associated secondary metabolites (SMs). SMs and BCs serve as the two main classes of objects in IMG-ABC, each with a rich collection of attributes. A unique feature of IMG-ABC is the incorporation of both experimentally validated and computationally predicted BCs in genomes as well as metagenomes, thus identifying BCs in uncultured populations and rare taxa. We demonstrate the strength of IMG-ABC's focused integrated analysis tools in enabling the exploration of microbial secondary metabolism on a global scale, through the discovery of phenazine-producing clusters for the first time in Alphaproteobacteria. IMG-ABC strives to fill the long-existent void of resources for computational exploration of the secondary metabolism universe; its underlying scalable framework enables traversal of uncovered phylogenetic and chemical structure space, serving as a doorway to a new era in the discovery of novel molecules. IMG-ABC is the largest publicly available database of predicted and experimental biosynthetic gene clusters and the secondary metabolites they produce. The system also includes powerful search and analysis tools that are integrated with IMG's extensive genomic/metagenomic data and analysis tool kits. As new research on biosynthetic gene clusters and secondary metabolites is published and more genomes are sequenced, IMG-ABC will continue to expand, with the goal of becoming an essential component of any bioinformatic exploration of the secondary metabolism world. Copyright © 2015 Hadjithomas et al.

Comparative genome analysis in the integrated microbial genomes (IMG) system.

PubMed

Markowitz, Victor M; Kyrpides, Nikos C

2007-01-01

Comparative genome analysis is critical for the effective exploration of a rapidly growing number of complete and draft sequences for microbial genomes. The Integrated Microbial Genomes (IMG) system (img.jgi.doe.gov) has been developed as a community resource that provides support for comparative analysis of microbial genomes in an integrated context. IMG allows users to navigate the multidimensional microbial genome data space and focus their analysis on a subset of genes, genomes, and functions of interest. IMG provides graphical viewers, summaries, and occurrence profile tools for comparing genes, pathways, and functions (terms) across specific genomes. Genes can be further examined using gene neighborhoods and compared with sequence alignment tools.

Phylogenetic relatedness determined between antibiotic resistance and 16S rRNA genes in actinobacteria.

PubMed

Sagova-Mareckova, Marketa; Ulanova, Dana; Sanderova, Petra; Omelka, Marek; Kamenik, Zdenek; Olsovska, Jana; Kopecky, Jan

2015-04-01

Distribution and evolutionary history of resistance genes in environmental actinobacteria provide information on intensity of antibiosis and evolution of specific secondary metabolic pathways at a given site. To this day, actinobacteria producing biologically active compounds were isolated mostly from soil but only a limited range of soil environments were commonly sampled. Consequently, soil remains an unexplored environment in search for novel producers and related evolutionary questions. Ninety actinobacteria strains isolated at contrasting soil sites were characterized phylogenetically by 16S rRNA gene, for presence of erm and ABC transporter resistance genes and antibiotic production. An analogous analysis was performed in silico with 246 and 31 strains from Integrated Microbial Genomes (JGI_IMG) database selected by the presence of ABC transporter genes and erm genes, respectively. In the isolates, distances of erm gene sequences were significantly correlated to phylogenetic distances based on 16S rRNA genes, while ABC transporter gene distances were not. The phylogenetic distance of isolates was significantly correlated to soil pH and organic matter content of isolation sites. In the analysis of JGI_IMG datasets the correlation between phylogeny of resistance genes and the strain phylogeny based on 16S rRNA genes or five housekeeping genes was observed for both the erm genes and ABC transporter genes in both actinobacteria and streptomycetes. However, in the analysis of sequences from genomes where both resistance genes occurred together the correlation was observed for both ABC transporter and erm genes in actinobacteria but in streptomycetes only in the erm gene. The type of erm resistance gene sequences was influenced by linkage to 16S rRNA gene sequences and site characteristics. The phylogeny of ABC transporter gene was correlated to 16S rRNA genes mainly above the genus level. The results support the concept of new specific secondary metabolite scaffolds occurring more likely in taxonomically distant producers but suggest that the antibiotic selection of gene pools is also influenced by site conditions.

20 CFR 229.65 - Initial reduction.

Code of Federal Regulations, 2010 CFR

2010-04-01

... wage (see § 225.2 of this chapter) used to compute the DIB O/M under the Social Security Act rules... that exceed the maximum used in computing social security benefits) for the 5 consecutive years after... earnings that exceed the maximum used in computing social security benefits) for the year of highest...

A survey of the computer literacy of undergraduate dental students at a University Dental School in Ireland during the academic year 1997-98.

PubMed

Ray, N J; Hannigan, A

1999-05-01

As dental practice management becomes more computer-based, the efficient functioning of the dentist will become dependent on adequate computer literacy. A survey has been carried out into the computer literacy of a cohort of 140 undergraduate dental students at a University Dental School in Ireland (years 1-5), in the academic year 1997-98. Aspects investigated by anonymous questionnaire were: (1) keyboard skills; (2) computer skills; (3) access to computer facilities; (4) software competencies and (5) use of medical library computer facilities. The students are relatively unfamiliar with basic computer hardware and software: 51.1% considered their expertise with computers as "poor"; 34.3% had taken a formal typewriting or computer keyboarding course; 7.9% had taken a formal computer course at university level and 67.2% were without access to computer facilities at their term-time residences. A majority of students had never used either word-processing, spreadsheet, or graphics programs. Programs relating to "informatics" were more popular, such as literature searching, accessing the Internet and the use of e-mail which represent the major use of the computers in the medical library. The lack of experience with computers may be addressed by including suitable computing courses at the secondary level (age 13-18 years) and/or tertiary level (FE/HE) education programmes. Such training may promote greater use of generic softwares, particularly in the library, with a more electronic-based approach to data handling.

Older men who use computers have lower risk of dementia.

PubMed

Almeida, Osvaldo P; Yeap, Bu B; Alfonso, Helman; Hankey, Graeme J; Flicker, Leon; Norman, Paul E

2012-01-01

To determine if older men who use computers have lower risk of developing dementia. Cohort study of 5506 community-dwelling men aged 69 to 87 years followed for up to 8.5 years. Use of computers measured as daily, weekly, less than weekly and never. Participants also reported their use of email, internet, word processors, games or other computer activities. The primary outcome was the incidence of ICD-10 diagnosis of dementia as recorded by the Western Australian Data Linkage System. 1857/5506 (33.7%) men reported using computers and 347 (6.3%) received a diagnosis of dementia during an average follow up of 6.0 years (range: 6 months to 8.5 years). The hazard ratio (HR) of dementia was lower among computer users than non-users (HR = 0.62, 95%CI = 0.47-0.81, after adjustment for age, educational attainment, size of social network, and presence of depression or of significant clinical morbidity). The HR of dementia appeared to decrease with increasing frequency of computer use: 0.68 (95%CI = 0.41-1.13), 0.61 (95%CI = 0.39-0.94) and 0.59 (95%CI = 0.40-0.87) for less than weekly, at least weekly and daily. The HR of dementia was 0.66 (95%CI = 0.50-0.86) after the analysis was further adjusted for baseline cognitive function, as measured by the Mini-Mental State Examination. Older men who use computers have lower risk of receiving a diagnosis of dementia up to 8.5 years later. Randomised trials are required to determine if the observed associations are causal.

IMG-ABC. A knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites

DOE PAGES

Hadjithomas, Michalis; Chen, I-Min Amy; Chu, Ken; ...

2015-07-14

In the discovery of secondary metabolites, analysis of sequence data is a promising exploration path that remains largely underutilized due to the lack of computational platforms that enable such a systematic approach on a large scale. In this work, we present IMG-ABC (https://img.jgi.doe.gov/abc), an atlas of biosynthetic gene clusters within the Integrated Microbial Genomes (IMG) system, which is aimed at harnessing the power of “big” genomic data for discovering small molecules. IMG-ABC relies on IMG’s comprehensive integrated structural and functional genomic data for the analysis of biosynthetic gene clusters (BCs) and associated secondary metabolites (SMs). SMs and BCs serve asmore » the two main classes of objects in IMG-ABC, each with a rich collection of attributes. A unique feature of IMG-ABC is the incorporation of both experimentally validated and computationally predicted BCs in genomes as well as metagenomes, thus identifying BCs in uncultured populations and rare taxa. We demonstrate the strength of IMG-ABC’s focused integrated analysis tools in enabling the exploration of microbial secondary metabolism on a global scale, through the discovery of phenazine-producing clusters for the first time in lphaproteobacteria. IMG-ABC strives to fill the long-existent void of resources for computational exploration of the secondary metabolism universe; its underlying scalable framework enables traversal of uncovered phylogenetic and chemical structure space, serving as a doorway to a new era in the discovery of novel molecules. IMG-ABC is the largest publicly available database of predicted and experimental biosynthetic gene clusters and the secondary metabolites they produce. The system also includes powerful search and analysis tools that are integrated with IMG’s extensive genomic/metagenomic data and analysis tool kits. As new research on biosynthetic gene clusters and secondary metabolites is published and more genomes are sequenced, IMG-ABC will continue to expand, with the goal of becoming an essential component of any bioinformatic exploration of the secondary metabolism world.« less

Historical changes in annual peak flows in Maine and implications for flood-frequency analyses

USGS Publications Warehouse

Hodgkins, Glenn A.

2010-01-01

Flood-frequency analyses use statistical methods to compute peak streamflows for selected recurrence intervals— the average number of years between peak flows that are equal to or greater than a specified peak flow. Analyses are based on annual peak flows at a stream. It has long been assumed that the annual peak streamflows used in these computations were stationary (non-changing) over very long periods of time, except in river basins subject to direct effects of human activities, such as urbanization and regulation. Because of the potential effects of global warming on peak flows, the assumption of peak-flow stationarity has recently been questioned. Maine has many streamgages with 50 to 105 years of recorded annual peak streamflows. In this study, this long-term record has been tested for historical flood-frequency stationarity, to provide some insight into future flood frequency. Changes over time in annual instantaneous peak streamflows at 28 U.S. Geological Survey streamgages with long-term data (50 or more years) and relatively complete records were investigated by examining linear trends for each streamgage’s period of record. None of the 28 streamgages had more than 5 years of missing data. Eight streamgages have substantial streamflow regulation. Because previous studies have suggested that changes over time may have occurred as a step change around 1970, step changes between each streamgage’s older record (start year to 1970) and newer record (1971 to 2006) also were computed. The median change over time for all 28 streamgages is an increase of 15.9 percent based on a linear change and an increase of 12.4 percent based on a step change. The median change for the 20 unregulated streamgages is slightly higher than for all 28 streamgages; it is 18.4 percent based on a linear change and 15.0 percent based on a step change. Peak flows with 100- and 5-year recurrence intervals were computed for the 28 streamgages using the full annual peak-flow record and multiple sub-periods of that record using the guidelines (Bulletin 17B) of the Interagency Advisory Committee on Water Data. Magnitudes of 100- and 5-year peak flows computed from sub-periods then were compared to those computed from the full period. Sub-periods of 30 years with starting years staggered by 10 years were evaluated (1907–36, 1917–46, 1927–56, 1937–66, 1947–76, 1957–86, 1967–96, and 1977–2006). Two other sub-periods were evaluated using older data (start-of-record to 1970) and newer data (1971 to 2006). The 5-year peak flow is used to represent small and relatively frequent flood flows in Maine, whereas the 100-year peak flow is used to represent large flood flows. The 1967–96 sub-period generated the highest 100- and 5-year peak flows overall when compared to peak flows based on the full period of record; the median difference for all 28 streamgages is 8 percent for 100- and 5-year peak flows. The 1977–2006 and 1971–2006 sub-periods also generated 100- and 5-year peak flows higher than peak flows based on the full period of record, but not as high as the peak flows based on the 1967–96 sub-period. The 1937–66 sub-period generated the lowest 100- and 5-year peak flows overall. The median difference from full-period peak flows is -11 percent for 100-year peak flows and -8 percent for 5-year peak flows. Overall, differences between peak flows based on the sub-periods and those based on the full periods, generated using the 20 unregulated streamgages, are similar to differences using all 28 streamgages. Increases in the 5- and 100-year peak flows based on recent years of record are, in general, modest when compared to peak flows based on complete periods of record. The highest peak flows are based on the 1967–96 sub-period rather than the most recent sub-period (1977-2006). Peak flows for selected recurrence intervals are sensitive to very high peak flows that may occur once in a century or even less frequently. It is difficult, therefore, to determine which approach will produce the most reliable future estimates of peak flows for selected recurrence intervals, using only recent years of record or the traditional method using the entire historical period. One possible conservative approach to computing peak flows of selected recurrence intervals would be to compute peak flows using recent annual peak flows and the entire period of record, then choose the higher computed value. Whether recent or entire periods of record are used to compute peak flows of selected recurrence intervals, the results of this study highlight the importance of using recent data in the computation of the peak flows. The use of older records alone could result in underestimation of peak flows, particularly peak flows with short recurrence intervals, such as the 5-year peak flows.

Knowledge and utilization of computer-software for statistics among Nigerian dentists.

PubMed

Chukwuneke, F N; Anyanechi, C E; Obiakor, A O; Amobi, O; Onyejiaka, N; Alamba, I

2013-01-01

The use of computer soft ware for generation of statistic analysis has transformed health information and data to simplest form in the areas of access, storage, retrieval and analysis in the field of research. This survey therefore was carried out to assess the level of knowledge and utilization of computer software for statistical analysis among dental researchers in eastern Nigeria. Questionnaires on the use of computer software for statistical analysis were randomly distributed to 65 practicing dental surgeons of above 5 years experience in the tertiary academic hospitals in eastern Nigeria. The focus was on: years of clinical experience; research work experience; knowledge and application of computer generated software for data processing and stastistical analysis. Sixty-two (62/65; 95.4%) of these questionnaires were returned anonymously, which were used in our data analysis. Twenty-nine (29/62; 46.8%) respondents fall within those with 5-10 years of clinical experience out of which none has completed the specialist training programme. Practitioners with above 10 years clinical experiences were 33 (33/62; 53.2%) out of which 15 (15/33; 45.5%) are specialists representing 24.2% (15/62) of the total number of respondents. All the 15 specialists are actively involved in research activities and only five (5/15; 33.3%) can utilize software statistical analysis unaided. This study has i dentified poor utilization of computer software for statistic analysis among dental researchers in eastern Nigeria. This is strongly associated with lack of exposure on the use of these software early enough especially during the undergraduate training. This call for introduction of computer training programme in dental curriculum to enable practitioners develops the attitude of using computer software for their research.

Older Men Who Use Computers Have Lower Risk of Dementia

PubMed Central

Almeida, Osvaldo P.; Yeap, Bu B.; Alfonso, Helman; Hankey, Graeme J.; Flicker, Leon; Norman, Paul E.

2012-01-01

Objective To determine if older men who use computers have lower risk of developing dementia. Methods Cohort study of 5506 community-dwelling men aged 69 to 87 years followed for up to 8.5 years. Use of computers measured as daily, weekly, less than weekly and never. Participants also reported their use of email, internet, word processors, games or other computer activities. The primary outcome was the incidence of ICD-10 diagnosis of dementia as recorded by the Western Australian Data Linkage System. Results 1857/5506 (33.7%) men reported using computers and 347 (6.3%) received a diagnosis of dementia during an average follow up of 6.0 years (range: 6 months to 8.5 years). The hazard ratio (HR) of dementia was lower among computer users than non-users (HR = 0.62, 95%CI = 0.47–0.81, after adjustment for age, educational attainment, size of social network, and presence of depression or of significant clinical morbidity). The HR of dementia appeared to decrease with increasing frequency of computer use: 0.68 (95%CI = 0.41–1.13), 0.61 (95%CI = 0.39–0.94) and 0.59 (95%CI = 0.40–0.87) for less than weekly, at least weekly and daily. The HR of dementia was 0.66 (95%CI = 0.50–0.86) after the analysis was further adjusted for baseline cognitive function, as measured by the Mini-Mental State Examination. Conclusion Older men who use computers have lower risk of receiving a diagnosis of dementia up to 8.5 years later. Randomised trials are required to determine if the observed associations are causal. PMID:22937167

The association between information and communication technology exposure and physical activity, musculoskeletal and visual symptoms and socio-economic status in 5-year-olds.

PubMed

Straker, L M; Pollock, C M; Zubrick, S R; Kurinczuk, J J

2006-05-01

Increasing use of computers by children has raised concerns over the potential impact on their cognitive, social, educational, visual and physical development. Despite this concern, there are no large-scale studies relating the use of computers to specific health indicators in children as they reach school age. A cross-sectional analysis of 1600 5-year-old Western Australian children participating in a longitudinal cohort study was conducted to ascertain their computer use, other activities (watching television and videos, playing electronic games, reading and looking at books, drawing on paper and moderate to vigorous physical activity), and specific health indicators. More than half (56%) of the children used computers each week. Computer use was significantly related to TV viewing (OR 1.97 weekday) and electronic game use (console games OR 2.48 weekday, 1.81 weekend; hand-held games OR 1.88 weekend) and negatively associated with vigorous physical activity on weekends (OR 0.72). Computer use was also significantly related to socio-economic indicators such as the mother being older (40+ years, OR 1.70 weekend, 1.73 weekday), tertiary educated (OR 1.63 weekend) and studying (OR 1.52 weekend, 1.41 weekday). Almost 1% children were reported to have complained of tired or sore muscles, and 2.2% had complained of tired or sore eyes, after watching television or using a computer. A substantial proportion of 5-year-old Western Australian children are using computers. Computer use was related to other sedentary activities and less vigorous activity. While musculoskeletal and vision problems are not widespread, their presence and the sedentary nature of computer use is of public health concern.

7 CFR 1786.153 - Discounted present value.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 2 1-year. 2 3 2-year. 3 4 3-year. 4 5 (1) 5 6 5-year. 6 7 (2) 7 8 7-year. 8 9 (3) 9 10 (3) 10 11 10... Maturities computed as above. 3 A straight line interpolated rate between the 7-year rate and the 10-year rate. (See formula below) 4 A straight line interpolated rate between the 10-year note and the 20-year...

7 CFR 1786.153 - Discounted present value.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 2 1-year. 2 3 2-year. 3 4 3-year. 4 5 (1) 5 6 5-year. 6 7 (2) 7 8 7-year. 8 9 (3) 9 10 (3) 10 11 10... Maturities computed as above. 3 A straight line interpolated rate between the 7-year rate and the 10-year rate. (See formula below) 4 A straight line interpolated rate between the 10-year note and the 20-year...

5 CFR 841.602 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... the Individual Retirement Record under consideration. Unexpended balance means the unrefunded amount... of this chapter; (b) Amounts deposited by an employee for periods of service (including military... service. Year of the computation means the calendar year when the unexpended balance is being computed. ...

Computer-associated health complaints and sources of ergonomic instructions in computer-related issues among Finnish adolescents: a cross-sectional study.

PubMed

Hakala, Paula T; Saarni, Lea A; Ketola, Ritva L; Rahkola, Erja T; Salminen, Jouko J; Rimpelä, Arja H

2010-01-11

The use of computers has increased among adolescents, as have musculoskeletal symptoms. There is evidence that these symptoms can be reduced through an ergonomics approach and through education. The purpose of this study was to examine where adolescents had received ergonomic instructions related to computer use, and whether receiving these instructions was associated with a reduced prevalence of computer-associated health complaints. Mailed survey with nationally representative sample of 12 to 18-year-old Finns in 2001 (n = 7292, response rate 70%). In total, 6961 youths reported using a computer. We tested the associations of computer use time and received ergonomic instructions (predictor variables) with computer-associated health complaints (outcome variables) using logistic regression analysis. To prevent computer-associated complaints, 61.2% reported having been instructed to arrange their desk/chair/screen in the right position, 71.5% to take rest breaks. The older age group (16-18 years) reported receiving instructions or being self-instructed more often than the 12- to 14-year-olds (p < 0.001). Among both age groups the sources of instructions included school (33.1%), family (28.6%), self (self-instructed) (12.5%), ICT-related (8.6%), friends (1.5%) and health professionals (0.8%). Receiving instructions was not related to lower prevalence of computer-associated health complaints. This report shows that ergonomic instructions on how to prevent computer-related musculoskeletal problems fail to reach a substantial number of children. Furthermore, the reported sources of instructions vary greatly in terms of reliability.

Computer-associated health complaints and sources of ergonomic instructions in computer-related issues among Finnish adolescents: A cross-sectional study

PubMed Central

2010-01-01

Background The use of computers has increased among adolescents, as have musculoskeletal symptoms. There is evidence that these symptoms can be reduced through an ergonomics approach and through education. The purpose of this study was to examine where adolescents had received ergonomic instructions related to computer use, and whether receiving these instructions was associated with a reduced prevalence of computer-associated health complaints. Methods Mailed survey with nationally representative sample of 12 to 18-year-old Finns in 2001 (n = 7292, response rate 70%). In total, 6961 youths reported using a computer. We tested the associations of computer use time and received ergonomic instructions (predictor variables) with computer-associated health complaints (outcome variables) using logistic regression analysis. Results To prevent computer-associated complaints, 61.2% reported having been instructed to arrange their desk/chair/screen in the right position, 71.5% to take rest breaks. The older age group (16-18 years) reported receiving instructions or being self-instructed more often than the 12- to 14-year-olds (p < 0.001). Among both age groups the sources of instructions included school (33.1%), family (28.6%), self (self-instructed) (12.5%), ICT-related (8.6%), friends (1.5%) and health professionals (0.8%). Receiving instructions was not related to lower prevalence of computer-associated health complaints. Conclusions This report shows that ergonomic instructions on how to prevent computer-related musculoskeletal problems fail to reach a substantial number of children. Furthermore, the reported sources of instructions vary greatly in terms of reliability. PMID:20064250

Radiological risk assessment of cosmic radiation at aviation altitudes (a trip from Houston Intercontinental Airport to Lagos International Airport).

PubMed

Enyinna, Paschal Ikenna

2016-01-01

Radiological risk parameters associated with aircrew members traveling from Houston Intercontinental Airport to Lagos International Airport have been computed using computer software called EPCARD (version 3.2). The mean annual effective dose of radiation was computed to be 2.94 mSv/year. This result is above the standard permissible limit of 1 mSv/year set for the public and pregnant aircrew members but below the limit set for occupationally exposed workers. The Risk of cancer mortality and excess career time cancer risk computed ranged from 3.5 × 10(-5) to 24.5 × 10(-5) (with average of 14.7 × 10(-5)) and 7 × 10(-4) to 49 × 10(-4) (with average of 29.4 × 10(-4)). Passengers and aircrew members should be aware of the extra cosmic radiation doses taken in during flights. All aircraft operators should monitor radiation doses incurred during aviation trips.

Radiological risk assessment of cosmic radiation at aviation altitudes (a trip from Houston Intercontinental Airport to Lagos International Airport)

PubMed Central

Enyinna, Paschal Ikenna

2016-01-01

Radiological risk parameters associated with aircrew members traveling from Houston Intercontinental Airport to Lagos International Airport have been computed using computer software called EPCARD (version 3.2). The mean annual effective dose of radiation was computed to be 2.94 mSv/year. This result is above the standard permissible limit of 1 mSv/year set for the public and pregnant aircrew members but below the limit set for occupationally exposed workers. The Risk of cancer mortality and excess career time cancer risk computed ranged from 3.5 × 10−5 to 24.5 × 10−5 (with average of 14.7 × 10−5) and 7 × 10−4 to 49 × 10−4 (with average of 29.4 × 10−4). Passengers and aircrew members should be aware of the extra cosmic radiation doses taken in during flights. All aircraft operators should monitor radiation doses incurred during aviation trips. PMID:27651568

7 CFR 5.3 - Selection of calendar year price data.

Code of Federal Regulations, 2014 CFR

2014-01-01

... payments as provided by section 301(a)(1)(B). For Maryland Tobacco, type 32, the price data for each... 7 Agriculture 1 2014-01-01 2014-01-01 false Selection of calendar year price data. 5.3 Section 5.3... year price data. In computing the adjusted base price for those commodities for which calendar year...

7 CFR 5.3 - Selection of calendar year price data.

Code of Federal Regulations, 2010 CFR

2010-01-01

... year price data. In computing the adjusted base price for those commodities for which calendar year price data are used, “* * * the average of the prices received by farmers for such commodity, at such... 7 Agriculture 1 2010-01-01 2010-01-01 false Selection of calendar year price data. 5.3 Section 5.3...

Efficient Graph Based Assembly of Short-Read Sequences on Hybrid Core Architecture

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

Sczyrba, Alex; Pratap, Abhishek; Canon, Shane

2011-03-22

Advanced architectures can deliver dramatically increased throughput for genomics and proteomics applications, reducing time-to-completion in some cases from days to minutes. One such architecture, hybrid-core computing, marries a traditional x86 environment with a reconfigurable coprocessor, based on field programmable gate array (FPGA) technology. In addition to higher throughput, increased performance can fundamentally improve research quality by allowing more accurate, previously impractical approaches. We will discuss the approach used by Convey?s de Bruijn graph constructor for short-read, de-novo assembly. Bioinformatics applications that have random access patterns to large memory spaces, such as graph-based algorithms, experience memory performance limitations on cache-based x86more » servers. Convey?s highly parallel memory subsystem allows application-specific logic to simultaneously access 8192 individual words in memory, significantly increasing effective memory bandwidth over cache-based memory systems. Many algorithms, such as Velvet and other de Bruijn graph based, short-read, de-novo assemblers, can greatly benefit from this type of memory architecture. Furthermore, small data type operations (four nucleotides can be represented in two bits) make more efficient use of logic gates than the data types dictated by conventional programming models.JGI is comparing the performance of Convey?s graph constructor and Velvet on both synthetic and real data. We will present preliminary results on memory usage and run time metrics for various data sets with different sizes, from small microbial and fungal genomes to very large cow rumen metagenome. For genomes with references we will also present assembly quality comparisons between the two assemblers.« less

The WRKY transcription factor family in Brachypodium distachyon.

PubMed

Tripathi, Prateek; Rabara, Roel C; Langum, Tanner J; Boken, Ashley K; Rushton, Deena L; Boomsma, Darius D; Rinerson, Charles I; Rabara, Jennifer; Reese, R Neil; Chen, Xianfeng; Rohila, Jai S; Rushton, Paul J

2012-06-22

A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors.

The WRKY transcription factor family in Brachypodium distachyon

PubMed Central

2012-01-01

Background A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. Results We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. Conclusions The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors. PMID:22726208

Parenting style, the home environment, and screen time of 5-year-old children; the 'be active, eat right' study.

PubMed

Veldhuis, Lydian; van Grieken, Amy; Renders, Carry M; Hirasing, Remy A; Raat, Hein

2014-01-01

The global increase in childhood overweight and obesity has been ascribed partly to increases in children's screen time. Parents have a large influence on their children's screen time. Studies investigating parenting and early childhood screen time are limited. In this study, we investigated associations of parenting style and the social and physical home environment on watching TV and using computers or game consoles among 5-year-old children. This study uses baseline data concerning 5-year-old children (n = 3067) collected for the 'Be active, eat right' study. Children of parents with a higher score on the parenting style dimension involvement, were more likely to spend >30 min/day on computers or game consoles. Overall, families with an authoritative or authoritarian parenting style had lower percentages of children's screen time compared to families with an indulgent or neglectful style, but no significant difference in OR was found. In families with rules about screen time, children were less likely to watch TV>2 hrs/day and more likely to spend >30 min/day on computers or game consoles. The number of TVs and computers or game consoles in the household was positively associated with screen time, and children with a TV or computer or game console in their bedroom were more likely to watch TV>2 hrs/day or spend >30 min/day on computers or game consoles. The magnitude of the association between parenting style and screen time of 5-year-olds was found to be relatively modest. The associations found between the social and physical environment and children's screen time are independent of parenting style. Interventions to reduce children's screen time might be most effective when they support parents specifically with introducing family rules related to screen time and prevent the presence of a TV or computer or game console in the child's room.

Parenting Style, the Home Environment, and Screen Time of 5-Year-Old Children; The ‘Be Active, Eat Right’ Study

PubMed Central

Veldhuis, Lydian; van Grieken, Amy; Renders, Carry M.; HiraSing, Remy A.; Raat, Hein

2014-01-01

Introduction The global increase in childhood overweight and obesity has been ascribed partly to increases in children's screen time. Parents have a large influence on their children's screen time. Studies investigating parenting and early childhood screen time are limited. In this study, we investigated associations of parenting style and the social and physical home environment on watching TV and using computers or game consoles among 5-year-old children. Methods This study uses baseline data concerning 5-year-old children (n = 3067) collected for the ‘Be active, eat right’ study. Results Children of parents with a higher score on the parenting style dimension involvement, were more likely to spend >30 min/day on computers or game consoles. Overall, families with an authoritative or authoritarian parenting style had lower percentages of children's screen time compared to families with an indulgent or neglectful style, but no significant difference in OR was found. In families with rules about screen time, children were less likely to watch TV>2 hrs/day and more likely to spend >30 min/day on computers or game consoles. The number of TVs and computers or game consoles in the household was positively associated with screen time, and children with a TV or computer or game console in their bedroom were more likely to watch TV>2 hrs/day or spend >30 min/day on computers or game consoles. Conclusion The magnitude of the association between parenting style and screen time of 5-year-olds was found to be relatively modest. The associations found between the social and physical environment and children's screen time are independent of parenting style. Interventions to reduce children's screen time might be most effective when they support parents specifically with introducing family rules related to screen time and prevent the presence of a TV or computer or game console in the child's room. PMID:24533092

Research on Using Computers with Preschool-age Children.

ERIC Educational Resources Information Center

Vartuli, Sue; And Others

Twenty-two 3-year-olds, 36 4-year-olds, and eight 5-year-olds were given the option of using two computers with selected, sequenced software games as one of their free-choice or work time activities. During the last half of the 33-week long study, children were also introduced to a floor turtle robot, a standing robot, and to Logo activities.…

Explicating Development of Personal Professional Theories from Higher Vocational Education to Beginning a Professional Career through Computer-Supported Drawing of Concept Maps

ERIC Educational Resources Information Center

van den Bogaart, Antoine C. M.; Hummel, Hans G. K.; Kirschner, Paul A.

2018-01-01

This article explores how personal professional theories (PPTs) develop. PPT development of nine junior accountants and nine novice teachers was monitored by repeated measurements over a period of 1.5 years, from the last year of vocational education until the second year of their professional careers. Computer-supported construction of PPT…

The Technology Refresh Program: Affording State-of-the Art Personal Computing.

ERIC Educational Resources Information Center

Spiwak, Rand

2000-01-01

Describes the Florida Community College Technology Refresh Program in which 28 Florida community colleges refresh their personal computer technology on a three-year cyclical basis through negotiation of a contract with Dell Computer Corporation. Discusses the contract highlights (such as a 22.5 percent discount on personal computers and on-site…

Excessive computer game playing among Norwegian adults: self-reported consequences of playing and association with mental health problems.

PubMed

Wenzel, H G; Bakken, I J; Johansson, A; Götestam, K G; Øren, Anita

2009-12-01

Computer games are the most advanced form of gaming. For most people, the playing is an uncomplicated leisure activity; however, for a minority the gaming becomes excessive and is associated with negative consequences. The aim of the present study was to investigate computer game-playing behaviour in the general adult Norwegian population, and to explore mental health problems and self-reported consequences of playing. The survey includes 3,405 adults 16 to 74 years old (Norway 2007, response rate 35.3%). Overall, 65.5% of the respondents reported having ever played computer games (16-29 years, 93.9%; 30-39 years, 85.0%; 40-59 years, 56.2%; 60-74 years, 25.7%). Among 2,170 players, 89.8% reported playing less than 1 hr. as a daily average over the last month, 5.0% played 1-2 hr. daily, 3.1% played 2-4 hr. daily, and 2.2% reported playing > 4 hr. daily. The strongest risk factor for playing > 4 hr. daily was being an online player, followed by male gender, and single marital status. Reported negative consequences of computer game playing increased strongly with average daily playing time. Furthermore, prevalence of self-reported sleeping problems, depression, suicide ideations, anxiety, obsessions/ compulsions, and alcohol/substance abuse increased with increasing playing time. This study showed that adult populations should also be included in research on computer game-playing behaviour and its consequences.

5 CFR 550.707 - Computation of severance pay fund.

Code of Federal Regulations, 2010 CFR

2010-01-01

... hours in the employee's basic work schedule (excluding overtime hours) varies during the year because of part-time work requirements, compute the weekly average of those hours and multiply that average by the... differential pay under 5 U.S.C. 5343(f) varies from week to week under a regularly recurring cycle of work...

Nurses' attitudes towards computers: cross sectional questionnaire study.

PubMed

Brumini, Gordan; Kovic, Ivor; Zombori, Dejvid; Lulic, Ileana; Petrovecki, Mladen

2005-02-01

To estimate the attitudes of hospital nurses towards computers and the influence of gender, age, education, and computer usage on these attitudes. The study was conducted in two Croatian hospitals where integrated hospital information system is being implemented. There were 1,081 nurses surveyed by an anonymous questionnaire consisting of 8 questions about demographic data, education, and computer usage, and 30 statements on attitudes towards computers. The statements were adapted to a Likert type scale. Differences in attitudes towards computers were compared using one-way ANOVA and Tukey-b post-hoc test. The total score was 120+/-15 (mean+/-standard deviation) out of maximal 150. Nurses younger than 30 years had a higher total score than those older than 30 years (124+/-13 vs 119+/-16 for 30-39 age groups and 117+/-15 for>39 age groups, P<0.001). Nurses with a bachelor's degree (119+/-16 vs 122+/-14, P=0.002) and nurses who had attended computer science courses had a higher total score compared to the others (124+/-13 vs 118+/-16, P<0.001). Nurses using computers more than 5 hours per week had higher total score than those who used computers less than 5 hours (127+/-13 vs 124+/-12 for 1-5 h and and 119+/-14 for <1 hour per day, P<0.001, post-hoc test). Nurses in general have positive attitudes towards computers. These results are important for the planning and implementing an integrated hospital information system.

5 CFR 550.707 - Computation of severance pay fund.

Code of Federal Regulations, 2011 CFR

2011-01-01

... pay for standby duty regularly varies throughout the year, compute the average standby duty premium...), compute the weekly average percentage, and multiply that percentage by the weekly scheduled rate of pay in... hours in a pay status (excluding overtime hours) and multiply that average by the hourly rate of basic...

Computer Generated View of Earth as seen from the Asteroid Toutatis

NASA Image and Video Library

1996-11-27

This computer generated image depicts a view of Earth as seen from the surface of the asteroid Toutatis on Nov 29th 1996. A 2.5 degree field-of-view synthetic computer camera was used for this simulation. Toutatis is visible on this date as a twelfth magnitude object in the night sky in the constellation of Virgo and could be viewed with a medium sized telescope. Toutatis currently approaches Earth once every four years and, on Nov. 29th, 1996 will be 5.2 million kilometers away (approx. 3.3 million miles). In approximately 8 years, on Sept. 29th, 2004, it will be less than 1.6 million kilometers from Earth. This is only 4 times the distance to the moon, and is the closest approach predicted for any known asteroid or comet during the next 60 years. http://photojournal.jpl.nasa.gov/catalog/PIA00515

A Study of the Utilization Patterns of an Elementary School-Based Health Clinic over a 5-Year Period

ERIC Educational Resources Information Center

Johnson, Veda; Hutcherson, Valerie

2006-01-01

The purpose of this study was to determine the utilization pattern of an elementary school-based clinic over a 5-year period. It involved a retrospective analysis of computer-based data for all patient visits during this study period. Results revealed high clinic utilization with an average of over 5 encounters for all users each year. The most…

26 CFR 54.4972-1 - Tax on excess contributions to plans benefiting self-employed individuals.

Code of Federal Regulations, 2010 CFR

2010-04-01

...) and this paragraph for the 1978 taxable year is $15,000, computed as follows: the difference between... paragraph for the 1980 taxable year is $5,000, computed as follows: the difference between (A) $25,000, the...)(4) and this paragraph for 1976 is $10,000 (the difference between (A) $40,000, the amount...

Tables of compound-discount interest rate multipliers for evaluating forestry investments.

Treesearch

Allen L. Lundgren

1971-01-01

Tables, prepared by computer, are presented for 10 selected compound-discount interest rate multipliers commonly used in financial analyses of forestry investments. Two set of tables are given for each of the 10 multipliers. The first set gives multipliers for each year from 1 to 40 years; the second set gives multipliers at 5-year intervals from 5 to 160 years....

Investigation of Intravenous Hydroxocobalamin Compared to Hextend for Resuscitation in a Swine Model of Uncontrolled Hemorrhagic Shock: A Preliminary Report

DTIC Science & Technology

2017-06-16

Iy Dlrec~ b. Is not ~j’lnll I’cr ~pport. res, ~ es or otollr~phs for pu -.. 2. Pilnt your ~me, r~nk;;. l ~Ge. sllln dll~ tt. ’brm In tt.e ~utho(s block...or e eledronl: slgnal1Jre. :> ..••• 1t21 a COP)’of the S9 [e.O.=e report, QA’ DWIR:E> IAC\\JC sl1JGY,progr ev~1 ~ the r8~arch ~ l ". ed l .1udy. If this...a ~chnl~1 U! l caU:,"!IJ~SCI’l~3I1on,~e the ~pe rn~DtlTllI.llon report. eft< , etc.) In the "P~co Tltee" t: x. 4 ..•••1tll a copy of your b’WIlc1

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

Klenk, Hans-Peter; Held, Brittany; Lucas, Susan

Saccharomonospora azurea Runmao et al. 1987 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonosoras are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist and over-heated grain, where they might play a role in the primary degradation of plant material by attacking hemicellulose. They are Gram-negative staining organisms classified among the usually Gram-positive actinomycetes. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for with a completely sequenced type strain genome willmore » be published. Here we describe the features of this organism, together with the complete genome sequence with project status 'permanent draft', and annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).« less

Genome Neighborhood Network Reveals Insights into Enediyne Biosynthesis and Facilitates Prediction and Prioritization for Discovery

PubMed Central

Rudolf, Jeffrey D.; Yan, Xiaohui; Shen, Ben

2015-01-01

The enediynes are one of the most fascinating families of bacterial natural products given their unprecedented molecular architecture and extraordinary cytotoxicity. Enediynes are rare with only 11 structurally characterized members and four additional members isolated in their cycloaromatized form. Recent advances in DNA sequencing have resulted in an explosion of microbial genomes. A virtual survey of the GenBank and JGI genome databases revealed 87 enediyne biosynthetic gene clusters from 78 bacteria strains, implying enediynes are more common than previously thought. Here we report the construction and analysis of an enediyne genome neighborhood network (GNN) as a high-throughput approach to analyze secondary metabolite gene clusters. Analysis of the enediyne GNN facilitated rapid gene cluster annotation, revealed genetic trends in enediyne biosynthetic gene clusters resulting in a simple prediction scheme to determine 9- vs 10-membered enediyne gene clusters, and supported a genomic-based strain prioritization method for enediyne discovery. PMID:26318027

Improving Microbial Genome Annotations in an Integrated Database Context

PubMed Central

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Anderson, Iain; Mavromatis, Konstantinos; Kyrpides, Nikos C.; Ivanova, Natalia N.

2013-01-01

Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. PMID:23424620

Effects of Volcanic Eruptions on Stratospheric Ozone Recovery

NASA Technical Reports Server (NTRS)

Rosenfield, Joan E.

2002-01-01

The effects of the stratospheric sulfate aerosol layer associated with the Mt. Pinatubo volcano and future volcanic eruptions on the recovery of the ozone layer is studied with an interactive two-dimensional photochemical model. The time varying chlorine loading and the stratospheric cooling due to increasing carbon dioxide have been taken into account. The computed ozone and temperature changes associated with the Mt. Pinatubo eruption in 1991 agree well with observations. Long model runs out to the year 2050 have been carried out, in which volcanoes having the characteristics of the Mount Pinatubo volcano were erupted in the model at 10-year intervals starting in the year 2010. Compared to a non-volcanic run using background aerosol loading, transient reductions of globally averaged column ozone of 2-3 percent were computed as a result of each of these eruptions, with the ozone recovering to that computed for the non-volcanic case in about 5 years after the eruption. Computed springtime Arctic column ozone losses of from 10 to 18 percent also recovered to the non-volcanic case within 5 years. These results suggest that the long-term recovery of ozone would not be strongly affected by infrequent volcanic eruptions with a sulfur loading approximating Mt. Pinatubo. Sensitivity studies in which the Arctic lower stratosphere was forced to be 4 K and 10 K colder resulted in transient ozone losses of which also recovered to the non-volcanic case in 5 years. A case in which a volcano five times Mt. Pinatubo was erupted in the year 2010 led to maximum springtime column ozone losses of 45 percent which took 10 years to recover to the background case. Finally, in order to simulate a situation in which frequent smaller volcanic eruptions result in increasing the background sulfate loading, a simulation was made in which the background aerosol was increased by 10 percent per year. This resulted in a delay of the recovery of column ozone to 1980 values of more than 10 years.

Performance of the MIR Cooperative Solar Array After 2.5 Years in Orbit

NASA Technical Reports Server (NTRS)

Kerslake, Thomas W.; Hoffman, David J.

1999-01-01

The Mir Cooperative Solar Array (MCSA) was developed jointly by the United States and Russia to produce 6 kW of power for the Russian space station Mir. Four, multi-orbit test sequences were executed between June 1996 and December 1998 to measure MCSA electrical performance. A dedicated Fortran computer code was developed to analyze the detailed thermal-electrical performance of the MCSA. The computational performance results compared very favorably with the measured flight data in most cases. Minor performance degradation was detected in one current generating section of the MCSA. Yet overall, the flight data indicated the MCSA was meeting and exceeding performance expectations. There was no precipitous performance loss due to contamination or other causes after 2.5 years of operation. In this paper, we review the MCSA flight electrical performance tests, data and computational modeling and discuss findings from data comparisons with the computational results.

Near Retirement Age (≥55 Years) Self-Reported Physical Symptoms and Use of Computers/Mobile Phones at Work and at Leisure

PubMed Central

Gobba, Fabriziomaria

2017-01-01

The aim of this research is to study the symptoms and use of computers/mobile phones of individuals nearing retirement age (≥55 years). A questionnaire was sent to 15,000 Finns (aged 18–65). People who were ≥55 years of age were compared to the rest of the population. Six thousand one hundred and twenty-one persons responded to the questionnaire; 1226 of them were ≥55 years of age. Twenty-four percent of the ≥55-year-old respondents used desktop computers daily for leisure; 47.8% of them frequently experienced symptoms in the neck, and 38.5% in the shoulders. Workers aged ≥55 years had many more physical symptoms than younger people, except with respect to symptoms of the neck. Female daily occupational users of desktop computers had more physical symptoms in the neck. It is essential to take into account that, for people aged ≥55 years, the use of technology can be a sign of wellness. However, physical symptoms in the neck can be associated with the use of computers. PMID:28991182

Tablet PCs: A Physical Educator's New Clipboard

ERIC Educational Resources Information Center

Nye, Susan B.

2010-01-01

Computers in education have come a long way from the abacus of 5,000 years ago to the desktop and laptop computers of today. Computers have transformed the educational environment, and with each new iteration of smaller and more powerful machines come additional advantages for teaching practices. The Tablet PC is one. Tablet PCs are fully…

Level-2 perspectives computed quickly and spontaneously: Evidence from eight- to 9.5-year-old children.

PubMed

Elekes, Fruzsina; Varga, Máté; Király, Ildikó

2017-11-01

It has been widely assumed that computing how a scene looks from another perspective (level-2 perspective taking, PT) is an effortful process, as opposed to the automatic capacity of tracking visual access to objects (level-1 PT). Recently, adults have been found to compute both forms of visual perspectives in a quick but context-sensitive way, indicating that the two functions share more features than previously assumed. However, the developmental literature still shows the dissociation between automatic level-1 and effortful level-2 PT. In the current paper, we report an experiment showing that in a minimally social situation, participating in a number verification task with an adult confederate, eight- to 9.5-year-old children demonstrate similar online level-2 PT capacities as adults. Future studies need to address whether online PT shows selectivity in children as well and develop paradigms that are adequate to test preschoolers' online level-2 PT abilities. Statement of Contribution What is already known on this subject? Adults can access how objects appear to others (level-2 perspective) spontaneously and online Online level-1, but not level-2 perspective taking (PT) has been documented in school-aged children What the present study adds? Eight- to 9.5-year-olds performed a number verification task with a confederate who had the same task Children showed similar perspective interference as adults, indicating spontaneous level-2 PT Not only agent-object relations but also object appearances are computed online by eight- to 9.5-year-olds. © 2017 The British Psychological Society.

Problematic computer game use as expression of Internet addiction and its association with self-rated health in the Lithuanian adolescent population.

PubMed

Ustinavičienė, Ruta; Škėmienė, Lina; Lukšienė, Dalia; Radišauskas, Ričardas; Kalinienė, Gintarė; Vasilavičius, Paulius

2016-01-01

Computers and the Internet have become an integral part of today's life. Problematic gaming is related to adolescent's health. The aim of our study was to evaluate the prevalence of Internet addiction among 13-18-year-old schoolchildren and its relation to sex, age, and time spent playing computer games, game type, and subjective health evaluation. A total of 1806 schoolchildren aged 13-18 years were interviewed. The evaluation of Internet addiction was conducted by the Diagnostic Questionnaire according to Young's methodology. The relation between the choice of computer games type, time spent while playing computer games and respondents' Internet addiction were assessed by using multivariate logistic regression analysis. One-tenth (10.6%) of the boys and 7.7% of the girls aged 13-18 years were Internet addicted. Internet addiction was associated with the type of computer game (action or combat vs. logic) among boys (OR=2.42; 95% CI, 1.03-5.67) and with the amount of time spent playing computer games per day during the last month (≥5 vs. <5h) among girls (OR=2.10; 95% CI, 1.19-3.70). The boys who were addicted to the Internet were more likely to rate their health poorer in comparison to their peers who were not addicted to the Internet (OR=2.48; 95% CI, 1.33-4.62). Internet addiction was significantly associated with poorer self-rated health among boys. Copyright © 2016 The Lithuanian University of Health Sciences. Production and hosting by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

The Effect of a Computer-Based Cartooning Tool on Children's Cartoons and Written Stories

ERIC Educational Resources Information Center

Madden, M.; Chung, P. W. H.; Dawson, C. W.

2008-01-01

This paper reports a study assessing a new computer tool for cartoon storytelling, created by the authors for a target audience in the upper half of the English and Welsh Key Stage 2 (years 5 and 6, covering ages 9-11 years). The tool attempts to provide users with more opportunities for expressive visualisation than previous educational software;…

The diagnostic value and accuracy of conjunctival impression cytology, dry eye symptomatology, and routine tear function tests in computer users.

PubMed

Bhargava, Rahul; Kumar, Prachi; Kaur, Avinash; Kumar, Manjushri; Mishra, Anurag

2014-07-01

To compare the diagnostic value and accuracy of dry eye scoring system (DESS), conjunctival impression cytology (CIC), tear film breakup time (TBUT), and Schirmer's test in computer users. A case-control study was done at two referral eye centers. Eyes of 344 computer users were compared to 371 eyes of age and sex matched controls. Dry eye questionnaire (DESS) was administered to both groups and they further underwent measurement of TBUT, Schirmer's, and CIC. Correlation analysis was performed between DESS, CIC, TBUT, and Schirmer's test scores. A Pearson's coefficient of the linear expression (R (2)) of 0.5 or more was statistically significant. The mean age in cases (26.05 ± 4.06 years) was comparable to controls (25.67 ± 3.65 years) (P = 0.465). The mean symptom score in computer users was significantly higher as compared to controls (P < 0.001). Mean TBUT, Schirmer's test values, and goblet cell density were significantly reduced in computer users (P < 0.001). TBUT, Schirmer's, and CIC were abnormal in 48.5%, 29.1%, and 38.4% symptomatic computer users respectively as compared to 8%, 6.7%, and 7.3% symptomatic controls respectively. On correlation analysis, there was a significant (inverse) association of dry eye symptoms (DESS) with TBUT and CIC scores (R (2) > 0.5), in contrast to Schirmer's scores (R(2) < 0.5). Duration of computer usage had a significant effect on dry eye symptoms severity, TBUT, and CIC scores as compared to Schirmer's test. DESS should be used in combination with TBUT and CIC for dry eye evaluation in computer users.

Final technical report for: Insertional Mutagenesis of Brachypodium distachyon DE-AI02-07ER64452

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

John, Vogel P.

Several bioenergy grasses are poised to become a major source of energy in the United States. Despite their increasing importance, we know little about the basic biology underlying the traits that control the utility of grasses as energy crops. Better knowledge of grass biology (e.g. identification of the genes that control cell wall composition, plant architecture, cell size, cell division, reproduction, nutrient uptake, carbon flux, etc.) could be used to design rational strategies for crop improvement and shorten the time required to domesticate these species. The use of an appropriate model system is an efficient way to gain this knowledge.more » Brachypodium distachyon is a small annual grass with all the attributes needed to be a modern model organism including simple growth requirements, fast generation time, small stature, small genome size and self-fertility. These attributes led to the recommendation in the DOE’s “Breaking the Biological Barriers to Cellulosic Ethanol: A Joint Research Agenda” report to propose developing and using B. distachyon as a model for energy crops to accelerate their domestication. Strategic investments (e.g. genome sequencing) in B. distachyon by the DOE are now bearing fruit and B. distachyon is being used as a model grass by hundreds of laboratories worldwide. Sequence indexed insertional mutants are an extremely powerful tool for both forward and reverse genetics. They allow researchers to order mutants in any gene tagged in the collection by simply emailing a request. The goal of this project was to create a collection of sequence indexed insertional mutants (T-DNA lines) for the model grass Brachypodium distachyon in order to facilitate research by the scientific community. During the course of this grant we created a collection of 23,649 B. distachyon T-DNA lines and identified 26,112 unique insertion sites. The collection can be queried through the project website (http://jgi.doe.gov/our-science/science-programs/plant-genomics/brachypodium/brachypodium-t-dna-collection/) and through the Phytozome genome browser (http://phytozome.jgi.doe.gov/pz/portal.html). The collection has been heavily utilized by the research community and, as of October 23, 2015, 223 orders for 12,069 seeds packets have been filled. In addition to creating this resource, we also optimized methods for transformation and sequencing DNA flanking insertion sites.« less

The New Film Technologies: Computerized Video-Assisted Film Production.

ERIC Educational Resources Information Center

Mott, Donald R.

Over the past few years, video technology has been used to assist film directors after they have shot a scene, to control costs, and to create special effects, especially computer assisted graphics. At present, a computer based editing system called "Film 5" combines computer technology and video tape with film to save as much as 50% of…

The association between acculturation and recreational computer use among Latino adolescents in California.

PubMed

Shi, L; van Meijgaard, J; Simon, P

2012-08-01

Physical inactivity like recreational computer use is a likely factor in the rising obesity prevalence among Latino adolescents. Using the data from California Health Interview Survey, we test the hypothesis whether acculturation is associated with recreational computer use among Latino adolescents. We run linear regressions of the weekly time spent on recreational computer use among Latino adolescents, stratified first by gender and then by age group (12-14 and 15-17 years). Years living in the United States and language at home are used as key variables for acculturation. For all four sub-populations, living in the United States for less than 5 years is significantly associated with fewer hours on recreational computer use, compared with those US-born. Among female adolescents, those who lived in the United States for 10 years or more spent fewer hours on recreational computer use than those US-born. Among adolescents under 15, speaking English only and speaking English plus another language are both significantly associated with more hours on recreational computer use, compared with those who speak a non-English language at home. Educators and health professionals should heed the Latino adolescents' possible increase in recreational computer use. © 2012 The Authors. Pediatric Obesity © 2012 International Association for the Study of Obesity.

ANL site response for the DOE FY1994 information resources management long-range plan

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

Boxberger, L.M.

1992-03-01

Argonne National Laboratory`s ANL Site Response for the DOE FY1994 Information Resources Management (IRM) Long-Range Plan (ANL/TM 500) is one of many contributions to the DOE information resources management long-range planning process and, as such, is an integral part of the DOE policy and program planning system. The Laboratory has constructed this response according to instructions in a Call issued in September 1991 by the DOE Office of IRM Policy, Plans and Oversight. As one of a continuing series, this Site Response is an update and extension of the Laboratory`s previous submissions. The response contains both narrative and tabular material.more » It covers an eight-year period consisting of the base year (FY1991), the current year (FY1992), the budget year (FY1993), the plan year (FY1994), and the out years (FY1995-FY1998). This Site Response was compiled by Argonne National Laboratory`s Computing and Telecommunications Division (CTD), which has the responsibility to provide leadership in optimizing computing and information services and disseminating computer-related technologies throughout the Laboratory. The Site Response consists of 5 parts: (1) a site overview, describes the ANL mission, overall organization structure, the strategic approach to meet information resource needs, the planning process, major issues and points of contact. (2) a software plan for DOE contractors, Part 2B, ``Software Plan FMS plan for DOE organizations, (3) computing resources telecommunications, (4) telecommunications, (5) printing and publishing.« less

ANL site response for the DOE FY1994 information resources management long-range plan

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

Boxberger, L.M.

1992-03-01

Argonne National Laboratory's ANL Site Response for the DOE FY1994 Information Resources Management (IRM) Long-Range Plan (ANL/TM 500) is one of many contributions to the DOE information resources management long-range planning process and, as such, is an integral part of the DOE policy and program planning system. The Laboratory has constructed this response according to instructions in a Call issued in September 1991 by the DOE Office of IRM Policy, Plans and Oversight. As one of a continuing series, this Site Response is an update and extension of the Laboratory's previous submissions. The response contains both narrative and tabular material.more » It covers an eight-year period consisting of the base year (FY1991), the current year (FY1992), the budget year (FY1993), the plan year (FY1994), and the out years (FY1995-FY1998). This Site Response was compiled by Argonne National Laboratory's Computing and Telecommunications Division (CTD), which has the responsibility to provide leadership in optimizing computing and information services and disseminating computer-related technologies throughout the Laboratory. The Site Response consists of 5 parts: (1) a site overview, describes the ANL mission, overall organization structure, the strategic approach to meet information resource needs, the planning process, major issues and points of contact. (2) a software plan for DOE contractors, Part 2B, Software Plan FMS plan for DOE organizations, (3) computing resources telecommunications, (4) telecommunications, (5) printing and publishing.« less

5 CFR 846.304 - Computing FERS annuities for persons with CSRS service.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) and (c). (d)(1) Except as specified in § 846.305, the average pay for computations under paragraphs (b... basic pay in effect over any 3 consecutive years of creditable service or, in the case of an annuity...

5 CFR 846.304 - Computing FERS annuities for persons with CSRS service.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) and (c). (d)(1) Except as specified in § 846.305, the average pay for computations under paragraphs (b... basic pay in effect over any 3 consecutive years of creditable service or, in the case of an annuity...

An Exploration of the Role of Visual Programming Tools in the Development of Young Children's Computational Thinking

ERIC Educational Resources Information Center

Rose, Simon P.; Habgood, M. P. Jacob; Jay, Tim

2017-01-01

Programming tools are being used in education to teach computer science to children as young as 5 years old. This research aims to explore young children's approaches to programming in two tools with contrasting programming interfaces, ScratchJr and Lightbot, and considers the impact of programming approaches on developing computational thinking.…

[The comparison of the expansion of polyps according to the Ki-67 and computed tomography scores].

PubMed

Aydin, Sedat; Sanli, Arif; Tezer, Ilter; Hardal, Umit; Barişik, Nagehan Ozdemir

2009-01-01

The disease extention in nasal polyps was compared by using the mitotic activity rates and the computed tomography scores. This study was conducted on 19 nasal polyposis patients (8 males, 11 females; mean age 40.0+/-13.7 years; range 20 to 63 years). The preoperative computed tomography records of the patients were evaluated according to the Lund-Mackay grading system. The polyp tissues of the same patients were stained with the Ki-67 antigen for immunohistochemical evaluation. The correlation between the radiologic results and the Ki-67 values was compared by means of the Spearman's correlation test. The mean computed tomography score was observed as 14.3+/-4.7 (range 7-24). The mean Ki-67 score resulting from the immunohistochemical staining was calculated as 24.3+/-18.5 (range 3.3-73.5%). A significant correlation was determined between the Ki-67 values and the computed tomography scores. ("Spearman's" correlation factor: 0.677; p<0.001). As the mitotic activity rate of nasal polyps increases, both the volume of the polyps and the computed tomography scores increase as a result of the blockage of the sinus ostiums by the increased polyp volume.

The impact of forest structure on near-ground temperatures during two years of contrasting temperature extremes

Treesearch

Brian E. Potter; Ronald M. Teclaw; John C. Zasada

2001-01-01

The thermal environment of clear-cut, partially cut, and uncut forest sites in northern Wisconsin are examined for a warm year and a cool year. Temperatures at 0.5 m above and 0.05m below ground, as well as base 5 degree C heat sums are computed for each site between May and September and differences between cut and uncut sites compared for the 2 years. differences in...

The outcomes of anxiety, confidence, and self-efficacy with Internet health information retrieval in older adults: a pilot study.

PubMed

Chu, Adeline; Mastel-Smith, Beth

2010-01-01

Technology has a great impact on nursing practice. With the increasing numbers of older Americans using computers and the Internet in recent years, nurses have the capability to deliver effective and efficient health education to their patients and the community. Based on the theoretical framework of Bandura's self-efficacy theory, the pilot project reported findings from a 5-week computer course on Internet health searches in older adults, 65 years or older, at a senior activity learning center. Twelve participants were recruited and randomized to either the intervention or the control group. Measures of computer anxiety, computer confidence, and computer self-efficacy scores were analyzed at baseline, at the end of the program, and 6 weeks after the completion of the program. Analysis was conducted with repeated-measures analysis of variance. Findings showed participants who attended a structured computer course on Internet health information retrieval reported lowered anxiety and increased confidence and self-efficacy at the end of the 5-week program and 6 weeks after the completion of the program as compared with participants who were not in the program. The study demonstrated that a computer course can help reduce anxiety and increase confidence and self-efficacy in online health searches in older adults.

Longitudinal study of low and high achievers in early mathematics.

PubMed

Navarro, Jose I; Aguilar, Manuel; Marchena, Esperanza; Ruiz, Gonzalo; Menacho, Inmaculada; Van Luit, Johannes E H

2012-03-01

Longitudinal studies allow us to identify, which specific maths skills are weak in young children, and whether there is a continuing weakness in these areas throughout their school years. This 2-year study investigated whether certain socio-demographic variables affect early mathematical competency in children aged 5-7 years. A randomly selected sample of 127 students (64 female; 63 male) participated. At the start of the study, the students were approximately 5 years old (M= 5.2; SD= 0.28; range = 4.5-5.8). The students were assessed using the Early Numeracy Test and then allocated to a high (n= 26), middle (n= 76), or low (n= 25) achievers group. The same children were assessed again with the Early Numeracy Test at 6 and 7 years old, respectively. Eight socio-demographic characteristics were also evaluated: family model, education of the parent(s), job of the parent(s), number of family members, birth order, number of computers at home, frequency of teacher visits, and hours watching television. Early Numeracy Test scores were more consistent for the high-achievers group than for the low-achievers group. Approximately 5.5% of low achievers obtained low scores throughout the study. A link between specific socio-demographic characteristics and early achievement in mathematics was only found for number of computers at home. The level of mathematical ability among students aged 5-7 years remains relatively stable regardless of the initial level of achievement. However, early screening for mathematics learning disabilities could be useful in helping low-achieving students overcome learning obstacles. ©2011 The British Psychological Society.

Water-surface profile and flood boundaries for the computed 100-year flood, lower Salt River, Lincoln County, Wyoming

USGS Publications Warehouse

Miller, Kirk A.; Mason, John P.

2000-01-01

The water-surface profile and flood boundaries for the computed 100-year flood were determined for a part of the lower Salt River in Lincoln County, Wyoming. Channel cross-section data were provided by Lincoln County. Cross-section data for bridges and other structures were collected and compiled by the U.S. Geological Survey. Roughness coefficients ranged from 0.034 to 0.100. The 100-year flood was computed using standard methods, ranged from 5,170 to 4,120 cubic feet per second through the study reach, and was adjusted proportional to contributing drainage area. Water-surface elevations were determined by the standard step-backwater method. Flood boundaries were plotted on digital basemaps.

High-Resolution Computed Tomography and Pulmonary Function Findings of Occupational Arsenic Exposure in Workers.

PubMed

Ergün, Recai; Evcik, Ender; Ergün, Dilek; Ergan, Begüm; Özkan, Esin; Gündüz, Özge

2017-05-05

The number of studies where non-malignant pulmonary diseases are evaluated after occupational arsenic exposure is very few. To investigate the effects of occupational arsenic exposure on the lung by high-resolution computed tomography and pulmonary function tests. Retrospective cross-sectional study. In this study, 256 workers with suspected respiratory occupational arsenic exposure were included, with an average age of 32.9±7.8 years and an average of 3.5±2.7 working years. Hair and urinary arsenic levels were analysed. High-resolution computed tomography and pulmonary function tests were done. In workers with occupational arsenic exposure, high-resolution computed tomography showed 18.8% pulmonary involvement. In pulmonary involvement, pulmonary nodule was the most frequently seen lesion (64.5%). The other findings of pulmonary involvement were 18.8% diffuse interstitial lung disease, 12.5% bronchiectasis, and 27.1% bullae-emphysema. The mean age of patients with pulmonary involvement was higher and as they smoked more. The pulmonary involvement was 5.2 times higher in patients with skin lesions because of arsenic. Diffusing capacity of lung for carbon monoxide was significantly lower in patients with pulmonary involvement. Besides lung cancer, chronic occupational inhalation of arsenic exposure may cause non-malignant pulmonary findings such as bronchiectasis, pulmonary nodules and diffuse interstitial lung disease. So, in order to detect pulmonary involvement in the early stages, workers who experience occupational arsenic exposure should be followed by diffusion test and high-resolution computed tomography.

Australian Infection Control Association members' use of skills and resources that promote evidence-based infection control.

PubMed

Murphy, C L; McLaws, M

2000-04-01

To adopt an evidence-based approach, professionals must be able to access, identify, interpret, and critically appraise best evidence. Critical appraisal requires essential skills, such as computer literacy and an understanding of research principles. These skills also are required for professionals to contribute to evidence. In 1996, members of the Australian Infection Control Association were surveyed to establish a profile including the extent to which they were reading infection control publications, using specific documents for policy and guideline development, developing and undertaking research, publishing research, and using computers. The relationships between demographics, computer use, and research activity were examined. The response rate was 63. 4% (630/993). The study group comprised mostly women (96.1%), and most (66.4%) were older than 40 years of age. Median infection control experience was 4 years (mean, 5.4 years; range, <12 months to 35 years). When developing guidelines and policies (92.7%; 584/630), infection control professionals reviewed State Health Department Infection Control Guidelines and Regulations. Research relating to infection control was undertaken by 21.5% (135/628) of the sample, and 27.6% (37/134) of this group published their research findings. Of the respondents (51.1%; 318/622) who used a computer to undertake infection control tasks, the majority (89.0%) used a personal computer for word processing. Regardless of infection control experience, Australian infection control professionals must be adequately prepared to contribute to, access, appraise, and where appropriate, apply best evidence to their practice. We suggest that computer literacy, an understanding of research principles, and familiarity with infection control literature are three essential skills that infection control professionals must possess and regularly exercise.

Command, Control, Communication, Computers and Information Technology (C4&IT). Strategic Plan, FY2008 - 2012

DTIC Science & Technology

2008-01-01

Intentionally Blank 5 Table of Contents INTRODUCTION...18 Goal 5 : Organizational Excellence...fully realized in the next 5 years, it is clear that coordinated activity must occur now to improve the Coast Guard’s operational capabilities

The DTIC Review. Information Terrorism. Volume 5, Number 1

DTIC Science & Technology

2000-03-01

ABSTRACT: (U) This document describes a PERSONAL AUTHORS: Llinas, James; proposed program of research into theories, Bisantz, Ann; Drury , Colin ; Seong...management computer. Before he finished he transferred more than $12 million to other banks and had access to the $500 billion daily transfer account . 3 By the...modem. The General Accounting Office recently estimated that Pentagon computers experience some 250,000 hacker attacks per year and 5 that 65 percent

Applications of personal computers in geophysics

NASA Astrophysics Data System (ADS)

Lee, W. H. K.; Lahr, J. C.; Habermann, R. E.

Since 1981, the use of personal computers (PCs) to increase productivity has become widespread. At present, more than 5 million personal computers are in operation for business, education, engineering, and scientific purposes. Activities within AGU reflect this trend: KOSMOS, the AGU electronic network, was introduced this year, and the AGU Committee on Personal Computers, chaired by W.H K. Lee (U.S. Geological Survey, Menlo Park, Calif.), was recently formed. In addition, in conjunction with the 1986 AGU Fall Meeting, this committee is organizing a personal computer session and hands-on demonstrations to promote applications of personal computers in geophysics.

Policy Information System Computer Program.

ERIC Educational Resources Information Center

Hamlin, Roger E.; And Others

The concepts and methodologies outlined in "A Policy Information System for Vocational Education" are presented in a simple computer format in this booklet. It also contains a sample output representing 5-year projections of various planning needs for vocational education. Computerized figures in the eight areas corresponding to those in the…

Hupa Natural Resources Dictionary.

ERIC Educational Resources Information Center

Bennett, Ruth, Ed.; And Others

Created by children in grades 5-8 who were enrolled in a year-long Hupa language class, this computer-generated, bilingual book contains descriptions and illustrations of local animals, birds, and fish. The introduction explains that students worked on a Macintosh computer able to print the Unifon alphabet used in writing the Hupa language.…

Critical Aspects of the Coastal Drought Index: Length of Salinity Data Record and Ecological Response Data

NASA Astrophysics Data System (ADS)

Conrads, P. A.; Tufford, D. L.; Darby, L. S.

2015-12-01

The phenomenon of coastal drought has a different dynamic from upland droughts that are typically characterized by agricultural, hydrologic, meteorological, and(or) socio-economic impacts. Because of the uniqueness of drought impacts on coastal ecosystems, a coastal drought index (CDI) that uses existing salinity datasets for sites in South Carolina, Georgia, and Florida was developed using an approach similar to the Standardized Precipitation Index (SPI). CDIs characterizing the 1- to 24-month salinity conditions were developed and the evaluation of the CDI indicates that the index can be used for different estuary types (for example, brackish, olioghaline, or mesohaline), for regional comparison between estuaries, and as an index for wet conditions (high freshwater inflow) in addition to drought conditions. Unlike the SPI where long-term precipitation datasets of 50 to 100 years are available for computing the index, there are a limited number of salinity data sets of greater than 10 or 15 years for computing the CDI. To evaluate the length of salinity record necessary to compute the CDI, a 29-year dataset was resampled into 5-, 10-, 15-, and 20-year interval datasets. Comparison of the CDI for the different periods of record show that the range of salinity conditions in the 10-, 15-, and 20-year datasets were similar and results were a close approximation to the CDI computed by using the full period of record. The CDI computed with the 5-year dataset had the largest differences with the CDI computed with the 29-year dataset but did provide useful information on coastal drought and freshwater conditions. An ongoing National Integrated Drought Information System (NIDIS) drought early warning project in the Carolinas is developing ecological linkages to the CDI and evaluating the effectiveness of the CDI as a prediction tool for adaptation planning for future droughts. However, identifying potential coastal drought response datasets is a challenge. Coastal drought is a relatively new concept and existing datasets may not have been collected or understood as "drought response" datasets. We have considered drought response datasets including tree growth and liter fall, harmful algal blooms occurrence, Vibrio infection occurrence, shellfish harvesting data, and shark attacks.

Low-dose computed tomography scans with automatic exposure control for patients of different ages undergoing cardiac PET/CT and SPECT/CT.

PubMed

Yang, Ching-Ching; Yang, Bang-Hung; Tu, Chun-Yuan; Wu, Tung-Hsin; Liu, Shu-Hsin

2017-06-01

This study aimed to evaluate the efficacy of automatic exposure control (AEC) in order to optimize low-dose computed tomography (CT) protocols for patients of different ages undergoing cardiac PET/CT and single-photon emission computed tomography/computed tomography (SPECT/CT). One PET/CT and one SPECT/CT were used to acquire CT images for four anthropomorphic phantoms representative of 1-year-old, 5-year-old and 10-year-old children and an adult. For the hybrid systems investigated in this study, the radiation dose and image quality of cardiac CT scans performed with AEC activated depend mainly on the selection of a predefined image quality index. Multiple linear regression methods were used to analyse image data from anthropomorphic phantom studies to investigate the effects of body size and predefined image quality index on CT radiation dose in cardiac PET/CT and SPECT/CT scans. The regression relationships have a coefficient of determination larger than 0.9, indicating a good fit to the data. According to the regression models, low-dose protocols using the AEC technique were optimized for patients of different ages. In comparison with the standard protocol with AEC activated for adult cardiac examinations used in our clinical routine practice, the optimized paediatric protocols in PET/CT allow 32.2, 63.7 and 79.2% CT dose reductions for anthropomorphic phantoms simulating 10-year-old, 5-year-old and 1-year-old children, respectively. The corresponding results for cardiac SPECT/CT are 8.4, 51.5 and 72.7%. AEC is a practical way to reduce CT radiation dose in cardiac PET/CT and SPECT/CT, but the AEC settings should be determined properly for optimal effect. Our results show that AEC does not eliminate the need for paediatric protocols and CT examinations using the AEC technique should be optimized for paediatric patients to reduce the radiation dose as low as reasonably achievable.

Thyroid cartilage invasion in laryngeal and hypopharyngeal squamous cell carcinoma treated with total laryngectomy.

PubMed

Koopmann, Mario; Weiss, Daniel; Steiger, Matthias; Elges, Sandra; Rudack, Claudia; Stenner, Markus

2016-11-01

The objective of this study is to analyze the accuracy of computed tomography in detecting malignant thyroid cartilage invasion. In a retrospective chart review, 120 patients with carcinoma of the larynx and hypopharynx underwent computed tomography before total laryngectomy. These data were compared with the histological specimens. Multidetector computed tomography (MDCT) scan had a positive predictive value (PPV) of 76 % and a negative predictive value (NPV) of 69 %. The specificity of MDCT was 89 % and sensitivity was 46 %. Comparison between radiologic suspected cartilage invasion and histologic results showed a significant correlation (p < 0.02). We found no significant impact of cartilage invasion concerning survival rates (5-year overall survival p = 0.683; 5-year disease-free survival p = 0.711). Preoperative CT scan is an important instrument in detecting neoplastic cartilage invasion.

Individual and family environmental correlates of television and computer time in 10- to 12-year-old European children: the ENERGY-project.

PubMed

Verloigne, Maïté; Van Lippevelde, Wendy; Bere, Elling; Manios, Yannis; Kovács, Éva; Grillenberger, Monika; Maes, Lea; Brug, Johannes; De Bourdeaudhuij, Ilse

2015-09-18

The aim was to investigate which individual and family environmental factors are related to television and computer time separately in 10- to-12-year-old children within and across five European countries (Belgium, Germany, Greece, Hungary, Norway). Data were used from the ENERGY-project. Children and one of their parents completed a questionnaire, including questions on screen time behaviours and related individual and family environmental factors. Family environmental factors included social, political, economic and physical environmental factors. Complete data were obtained from 2022 child-parent dyads (53.8 % girls, mean child age 11.2 ± 0.8 years; mean parental age 40.5 ± 5.1 years). To examine the association between individual and family environmental factors (i.e. independent variables) and television/computer time (i.e. dependent variables) in each country, multilevel regression analyses were performed using MLwiN 2.22, adjusting for children's sex and age. In all countries, children reported more television and/or computer time, if children and their parents thought that the maximum recommended level for watching television and/or using the computer was higher and if children had a higher preference for television watching and/or computer use and a lower self-efficacy to control television watching and/or computer use. Most physical and economic environmental variables were not significantly associated with television or computer time. Slightly more individual factors were related to children's computer time and more parental social environmental factors to children's television time. We also found different correlates across countries: parental co-participation in television watching was significantly positively associated with children's television time in all countries, except for Greece. A higher level of parental television and computer time was only associated with a higher level of children's television and computer time in Hungary. Having rules regarding children's television time was related to less television time in all countries, except for Belgium and Norway. Most evidence was found for an association between screen time and individual and parental social environmental factors, which means that future interventions aiming to reduce screen time should focus on children's individual beliefs and habits as well parental social factors. As we identified some different correlates for television and computer time and across countries, cross-European interventions could make small adaptations per specific screen time activity and lay different emphases per country.

26 CFR 1.441-0 - Table of contents.

Code of Federal Regulations, 2010 CFR

2010-04-01

...) Computation of taxable income. (1) In general. (2) Length of taxable year. (b) General rules and definitions... accounting period. (4) Calendar year. (5) Fiscal year. (i) Definition. (ii) Recognition. (6) Grandfathered...) INCOME TAXES Accounting Periods § 1.441-0 Table of contents. This section lists the captions contained in...

Prediction of 5-year overall survival in cervical cancer patients treated with radical hysterectomy using computational intelligence methods.

PubMed

Obrzut, Bogdan; Kusy, Maciej; Semczuk, Andrzej; Obrzut, Marzanna; Kluska, Jacek

2017-12-12

Computational intelligence methods, including non-linear classification algorithms, can be used in medical research and practice as a decision making tool. This study aimed to evaluate the usefulness of artificial intelligence models for 5-year overall survival prediction in patients with cervical cancer treated by radical hysterectomy. The data set was collected from 102 patients with cervical cancer FIGO stage IA2-IIB, that underwent primary surgical treatment. Twenty-three demographic, tumor-related parameters and selected perioperative data of each patient were collected. The simulations involved six computational intelligence methods: the probabilistic neural network (PNN), multilayer perceptron network, gene expression programming classifier, support vector machines algorithm, radial basis function neural network and k-Means algorithm. The prediction ability of the models was determined based on the accuracy, sensitivity, specificity, as well as the area under the receiver operating characteristic curve. The results of the computational intelligence methods were compared with the results of linear regression analysis as a reference model. The best results were obtained by the PNN model. This neural network provided very high prediction ability with an accuracy of 0.892 and sensitivity of 0.975. The area under the receiver operating characteristics curve of PNN was also high, 0.818. The outcomes obtained by other classifiers were markedly worse. The PNN model is an effective tool for predicting 5-year overall survival in cervical cancer patients treated with radical hysterectomy.

DUK - A Fast and Efficient Kmer Based Sequence Matching Tool

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

Li, Mingkun; Copeland, Alex; Han, James

2011-03-21

A new tool, DUK, is developed to perform matching task. Matching is to find whether a query sequence partially or totally matches given reference sequences or not. Matching is similar to alignment. Indeed many traditional analysis tasks like contaminant removal use alignment tools. But for matching, there is no need to know which bases of a query sequence matches which position of a reference sequence, it only need know whether there exists a match or not. This subtle difference can make matching task much faster than alignment. DUK is accurate, versatile, fast, and has efficient memory usage. It uses Kmermore » hashing method to index reference sequences and Poisson model to calculate p-value. DUK is carefully implemented in C++ in object oriented design. The resulted classes can also be used to develop other tools quickly. DUK have been widely used in JGI for a wide range of applications such as contaminant removal, organelle genome separation, and assembly refinement. Many real applications and simulated dataset demonstrate its power.« less

Comparison of the 2-, 25-, and 100-year recurrence interval floods computed from observed data with the 1995 urban flood-frequency estimating equations for Georgia

USGS Publications Warehouse

Inman, Ernest J.

1997-01-01

Flood-frequency relations were computed for 28 urban stations, for 2-, 25-, and 100-year recurrence interval floods and the computations were compared to corresponding recurrence interval floods computed from the estimating equations from a 1995 investigation. Two stations were excluded from further comparisons or analyses because neither station had a significant flood during the period of observed record. The comparisons, based on the student's t-test statistics at the 0.05 level of significance, indicate that the mean residuals of the 25- and 100-year floods were negatively biased by 26.2 percent and 31.6 percent, respectively, at the 26 stations. However, the mean residuals of the 2-year floods were 2.5 percent lower than the mean of the 2-year floods computed from the equations, and were not significantly biased. The reason for this negative bias is that the period of observed record at the 26 stations was a relatively dry period. At 25 of the 26 stations, the two highest simulated peaks used to develop the estimating equations occurred many years before the observed record began. However, no attempt was made to adjust the estimating equations because higher peaks could occur after the period of observed record and an adjustment to the equations would cause an underestimation of design floods.

26 CFR 1.263A-9 - The avoided cost method.

Code of Federal Regulations, 2012 CFR

2012-04-01

... least four times during the taxable year (or consecutive 12-month period in the case of a short taxable... computation period with two measurement dates within each computation period. Corporation X must identify... date during the period and dividing the sum of these amounts by two. Under paragraph (c)(5)(iii)(C) of...

26 CFR 1.263A-9 - The avoided cost method.

Code of Federal Regulations, 2013 CFR

2013-04-01

... least four times during the taxable year (or consecutive 12-month period in the case of a short taxable... computation period with two measurement dates within each computation period. Corporation X must identify... date during the period and dividing the sum of these amounts by two. Under paragraph (c)(5)(iii)(C) of...

26 CFR 1.263A-9 - The avoided cost method.

Code of Federal Regulations, 2011 CFR

2011-04-01

... least four times during the taxable year (or consecutive 12-month period in the case of a short taxable... computation period with two measurement dates within each computation period. Corporation X must identify... date during the period and dividing the sum of these amounts by two. Under paragraph (c)(5)(iii)(C) of...

Problem Solving by 5-6 Years Old Kindergarten Children in a Computer Programming Environment: A Case Study

ERIC Educational Resources Information Center

Fessakis, G.; Gouli, E.; Mavroudi, E.

2013-01-01

Computer programming is considered an important competence for the development of higher-order thinking in addition to algorithmic problem solving skills. Its horizontal integration throughout all educational levels is considered worthwhile and attracts the attention of researchers. Towards this direction, an exploratory case study is presented…

Mathematical Language Development and Talk Types in Computer Supported Collaborative Learning Environments

ERIC Educational Resources Information Center

Symons, Duncan; Pierce, Robyn

2015-01-01

In this study we examine the use of cumulative and exploratory talk types in a year 5 computer supported collaborative learning environment. The focus for students in this environment was to participate in mathematical problem solving, with the intention of developing the proficiencies of problem solving and reasoning. Findings suggest that…

Modelling the Landing of a Plane in a Calculus Lab

ERIC Educational Resources Information Center

Morante, Antonio; Vallejo, Jose A.

2012-01-01

We exhibit a simple model of a plane landing that involves only basic concepts of differential calculus, so it is suitable for a first-year calculus lab. We use the computer algebra system Maxima and the interactive geometry software GeoGebra to do the computations and graphics. (Contains 5 figures and 1 note.)

48 CFR 9904.412-60 - Illustrations.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 7 2014-10-01 2014-10-01 false Illustrations. 9904.412-60... computed for 2017, the current year, is $1.5 million. This computed cost is based on the components of... pension cost for 2017 is limited to $1.3 million. In addition, all amounts that were previously being...

26 CFR 1.460-4 - Methods of accounting for long-term contracts.

Code of Federal Regulations, 2014 CFR

2014-04-01

... (CCM), which is one of the permissible methods of accounting for exempt construction contracts... computing taxable income. (3) Post-completion-year income. If a taxpayer has not included the total contract... completion year. For the treatment of post-completion-year costs, see paragraph (b)(5)(v) of this section...

26 CFR 1.460-4 - Methods of accounting for long-term contracts.

Code of Federal Regulations, 2011 CFR

2011-04-01

... (CCM), which is one of the permissible methods of accounting for exempt construction contracts... computing taxable income. (3) Post-completion-year income. If a taxpayer has not included the total contract... completion year. For the treatment of post-completion-year costs, see paragraph (b)(5)(v) of this section...

26 CFR 1.460-4 - Methods of accounting for long-term contracts.

Code of Federal Regulations, 2012 CFR

2012-04-01

... (CCM), which is one of the permissible methods of accounting for exempt construction contracts... computing taxable income. (3) Post-completion-year income. If a taxpayer has not included the total contract... completion year. For the treatment of post-completion-year costs, see paragraph (b)(5)(v) of this section...

26 CFR 1.460-4 - Methods of accounting for long-term contracts.

Code of Federal Regulations, 2010 CFR

2010-04-01

... (CCM), which is one of the permissible methods of accounting for exempt construction contracts... computing taxable income. (3) Post-completion-year income. If a taxpayer has not included the total contract... completion year. For the treatment of post-completion-year costs, see paragraph (b)(5)(v) of this section...

26 CFR 1.460-4 - Methods of accounting for long-term contracts.

Code of Federal Regulations, 2013 CFR

2013-04-01

... (CCM), which is one of the permissible methods of accounting for exempt construction contracts... computing taxable income. (3) Post-completion-year income. If a taxpayer has not included the total contract... completion year. For the treatment of post-completion-year costs, see paragraph (b)(5)(v) of this section...

The Use and Misuse of Computers in Education: Evidence from a Randomized Experiment in Colombia. Impact Evaluation Series No. 29. Policy Research Working Paper 4836

ERIC Educational Resources Information Center

Barrera-Osorio, Felipe; Linden, Leigh L.

2009-01-01

This paper presents the evaluation of the program Computers for Education. The program aims to integrate computers, donated by the private sector, into the teaching of language in public schools. The authors conduct a two-year randomized evaluation of the program using a sample of 97 schools and 5,201 children. Overall, the program seems to have…

[Physiological mechanisms of the etiology of visual fatigue during work involving visual stress].

PubMed

Korniushina, T A

2000-01-01

Physiological parameters of vision were studied in three professional groups (a total of 1204 subjects): microscope operators, subjects working with magnifying glasses, and computer users. General and specific features of visual system fatigue formation were identified. Because of complete (in microscope operators) or partial (in subjects working with magnifying glasses and display users) "deprivation" of accommodation, these subjects develop early presbyopia (at the age of 30-35 years). In microscope operators long strain of accommodation system leads to professional myopia, while display users develop pseudomyopia. The highest overstrain is observed after 4 years of work in microscope operators, after 5 years in magnifying glass users, and after 6 years in computer users.

The mortality impacts of fine particles in France.

PubMed

Pascal, Mathilde; de Crouy Chanel, Perrine; Wagner, Vérène; Corso, Magali; Tillier, Claude; Bentayeb, Malek; Blanchard, Myriam; Cochet, Amandine; Pascal, Laurence; Host, Sabine; Goria, Sarah; Le Tertre, Alain; Chatignoux, Edouard; Ung, Aymeric; Beaudeau, Pascal; Medina, Sylvia

2016-11-15

Worldwide, air pollution has become a main environmental cause of premature mortality. This burden is largely due to fine particles. Recent cohort studies have confirmed the health risks associated with chronic exposure to PM2.5 for European and French populations. We assessed the mortality impact of PM2.5 in continental France using these new results. Based on a meta-analysis of French and European cohorts, we computed a shrunken estimate of PM2.5-mortality relationship for the French population (RR 1.15 [1.05:1.25] for a 10μg/m(3) increase in PM2.5). This RR was applied to PM2.5 annual concentrations estimated at a fine spatial scale, using a classical health impacts assessment method. The health benefits associated with alternative scenarios of improving air quality were computed for 36,219 French municipalities for 2007-2008. 9% of the total mortality in continental France is attributable to anthropogenic PM2.5. This represents >48,000 deaths per year, and 950,000years of life lost per year, more than half occurring in urban areas larger than 100,000 inhabitants. If none of the municipalities exceeded the World Health Organization guideline value for PM2.5 (10μg/m(3)), the total mortality could be decreased by 3%, corresponding to 400,000years of life saved per year. Results were consistent with previous estimates of the long-term mortality impacts of fine particles in France. These findings show that further actions to improve air quality in France would substantially improve health. Copyright © 2016 Elsevier B.V. All rights reserved.

Selected Streamflow Statistics for Streamgaging Stationsin Northeastern Maryland, 2006

USGS Publications Warehouse

Ries, Kernell G.

2006-01-01

Streamflow statistics were calculated for 47 U.S. Geological Survey (USGS) streamgaging stations in northeastern Maryland, in cooperation with (1) the University of Maryland, Baltimore County, Center for Urban Environmental Research and Education; (2) the Baltimore City Department of Public Works; and (3) the Baltimore County Department of Environmental Protection and Resource Management. The statistics include the mean, minimum, maximum, and standard deviation of the daily mean discharges for the periods of record at the stations, as well as flow-duration and low-flow frequency statistics. The flow-duration statistics include the 1-, 2-, 5-, 10-, 15-, 20-, 25-, 30-, 40-, 50-, 60-, 70-, 75-, 80-, 85-, 90-, 95-, 98-, and 99-percent duration discharges. The low-flow frequency statistics include the average discharges for 1, 7, 14, and 30 days that recur, on average, once in 1.01, 2, 5, 10, 20, 50, and 100 years. The statistics were computed only for the 25 stations with periods of record of 10 years or more. The statistics were computed from records available through September 30, 2004 using standard methods and computer software developed by the USGS. A comparison between low-flow frequency statistics computed for this study and for a previous study that used data available through September 30, 1989 was done for seven stations. The comparison indicated that, for the 7-day mean low flow, the newer values were 19.8 and 15.3 percent lower for the 20- and 10-year recurrence intervals, respectively, and 2.1 percent higher for the 2-year recurrence interval, than the older values. For the 14-day mean low flow, the newer 20- and 10-year values were 25.2 and 15.5 percent lower, respectively, and the 2-year value was 2.9 percent higher than the older values. For the 30-day mean low flow, the newer 20-, 10-, and 2-year values were 10.8, 7.9, and 0.8 percent lower, respectively, than the older values. The newer values are generally lower than the older ones most likely because two major droughts have occurred since the older study was completed.

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

DOE PAGES

Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.; ...

2014-06-15

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. The two major goals of that project were (a) to test the hypothesis that there are many benefits to the use the phylogenetic diversity of organisms in the tree of life as a primary criterion for generating their genome sequence and (b) to develop the necessary framework, technology and organization for large-scale sequencing of microbial isolate genomes. While the GEBA pilot project has not yet been entirely completed, both ofmore » the original goals have already been successfully accomplished, leading the way for the next phase of the project. Here we propose taking the GEBA project to the next level, by generating high quality draft genomes for 1,000 bacterial and archaeal strains. This represents a combined 16-fold increase in both scale and speed as compared to the GEBA pilot project (250 isolate genomes in 4+ years). We will follow a similar approach for organism selection and sequencing prioritization as was done for the GEBA pilot project (i.e. phylogenetic novelty, availability and growth of cultures of type strains and DNA extraction capability), focusing on type strains as this ensures reproducibility of our results and provides the strongest linkage between genome sequences and other knowledge about each strain. In turn, this project will constitute a pilot phase of a larger effort that will target the genome sequences of all available type strains of the Bacteria and Archaea.« less

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project

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

Kyrpides, Nikos C.; Woyke, Tanja; Eisen, Jonathan A.

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. The two major goals of that project were (a) to test the hypothesis that there are many benefits to the use the phylogenetic diversity of organisms in the tree of life as a primary criterion for generating their genome sequence and (b) to develop the necessary framework, technology and organization for large-scale sequencing of microbial isolate genomes. While the GEBA pilot project has not yet been entirely completed, both ofmore » the original goals have already been successfully accomplished, leading the way for the next phase of the project. Here we propose taking the GEBA project to the next level, by generating high quality draft genomes for 1,000 bacterial and archaeal strains. This represents a combined 16-fold increase in both scale and speed as compared to the GEBA pilot project (250 isolate genomes in 4+ years). We will follow a similar approach for organism selection and sequencing prioritization as was done for the GEBA pilot project (i.e. phylogenetic novelty, availability and growth of cultures of type strains and DNA extraction capability), focusing on type strains as this ensures reproducibility of our results and provides the strongest linkage between genome sequences and other knowledge about each strain. In turn, this project will constitute a pilot phase of a larger effort that will target the genome sequences of all available type strains of the Bacteria and Archaea.« less

Mid-term survival analysis of closed wedge high tibial osteotomy: A comparative study of computer-assisted and conventional techniques.

PubMed

Bae, Dae Kyung; Song, Sang Jun; Kim, Kang Il; Hur, Dong; Jeong, Ho Yeon

2016-03-01

The purpose of the present study was to compare the clinical and radiographic results and survival rates between computer-assisted and conventional closing wedge high tibial osteotomies (HTOs). Data from a consecutive cohort comprised of 75 computer-assisted HTOs and 75 conventional HTOs were retrospectively reviewed. The Knee Society knee and function scores, Hospital for Special Surgery (HSS) score and femorotibial angle (FTA) were compared between the two groups. Survival rates were also compared with procedure failure. The knee and function scores at one year postoperatively were slightly better in the computer-assisted group than those in conventional group (90.1 vs. 86.1) (82.0 vs. 76.0). The HSS scores at one year postoperatively were slightly better for the computer-assisted HTOs than those of conventional HTOs (89.5 vs. 81.8). The inlier of the postoperative FTA was wider in the computer-assisted group than that in the conventional HTO group (88.0% vs. 58.7%), and mean postoperative FTA was greater in the computer-assisted group that in the conventional HTO group (valgus 9.0° vs. valgus 7.6°, p<0.001). The five- and 10-year survival rates were 97.1% and 89.6%, respectively. No difference was detected in nine-year survival rates (p=0.369) between the two groups, although the clinical and radiographic results were better in the computer-assisted group that those in the conventional HTO group. Mid-term survival rates did not differ between computer-assisted and conventional HTOs. A comparative analysis of longer-term survival rate is required to demonstrate the long-term benefit of computer-assisted HTO. III. Copyright © 2015 Elsevier B.V. All rights reserved.

Comfort and experience with online learning: trends over nine years and associations with knowledge.

PubMed

Cook, David A; Thompson, Warren G

2014-07-01

Some evidence suggests that attitude toward computer-based instruction is an important determinant of success in online learning. We sought to determine how comfort using computers and perceptions of prior online learning experiences have changed over the past decade, and how these associate with learning outcomes. Each year from 2003-2011 we conducted a prospective trial of online learning. As part of each year's study, we asked medicine residents about their comfort using computers and if their previous experiences with online learning were favorable. We assessed knowledge using a multiple-choice test. We used regression to analyze associations and changes over time. 371 internal medicine and family medicine residents participated. Neither comfort with computers nor perceptions of prior online learning experiences showed a significant change across years (p > 0.61), with mean comfort rating 3.96 (maximum 5 = very comfortable) and mean experience rating 4.42 (maximum 6 = strongly agree [favorable]). Comfort showed no significant association with knowledge scores (p = 0.39) but perceptions of prior experiences did, with a 1.56% rise in knowledge score for a 1-point rise in experience score (p = 0.02). Correlations among comfort, perceptions of prior experiences, and number of prior experiences were all small and not statistically significant. Comfort with computers and perceptions of prior experience with online learning remained stable over nine years. Prior good experiences (but not comfort with computers) demonstrated a modest association with knowledge outcomes, suggesting that prior course satisfaction may influence subsequent learning.

Evaluating the risk of appendiceal perforation when using ultrasound as the initial diagnostic imaging modality in children with suspected appendicitis.

PubMed

Alerhand, Stephen; Meltzer, James; Tay, Ee Tein

2017-08-01

Ultrasound scan has gained attention for diagnosing appendicitis due to its avoidance of ionizing radiation. However, studies show that ultrasound scan carries inferior sensitivity to computed tomography scan. A non-diagnostic ultrasound scan could increase the time to diagnosis and appendicectomy, particularly if follow-up computed tomography scan is needed. Some studies suggest that delaying appendicectomy increases the risk of perforation. To investigate the risk of appendiceal perforation when using ultrasound scan as the initial diagnostic imaging modality in children with suspected appendicitis. We retrospectively reviewed 1411 charts of children ≤17 years old diagnosed with appendicitis at two urban academic medical centers. Patients who underwent ultrasound scan first were compared to those who underwent computed tomography scan first. In the sub-group analysis, patients who only received ultrasound scan were compared to those who received initial ultrasound scan followed by computed tomography scan. Main outcome measures were appendiceal perforation rate and time from triage to appendicectomy. In 720 children eligible for analysis, there was no significant difference in perforation rate between those who had initial ultrasound scan and those who had initial computed tomography scan (7.3% vs. 8.9%, p = 0.44), nor in those who had ultrasound scan only and those who had initial ultrasound scan followed by computed tomography scan (8.0% vs. 5.6%, p = 0.42). Those patients who had ultrasound scan first had a shorter triage-to-incision time than those who had computed tomography scan first (9.2 (IQR: 5.9, 14.0) vs. 10.2 (IQR: 7.3, 14.3) hours, p = 0.03), whereas those who had ultrasound scan followed by computed tomography scan took longer than those who had ultrasound scan only (7.8 (IQR: 5.3, 11.6) vs. 15.1 (IQR: 10.6, 20.6), p < 0.001). Children < 12 years old receiving ultrasound scan first had lower perforation rate (p = 0.01) and shorter triage-to-incision time (p = 0.003). Children with suspected appendicitis receiving ultrasound scan as the initial diagnostic imaging modality do not have increased risk of perforation compared to those receiving computed tomography scan first. We recommend that children <12 years of age receive ultrasound scan first.

5 CFR 847.903 - How is the monthly reduction to the retirement annuity computed?

Code of Federal Regulations, 2010 CFR

2010-01-01

... reduction to the retirement annuity computed? (a) The reduction equals: (1) The difference in the present value of the immediate annuity with credit for NAFI service and the deferred annuity without credit for NAFI service, divided by (2) The present value factor for the retiree's attained age (in full years) at...

Evidence for a Non-Lexical Influence on Children's Auditory Repetition of Familiar Words

ERIC Educational Resources Information Center

Budd, Mary-Jane; Hanley, J. Richard; Nozari, Nazbanou

2012-01-01

This paper examines evidence for a nonlexical influence on children's repetition of real words. We investigate the extent to which two computational models of auditory repetition can simulate the performance of 68 children aged between 5 and 11 years-old when they are attempting to repeat familiar words. Both computational accounts were derived…

Technical Specifications for Hardware and Software, and Maintenance in Support of Computer Literacy Program. Volume II.

ERIC Educational Resources Information Center

District of Columbia Public Schools, Washington, DC.

Designed for use by vendors, this guide provides an overview of the objectives for the 5-year computer literacy program to be implemented in the District of Columbia Public Schools; outlines requirements which are mandatory elements of vendors' bids unless explicitly designated "desirable"; and details specifications for computing…

Examining Computational Skills in Prekindergarteners: The Effects of Traditional and Digital Manipulatives in a Prekindergarten Classroom

ERIC Educational Resources Information Center

Mattoon, Cassandra; Bates, Alan; Shifflet, Rena; Latham, Nancy; Ennis, Sarah

2015-01-01

The authors investigated benefits of digital technology compared with traditional manipulatives in relation to preschoolers' development and learning of computational skills. The sample consisted of twenty four 4-and 5-year old children who attended a half-day prekindergarten program five times a week in a university laboratory school in the…

Productivity associated with visual status of computer users.

PubMed

Daum, Kent M; Clore, Katherine A; Simms, Suzanne S; Vesely, Jon W; Wilczek, Dawn D; Spittle, Brian M; Good, Greg W

2004-01-01

The aim of this project is to examine the potential connection between the astigmatic refractive corrections of subjects using computers and their productivity and comfort. We hypothesize that improving the visual status of subjects using computers results in greater productivity, as well as improved visual comfort. Inclusion criteria required subjects 19 to 30 years of age with complete vision examinations before being enrolled. Using a double-masked, placebo-controlled, randomized design, subjects completed three experimental tasks calculated to assess the effects of refractive error on productivity (time to completion and the number of errors) at a computer. The tasks resembled those commonly undertaken by computer users and involved visual search tasks of: (1) counties and populations; (2) nonsense word search; and (3) a modified text-editing task. Estimates of productivity for time to completion varied from a minimum of 2.5% upwards to 28.7% with 2 D cylinder miscorrection. Assuming a conservative estimate of an overall 2.5% increase in productivity with appropriate astigmatic refractive correction, our data suggest a favorable cost-benefit ratio of at least 2.3 for the visual correction of an employee (total cost 268 dollars) with a salary of 25,000 dollars per year. We conclude that astigmatic refractive error affected both productivity and visual comfort under the conditions of this experiment. These data also suggest a favorable cost-benefit ratio for employers who provide computer-specific eyewear to their employees.

Examination of the Relationship between Technology Use of 5-6 Year-Old Children and Their Social Skills and Social Status

ERIC Educational Resources Information Center

Gülay Ogelman, Hülya; Güngör, Hande; Körükçü, Özlem; Erten Sarkaya, Hatice

2018-01-01

The primary objective of this study is to determine the predictive effect of technology use durations of 5-6 year-old children on their social skill levels and social status. In this study, children's technology usage is restricted to the use of television, portable computers, tablets and smartphones. The sample group of the study consisted of 162…

26 CFR 25.2502-1 - Rate of tax.

Code of Federal Regulations, 2010 CFR

2010-04-01

... schedule) 18,900 (6) Tax for year 1955 (item 4 minus item 5) 12,825 Example 3. (i) Facts. During the...,000 Amount of taxable gifts for year 12,000 (b) Computation of tax. The steps set forth in paragraph (a) of this section are followed. (1) Amount of taxable gifts for year $12,000 (2) Total taxable...

Computer-based simulation training in emergency medicine designed in the light of malpractice cases.

PubMed

Karakuş, Akan; Duran, Latif; Yavuz, Yücel; Altintop, Levent; Calişkan, Fatih

2014-07-27

Using computer-based simulation systems in medical education is becoming more and more common. Although the benefits of practicing with these systems in medical education have been demonstrated, advantages of using computer-based simulation in emergency medicine education are less validated. The aim of the present study was to assess the success rates of final year medical students in doing emergency medical treatment and evaluating the effectiveness of computer-based simulation training in improving final year medical students' knowledge. Twenty four Students trained with computer-based simulation and completed at least 4 hours of simulation-based education between the dates Feb 1, 2010 - May 1, 2010. Also a control group (traditionally trained, n =24) was chosen. After the end of training, students completed an examination about 5 randomized medical simulation cases. In 5 cases, an average of 3.9 correct medical approaches carried out by computer-based simulation trained students, an average of 2.8 correct medical approaches carried out by traditionally trained group (t = 3.90, p < 0.005). We found that the success of students trained with simulation training in cases which required complicated medical approach, was statistically higher than the ones who didn't take simulation training (p ≤ 0.05). Computer-based simulation training would be significantly effective in learning of medical treatment algorithms. We thought that these programs can improve the success rate of students especially in doing adequate medical approach to complex emergency cases.

Computer use, sleep duration and health symptoms: a cross-sectional study of 15-year olds in three countries.

PubMed

Nuutinen, Teija; Roos, Eva; Ray, Carola; Villberg, Jari; Välimaa, Raili; Rasmussen, Mette; Holstein, Bjørn; Godeau, Emmanuelle; Beck, Francois; Léger, Damien; Tynjälä, Jorma

2014-08-01

This study investigated whether computer use is associated with health symptoms through sleep duration among 15-year olds in Finland, France and Denmark. We used data from the WHO cross-national Health Behaviour in School-aged Children study collected in Finland, France and Denmark in 2010, including data on 5,402 adolescents (mean age 15.61 (SD 0.37), girls 53%). Symptoms assessed included feeling low, irritability/bad temper, nervousness, headache, stomachache, backache, and feeling dizzy. We used structural equation modeling to explore the mediating effect of sleep duration on the association between computer use and symptom load. Adolescents slept approximately 8 h a night and computer use was approximately 2 h a day. Computer use was associated with shorter sleep duration and higher symptom load. Sleep duration partly mediated the association between computer use and symptom load, but the indirect effects of sleep duration were quite modest in all countries. Sleep duration may be a potential underlying mechanism behind the association between computer use and health symptoms.

Evolution of product lifespan and implications for environmental assessment and management: a case study of personal computers in higher education.

PubMed

Babbitt, Callie W; Kahhat, Ramzy; Williams, Eric; Babbitt, Gregory A

2009-07-01

Product lifespan is a fundamental variable in understanding the environmental impacts associated with the life cycle of products. Existing life cycle and materials flow studies of products, almost without exception, consider lifespan to be constant over time. To determine the validity of this assumption, this study provides an empirical documentation of the long-term evolution of personal computer lifespan, using a major U.S. university as a case study. Results indicate that over the period 1985-2000, computer lifespan (purchase to "disposal") decreased steadily from a mean of 10.7 years in 1985 to 5.5 years in 2000. The distribution of lifespan also evolved, becoming narrower over time. Overall, however, lifespan distribution was broader than normally considered in life cycle assessments or materials flow forecasts of electronic waste management for policy. We argue that these results suggest that at least for computers, the assumption of constant lifespan is problematic and that it is important to work toward understanding the dynamics of use patterns. We modify an age-structured model of population dynamics from biology as a modeling approach to describe product life cycles. Lastly, the purchase share and generation of obsolete computers from the higher education sector is estimated using different scenarios for the dynamics of product lifespan.

TRADOC Union List of Periodicals.

DTIC Science & Technology

1988-08-01

Comp11t er Products TSO Nov 1987+ Compul er Rev iew TRQ 1980. Computer Security Journal TRADOC UNION LIST OF SERIALS P\\GE 103 TSO 1987+ Computer Shopper...c:urrcnrt monith onl.N TSP 1988+ TS( cu-rrenft year only TTF Ap1)r 21 , ŝ 86 + TT1T[’ rr-erit ,ear only De fvii <t - v ’P,’ort T s : 12+ Dfe r :iS 5...Executive Orders TTG 1948-1962. Executive Proclamations TTG 1955-1960. Executive Productivity TSR 0277-5298 current year only Executive Risk Assessment TRC V

The value of computed tomography in myasthenia gravis

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

Brown, L.R.; Muhm, J.R.; Sheedy, P.F. II

1983-01-01

In a 5 year study, 19 patients with myasthenia gravis were studied by computed tomography (CT) and underwent thymectomy. CT was accurate in detecting the nine true thymic masses but could not differentiate thymomas from nonthymomatous masses, including thymic cysts. No thymoma was found in a patient under 25 years of age. In one case, the 18 sec scanner could not differentiate a large gland from a thymoma. In eight cases, glands with histologic thymic hyperplasia and histologically normal thymus appeared to be similar and could not be differentiated by CT.

26 CFR 1.381(c)(1)-1 - Net operating loss carryovers in certain corporate acquisitions.

Code of Federal Regulations, 2011 CFR

2011-04-01

... loss $10,000 Less: X's 1954 taxable income 0 X's 1956 taxable income 0 0 Carryover to X's 8/31/57-year 10,000 Less: X's 8/31/57-year taxable income before net operating loss deduction $1,000 Minus X's net... postacquisition part year 10,000 Less: Y's postacquisition part year taxable income computed under paragraph (f)(5...

Estimates of long-term suspended-sediment loads in Bay Creek at Nebo, Pike County, Illinois, 1940-80

USGS Publications Warehouse

Lazaro, Timothy R.; Fitzgerald, Kathleen K.; Frost, Leonard R.

1984-01-01

Five years of daily suspended-sediment discharges (1968, 1969, 1975, 1976, and 1980) for Bay Creek at Nebo, Illinois, computed from once- or twice-weekly samples (more often during storm events), were used to develop transport equations that can be used to estimate long-term suspended-sediment discharges from long-term water-discharge records. Discharge was divided into three groups based on changes in slope on a graph of logarithms of water discharge versus suspended-sediment discharge. Two subgroups were formed within each of the three groups by determining whether the flow was steady or increasing, or was decreasing. Seasonality was accounted for by introducing day of the year in sine and cosine functions. The suspended-sediment load estimated from the equations for the 5 years was 77.3 percent of that computed from daily sediment- and water-discharge records for those years. The mean annual suspended-sediment load for 41 years of estimated loads was 359 ,500 tons, which represents a yield of about 3.5 tons per acre from the Bay Creek drainage basin. (USGS)

Pulmonary infection caused by Mycobacterium kansasii: findings on computed tomography of the chest*

PubMed Central

Mogami, Roberto; Goldenberg, Telma; de Marca, Patricia Gomes Cytrangulo; Mello, Fernanda Carvalho de Queiroz; Lopes, Agnaldo José

2016-01-01

Objective To describe the main tomography findings in patients diagnosed with pulmonary infection caused by Mycobacterium kansasii. Materials and Methods Retrospective study of computed tomography scans of 19 patients with pulmonary infection by M. kansasii. Results Of the 19 patients evaluated, 10 (52.6%) were male and 9 (47.4%) were female. The mean age of the patients was 58 years (range, 33-76 years). Computed tomography findings were as follows: architectural distortion, in 17 patients (89.5%); reticular opacities and bronchiectasis, in 16 (84.2%); cavities, in 14 (73.7%); centrilobular nodules, in 13 (68.4%); small consolidations, in 10 (52.6%); atelectasis and large consolidations, in 9 (47.4%); subpleural blebs and emphysema, in 6 (31.6%); and adenopathy, in 1 (5.3%). Conclusion There was a predominance of cavities, as well as of involvement of the small and large airways. The airway disease was characterized by bronchiectasis and bronchiolitis presenting as centrilobular nodules. PMID:27777472

Conventional versus computer-assisted technique for total knee arthroplasty: a minimum of 5-year follow-up of 200 patients in a prospective randomized comparative trial.

PubMed

Cip, Johannes; Widemschek, Mark; Luegmair, Matthias; Sheinkop, Mitchell B; Benesch, Thomas; Martin, Arno

2014-09-01

In the literature, studies of computer-assisted total knee arthroplasty (TKA) after mid-term period are not conclusive and long-term data are rare. In a prospective, randomized, comparative study 100 conventional TKAs (group REG) were compared with 100 computer-assisted TKAs (group NAV). Minimum follow-up was 5years. No difference in implant failure was found with 1.1% in group NAV versus 4.6% in group REG (P=0.368). Group NAV showed a significantly less mean deviation of mechanical limb axis (P=0.015), more TKAs (90% versus 81% in group REG) were within 3° varus/valgus and a higher tibial slope and lateral distal femoral angle (LDFA) accuracy was found (P≤0.034). Clinical investigational parameters showed no differences (P≥0.058). Insall and HSS score total were also higher in group NAV (P≤0.016). Copyright © 2014 Elsevier Inc. All rights reserved.

Simulation of Flood Profiles for Catoma Creek near Montgomery, Alabama, 2008

USGS Publications Warehouse

Lee, K.G.; Hedgecock, T.S.

2008-01-01

A one-dimensional step-backwater model was used to simulate flooding conditions for Catoma Creek near Montgomery, Alabama. A peak flow of 50,000 cubic feet per second was computed by the U.S. Geological Survey for the March 1990 flood at the Norman Bridge Road gaging station. Using this estimated peak flow, flood-plain surveys with associated roughness coefficients, and surveyed high-water marks for the March 1990 flood, a flow model was calibrated to closely match the known event. The calibrated model then was used to simulate flooding for the 10-, 50-, 100-, and 500-year recurrence-interval floods. The 100-year flood stage for the Alabama River also was computed in the vicinity of the Catoma Creek confluence using observed high-water profiles from the 1979 and 1990 floods and gaging-station data. The results indicate that the 100-year flood profile for Catoma Creek within the 15-mile study reach is about 2.5 feet higher, on average, than the profile published by the Federal Emergency Management Agency. The maximum and minimum differences are 6.0 feet and 0.8 foot, respectively. All water-surface elevations computed for the 100-year flood are higher than those published by the Federal Emergency Management Agency. The 100-year flood stage computed for the Alabama River in the vicinity of the Catoma Creek confluence was about 4.5 feet lower than the elevation published by the Federal Emergency Management Agency. The results of this study provide the community with flood-profile information that can be used for flood-plain mitigation, future development, and safety plans for the city.

Interaction between smoking and depressive symptoms with subclinical heart disease in the Coronary Artery Risk Development in Young Adults (CARDIA) study.

PubMed

Carroll, Allison J; Carnethon, Mercedes R; Liu, Kiang; Jacobs, David R; Colangelo, Laura A; Stewart, Jesse C; Carr, J Jeffrey; Widome, Rachel; Auer, Reto; Hitsman, Brian

2017-02-01

Evaluate whether smoking exposure and depressive symptoms accumulated over 25 years are synergistically associated with subclinical heart disease, measured by coronary artery calcification (CAC). Participants (baseline: 54.5% women; 51.5% Black; age range = 18-30 years) were followed prospectively from 1985 to 2010 in the Coronary Artery Risk Development in Young Adults (CARDIA) study. Smoking status was queried yearly from Year 0 to Year 25 to compute packyears of smoking exposure. Depressive symptoms were measured on the Center for Epidemiologic Studies Depression (CES-D) scale every 5 years to compute cumulative scores from Year 5 to Year 25. A three-level multinomial logistic regression was used to evaluate the association between cumulative smoking, cumulative depressive symptoms, and their interaction with moderate-risk CAC (score 1-99) and higher-risk CAC (score ≥100) compared with no CAC (score = 0) at Year 25. Models were adjusted for sociodemographic, clinical, and behavioral covariates. Among 3,189 adults, the cumulative Smoking × Depressive Symptoms interaction was not significant for moderate-risk CAC (p = .057), but was significant for higher-risk CAC (p = .001). For adults with a 30-packyear smoking history, average CES-D scores 2, 10, and 16 were, respectively, associated with odds ratios (95% confidence intervals) 3.40 (2.36-4.90), 4.82 (3.03-7.66), and 6.25 (3.31-11.83) for higher-risk CAC (all ps < .05). Cumulative smoking exposure and cumulative depressive symptoms have a synergistic association with subclinical heart disease, where higher lifetime smoking exposure and depressive symptoms are associated with greater odds of CAC. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Five-Year Technology Plan. Educational Planning Center.

ERIC Educational Resources Information Center

Virginia Beach City Public Schools, VA.

This 5-year plan is based on "A Comprehensive Plan for Instructional and Administrative Use of Computers in the Virginia Beach Public Schools" ("The Pogrow Report," completed in December 1984) and the "Task Force Report on Information Systems" (completed in July 1988). These reports document the importance of making…

Prosthetic liner wear in total hip replacement: a longitudinal 13-year study with computed tomography.

PubMed

Weidenhielm, Lars; Olivecrona, Henrik; Maguire, Gerald Q; Noz, Marilyn E

2018-06-01

This case report follows a woman who had a total hip replacement in 1992 when she was 45 years old. Six serial computed tomography (CT) examinations over a period of 13 years provided information that allowed her revision surgery to be limited to liner replacement as opposed to replacement of the entire prosthesis. Additionally, they provided data that ruled out the presence of osteolysis and indeed none was found at surgery. In 2004, when the first CT was performed, the 3D distance the femoral head had penetrated into the cup was determined to be 2.6 mm. By 2017, femoral head penetration had progressed to 5.0 mm. The extracted liner showed wear at the thinnest part to be 5.5 mm, as measured with a micrometer. The use of modern CT techniques can identify problems, while still correctable without major surgery. Furthermore, the ability of CT to assess the direction of wear revealed that the liner wear changed from the cranial to dorsal direction.

Examining the Relationship between Digital Game Preferences and Computational Thinking Skills

ERIC Educational Resources Information Center

Yildiz, Hatice Durak; Yilmaz, Fatma Gizem Karaoglan; Yilmaz, Ramazan

2017-01-01

The purpose of this study is to identify whether computational thinking skills among secondary school students differ depending on the type of digital games they play. The participants of this study were 202 secondary school students at 5th, 6th, 7th and 8th grades during 2016-2017 academic year. Correlational survey method was used during this…

26 CFR 25.2512-5 - Valuation of annuities, unitrust interests, interests for life or term of years, and remainder or...

Code of Federal Regulations, 2010 CFR

2010-04-01

... transferred by gift is the present value of the interests determined under paragraph (d) of this section... standard actuarial factors and examples that illustrate how to use the tables to compute the present value... and special actuarial factors that may be necessary to compute the present value of similar interests...

Hotline and Walk-In Consulting. Microcomputing Working Paper Series.

ERIC Educational Resources Information Center

Wozny, Lucy Anne

In the Fall of 1982, Drexel University introduced a new educational program for the 1983-84 academic year that required every freshman to have access to a personal computer for use in all areas of the curriculum. The computer selected was the 128K Macintosh. As of January 1985, approximately 5,000 students, faculty, and staff on the Drexel campus…

Computed tomography diagnosis of a thoracic and abdominal penetrating foreign body in a dog

PubMed Central

Appleby, Ryan; zur Linden, Alex; Singh, Ameet; Finck, Cyrielle; Crawford, Evan

2015-01-01

A 1.5-year-old, spayed female, mixed-breed dog was presented for hemoabdomen associated with an abdominal mass. Upon presentation bicavitary effusion was diagnosed. A penetrating intra-abdominal wooden foreign body was identified using computed tomography. This case describes a thoracic penetrating wooden foreign body causing bicavitary effusion following migration into the retroperitoneal space. PMID:26538669

Pain, Work-related Characteristics, and Psychosocial Factors among Computer Workers at a University Center.

PubMed

Mainenti, Míriam Raquel Meira; Felicio, Lilian Ramiro; Rodrigues, Erika de Carvalho; Ribeiro da Silva, Dalila Terrinha; Vigário Dos Santos, Patrícia

2014-04-01

[Purpose] Complaint of pain is common in computer workers, encouraging the investigation of pain-related workplace factors. This study investigated the relationship among work-related characteristics, psychosocial factors, and pain among computer workers from a university center. [Subjects and Methods] Fifteen subjects (median age, 32.0 years; interquartile range, 26.8-34.5 years) were subjected to measurement of bioelectrical impedance; photogrammetry; workplace measurements; and pain complaint, quality of life, and motivation questionnaires. [Results] The low back was the most prevalent region of complaint (76.9%). The number of body regions for which subjects complained of pain was greater in the no rest breaks group, which also presented higher prevalences of neck (62.5%) and low back (100%) pain. There were also observed associations between neck complaint and quality of life; neck complaint and head protrusion; wrist complaint and shoulder angle; and use of a chair back and thoracic pain. [Conclusion] Complaint of pain was associated with no short rest breaks, no use of a chair back, poor quality of life, high head protrusion, and shoulder angle while using the mouse of a computer.

[Cost analysis for navigation in knee endoprosthetics].

PubMed

Cerha, O; Kirschner, S; Günther, K-P; Lützner, J

2009-12-01

Total knee arthroplasty (TKA) is one of the most frequent procedures in orthopaedic surgery. The outcome depends on a range of factors including alignment of the leg and the positioning of the implant in addition to patient-associated factors. Computer-assisted navigation systems can improve the restoration of a neutral leg alignment. This procedure has been established especially in Europe and North America. The additional expenses are not reimbursed in the German DRG system (Diagnosis Related Groups). In the present study a cost analysis of computer-assisted TKA compared to the conventional technique was performed. The acquisition expenses of various navigation systems (5 and 10 year depreciation), annual costs for maintenance and software updates as well as the accompanying costs per operation (consumables, additional operating time) were considered. The additional operating time was determined on the basis of a meta-analysis according to the current literature. Situations with 25, 50, 100, 200 and 500 computer-assisted TKAs per year were simulated. The amount of the incremental costs of the computer-assisted TKA depends mainly on the annual volume and the additional operating time. A relevant decrease of the incremental costs was detected between 50 and 100 procedures per year. In a model with 100 computer-assisted TKAs per year an additional operating time of 14 mins and a 10 year depreciation of the investment costs, the incremental expenses amount to 300-395 depending on the navigation system. Computer-assisted TKA is associated with additional costs. From an economical point of view an amount of more than 50 procedures per year appears to be favourable. The cost-effectiveness could be estimated if long-term results will show a reduction of revisions or a better clinical outcome.

The quality and impact of computer supported collaborative learning (CSCL) in radiology case-based learning.

PubMed

Kourdioukova, Elena V; Verstraete, Koenraad L; Valcke, Martin

2011-06-01

The aim of this research was to explore (1) clinical years students' perceptions about radiology case-based learning within a computer supported collaborative learning (CSCL) setting, (2) an analysis of the collaborative learning process, and (3) the learning impact of collaborative work on the radiology cases. The first part of this study focuses on a more detailed analysis of a survey study about CSCL based case-based learning, set up in the context of a broader radiology curriculum innovation. The second part centers on a qualitative and quantitative analysis of 52 online collaborative learning discussions from 5th year and nearly graduating medical students. The collaborative work was based on 26 radiology cases regarding musculoskeletal radiology. The analysis of perceptions about collaborative learning on radiology cases reflects a rather neutral attitude that also does not differ significantly in students of different grade levels. Less advanced students are more positive about CSCL as compared to last year students. Outcome evaluation shows a significantly higher level of accuracy in identification of radiology key structures and in radiology diagnosis as well as in linking the radiological signs with available clinical information in nearly graduated students. No significant differences between different grade levels were found in accuracy of using medical terminology. Students appreciate computer supported collaborative learning settings when tackling radiology case-based learning. Scripted computer supported collaborative learning groups proved to be useful for both 5th and 7th year students in view of developing components of their radiology diagnostic approaches. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Coronary revascularization vs. medical therapy following coronary-computed tomographic angiography in patients with low-, intermediate- and high-risk coronary artery disease: results from the CONFIRM long-term registry

PubMed Central

Schulman-Marcus, Joshua; Lin, Fay Y.; Gransar, Heidi; Berman, Daniel; Callister, Tracy; DeLago, Augustin; Hadamitzky, Martin; Hausleiter, Joerg; Al-Mallah, Mouaz; Budoff, Matthew; Kaufmann, Philipp; Achenbach, Stephan; Raff, Gilbert; Chinnaiyan, Kavitha; Cademartiri, Filippo; Maffei, Erica; Villines, Todd; Kim, Yong-Jin; Leipsic, Jonathon; Feuchtner, Gudrun; Rubinshtein, Ronen; Pontone, Gianluca; Andreini, Daniele; Marques, Hugo; Chang, Hyuk-Jae; Chow, Benjamin J.W.; Cury, Ricardo C.; Dunning, Allison; Shaw, Leslee; Min, James K.

2017-01-01

Abstract Aims To identify the effect of early revascularization on 5-year survival in patients with CAD diagnosed by coronary-computed tomographic angiography (CCTA). Methods and results We examined 5544 stable patients with suspected CAD undergoing CCTA who were followed a median of 5.5 years in a large international registry. Patients were categorized as having low-, intermediate-, or high-risk CAD based on CCTA findings. Two treatment groups were defined: early revascularization within 90 days of CCTA (n = 1171) and medical therapy (n = 4373). To account for the non-randomized referral to revascularization, we developed a propensity score by logistic regression. This score was incorporated into Cox proportional hazard models to calculate the effect of revascularization on all-cause mortality. Death occurred in 363 (6.6%) patients and was more frequent in medical therapy. In multivariable models, when compared with medical therapy, the mortality benefit of revascularization varied significantly over time and by CAD risk (P for interaction 0.04). In high-risk CAD, revascularization was significantly associated with lower mortality at 1 year (hazard ratio [HR] 0.22, 95% confidence interval [CI] 0.11–0.47) and 5 years (HR 0.31, 95% CI 0.18–0.54). For intermediate-risk CAD, revascularization was associated with reduced mortality at 1 year (HR 0.45, 95% CI 0.22–0.93) but not 5 years (HR 0.63, 95% CI 0.33–1.20). For low-risk CAD, there was no survival benefit at either time point. Conclusions Early revascularization was associated with reduced 1-year mortality in intermediate- and high-risk CAD detected by CCTA, but this association only persisted for 5-year mortality in high-risk CAD. PMID:28329294

[Foot arch shape in children aged 2-5 years according to the data of plantography and holographic interferometry].

PubMed

bol'shakov, O P; Kotov, I R; Poliakova, E L

2014-01-01

25 children aged 2 to 5 years were examined orthopedically using the methods of plantometry and holographic interferometry of three-dimensional casts of footprints. The computer maps of the foot arch surface were obtained and the graphic reconstruction of the arch shape was performed in normal cases and in children with flatfoot. Most significant deviations of the foot arch shape, probably associated with the development delay, were detected in 4-5-year-old children under the dynamic load. Some additional advantages of holographic interferometry for the early diagnosis of flatfoot in children were demonstrated.

Motivation in computer-assisted instruction.

PubMed

Hu, Amanda; Shewokis, Patricia A; Ting, Kimberly; Fung, Kevin

2016-08-01

Computer-aided instruction (CAI) is defined as instruction in which computers play a central role as the means of information delivery and direct interaction with learners. Computer-aided instruction has become mainstream in medical school curricula. For example, a three-dimensional (3D) computer module of the larynx has been created to teach laryngeal anatomy. Although the novelty and educational potential of CAI has garnered much attention, these new technologies have been plagued with low utilization rates. Several experts attribute this problem to lack of motivation in students. Motivation is defined as the desire and action toward goal-oriented behavior. Psychologist Dr. John Keller developed the ARCS theory of motivational learning, which proposed four components: attention (A), relevance (R), concentration (C), and satisfaction (S). Keller believed that motivation is not only an innate characteristic of the pupil; it can also be influenced by external factors, such as the instructional design of the curriculum. Thus, understanding motivation is an important step to designing CAI appropriately. Keller also developed a 36-item validated instrument called the Instructional Materials Motivation Survey (IMMS) to measure motivation. The objective of this study was to study motivation in CAI. Medical students learning anatomy with the 3D computer module will have higher laryngeal anatomy test scores and higher IMMS motivation scores. Higher anatomy test scores will be positively associated with higher IMMS scores. Prospective, randomized, controlled trial. After obtaining institutional review board approval, 100 medical students (mean age 25.5 ± 2.5, 49% male) were randomized to either the 3D computer module (n = 49) or written text (n = 51). Information content was identical in both arms. Students were given 30 minutes to study laryngeal anatomy and then completed the laryngeal anatomy test and IMMS. Students were categorized as either junior (year 1 and 2) or senior (year 3 and 4). There were no significant differences in anatomy scores based on educational modality. There was significant interaction of educational modality by year [F(1,96) = 4.12, P = 0.045, ω(2)  = 0.031]. For the total score, there was a significant effect of year [F(1,96) = 22.28, P < 0.001, ω(2)  = 0.178], with seniors (15.4 ± 2.6) scoring significantly higher than juniors (12.8 ± 3.1). For the motivational score, the total IMMS score had two significant effects. With educational modality [F(1,96) = 5.18, P = 0.025, ω(2)  = 0.041], the 3D group (12.4 ± 2.8) scored significantly higher than the written text group (11.7 ± 3.2). With year [F(1,96) = 25.31, P < 0.001, ω(2)  = 0.198], seniors (13.4 ± 3.0) scored significantly higher than juniors (10.8 ± 2.5). Pearson's correlation showed positive associations (r = 0.22-0.91) between anatomy scores and IMMS motivation scores (P < 0.05). Computer-aided instruction conferred no measurable educational benefit over traditional written text in medical students; however, CAI was associated with higher motivational levels. Computer-aided instruction was found to have a greater positive impact on senior medical students with higher anatomy and motivational scores. Higher anatomy scores were positively associated with higher motivational scores. Computer-aided instruction may be better targeted toward senior students. N/A. Laryngoscope, 126:S5-S13, 2016. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

Need Assessment of Computer Science and Engineering Graduates

NASA Astrophysics Data System (ADS)

Surakka, Sami; Malmi, Lauri

2005-06-01

This case study considered the syllabus of the first and second year studies in computer science. The aim of the study was to reveal which topics covered in the syllabi were really needed during the following years of study or in working life. The program that was assessed in the study was a Masters program in computer science and engineering at a university of technology in Finland. The necessity of different subjects for the advanced studies (years 3? ?5) and for working life was assessed using four content analyses: (a) the course catalog of the institution where this study was carried out, (b) employment reports that were attached to the applications for internship credits, (c) masters theses, and (d) job advertisements in a newspaper. The results of the study imply that the necessity of physics for the advanced study and work was very low compared to the extent to which it was studied. On the other hand, the necessity for mathematics was moderate, and it had remained quite steady during the period 1989? ?2002. The most necessary computer science topic was programming. Also telecommunications and networking was needed often, whereas theoretical computer science was needed quite rarely.

Information Resources Management Long Range Plan, FY 1995-1999

NASA Technical Reports Server (NTRS)

1994-01-01

Table of Contents: Introduction; Agency 5-Year IRM Investment Projections; Major IRM Program Accomplishments for FY 1993; Information Collection Budget; Summary of Computer Security Plans; Appendix: Acronym List.

Parathyroid Cancer Treatment

MedlinePlus

... of the head and neck. SPECT scan (single photon emission computed tomography scan) : A procedure that uses ... a recurrence. The parathyroid cancer usually recurs between 2 and 5 years after the first surgery , but ...

Computing at h1 - Experience and Future

NASA Astrophysics Data System (ADS)

Eckerlin, G.; Gerhards, R.; Kleinwort, C.; KrÜNer-Marquis, U.; Egli, S.; Niebergall, F.

The H1 experiment has now been successfully operating at the electron proton collider HERA at DESY for three years. During this time the computing environment has gradually shifted from a mainframe oriented environment to the distributed server/client Unix world. This transition is now almost complete. Computing needs are largely determined by the present amount of 1.5 TB of reconstructed data per year (1994), corresponding to 1.2 × 107 accepted events. All data are centrally available at DESY. In addition to data analysis, which is done in all collaborating institutes, most of the centrally organized Monte Carlo production is performed outside of DESY. New software tools to cope with offline computing needs include CENTIPEDE, a tool for the use of distributed batch and interactive resources for Monte Carlo production, and H1 UNIX, a software package for automatic updates of H1 software on all UNIX platforms.

Frequent computer-related activities increase the risk of neck-shoulder and low back pain in adolescents.

PubMed

Hakala, Paula T; Rimpelä, Arja H; Saarni, Lea A; Salminen, Jouko J

2006-10-01

Neck-shoulder pain (NSP) and low back pain (LBP) increased among adolescents in the 1990s and the beginning of 2000. A potential risk factor for this increase is the use of information and communication technology. We studied how the use of computers, the Internet, and mobile phones, playing digital games and viewing television are related to NSP and LBP in adolescents. Mailed survey with nationally representative samples of 14-, 16-, and 18-year-old Finns in 2003 (n = 6003, response rate 68%). The outcome variables were weekly NSP and LBP. NSP was perceived by 26% and LBP by 12%. When compared with non-users, the risk of NSP was 1.3 (adjusted odds ratios) when using computers > 2-3 h/day, and 1.8 when using 4-5 h/day; 2.5 when using computers > or = 42 h/week, and 1.7 when using the Internet > or = 42 h/week. Compared with non-users, the risk of LBP was 2.0 when using computers > 5 h/day, 1.7 when using > or = 42 h/week, 1.8 when using the Internet > or = 42 h/week, and 2.0 when playing digital games > 5 h/day. Times spent on digital gaming, viewing television, and using mobile phones were not associated with NSP, nor were use of mobile phones and viewing television with LBP after adjusting for confounding factors. Frequent computer-related activities are an independent risk factor for NSP and LBP. Daily use of computers exceeding 2-3 h seems to be a threshold for NSP and exceeding 5 h for LBP. Computer-related activities may explain the increase of NSP and LBP in the 1990s and the beginning of 2000.

Screen and nonscreen sedentary behavior and sleep in adolescents.

PubMed

Brunetti, Vanessa C; O'Loughlin, Erin K; O'Loughlin, Jennifer; Constantin, Evelyn; Pigeon, Étienne

2016-12-01

This study examined the associations between screen (computer, videogame, TV) and nonscreen (talking on the phone, doing homework, reading) sedentary time, and sleep in adolescents. Data were drawn from AdoQuest, a prospective investigation of 1843 grade 5 students aged 10-12 years at inception in the greater Montreal (Canada) area. Data for this cross-sectional analysis on screen and nonscreen sedentary time, sleep duration, and daytime sleepiness were collected in 2008-2009 from 1233 participants (67% of 1843) aged 14-16 years. Computer and videogame use >2 hours per day was associated with 17 and 11 fewer minutes of sleep per night, respectively. Computer use and talking on the phone were both associated with being a short sleeper (<8 hour per night) (odds ratio =2.2 [1.4-3.4] and 3.0 [1.5-6.2], respectively), whereas TV time was protective (odds ratio=0.5 [0.3-0.8]). Participants who reported >2 hours of computer use or talking on the phone per day had higher daytime sleepiness scores (11.9 and 13.9, respectively) than participants who reported d2 hours per day (9.7 and 10.3, respectively). Computer use and time spent talking on the phone are associated with short sleep and more daytime sleepiness in adolescents. Videogame time is also associated with less sleep. Clinicians, parents, and adolescents should be made aware that sedentary behavior and especially screen-related sedentary behavior may affect sleep duration negatively and is possibly associated with daytime sleepiness. Copyright \\© 2016 National Sleep Foundation. Published by Elsevier Inc. All rights reserved.

7-year follow-up after stereotactic ablative radiotherapy for patients with stage I non-small cell lung cancer: Results of a phase 2 clinical trial.

PubMed

Sun, Bing; Brooks, Eric D; Komaki, Ritsuko U; Liao, Zhongxing; Jeter, Melenda D; McAleer, Mary F; Allen, Pamela K; Balter, Peter A; Welsh, James D; O'Reilly, Michael S; Gomez, Daniel; Hahn, Stephen M; Roth, Jack A; Mehran, Reza J; Heymach, John V; Chang, Joe Y

2017-08-15

The authors evaluated the efficacy, patterns of failure, and toxicity of stereotactic ablative radiotherapy (SABR) for patients with medically inoperable, clinical stage I non-small cell lung cancer (NSCLC) in a prospective clinical trial with 7 years of follow-up. Clinical staging was performed according to the seventh edition of the American Joint Committee on Cancer TNM staging system. Eligible patients with histologically confirmed NSCLC of clinical stage I as determined using positron emission tomography staging were treated with SABR (50 grays in 4 fractions). The primary endpoint was progression-free survival. Patients were followed with computed tomography and/or positron emission tomography/computed tomography every 3 months for the first 2 years, every 6 months for the next 3 years, and then annually thereafter. A total of 65 patients were eligible for analysis. The median age of the patients was 71 years, and the median follow-up was 7.2 years. A total of 18 patients (27.7%) developed disease recurrence at a median of 14.5 months (range, 4.3-71.5 months) after SABR. Estimated incidences of local, regional, and distant disease recurrence using competing risk analysis were 8.1%, 10.9%, and 11.0%, respectively, at 5 years and 8.1%, 13.6%, and 13.8%, respectively, at 7 years. A second primary lung carcinoma developed in 12 patients (18.5%) at a median of 35 months (range, 5-67 months) after SABR. Estimated 5-year and 7-year progression-free survival rates were 49.5% and 38.2%, respectively; the corresponding overall survival rates were 55.7% and 47.5%, respectively. Three patients (4.6%) experienced grade 3 treatment-related adverse events. No patients developed grade 4 or 5 adverse events (toxicity was graded according to the National Cancer Institute Common Terminology Criteria for Adverse Events [version 3.0]). With long-term follow-up, the results of the current prospective study demonstrated outstanding local control and low toxicity after SABR in patients with clinical stage I NSCLC. Regional disease recurrence and distant metastases were the dominant manifestations of failure. Surveillance for second primary lung carcinoma is recommended. Cancer 2017;123:3031-39. © 2017 American Cancer Society. © 2017 American Cancer Society.

5 CFR 841.603 - Rate of interest.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Rate of interest. 841.603 Section 841.603... EMPLOYEES RETIREMENT SYSTEM-GENERAL ADMINISTRATION Computation of Interest § 841.603 Rate of interest. For... to notify the public of the interest rate that will be in effect during that calendar year. ...

Stages of Parathyroid Cancer

MedlinePlus

... of the head and neck. SPECT scan (single photon emission computed tomography scan) : A procedure that uses ... a recurrence. The parathyroid cancer usually recurs between 2 and 5 years after the first surgery , but ...

Initial Investigation of the relation between extended computer use and temporomandibular joint disorders.

PubMed

Perri, Romina; Huta, Veronika; Pinchuk, Leonard; Pinchuk, Cindy; Ostry, David J; Lund, James P

2008-09-01

To determine if temporomandibular joint disorders (TMDs) are associated with extended computer use. People with chronic pain and extensive computer use were recruited by means of a newspaper advertisement. Those who responded to the ad were asked to complete an online survey, which included questions on computer use, medical history, pain symptoms, lifestyle and mood. Ninety-two people completed the online survey, but none of them responded to all questions in the survey. Of the 88 respondents who reported their sex, 49 (56%) were female. Most of the respondents had used computers for more than 5 hours per day for more than 5 years, and most believed that their pain was linked to computer use. The great majority had pain in the neck (73/89 [82%]) or shoulder (67/89 [75%]), but many (40/91 [44%]) also had symptoms of TMD. About half of the participants reported poor sleep and fatigue, and many linked their pain to negative effects on lifestyle and poor quality of life. Two multiple regressions, with duration of pain as the dependent variable, were carried out, one using the entire sample of respondents who had completed the necessary sections of the survey (n = 91) and the other using the subset of people with symptoms suggestive of TMD (n = 40). Duration of computer use was associated with duration of pain in both analyses, but 6 other independent variables (injury or arthritis, hours of daily computer use, stress, position of computer screen relative to the eyes, sex, and age) were without effect. In these regression analyses, the intercept was close to 0 years, which suggests that the pain began at about the same time as computer use. This web-based survey provides the first evidence that chronic pain in jaw muscles and other symptoms of TMD are associated with long-term, heavy use of computers. However, the great majority of people with these symptoms probably also suffer from pain in the shoulder and neck.

Recruiting Older Youths: Insights from a New Survey of Army Recruits

DTIC Science & Technology

2014-01-01

remaining in the service at the time to be considered for promotion 8. the unconditional probability of achieving the military grade of E-5 at four years...of service 9. the unconditional probability of achieving the military grade of E-5 at six years of ser- vice. We examined both the total effects of...career outcomes for Army enlist- ees. These effects are computed from separate linear probability regression models that include only dummy variables

Evaluation of a Computer-Based Patient Education and Motivation Tool on Knowledge, Attitudes and Practice towards Influenza Vaccination

ERIC Educational Resources Information Center

Joshi, Ashish; Lichenstein, Richard; King, James; Arora, Mohit; Khan, Salwa

2009-01-01

The objective of this pilot study was to assess and describe changes in knowledge, attitudes and practice regarding influenza vaccination in an inner city setting using an interactive computer-based educational program. A convenience sample of ninety participants whose children were in the age group of 6 months to 5 years was enrolled in this…

Can computed tomography aid in diagnosis of intramural hematomas of the intestinal wall?

PubMed

Ulusan, Serife; Pekoz, Burcak; Sariturk, Cagla

2015-12-01

We sought to use computed tomography (CT) data to support the correct differential diagnosis of patients with spontaneous intramural hematomas of the gastrointestinal tract, to aid in the clinical management of those using oral anticoagulants. Patient data were retrospectively analyzed and patients were divided into two groups. The first group contained 10 patients (5 females, 5 males, median age 65 years [range 35-79 years]) who had been diagnosed with spontaneous intramural hematomas of the gastrointestinal tract. The second group contained nine patients (5 females, 4 males, median age 41 years [range 24-56 years]) who exhibited intestinal wall thickening on CT, and who had been diagnosed with ulcerative colitis, Crohn's disease, ameboma, and lymphoma. The enhancement patterns in the CT images of the two groups were compared by an experienced and inexperienced radiologist. The differences in values were subjected to ROC analysis. Inter-observer variability was excellent (0.84) when post-contrast CT images were evaluated, as were the subtraction values (0.89). The subtracted values differed significantly between the two groups (p=0.0001). A cutoff of +31.5 HU was optimal in determining whether a hematoma was or was not present. Contrast enhancement of an intestinal wall hematoma is less than that of other intestinal wall pathologies associated with increased wall thickness. If the post-contrast enhancement of a thickened intestinal wall is less than +31.5 HU, a wall hematoma is possible. © Acta Gastro-Enterologica Belgica.

40 CFR 63.1416 - Recordkeeping requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... subpart for at least 5 years, as specified in paragraph (a)(1) of this section, with the exception listed... hours after a request. The remaining 4 and one-half years of records may be retained offsite. Records may be maintained in hard copy or computer-readable form including, but not limited to, on paper...

Whatever Happened to Richard Reid's List of First Programming Languages?

ERIC Educational Resources Information Center

Siegfried, Robert M.; Greco, Daniel M.; Miceli, Nicholas G.; Siegfried, Jason P.

2012-01-01

Throughout the 1990s, Richard Reid of Michigan State University maintained a list showing the first programming language used in introductory programming courses taken by computer science and information systems majors; it was updated for several years afterwards by Frances Van Scoy of West Virginia University. However, it has been 5 years since…

Persistent of Neck/Shoulder Pain among Computer Office Workers with Specific Attention to Pain Expectation, Somatization Tendency, and Beliefs.

PubMed

Sadeghian, Farideh; Raei, Mehdi; Amiri, Mohammad

2014-09-01

Neck and shoulder pains are the prevalent complaints among computer office workers. The purpose of this study was to assess the relationship of somatization tendency, expectation of pain, mental health and beliefs about causation of pain with persistence of neck/shoulder pains among computer office workers. This research is a kind of prospective cohort study with 1-year follow-up. It has done among all eligible computer office workers of Shahroud universities (n = 182) in 2008-2009 and 1-year later. Data were collected using the Cultural and Psychosocial Influences on Disability questionnaire. Multiple logistic regression analysis was used to analyze the data through SPSS (P < 0.05). At the baseline 100 (54.9%) of participants reported neck/shoulder pains and at follow-up 34.3% of them reported persistence pains. Significant relationships were found between persistence of neck/shoulder pains and negative expectation about pain in next 1-year P = 0.002, (odds ratio [OR] =8.3, 95% confidence interval [CI]: 2.1-32.9) and somatization tendency P = 0.01, (OR = 6.5, 95% CI: 1.6-27.4). Pain expectation and somatization tendency recognized as associated risk factors of persistent neck/shoulder pain among computer operators. This confirmed some other similar studies on work-related musculoskeletal disorders in Europe countries in recent years.

Mapping the Themes, Impact, and Cohesion of Creativity Research over the Last 25 Years

ERIC Educational Resources Information Center

Williams, Rich; Runco, Mark A.; Berlow, Eric

2016-01-01

This article describes the themes found in the past 25 years of creativity research. Computational methods and network analysis were used to map keyword theme development across ~1,400 documents and ~5,000 unique keywords from 1990 (the first year keywords are available in Web of Science) to 2015. Data were retrieved from Web of Science using the…

Dynamic electronic institutions in agent oriented cloud robotic systems.

PubMed

Nagrath, Vineet; Morel, Olivier; Malik, Aamir; Saad, Naufal; Meriaudeau, Fabrice

2015-01-01

The dot-com bubble bursted in the year 2000 followed by a swift movement towards resource virtualization and cloud computing business model. Cloud computing emerged not as new form of computing or network technology but a mere remoulding of existing technologies to suit a new business model. Cloud robotics is understood as adaptation of cloud computing ideas for robotic applications. Current efforts in cloud robotics stress upon developing robots that utilize computing and service infrastructure of the cloud, without debating on the underlying business model. HTM5 is an OMG's MDA based Meta-model for agent oriented development of cloud robotic systems. The trade-view of HTM5 promotes peer-to-peer trade amongst software agents. HTM5 agents represent various cloud entities and implement their business logic on cloud interactions. Trade in a peer-to-peer cloud robotic system is based on relationships and contracts amongst several agent subsets. Electronic Institutions are associations of heterogeneous intelligent agents which interact with each other following predefined norms. In Dynamic Electronic Institutions, the process of formation, reformation and dissolution of institutions is automated leading to run time adaptations in groups of agents. DEIs in agent oriented cloud robotic ecosystems bring order and group intellect. This article presents DEI implementations through HTM5 methodology.

Treatment Option Overview (Parathyroid Cancer)

MedlinePlus

... of the head and neck. SPECT scan (single photon emission computed tomography scan) : A procedure that uses ... a recurrence. The parathyroid cancer usually recurs between 2 and 5 years after the first surgery , but ...

Computed tomography screening for lung cancer: results of ten years of annual screening and validation of cosmos prediction model.

PubMed

Veronesi, G; Maisonneuve, P; Rampinelli, C; Bertolotti, R; Petrella, F; Spaggiari, L; Bellomi, M

2013-12-01

It is unclear how long low-dose computed tomographic (LDCT) screening should continue in populations at high risk of lung cancer. We assessed outcomes and the predictive ability of the COSMOS prediction model in volunteers screened for 10 years. Smokers and former smokers (>20 pack-years), >50 years, were enrolled over one year (2000-2001), receiving annual LDCT for 10 years. The frequency of screening-detected lung cancers was compared with COSMOS and Bach risk model estimates. Among 1035 recruited volunteers (71% men, mean age 58 years) compliance was 65% at study end. Seventy-one (6.95%) lung cancers were diagnosed, 12 at baseline. Disease stage was: IA in 48 (66.6%); IB in 6; IIA in 5; IIB in 2; IIIA in 5; IIIB in 1; IV in 5; and limited small cell cancer in 3. Five- and ten-year survival were 64% and 57%, respectively, 84% and 65% for stage I. Ten (12.1%) received surgery for a benign lesion. The number of lung cancers detected during the first two screening rounds was close to that predicted by the COSMOS model, while the Bach model accurately predicted frequency from the third year on. Neither cancer frequency nor proportion at stage I decreased over 10 years, indicating that screening should not be discontinued. Most cancers were early stage, and overall survival was high. Only a limited number of invasive procedures for benign disease were performed. The Bach model - designed to predict symptomatic cancers - accurately predicted cancer frequency from the third year, suggesting that overdiagnosis is a minor problem in lung cancer screening. The COSMOS model - designed to estimate screening-detected lung cancers - accurately predicted cancer frequency at baseline and second screening round. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A Universal Genome Array and Transcriptome Atlas for Brachypodium Distachyon

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

Mockler, Todd

Brachypodium distachyon is the premier experimental model grass platform and is related to candidate feedstock crops for bioethanol production. Based on the DOE-JGI Brachypodium Bd21 genome sequence and annotation we designed a whole genome DNA microarray platform. The quality of this array platform is unprecedented due to the exceptional quality of the Brachypodium genome assembly and annotation and the stringent probe selection criteria employed in the design. We worked with members of the international community and the bioinformatics/design team at Affymetrix at all stages in the development of the array. We used the Brachypodium arrays to interrogate the transcriptomes ofmore » plants grown in a variety of environmental conditions including diurnal and circadian light/temperature conditions and under a variety of environmental conditions. We examined the transciptional responses of Brachypodium seedlings subjected to various abiotic stresses including heat, cold, salt, and high intensity light. We generated a gene expression atlas representing various organs and developmental stages. The results of these efforts including all microarray datasets are published and available at online public databases.« less

Selected Streamflow Statistics for Streamgaging Stations in Delaware, 2003

USGS Publications Warehouse

Ries, Kernell G.

2004-01-01

Flow-duration and low-flow frequency statistics were calculated for 15 streamgaging stations in Delaware, in cooperation with the Delaware Geological Survey. The flow-duration statistics include the 1-, 2-, 5-, 10-, 20-, 30-, 40-, 50-, 60-, 70-, 80-, 90-, 95-, 98-, and 99-percent duration discharges. The low-flow frequency statistics include the average discharges for 1, 7, 14, 30, 60, 90, and 120 days that recur, on average, once in 1.01, 2, 5, 10, 20, 50, and 100 years. The statistics were computed using U.S. Geological Survey computer programs that can be downloaded from the World Wide Web at no cost. The computer programs automate standard U.S. Geological Survey methods for computing the statistics. Documentation is provided at the Web sites for the individual programs. The computed statistics are presented in tabular format on a separate page for each station, along with the station name, station number, the location, the period of record, and remarks.

Visual problems in young adults due to computer use.

PubMed

Moschos, M M; Chatziralli, I P; Siasou, G; Papazisis, L

2012-04-01

Computer use can cause visual problems. The purpose of our study was to evaluate visual problems due to computer use in young adults. Participants in our study were 87 adults, 48 male and 39 female, mean aged 31.3 years old (SD 7.6). All the participants completed a questionnaire regarding visual problems detected after computer use. The mean daily use of computers was 3.2 hours (SD 2.7). 65.5 % of the participants complained for dry eye, mainly after more than 2.5 hours of computer use. 32 persons (36.8 %) had a foreign body sensation in their eyes, while 15 participants (17.2 %) complained for blurred vision which caused difficulties in driving, after 3.25 hours of continuous computer use. 10.3 % of the participants sought medical advice for their problem. There was a statistically significant correlation between the frequency of visual problems and the duration of computer use (p = 0.021). 79.3 % of the participants use artificial tears during or after long use of computers, so as not to feel any ocular discomfort. The main symptom after computer use in young adults was dry eye. All visual problems associated with the duration of computer use. Artificial tears play an important role in the treatment of ocular discomfort after computer use. © Georg Thieme Verlag KG Stuttgart · New York.

Fluvial sediment in Double Creek subwatershed No. 5, Washington County, Oklahoma

USGS Publications Warehouse

Bednar, Gene A.; Waldrep, Thomas E.

1973-01-01

A total of 21,370 tons of fluvial sediment was transported into reservoir No. 5 and a total of 19,930 tons was deposited. Seventy-eight percent of the total fluvial sediment was deposited during the first 9.2 years, or 63 percent of time of reservoir operation. The computed trap efficiency of reservoir No. 5 was 93 percent.

Computer-guided percutaneous interbody fixation and fusion of the L5-S1 disc: a 2-year prospective study.

PubMed

Mac Millan, Michael

2005-02-01

The clinical outcomes of lumbar fusion are diminished by the complications associated with the surgical approach. Posterior approaches cause segmental muscular necrosis and anterior approaches risk visceral and vascular injury. This report details a two-year prospective study of a percutaneous method which avoids the major problems associated with existing approaches. Seventeen patients underwent percutaneous, trans-sacral fusion and fixation of L5-S1 with the assistance of computer guidance. Each patient was followed for a minimum of two years post surgery. SF-36 questionnaires and radiographs were obtained preoperatively and at two years post-operatively. Fusion was assessed with post-operative radiographs and/or CT scan. Ninety-three percent of the people fused as judged by plain AP films, Ferguson's view radiographs, and/or CT scans at the two year follow-up. Prospective health and functional SF-36 scores showed significant improvement from the preoperative to the postoperative period. There were no significant complications related to the approach or to the placement of the implants. Percutaneous fusion of the lumbosacral spine appears safe and provides excellent clinical results with a minimal amount of associated tissue trauma.

New estimates of the CMB angular power spectra from the WMAP 5 year low-resolution data

NASA Astrophysics Data System (ADS)

Gruppuso, A.; de Rosa, A.; Cabella, P.; Paci, F.; Finelli, F.; Natoli, P.; de Gasperis, G.; Mandolesi, N.

2009-11-01

A quadratic maximum likelihood (QML) estimator is applied to the Wilkinson Microwave Anisotropy Probe (WMAP) 5 year low-resolution maps to compute the cosmic microwave background angular power spectra (APS) at large scales for both temperature and polarization. Estimates and error bars for the six APS are provided up to l = 32 and compared, when possible, to those obtained by the WMAP team, without finding any inconsistency. The conditional likelihood slices are also computed for the Cl of all the six power spectra from l = 2 to 10 through a pixel-based likelihood code. Both the codes treat the covariance for (T, Q, U) in a single matrix without employing any approximation. The inputs of both the codes (foreground-reduced maps, related covariances and masks) are provided by the WMAP team. The peaks of the likelihood slices are always consistent with the QML estimates within the error bars; however, an excellent agreement occurs when the QML estimates are used as a fiducial power spectrum instead of the best-fitting theoretical power spectrum. By the full computation of the conditional likelihood on the estimated spectra, the value of the temperature quadrupole CTTl=2 is found to be less than 2σ away from the WMAP 5 year Λ cold dark matter best-fitting value. The BB spectrum is found to be well consistent with zero, and upper limits on the B modes are provided. The parity odd signals TB and EB are found to be consistent with zero.

Energy expenditure in adolescents playing new generation computer games.

PubMed

Graves, Lee; Stratton, Gareth; Ridgers, N D; Cable, N T

2008-07-01

To compare the energy expenditure of adolescents when playing sedentary and new generation active computer games. Cross sectional comparison of four computer games. Setting Research laboratories. Six boys and five girls aged 13-15 years. Participants were fitted with a monitoring device validated to predict energy expenditure. They played four computer games for 15 minutes each. One of the games was sedentary (XBOX 360) and the other three were active (Wii Sports). Predicted energy expenditure, compared using repeated measures analysis of variance. Mean (standard deviation) predicted energy expenditure when playing Wii Sports bowling (190.6 (22.2) kl/kg/min), tennis (202.5 (31.5) kl/kg/min), and boxing (198.1 (33.9) kl/kg/min) was significantly greater than when playing sedentary games (125.5 (13.7) kl/kg/min) (P<0.001). Predicted energy expenditure was at least 65.1 (95% confidence interval 47.3 to 82.9) kl/kg/min greater when playing active rather than sedentary games. Playing new generation active computer games uses significantly more energy than playing sedentary computer games but not as much energy as playing the sport itself. The energy used when playing active Wii Sports games was not of high enough intensity to contribute towards the recommended daily amount of exercise in children.

Computer vision syndrome in presbyopia and beginning presbyopia: effects of spectacle lens type.

PubMed

Jaschinski, Wolfgang; König, Mirjam; Mekontso, Tiofil M; Ohlendorf, Arne; Welscher, Monique

2015-05-01

This office field study investigated the effects of different types of spectacle lenses habitually worn by computer users with presbyopia and in the beginning stages of presbyopia. Computer vision syndrome was assessed through reported complaints and ergonomic conditions. A questionnaire regarding the type of habitually worn near-vision lenses at the workplace, visual conditions and the levels of different types of complaints was administered to 175 participants aged 35 years and older (mean ± SD: 52.0 ± 6.7 years). Statistical factor analysis identified five specific aspects of the complaints. Workplace conditions were analysed based on photographs taken in typical working conditions. In the subgroup of 25 users between the ages of 36 and 57 years (mean 44 ± 5 years), who wore distance-vision lenses and performed more demanding occupational tasks, the reported extents of 'ocular strain', 'musculoskeletal strain' and 'headache' increased with the daily duration of computer work and explained up to 44 per cent of the variance (rs = 0.66). In the other subgroups, this effect was smaller, while in the complete sample (n = 175), this correlation was approximately rs = 0.2. The subgroup of 85 general-purpose progressive lens users (mean age 54 years) adopted head inclinations that were approximately seven degrees more elevated than those of the subgroups with single vision lenses. The present questionnaire was able to assess the complaints of computer users depending on the type of spectacle lenses worn. A missing near-vision addition among participants in the early stages of presbyopia was identified as a risk factor for complaints among those with longer daily durations of demanding computer work. © 2015 The Authors. Clinical and Experimental Optometry © 2015 Optometry Australia.

Structural dynamics division research and technology accomplishments for fiscal year 1990 and plans for fiscal year 1991

NASA Technical Reports Server (NTRS)

Wynne, Eleanor C.

1991-01-01

The research accomplishments of the Structural Dynamics Division for F.Y. 1991 are presented. The work is discussed in terms of highlights of accomplishments during the past year and plans for the current year as they relate to 5-year plans and the objectives of each technical area. Included is research on unsteady aerodynamics, helicopter rotors, computational fluid dynamics, oscillations of leading edge flaps of a delta wing, and aircraft wing loads.

Computational Investigations of Noise Suppression in Subsonic Round Jets

NASA Technical Reports Server (NTRS)

Pruett, C. David

1997-01-01

NASA Grant NAG1-1802, originally submitted in June 1996 as a two-year proposal, was awarded one-year's funding by NASA LaRC for the period 5 Oct., 1996, through 4 Oct., 1997. Because of the inavailability (from IT at NASA ARC) of sufficient supercomputer time in fiscal 1998 to complete the computational goals of the second year of the original proposal (estimated to be at least 400 Cray C-90 CPU hours), those goals have been appropriately amended, and a new proposal has been submitted to LaRC as a follow-on to NAG1-1802. The current report documents the activities and accomplishments on NAG1-1802 during the one-year period from 5 Oct., 1996, through 4 Oct., 1997. NASA Grant NAG1-1802, and its predecessor, NAG1-1772, have been directed toward adapting the numerical tool of Large-Eddy Simulation (LES) to aeroacoustic applications, with particular focus on noise suppression in subsonic round jets. In LES, the filtered Navier-Stokes equations are solved numerically on a relatively coarse computational grid. Residual stresses, generated by scales of motion too small to be resolved on the coarse grid, are modeled. Although most LES incorporate spatial filtering, time-domain filtering affords certain conceptual and computational advantages, particularly for aeroacoustic applications. Consequently, this work has focused on the development of SubGrid-Scale (SGS) models that incorporate time- domain filters. The author is unaware of any previous attempt at purely time-filtered LES; however, Aldama and Dakhoul and Bedford have considered approaches that combine both spatial and temporal filtering. In our view, filtering in both space and time is redundant, because removal of high frequencies effects the removal of small spatial scales and vice versa.

Prevalence and correlates of problematic internet experiences and computer-using time: a two-year longitudinal study in korean school children.

PubMed

Yang, Su-Jin; Stewart, Robert; Lee, Ju-Yeon; Kim, Jae-Min; Kim, Sung-Wan; Shin, Il-Seon; Yoon, Jin-Sang

2014-01-01

To measure the prevalence of and factors associated with online inappropriate sexual exposure, cyber-bullying victimisation, and computer-using time in early adolescence. A two-year, prospective school survey was performed with 1,173 children aged 13 at baseline. Data collected included demographic factors, bullying experience, depression, anxiety, coping strategies, self-esteem, psychopathology, attention-deficit hyperactivity disorder symptoms, and school performance. These factors were investigated in relation to problematic Internet experiences and computer-using time at age 15. The prevalence of online inappropriate sexual exposure, cyber-bullying victimisation, academic-purpose computer overuse, and game-purpose computer overuse was 31.6%, 19.2%, 8.5%, and 21.8%, respectively, at age 15. Having older siblings, more weekly pocket money, depressive symptoms, anxiety symptoms, and passive coping strategy were associated with reported online sexual harassment. Male gender, depressive symptoms, and anxiety symptoms were associated with reported cyber-bullying victimisation. Female gender was associated with academic-purpose computer overuse, while male gender, lower academic level, increased height, and having older siblings were associated with game-purpose computer-overuse. Different environmental and psychological factors predicted different aspects of problematic Internet experiences and computer-using time. This knowledge is important for framing public health interventions to educate adolescents about, and prevent, internet-derived problems.

Prevalence and factors associated with neck, shoulder and low back pains among medical students in a Malaysian Medical College.

PubMed

Alshagga, Mustafa Ahmed; Nimer, Amal R; Yan, Looi Pui; Ibrahim, Ibrahim Abdel Aziz; Al-Ghamdi, Saeed S; Radman Al-Dubai, Sami Abdo

2013-07-01

The main purpose of the study was to assess the prevalence, body distributions and factors associated with musculoskeletal pain (MSP) among medical students in a private Malaysian medical college. This cross-sectional study was conducted among 232 medical students in a private medical college using an online questionnaire. The questionnaire was a modified Standardized Nordic Questionnaire focused on neck, shoulder and low back pain in the past week and the past year. Two hundred and thirty two medical students responded to the questionnaire out of 642. Mean age was 20.7 ± 2.1 years. The majority were female (62.9%), Malay (80.6%) and in the preclinical years (72%). One hundred and six (45.7%) of all students had at least one site of MSP in the past week and 151 (65.1%) had at least one site of MSP in the past year. MSP in the past week was associated significantly with the academic year, (OR 2.0, 95% CI 1.15-3.67, P = 0.015), history of trauma (OR 2.6, 95% CI 1.2-5.3, P = 0.011), family history of MSP (OR 2.1, 95% CI 1.1-3.9, P = 0.023) and Body Mass Index (BMI) (P = 0.028). MSP in the past year was significantly associated with computer use (P = 0.027), daily hours of computer use (median ± IQR (5.0 ±3.0), history of trauma (OR 7.5, 95% CI 2.24-2.56, P < 0.01) and family history of MSP (OR 2.5, 95% CI 1.31-4.90, P = 0.006). On multivariate analysis, factors associated with MSP during the past week were a family history of MSP (p = 0.029) and BMI (p = 0.03). Factors associated with MSP during the past year were being in clinical years (p = 0.002, computer use (p = 0.038), and a history of trauma (p = 0.030). MSP among medical students was relatively high, thus, further clinical assessment is needed in depth study of ergonomics. The study results indicate that medical school authorities should take measures to prevent MSP due to factors related to medical school. Students should make aware of importance of weight reduction to reduce MSP.

Effect of More vs Less Frequent Follow-up Testing on Overall and Colorectal Cancer-Specific Mortality in Patients With Stage II or III Colorectal Cancer: The COLOFOL Randomized Clinical Trial.

PubMed

Wille-Jørgensen, Peer; Syk, Ingvar; Smedh, Kenneth; Laurberg, Søren; Nielsen, Dennis T; Petersen, Sune H; Renehan, Andrew G; Horváth-Puhó, Erzsébet; Påhlman, Lars; Sørensen, Henrik T

2018-05-22

Intensive follow-up of patients after curative surgery for colorectal cancer is common in clinical practice, but evidence of a survival benefit is limited. To examine overall mortality, colorectal cancer-specific mortality, and colorectal cancer-specific recurrence rates among patients with stage II or III colorectal cancer who were randomized after curative surgery to 2 alternative schedules for follow-up testing with computed tomography and carcinoembryonic antigen. Unblinded randomized trial including 2509 patients with stage II or III colorectal cancer treated at 24 centers in Sweden, Denmark, and Uruguay from January 2006 through December 2010 and followed up for 5 years; follow-up ended on December 31, 2015. Patients were randomized either to follow-up testing with computed tomography of the thorax and abdomen and serum carcinoembryonic antigen at 6, 12, 18, 24, and 36 months after surgery (high-frequency group; n = 1253 patients) or at 12 and 36 months after surgery (low-frequency group; n = 1256 patients). The primary outcomes were 5-year overall mortality and colorectal cancer-specific mortality rates. The secondary outcome was the colorectal cancer-specific recurrence rate. Both intention-to-treat and per-protocol analyses were performed. Among 2555 patients who were randomized, 2509 were included in the intention-to-treat analysis (mean age, 63.5 years; 1128 women [45%]) and 2365 (94.3%) completed the trial. The 5-year overall patient mortality rate in the high-frequency group was 13.0% (161/1253) compared with 14.1% (174/1256) in the low-frequency group (risk difference, 1.1% [95% CI, -1.6% to 3.8%]; P = .43). The 5-year colorectal cancer-specific mortality rate in the high-frequency group was 10.6% (128/1248) compared with 11.4% (137/1250) in the low-frequency group (risk difference, 0.8% [95% CI, -1.7% to 3.3%]; P = .52). The colorectal cancer-specific recurrence rate was 21.6% (265/1248) in the high-frequency group compared with 19.4% (238/1250) in the low-frequency group (risk difference, 2.2% [95% CI, -1.0% to 5.4%]; P = .15). Among patients with stage II or III colorectal cancer, follow-up testing with computed tomography and carcinoembryonic antigen more frequently compared with less frequently did not result in a significant rate reduction in 5-year overall mortality or colorectal cancer-specific mortality. clinicaltrials.gov Identifier: NCT00225641.

31 CFR 332.5 - Limitation on holdings.

Code of Federal Regulations, 2014 CFR

2014-07-01

..., DEPARTMENT OF THE TREASURY BUREAU OF THE FISCAL SERVICE OFFERING OF UNITED STATES SAVINGS BONDS, SERIES H § 332.5 Limitation on holdings. The amount of Series H bonds, originally issued during any one calendar year, that could be held by any one person, at any one time, computed in accordance with the governing...

31 CFR 332.5 - Limitation on holdings.

Code of Federal Regulations, 2011 CFR

2011-07-01

..., DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT OFFERING OF UNITED STATES SAVINGS BONDS, SERIES H § 332.5 Limitation on holdings. The amount of Series H bonds, originally issued during any one calendar year, that could be held by any one person, at any one time, computed in accordance with the governing...

31 CFR 332.5 - Limitation on holdings.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT OFFERING OF UNITED STATES SAVINGS BONDS, SERIES H § 332.5 Limitation on holdings. The amount of Series H bonds, originally issued during any one calendar year, that could be held by any one person, at any one time, computed in accordance with the governing...

31 CFR 332.5 - Limitation on holdings.

Code of Federal Regulations, 2012 CFR

2012-07-01

..., DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT OFFERING OF UNITED STATES SAVINGS BONDS, SERIES H § 332.5 Limitation on holdings. The amount of Series H bonds, originally issued during any one calendar year, that could be held by any one person, at any one time, computed in accordance with the governing...

31 CFR 332.5 - Limitation on holdings.

Code of Federal Regulations, 2013 CFR

2013-07-01

..., DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT OFFERING OF UNITED STATES SAVINGS BONDS, SERIES H § 332.5 Limitation on holdings. The amount of Series H bonds, originally issued during any one calendar year, that could be held by any one person, at any one time, computed in accordance with the governing...

Progress Monitoring in Grade 5 Science for Low Achievers

ERIC Educational Resources Information Center

Vannest, Kimberly J.; Parker, Richard; Dyer, Nicole

2011-01-01

This article presents procedures and results from a 2-year project developing science key vocabulary (KV) short tests suitable for progress monitoring Grade 5 science in Texas public schools using computer-generated, -administered, and -scored assessments. KV items included KV definitions and important usages in a multiple-choice cloze format. A…

Mobile computing initiatives within pharmacy education.

PubMed

Cain, Jeff; Bird, Eleanora R; Jones, Mikael

2008-08-15

To identify mobile computing initiatives within pharmacy education, including how devices are obtained, supported, and utilized within the curriculum. An 18-item questionnaire was developed and delivered to academic affairs deans (or closest equivalent) of 98 colleges and schools of pharmacy. Fifty-four colleges and schools completed the questionnaire for a 55% completion rate. Thirteen of those schools have implemented mobile computing requirements for students. Twenty schools reported they were likely to formally consider implementing a mobile computing initiative within 5 years. Numerous models of mobile computing initiatives exist in terms of device obtainment, technical support, infrastructure, and utilization within the curriculum. Responders identified flexibility in teaching and learning as the most positive aspect of the initiatives and computer-aided distraction as the most negative, Numerous factors should be taken into consideration when deciding if and how a mobile computing requirement should be implemented.

Evaluating Thin Client Computers for Use by the Polish Army

DTIC Science & Technology

2006-06-01

43 Figure 15. Annual Electricity Cost and Savings for 5 to 100 Users (source: Thin Client Computing...50 percent in hard costs in the first year of thin client network deployment.20 However, the greatest savings come from the reduction in soft costs ...resources from both the classrooms and home. The thin client solution increased the reliability of the IT infrastructure and resulted in cost savings

JPRS Report, Soviet Union, Foreign Military Review, No. 8, August 1987

DTIC Science & Technology

1988-01-28

Hinkley Point (1.5 million) and Hartlepool (1.3 million). In recent years the country has begun building large hydro- electric pumped storage power ...antenna 6. Interface equipment 7. Data transmission line terminal 8. Computer 9. Power supply plant control station 10. Radio-relay station terminals... stations and data transmission line, interface equipment, and power distribution unit (Fig. 3). The parallel computer, which performs operations on

[Value of computer tomography in the managment of brain injuries].

PubMed

Keita, A D; Toure, M; Sissako, A; Doumbia, S; Coulibaly, Y; Doumbia, D; Kane, M; Diallo, A K; Toure, A A; Traore, I

2005-11-01

The purpose of this prospective study conducted from January 2001 to December 2001 was to ascertain the value of computer tomography for evaluation of brain injuries. Computer tomography was performed using a Toshiba X VID system with contiguous 5 mm axial sections through the posterior fossa and 10 mm contiguous axial sections through the subtentorial region without contrast injection. A total of 107 patients with brain injuries were enrolled over the one-year study period. These patients accounted for 0.8% of all admissions to surgical emergency unit of Gabriel Toure Hospital in Bamako, Mali. The predominant age group for brain injuries was the 20- to 29-year-old group (35 cases). The male-to-female sex ratio was 5:1. Vehicular accident was the most frequent cause of brain injury (76 cases). Trauma was severe in 48 patients with a Glasgow score less than 8. Coma occurred immediately after injury in 90 cases. Ventricular hemorrhage led to coma in 100% of cases whereas brain hemorrhage and hematoma led to coma in 93.3% and 83.3% of cases respectively. Treatment was medical in 99 cases and neurosurgical in 8. The mortality rate was 34% and the morbidity rate (permanent sequels) was 36%. Computer tomography is a valuable tool for therapeutic decision-making in medico-surgical emergencies involving brain injuries.

Feasibility of simultaneous computed tomographic colonography and fully automated bone mineral densitometry in a single examination.

PubMed

Summers, Ronald M; Baecher, Nicolai; Yao, Jianhua; Liu, Jiamin; Pickhardt, Perry J; Choi, J Richard; Hill, Suvimol

2011-01-01

To show the feasibility of calculating the bone mineral density (BMD) from computed tomographic colonography (CTC) scans using fully automated software. Automated BMD measurement software was developed that measures the BMD of the first and second lumbar vertebrae on computed tomography and calculates the mean of the 2 values to provide a per patient BMD estimate. The software was validated in a reference population of 17 consecutive women who underwent quantitative computed tomography and in a population of 475 women from a consecutive series of asymptomatic patients enrolled in a CTC screening trial conducted at 3 medical centers. The mean (SD) BMD was 133.6 (34.6) mg/mL (95% confidence interval, 130.5-136.7; n = 475). In women aged 42 to 60 years (n = 316) and 61 to 79 years (n = 159), the mean (SD) BMDs were 143.1 (33.5) and 114.7 (28.3) mg/mL, respectively (P < 0.0001). Fully automated BMD measurements were reproducible for a given patient with 95% limits of agreement of -9.79 to 8.46 mg/mL for the mean difference between paired assessments on supine and prone CTC. Osteoporosis screening can be performed simultaneously with screening for colorectal polyps.

Incidental renal tumours on low-dose CT lung cancer screening exams.

PubMed

Pinsky, Paul F; Dunn, Barbara; Gierada, David; Nath, P Hrudaya; Munden, Reginald; Berland, Lincoln; Kramer, Barnett S

2017-06-01

Introduction Renal cancer incidence has increased markedly in the United States in recent decades, largely due to incidentally detected tumours from computed tomography imaging. Here, we analyze the potential for low-dose computed tomography lung cancer screening to detect renal cancer. Methods The National Lung Screening Trial randomized subjects to three annual screens with either low-dose computed tomography or chest X-ray. Eligibility criteria included 30 + pack-years, current smoking or quit within 15 years, and age 55-74. Subjects were followed for seven years. Low-dose computed tomography screening forms collected information on lung cancer and non-lung cancer abnormalities, including abnormalities below the diaphragm. A reader study was performed on a sample of National Lung Screening Trial low-dose computed tomography images assessing presence of abnormalities below the diaphragms and abnormalities suspicious for renal cancer. Results There were 26,722 and 26,732 subjects enrolled in the low-dose computed tomography and chest X-ray arms, respectively, and there were 104 and 85 renal cancer cases diagnosed, respectively (relative risk = 1.22, 95% CI: 0.9-1.5). From 75,126 low-dose computed tomography screens, there were 46 renal cancer diagnoses within one year. Abnormalities below the diaphragm rates were 39.1% in screens with renal cancer versus 4.1% in screens without (P < 0.001). Cases with abnormalities below the diaphragms had shorter median time to diagnosis than those without (71 vs. 160 days, P = 0.004). In the reader study, 64% of renal cancer cases versus 13% of non-cases had abnormalities below the diaphragms; 55% of cases and 0.8% of non-cases had a finding suspicious for renal cancer (P < 0.001). Conclusion Low-dose computed tomography screens can potentially detect renal cancers. The benefits to harms tradeoff of incidental detection of renal tumours on low-dose computed tomography is unknown.

Dilatation of aortic grafts over time: what to expect and when to be concerned.

PubMed

Schroeder, Torben V; Eldrup, Nikolaj; Just, Sven; Hansen, Marc; Nyhuus, Bo; Sillesen, Henrik

2009-06-01

Dilatation of aortic prosthetic grafts is commonly reported, but most reports are anecdotal, with little objective data in the literature. We performed a prospective trial of 303 patients who underwent prosthetic graft repair for aortic aneurysm or occlusive disease, randomizing patients between insertion of a woven polyester or expanded polytetrafluoroethylene (ePTFE) graft. Patients were followed with computed tomography and ultrasonography for up to 5 years in order to assess the frequency and magnitude of postoperative dilatation. Graft dilatation was documented in patients with polyester grafts at 12 months. Thereafter and up to 60 months, polyester grafts did not dilate further. After 5 years, polyester prostheses had dilated by 25% and ePTFE by 12.5%, as determined by computed tomography imaging. These observations suggest that dilatation of prosthetic grafts is more frequent with knitted polyester grafts compared with ePTFE. Dilatation occurs within the first year after implantation and can be, in part, explained by a discrepancy between the initial nominal graft diameter and its diameter after clamp release, probably due to an in vivo adaptation of the textile structure. Interestingly, graft dilatation did not appear to be associated with an increased frequency of graft-related complications.

Comfort and experience with online learning: trends over nine years and associations with knowledge

PubMed Central

2014-01-01

Background Some evidence suggests that attitude toward computer-based instruction is an important determinant of success in online learning. We sought to determine how comfort using computers and perceptions of prior online learning experiences have changed over the past decade, and how these associate with learning outcomes. Methods Each year from 2003–2011 we conducted a prospective trial of online learning. As part of each year’s study, we asked medicine residents about their comfort using computers and if their previous experiences with online learning were favorable. We assessed knowledge using a multiple-choice test. We used regression to analyze associations and changes over time. Results 371 internal medicine and family medicine residents participated. Neither comfort with computers nor perceptions of prior online learning experiences showed a significant change across years (p > 0.61), with mean comfort rating 3.96 (maximum 5 = very comfortable) and mean experience rating 4.42 (maximum 6 = strongly agree [favorable]). Comfort showed no significant association with knowledge scores (p = 0.39) but perceptions of prior experiences did, with a 1.56% rise in knowledge score for a 1-point rise in experience score (p = 0.02). Correlations among comfort, perceptions of prior experiences, and number of prior experiences were all small and not statistically significant. Conclusions Comfort with computers and perceptions of prior experience with online learning remained stable over nine years. Prior good experiences (but not comfort with computers) demonstrated a modest association with knowledge outcomes, suggesting that prior course satisfaction may influence subsequent learning. PMID:24985690

Emotion Recognition in Children and Adolescents with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Kuusikko, Sanna; Haapsamo, Helena; Jansson-Verkasalo, Eira; Hurtig, Tuula; Mattila, Marja-Leena; Ebeling, Hanna; Jussila, Katja; Bolte, Sven; Moilanen, Irma

2009-01-01

We examined upper facial basic emotion recognition in 57 subjects with autism spectrum disorders (ASD) (M = 13.5 years) and 33 typically developing controls (M = 14.3 years) by using a standardized computer-aided measure (The Frankfurt Test and Training of Facial Affect Recognition, FEFA). The ASD group scored lower than controls on the total…

Longitudinal patterns of problematic computer game use among adolescents and adults--a 2-year panel study.

PubMed

Scharkow, Michael; Festl, Ruth; Quandt, Thorsten

2014-11-01

To investigate the longitudinal patterns (stability and change) of problematic computer game use and its interdependencies with psychosocial wellbeing in different age groups. Three-wave, annual panel study using computer-assisted telephone surveys. Germany. A total of 112 adolescents aged between 14 and 18 years, 363 younger adults between 19-39 years and 427 adults aged 40 years and older (overall n = 902). Problematic game use was measured with the Gaming Addiction Short Scale (GAS), which covers seven criteria including salience, withdrawal and conflict. Additionally, gaming behaviour and psychosocial wellbeing (social capital and support, life satisfaction and success) were measured in all three panel waves. The generally low GAS scores were very stable in yearly intervals [average autocorrelation across waves and age groups: r = 0.74, confidence interval (CI) = 0.71, 0.77]. Only nine respondents (1%, CI = 0.5, 1.9) consistently exhibited symptoms of problematic game use across all waves, while no respondent could be classified consistently as being addicted according to the GAS criteria. Changes in problematic gaming were not related consistently to changes in psychosocial wellbeing, although some cross-lagged effects were statistically significant in younger and older adult groups. Within a 2-year time-frame, problematic use of computer games appears to be a less stable behaviour than reported previously and not related systematically to negative changes in the gamers' lives. © 2014 Society for the Study of Addiction.

Computer-Aided Drug Discovery Approaches against the Tropical Infectious Diseases Malaria, Tuberculosis, Trypanosomiasis, and Leishmaniasis.

PubMed

Njogu, Peter M; Guantai, Eric M; Pavadai, Elumalai; Chibale, Kelly

2016-01-08

Despite the tremendous improvement in overall global health heralded by the adoption of the Millennium Declaration in the year 2000, tropical infections remain a major health problem in the developing world. Recent estimates indicate that the major tropical infectious diseases, namely, malaria, tuberculosis, trypanosomiasis, and leishmaniasis, account for more than 2.2 million deaths and a loss of approximately 85 million disability-adjusted life years annually. The crucial role of chemotherapy in curtailing the deleterious health and economic impacts of these infections has invigorated the search for new drugs against tropical infectious diseases. The research efforts have involved increased application of computational technologies in mainstream drug discovery programs at the hit identification, hit-to-lead, and lead optimization stages. This review highlights various computer-aided drug discovery approaches that have been utilized in efforts to identify novel antimalarial, antitubercular, antitrypanosomal, and antileishmanial agents. The focus is largely on developments over the past 5 years (2010-2014).

Toward a Global Bundle Adjustment of SPOT 5 - HRS Images

NASA Astrophysics Data System (ADS)

Massera, S.; Favé, P.; Gachet, R.; Orsoni, A.

2012-07-01

The HRS (High Resolution Stereoscopic) instrument carried on SPOT 5 enables quasi-simultaneous acquisition of stereoscopic images on wide segments - 120 km wide - with two forward and backward-looking telescopes observing the Earth with an angle of 20° ahead and behind the vertical. For 8 years IGN (Institut Géographique National) has been developing techniques to achieve spatiotriangulation of these images. During this time the capacities of bundle adjustment of SPOT 5 - HRS spatial images have largely improved. Today a global single block composed of about 20,000 images can be computed in reasonable calculation time. The progression was achieved step by step: first computed blocks were only composed of 40 images, then bigger blocks were computed. Finally only one global block is now computed. In the same time calculation tools have improved: for example the adjustment of 2,000 images of North Africa takes about 2 minutes whereas 8 hours were needed two years ago. To reach such a result a new independent software was developed to compute fast and efficient bundle adjustments. In the same time equipment - GCPs (Ground Control Points) and tie points - and techniques have also evolved over the last 10 years. Studies were made to get recommendations about the equipment in order to make an accurate single block. Tie points can now be quickly and automatically computed with SURF (Speeded Up Robust Features) techniques. Today the updated equipment is composed of about 500 GCPs and studies show that the ideal configuration is around 100 tie points by square degree. With such an equipment, the location of the global HRS block becomes a few meters accurate whereas non adjusted images are only 15 m accurate. This paper will describe the methods used in IGN Espace to compute a global single block composed of almost 20,000 HRS images, 500 GCPs and several million of tie points in reasonable calculation time. Many advantages can be found to use such a block. Because the global block is unique it becomes easier to manage the historic and the different evolutions of the computations (new images, new GCPs or tie points). The location is now unique and consequently coherent all around the world, avoiding steps and artifacts on the borders of DSMs (Digital Surface Models) and OrthoImages historically calculated from different blocks. No extrapolation far from GCPs in the limits of images is done anymore. Using the global block as a reference will allow new images from other sources to be easily located on this reference.

Television viewing, computer game play and book reading during meals are predictors of meal skipping in a cross-sectional sample of 12-, 14- and 16-year-olds.

PubMed

Custers, Kathleen; Van den Bulck, Jan

2010-04-01

To examine whether television viewing, computer game playing or book reading during meals predicts meal skipping with the aim of watching television, playing computer games or reading books (media meal skipping). A cross-sectional study was conducted using a standardized self-administered questionnaire. Analyses were controlled for age, gender and BMI. Data were obtained from a random sample of adolescents in Flanders, Belgium. Seven hundred and ten participants aged 12, 14 and 16 years. Of the participants, 11.8 % skipped meals to watch television, 10.5 % skipped meals to play computer games and 8.2 % skipped meals to read books. Compared with those who did not use these media during meals, the risk of skipping meals in order to watch television was significantly higher for those children who watched television during meals (2.9 times higher in those who watched television during at least one meal a day). The risk of skipping meals for computer game playing was 9.5 times higher in those who played computer games weekly or more while eating, and the risk of meal skipping in order to read books was 22.9 times higher in those who read books during meals less than weekly. The more meals the respondents ate with the entire family, the less likely they were to skip meals to watch television. The use of media during meals predicts meal skipping for using that same medium. Family meals appear to be inversely related to meal skipping for television viewing.

IPSL-CM5A2. An Earth System Model designed to run long simulations for past and future climates.

NASA Astrophysics Data System (ADS)

Sepulchre, Pierre; Caubel, Arnaud; Marti, Olivier; Hourdin, Frédéric; Dufresne, Jean-Louis; Boucher, Olivier

2017-04-01

The IPSL-CM5A model was developed and released in 2013 "to study the long-term response of the climate system to natural and anthropogenic forcings as part of the 5th Phase of the Coupled Model Intercomparison Project (CMIP5)" [Dufresne et al., 2013]. Although this model also has been used for numerous paleoclimate studies, a major limitation was its computation time, which averaged 10 model-years / day on 32 cores of the Curie supercomputer (on TGCC computing center, France). Such performances were compatible with the experimental designs of intercomparison projects (e.g. CMIP, PMIP) but became limiting for modelling activities involving several multi-millenial experiments, which are typical for Quaternary or "deeptime" paleoclimate studies, in which a fully-equilibrated deep-ocean is mandatory. Here we present the Earth-System model IPSL-CM5A2. Based on IPSL-CM5A, technical developments have been performed both on separate components and on the coupling system in order to speed up the whole coupled model. These developments include the integration of hybrid parallelization MPI-OpenMP in LMDz atmospheric component, the use of a new input-ouput library to perform parallel asynchronous input/output by using computing cores as "IO servers", the use of a parallel coupling library between the ocean and the atmospheric components. Running on 304 cores, the model can now simulate 55 years per day, opening new gates towards multi-millenial simulations. Apart from obtaining better computing performances, one aim of setting up IPSL-CM5A2 was also to overcome the cold bias depicted in global surface air temperature (t2m) in IPSL-CM5A. We present the tuning strategy to overcome this bias as well as the main characteristics (including biases) of the pre-industrial climate simulated by IPSL-CM5A2. Lastly, we shortly present paleoclimate simulations run with this model, for the Holocene and for deeper timescales in the Cenozoic, for which the particular continental configuration was overcome by a new design of the ocean tripolar grid.

Twelve-Year Follow-Up of Navigated Computer-Assisted Versus Conventional Total Knee Arthroplasty: A Prospective Randomized Comparative Trial.

PubMed

Cip, Johannes; Obwegeser, Florian; Benesch, Thomas; Bach, Christian; Ruckenstuhl, Paul; Martin, Arno

2018-05-01

Navigated computer-assisted total knee arthroplasty (TKA) was introduced to expedite long-term survival based on improved postoperative implantation accuracy. However, long-term outcome data after 10 years or more are rare, even available meta-analyses show controversial study results. In a prospective randomized trial, 100 conventional TKAs (group CONV) were compared with 100 computer-assisted TKAs (group NAV) after a mean follow-up of 12 years postoperatively. A long-leg weight-bearing X-ray was performed for measuring mechanical axis of the limb, lateral distal femoral angle, and medial proximal tibial angle. Tibial slope, patella alpha angle, and radiolucent lines were also observed. Clinical investigation included evaluation of 4 different scores: Insall Knee Score, Western Ontario and MacMaster University Index score, Hospital for Special Surgery Knee Score, and visual analog scale. Based on a follow-up rate of at least 75%, no difference in TKA survival was found 12 years postoperatively: 91.5% in group CONV vs 98.2% in group NAV (P = .181). Since 5-year follow-up, no additional TKA revision had been performed in both groups. Group CONV showed a nonsignificant higher inaccuracy of neutral lower limb axis (1.8° ± 1.4°) compared to group NAV (1.6° ± 1.7°, P = .700). All X-ray assessments were not significant different within both study groups (P ≥ .068). Clinical examination showed no differences in evaluations (P ≥ .204). All collected outcome score results were similar (P ≥ .222). Twelve years postoperatively, no differences were found in terms of long-term survival, implantation accuracy, clinical outcome or score results. Copyright © 2017 Elsevier Inc. All rights reserved.

Novel Assessment of Renal Motion in Children as Measured via Four-Dimensional Computed Tomography

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

Pai Panandiker, Atmaram S., E-mail: atmaram.pai-panandiker@stjude.org; Sharma, Shelly; Naik, Mihir H.

Objectives: Abdominal intensity-modulated radiation therapy and proton therapy require quantification of target and organ motion to optimize localization and treatment. Although addressed in adults, there is no available literature on this issue in pediatric patients. We assessed physiologic renal motion in pediatric patients. Methods and Materials: Twenty free-breathing pediatric patients at a median age of 8 years (range, 2-18 years) with intra-abdominal tumors underwent computed tomography simulation and four-dimensional computed tomography acquisition (slice thickness, 3 mm). Kidneys and diaphragms were contoured during eight phases of respiration to estimate center-of-mass motion. We quantified center of kidney mass mobility vectors in threemore » dimensions: anteroposterior (AP), mediolateral (ML), and superoinferior (SI). Results: Kidney motion decreases linearly with decreasing age and height. The 95% confidence interval for the averaged minima and maxima of renal motion in children younger than 9 years was 5-9 mm in the ML direction, 4-11 mm in the AP direction, and 12-25 mm in the SI dimension for both kidneys. In children older than 9 years, the same confidence interval reveals a widening range of motion that was 5-16 mm in the ML direction, 6-17 mm in the AP direction, and 21-52 mm in the SI direction. Although not statistically significant, renal motion correlated with diaphragm motion in older patients. The correlation between diaphragm motion and body mass index was borderline (r = 0.52, p = 0.0816) in younger patients. Conclusions: Renal motion is age and height dependent. Measuring diaphragmatic motion alone does not reliably quantify pediatric renal motion. Renal motion in young children ranges from 5 to 25 mm in orientation-specific directions. The vectors of motion range from 5 to 52 mm in older children. These preliminary data represent novel analyses of pediatric intra-abdominal organ motion.« less

Change in Intra-Abdominal Fat Predicts the Risk of Hypertension in Japanese Americans.

PubMed

Sullivan, Catherine A; Kahn, Steven E; Fujimoto, Wilfred Y; Hayashi, Tomoshige; Leonetti, Donna L; Boyko, Edward J

2015-07-01

In Japanese Americans, intra-abdominal fat area measured by computed tomography is positively associated with the prevalence and incidence of hypertension. Evidence in other populations suggests that other fat areas may be protective. We sought to determine whether a change in specific fat depots predicts the development of hypertension. We prospectively followed up 286 subjects (mean age, 49.5 years; 50.4% men) from the Japanese American Community Diabetes Study for 10 years. At baseline, subjects did not have hypertension (defined as blood pressure ≥140/90 mm Hg) and were not taking blood pressure or glucose-lowering medications. Mid-thigh subcutaneous fat area, abdominal subcutaneous fat area, and intra-abdominal fat area were directly measured by computed tomography at baseline and 5 years. Logistic regression was used to estimate odds of incident hypertension over 10 years in relation to a 5-year change in fat area. The relative odds of developing hypertension for a 5-year increase in intra-abdominal fat was 1.74 (95% confidence interval, 1.28-2.37), after adjusting for age, sex, body mass index, baseline intra-abdominal fat, alcohol use, smoking status, and weekly exercise energy expenditure. This relationship remained significant when adjusted for baseline fasting insulin and 2-hour glucose levels or for diabetes mellitus and pre-diabetes mellitus classification. There were no significant associations between baseline and change in thigh or abdominal subcutaneous fat areas and incident hypertension. In conclusion, in this cohort of Japanese Americans, the risk of developing hypertension is related to the accumulation of intra-abdominal fat rather than the accrual of subcutaneous fat in either the thigh or the abdominal areas. © 2015 American Heart Association, Inc.

Relation of aortic valve calcium detected by cardiac computed tomography to all-cause mortality.

PubMed

Blaha, Michael J; Budoff, Matthew J; Rivera, Juan J; Khan, Atif N; Santos, Raul D; Shaw, Leslee J; Raggi, Paolo; Berman, Daniel; Rumberger, John A; Blumenthal, Roger S; Nasir, Khurram

2010-12-15

Aortic valve calcium (AVC) can be quantified on the same computed tomographic scan as coronary artery calcium (CAC). Although CAC is an established predictor of cardiovascular events, limited evidence is available for an independent predictive value for AVC. We studied a cohort of 8,401 asymptomatic subjects (mean age 53 ± 10 years, 69% men), who were free of known coronary heart disease and were undergoing electron beam computed tomography for assessment of subclinical atherosclerosis. The patients were followed for a median of 5 years (range 1 to 7) for the occurrence of mortality from any cause. Multivariate Cox regression models were developed to predict all-cause mortality according to the presence of AVC. A total of 517 patients (6%) had AVC on electron beam computed tomography. During follow-up, 124 patients died (1.5%), for an overall survival rate of 96.1% and 98.7% for those with and without AVC, respectively (hazard ratio 3.39, 95% confidence interval 2.09 to 5.49). After adjustment for age, gender, hypertension, dyslipidemia, diabetes mellitus, smoking, and a family history of premature coronary heart disease, AVC remained a significant predictor of mortality (hazard ratio 1.82, 95% confidence interval 1.11 to 2.98). Likelihood ratio chi-square statistics demonstrated that the addition of AVC contributed significantly to the prediction of mortality in a model adjusted for traditional risk factors (chi-square = 5.03, p = 0.03) as well as traditional risk factors plus the presence of CAC (chi-square = 3.58, p = 0.05). In conclusion, AVC was associated with increased all-cause mortality, independent of the traditional risk factors and the presence of CAC. Copyright © 2010. Published by Elsevier Inc.

Siemens, Philips megaproject to yield superchip in 5 years

NASA Astrophysics Data System (ADS)

1985-02-01

The development of computer chips using complementary metal oxide semiconductor (CMOS) memory technology is described. The management planning and marketing strategy of the Philips and Siemens corporations with regard to the memory chip are discussed.

Conservative orthodontic treatment of mandibular bilateral condyle fracture.

PubMed

Gašpar, Goran; Brakus, Ivan; Kovačić, Ivan

2014-09-01

Maxillofacial trauma is rare in children younger than the age of 5 years (range 0.6%-1.2%), and they can require different clinical treatment strategies compared with fractures in the adult population because of concerns regarding mandibular growth and development of dentition. A 5-year-old girl with a history of falling from a bicycle 7 hours earlier was referred to the department of oral and maxillofacial surgery. Multislice computed tomographic examination demonstrated a bilateral fracture of the mandibular condyle neck associated with minimal fracture of the alveolar ridge of the maxilla. The multislice computed tomographic scan also demonstrated dislocation on the right condyle neck and, on the left side, a medial inclination of approximately 45 degrees associated with greenstick fracture of the right parasymphysis region. In this particular case, orthodontic rubber elastics in combination with fixed orthodontic brackets provided good results in the treatment of bilateral condyle neck fractures associated with greenstick fracture of parasymphysis.

Short-term outcome of 1,465 computer-navigated primary total knee replacements 2005-2008.

PubMed

Gøthesen, Oystein; Espehaug, Birgitte; Havelin, Leif; Petursson, Gunnar; Furnes, Ove

2011-06-01

and purpose Improvement of positioning and alignment by the use of computer-assisted surgery (CAS) might improve longevity and function in total knee replacements, but there is little evidence. In this study, we evaluated the short-term results of computer-navigated knee replacements based on data from the Norwegian Arthroplasty Register. Primary total knee replacements without patella resurfacing, reported to the Norwegian Arthroplasty Register during the years 2005-2008, were evaluated. The 5 most common implants and the 3 most common navigation systems were selected. Cemented, uncemented, and hybrid knees were included. With the risk of revision for any cause as the primary endpoint and intraoperative complications and operating time as secondary outcomes, 1,465 computer-navigated knee replacements (CAS) and 8,214 conventionally operated knee replacements (CON) were compared. Kaplan-Meier survival analysis and Cox regression analysis with adjustment for age, sex, prosthesis brand, fixation method, previous knee surgery, preoperative diagnosis, and ASA category were used. Kaplan-Meier estimated survival at 2 years was 98% (95% CI: 97.5-98.3) in the CON group and 96% (95% CI: 95.0-97.8) in the CAS group. The adjusted Cox regression analysis showed a higher risk of revision in the CAS group (RR = 1.7, 95% CI: 1.1-2.5; p = 0.02). The LCS Complete knee had a higher risk of revision with CAS than with CON (RR = 2.1, 95% CI: 1.3-3.4; p = 0.004)). The differences were not statistically significant for the other prosthesis brands. Mean operating time was 15 min longer in the CAS group. With the introduction of computer-navigated knee replacement surgery in Norway, the short-term risk of revision has increased for computer-navigated replacement with the LCS Complete. The mechanisms of failure of these implantations should be explored in greater depth, and in this study we have not been able to draw conclusions regarding causation.

[Etiological factors for developing carpal tunnel syndrome in people who work with computers].

PubMed

Lewańska, Magdalena; Wagrowska-Koski, Ewa; Walusiak-Skorupa, Jolanta

2013-01-01

Carpal tunnel syndrome (CTS) is the most frequent mononeuropathy of upper extremities. From the early 1990's it has been suggested that intensive work with computers can result in CTS development, however, this relationship has not as yet been proved. The aim of the study was to evaluate occupational and non-occupational risk factors for developing CTS in the population of computer-users. The study group comprised 60 patients (58 women and 2 men; mean age: 53.8 +/- 6.35 years) working with computers and suspected of occupational CTS. A survey as well as both median and ulnar nerve conduction examination (NCS) were performed in all the subjects. The patients worked with use of computer for 6.43 +/- 1.71 h per day. The mean latency between the beginning of employment and the occurrence of first CTS symptoms was 12.09 +/- 5.94 years. All patients met the clinical and electrophysiological diagnostic criteria of CTS. In the majority of patients etiological factors for developing CTS were non-occupational: obesity, hypothyroidism, oophorectomy, past hysterectomy, hormonal replacement therapy or oral contraceptives, recent menopause, diabetes, tendovaginitis. In 7 computer-users etiological factors were not identified. The results of our study show that CTS is usually generated by different causes not related with using computers at work.

Department of Defense In-House RDT and E Activities: Management Analysis Report for Fiscal Year 1993

DTIC Science & Technology

1994-11-01

A worldwide unique lab because it houses a high - speed modeling and simulation system, a prototype...E Division, San Diego, CA: High Performance Computing Laboratory providing a wide range of advanced computer systems for the scientific investigation...Machines CM-200 and a 256-node Thinking Machines CM-S. The CM-5 is in a very large memory, ( high performance 32 Gbytes, >4 0 OFlop) coafiguration,

Tuition Assistance Program (TAP) at ASA Institute of Computer and Business Technology, Inc. Audit for 1991-1992 through 1993-1994 Academic Years. Report 95-T-5 (Revised).

ERIC Educational Resources Information Center

Maldonado, Carmen

In an audit of the records and procedures for ASA Institute of Computer and Business Technology, Inc. (ASA), the New York Office of the State Comptroller determined that ASA was overpaid $696,352 because school officials incorrectly certified certain students as eligible for Tuition Assistance Program (TAP) awards. This error was discovered using…

Put Your Robot In, Put Your Robot Out: Sequencing through Programming Robots in Early Childhood

ERIC Educational Resources Information Center

Kazakoff, Elizabeth R.; Bers, Marina Umaschi

2014-01-01

This article examines the impact of programming robots on sequencing ability in early childhood. Thirty-four children (ages 4.5-6.5 years) participated in computer programming activities with a developmentally appropriate tool, CHERP, specifically designed to program a robot's behaviors. The children learned to build and program robots over three…

A STATEMENT OF GUIDELINES CONCERNING ARTICULATION BETWEEN TWO-YEAR AND FOUR-YEAR COLLEGES, WASHINGTON FOLLOW-UP CONFERENCE OF THE NATIONAL PROJECT FOR IMPROVEMENT OF ARTICULATION BETWEEN 2-YEAR AND 4-YEAR COLLEGES (U. OF WASHINGTON, MAY 3-5, 1965).

ERIC Educational Resources Information Center

GILES, FREDERIC T.; NELSON, JAMES H.

THE AUTHORS PRESENT A SET OF SPECIFIC GUIDELINES WITHIN A FRAMEWORK OF FIVE PRINCIPLES. (1) MAXIMUM FREEDOM TO TRANSFER SHOULD BE PRESERVED FOR STUDENTS WHO MAKE SATISFACTORY JUNIOR COLLEGE RECORDS. ATTENTION IS GIVEN TO THE PLACE OF HIGH SCHOOL RECORDS, TEST SCORES, INSTITUTIONAL GRADE DIFFERENTIALS, FLEXIBILITY, AND METHODS OF COMPUTING GRADE…

Historical Inflation Program. A Computer Program Generating Historical Inflation Indices for Army Aircraft. Revision.

DTIC Science & Technology

1984-01-01

data comes in three published formats: (1) a cumulative history coverina past years on a monthly basis, 5 (2) yearly supplements (such as wage and...all fisca. ea’r :. ma. Outzu: _ dNx’resse as monthly, quarterly, fiscal vear, and .-r ear 4n- :~n.e (in calen- dar year 1967 base) and inflation faCt...These indices and factors provide a means of adjusting historical cost data for the procurement of Army aircraft to constant year dollars. Additional

Prognostic value of coronary computed tomographic angiography findings in asymptomatic individuals: a 6-year follow-up from the prospective multicentre international CONFIRM study.

PubMed

Cho, Iksung; Al'Aref, Subhi J; Berger, Adam; Ó Hartaigh, Bríain; Gransar, Heidi; Valenti, Valentina; Lin, Fay Y; Achenbach, Stephan; Berman, Daniel S; Budoff, Matthew J; Callister, Tracy Q; Al-Mallah, Mouaz H; Cademartiri, Filippo; Chinnaiyan, Kavitha; Chow, Benjamin J W; DeLago, Augustin; Villines, Todd C; Hadamitzky, Martin; Hausleiter, Joerg; Leipsic, Jonathon; Shaw, Leslee J; Kaufmann, Philipp A; Feuchtner, Gudrun; Kim, Yong-Jin; Maffei, Erica; Raff, Gilbert; Pontone, Gianluca; Andreini, Daniele; Marques, Hugo; Rubinshtein, Ronen; Chang, Hyuk-Jae; Min, James K

2018-03-14

The long-term prognostic benefit of coronary computed tomographic angiography (CCTA) findings of coronary artery disease (CAD) in asymptomatic populations is unknown. From the prospective multicentre international CONFIRM long-term study, we evaluated asymptomatic subjects without known CAD who underwent both coronary artery calcium scoring (CACS) and CCTA (n = 1226). Coronary computed tomographic angiography findings included the severity of coronary artery stenosis, plaque composition, and coronary segment location. Using the C-statistic and likelihood ratio tests, we evaluated the incremental prognostic utility of CCTA findings over a base model that included a panel of traditional risk factors (RFs) as well as CACS to predict long-term all-cause mortality. During a mean follow-up of 5.9 ± 1.2 years, 78 deaths occurred. Compared with the traditional RF alone (C-statistic 0.64), CCTA findings including coronary stenosis severity, plaque composition, and coronary segment location demonstrated improved incremental prognostic utility beyond traditional RF alone (C-statistics range 0.71-0.73, all P < 0.05; incremental χ2 range 20.7-25.5, all P < 0.001). However, no added prognostic benefit was offered by CCTA findings when added to a base model containing both traditional RF and CACS (C-statistics P > 0.05, for all). Coronary computed tomographic angiography improved prognostication of 6-year all-cause mortality beyond a set of conventional RF alone, although, no further incremental value was offered by CCTA when CCTA findings were added to a model incorporating RF and CACS.

Pacific Symposium on Biocomputing 2002/2003/2004

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

A.Keith Dunker

2004-10-26

Brief introduction to Pacific Symposium on Biocomputing The Pacific Symposium on Biocomputing is an international, multidisciplinary conference covering current research in the theory and the application of computational methods in problems of biological significance. Researchers from the United States, the Asian Pacific nations and around the world gather each year at PSB to exchange research results and discuss open issues in all aspects of computational biology. PSB provides a forum for work on databases, algorithms, interfaces, visualization, modeling and other computational methods, as applied to biological problems. The data-rich areas of molecular biology are emphasized. PSB is the only meetingmore » in the bioinformatics field with sessions defined dynamically each year in response to specific proposals from the participants. Sessions are organized by leaders in emerging areas to provide forums for publication and for discussion of research in biocomputing ''hot topics''. PSB therefore enables discussion of emerging methods and approaches in this rapidly changing field. PSB has been designated as one of the major meetings in this field by the recently established International Society for Computational Biology (see www.iscb.org). Papers and presentations are peer reviewed typically with 3 reviews per paper plus editorial oversight from the conference organizers. The accepted papers are published in an archival proceedings volume, which is indexed by PubMed, and electronically (see http://psb.stanford.edu/). Finally, given the tight schedule from submission of papers to their publication, typically 5 to 5 1/2 months, the PSB proceedings each year represents one of the most up-to-date surveys of current trends in bioinformatics.« less

Examining the Impact of ABRACADABRA on Early Literacy in Northern Australia: An Implementation Fidelity Analysis

ERIC Educational Resources Information Center

Wolgemuth, Jennifer R.; Abrami, Philip C.; Helmer, Janet; Savage, Robert; Harper, Helen; Lea, Tess

2014-01-01

To address students' poor literacy outcomes, an intervention using a computer-based literacy tool, ABRACADABRA, was implemented in 6 Northern Australia primary schools. A pretest, posttest parallel group, single blind multisite randomized controlled trial was conducted with 308 students between the ages of 4 and 8 years old (M age = 5.8 years, SD…

Comparison of energy expenditure in adolescents when playing new generation and sedentary computer games: cross sectional study

PubMed Central

2007-01-01

Objective To compare the energy expenditure of adolescents when playing sedentary and new generation active computer games. Design Cross sectional comparison of four computer games. Setting Research laboratories. Participants Six boys and five girls aged 13-15 years. Procedure Participants were fitted with a monitoring device validated to predict energy expenditure. They played four computer games for 15 minutes each. One of the games was sedentary (XBOX 360) and the other three were active (Wii Sports). Main outcome measure Predicted energy expenditure, compared using repeated measures analysis of variance. Results Mean (standard deviation) predicted energy expenditure when playing Wii Sports bowling (190.6 (22.2) kJ/kg/min), tennis (202.5 (31.5) kJ/kg/min), and boxing (198.1 (33.9) kJ/kg/min) was significantly greater than when playing sedentary games (125.5 (13.7) kJ/kg/min) (P<0.001). Predicted energy expenditure was at least 65.1 (95% confidence interval 47.3 to 82.9) kJ/kg/min greater when playing active rather than sedentary games. Conclusions Playing new generation active computer games uses significantly more energy than playing sedentary computer games but not as much energy as playing the sport itself. The energy used when playing active Wii Sports games was not of high enough intensity to contribute towards the recommended daily amount of exercise in children. PMID:18156227

Comparison of energy expenditure in adolescents when playing new generation and sedentary computer games: cross sectional study.

PubMed

Graves, Lee; Stratton, Gareth; Ridgers, N D; Cable, N T

2007-12-22

To compare the energy expenditure of adolescents when playing sedentary and new generation active computer games. Cross sectional comparison of four computer games. Research laboratories. Six boys and five girls aged 13-15 years. Procedure Participants were fitted with a monitoring device validated to predict energy expenditure. They played four computer games for 15 minutes each. One of the games was sedentary (XBOX 360) and the other three were active (Wii Sports). Predicted energy expenditure, compared using repeated measures analysis of variance. Mean (standard deviation) predicted energy expenditure when playing Wii Sports bowling (190.6 (22.2) kJ/kg/min), tennis (202.5 (31.5) kJ/kg/min), and boxing (198.1 (33.9) kJ/kg/min) was significantly greater than when playing sedentary games (125.5 (13.7) kJ/kg/min) (P<0.001). Predicted energy expenditure was at least 65.1 (95% confidence interval 47.3 to 82.9) kJ/kg/min greater when playing active rather than sedentary games. Playing new generation active computer games uses significantly more energy than playing sedentary computer games but not as much energy as playing the sport itself. The energy used when playing active Wii Sports games was not of high enough intensity to contribute towards the recommended daily amount of exercise in children.

Work-site health promotion of frequent computer users: comparing selected interventions.

PubMed

Blasche, Gerhard; Pfeffer, Manuela; Thaler, Helga; Gollner, Erwin

2013-01-01

Frequent computer use is associated with an increase in musculoskeletal complaints. The present study aims at comparing the relative efficacy of three novel interventions for the preventions of musculoskeletal complaints in frequent computer users. 93 employees (56 woman, 37 men, mean age 40.1 ± 8.8 years) with frequent computer use. Participants were assigned on the basis of preference to one of the following interventions of 8 week duration: Nordic Walking (NW), biofeedback assisted relaxation and stretching (BFB), balance exercises on a wobble board (BAL) or a waiting list control group. Outcome measures were musculoskeletal complaints, emotional well-being, fatigue, job dissatisfaction as well as neuromuscular activity in the neck/shoulder region at rest and during computer work assessed before and after the intervention and at 3 months follow-up. The average number of training-units per week was 2.2 ± 0.8, 5.5 ± 3.5 and 4.1 ± 2.9 for NW, BFB and BAL, respectively. NW led to short and medium term improvement of musculoskeletal complaints, BFB to a short term improvement of musculoskeletal complaints. Effects on the well-being related variables or on neuromuscular activity were not found. BAL had no effect on the studied variables. NW and to a limited extent BFB are interventions potentially useful for reducing musculoskeletal complaints in frequent computer users.

An optimized network for phosphorus load monitoring for Lake Okeechobee, Florida

USGS Publications Warehouse

Gain, W.S.

1997-01-01

Phosphorus load data were evaluated for Lake Okeechobee, Florida, for water years 1982 through 1991. Standard errors for load estimates were computed from available phosphorus concentration and daily discharge data. Components of error were associated with uncertainty in concentration and discharge data and were calculated for existing conditions and for 6 alternative load-monitoring scenarios for each of 48 distinct inflows. Benefit-cost ratios were computed for each alternative monitoring scenario at each site by dividing estimated reductions in load uncertainty by the 5-year average costs of each scenario in 1992 dollars. Absolute and marginal benefit-cost ratios were compared in an iterative optimization scheme to determine the most cost-effective combination of discharge and concentration monitoring scenarios for the lake. If the current (1992) discharge-monitoring network around the lake is maintained, the water-quality sampling at each inflow site twice each year is continued, and the nature of loading remains the same, the standard error of computed mean-annual load is estimated at about 98 metric tons per year compared to an absolute loading rate (inflows and outflows) of 530 metric tons per year. This produces a relative uncertainty of nearly 20 percent. The standard error in load can be reduced to about 20 metric tons per year (4 percent) by adopting an optimized set of monitoring alternatives at a cost of an additional $200,000 per year. The final optimized network prescribes changes to improve both concentration and discharge monitoring. These changes include the addition of intensive sampling with automatic samplers at 11 sites, the initiation of event-based sampling by observers at another 5 sites, the continuation of periodic sampling 12 times per year at 1 site, the installation of acoustic velocity meters to improve discharge gaging at 9 sites, and the improvement of a discharge rating at 1 site.

Prevalence and Correlates of Problematic Internet Experiences and Computer-Using Time: A Two-Year Longitudinal Study in Korean School Children

PubMed Central

Stewart, Robert; Lee, Ju-Yeon; Kim, Jae-Min; Kim, Sung-Wan; Shin, Il-Seon; Yoon, Jin-Sang

2014-01-01

Objective To measure the prevalence of and factors associated with online inappropriate sexual exposure, cyber-bullying victimisation, and computer-using time in early adolescence. Methods A two-year, prospective school survey was performed with 1,173 children aged 13 at baseline. Data collected included demographic factors, bullying experience, depression, anxiety, coping strategies, self-esteem, psychopathology, attention-deficit hyperactivity disorder symptoms, and school performance. These factors were investigated in relation to problematic Internet experiences and computer-using time at age 15. Results The prevalence of online inappropriate sexual exposure, cyber-bullying victimisation, academic-purpose computer overuse, and game-purpose computer overuse was 31.6%, 19.2%, 8.5%, and 21.8%, respectively, at age 15. Having older siblings, more weekly pocket money, depressive symptoms, anxiety symptoms, and passive coping strategy were associated with reported online sexual harassment. Male gender, depressive symptoms, and anxiety symptoms were associated with reported cyber-bullying victimisation. Female gender was associated with academic-purpose computer overuse, while male gender, lower academic level, increased height, and having older siblings were associated with game-purpose computer-overuse. Conclusion Different environmental and psychological factors predicted different aspects of problematic Internet experiences and computer-using time. This knowledge is important for framing public health interventions to educate adolescents about, and prevent, internet-derived problems. PMID:24605120

Violence Against Women and Household Ownership of Radios, Computers, and Phones in 20 Countries.

PubMed

Cardoso, Lauren F; Sorenson, Susan B

2017-07-01

To examine the relationship between household ownership of information and communication technologies (ICTs) and justifications for wife beating. Women aged 15 to 49 years in 20 countries were surveyed via UNICEF's Multiple Indicator Cluster Surveys between 2006 and 2014. Multivariate logistic regressions accounted for individual-, household-, and structural-level variables. Household ownership of any ICT (radio, computer, fixed phone, or mobile phone but not television) was associated with increased odds of women rejecting wife beating. The largest association was with computer ownership: women in homes with a computer were more likely to reject wife beating (adjusted odds ratio [AOR] = 1.81; 97.5% confidence interval [CI] = 1.69, 1.93). Number of ICTs was important: women in households with 1, 2, 3, 4, and 5 ICTs (vs 0) were more likely to reject wife-beating justifications (AOR = 1.10 [97.5% CI = 1.03, 1.17]; AOR = 1.10 [97.5% CI = 1.03, 1.18]; AOR = 1.19 [97.5% CI = 1.11, 1.29]; AOR = 1.71 [97.5% CI = 1.54, 1.88]; and AOR = 2.85 [97.5% CI = 2.48, 3.26]; respectively). Independent of household wealth, country development, and other sociodemographic factors, the more ICTs in a household, the more likely that women will reject wife-beating justifications. Policymakers and program planners should consider potential implications of ICT access relating to intimate partner violence.

Media use as a reason for meal skipping and fast eating in secondary school children.

PubMed

Van den Bulck, J; Eggermont, S

2006-04-01

This study examined self-reported meal skipping and eating faster than usual with the goal of watching television or playing computer games. Respondents reported their media use and indicated how often they skipped a meal to watch a favourite television programme or to play a computer game, and how often they ate faster than usual in order to watch television or play a computer game. Respondents were 2546 adolescents of 13 (first year of secondary school) and 16 years (fourth year of secondary school) of age. About one respondent in 10 skipped at least one meal every week for either television viewing or computer game playing. Weekly meal skipping for television viewing occurs more regularly in boys and first-year students, but particularly in teenagers who view 5 h or more daily (15% of the sample). The category of teenagers who play computer games four times a week or more (25.3% of the sample) is at increased risk of meal skipping; those who play more than four times a week are 10 times more likely weekly to skip a meal. A quarter of the adolescents eat faster at least once a week to be able to watch television or play a computer game. Regardless of gender and school year, teenagers' risk of eating faster progressively increases with their use of the media. Those who watch 4 h or more daily are about seven times more likely to skip a meal for television and those who play computer games at least four times a week are nine times more likely weekly to skip a meal. Unhealthy eating habits can be a side effect of heavy or excessive media use. Teenagers' use of television or game computers during nonworking or out-of-school hours partly displaces the amount of time that needs to be spent at meals. Practitioners and educators may try to encourage or restore a pattern of healthful meal consumption habits by reducing the amount of media use, and by supporting parental rule-making regarding children's eating habits and media use.

NASA Information Resources Management Long Range Plan, FY 1994-1998

NASA Technical Reports Server (NTRS)

1993-01-01

Table of Contents: Introduction; Agency 5-Year IRM Investment Projections; Program Specific IRM Activities by Program Office; Major IRM Program Accomplishments for FY 1992; Information Collection Budget; Summary of Computer Security Plans; and Appendix: Acronym List.

25 CFR 36.23 - Standard VIII-Junior high/middle school instructional program.

Code of Federal Regulations, 2014 CFR

2014-04-01

.... (4) Science. One unit shall be required of each student every year. (5) Fine arts and practical arts.... (6) Computer literacy. One unit shall be required of each student in the junior high/middle school...

25 CFR 36.23 - Standard VIII-Junior high/middle school instructional program.

Code of Federal Regulations, 2013 CFR

2013-04-01

.... (4) Science. One unit shall be required of each student every year. (5) Fine arts and practical arts.... (6) Computer literacy. One unit shall be required of each student in the junior high/middle school...

25 CFR 36.23 - Standard VIII-Junior high/middle school instructional program.

Code of Federal Regulations, 2011 CFR

2011-04-01

.... (4) Science. One unit shall be required of each student every year. (5) Fine arts and practical arts.... (6) Computer literacy. One unit shall be required of each student in the junior high/middle school...

25 CFR 36.23 - Standard VIII-Junior high/middle school instructional program.

Code of Federal Regulations, 2012 CFR

2012-04-01

.... (4) Science. One unit shall be required of each student every year. (5) Fine arts and practical arts.... (6) Computer literacy. One unit shall be required of each student in the junior high/middle school...

A comparative evaluation of computer literacy amongst dental educators and students.

PubMed

Mattheos, N; Schittek, M Janda; Nattestad, A; Shanley, D; Attström, R

2005-02-01

A task-oriented questionnaire was designed, aiming to quickly assess competence with the use of computers. The questionnaire consisted of distinct computer-related skills, representing various competences in educational computer use. A total score from 0 to 49 was calculated upon completion of the questionnaire, based on the sum of all the positively identified competences. The questionnaire was distributed to an international group of leading dental educators during the DentEd Global Congress in Prague in 2001 and to a cohort of first year dental students (2001) in the Dental Faculty, University of Malmo, Sweden. Certain attitudes towards the role of information and communication technology (ICT) in dental education were also measured through Visual Analogue Scales in the educator's group. A total of 149 questionnaires were collected from the educators' group and 58 from the dental students. There was no significant difference in the average computer competence score between the two groups. The educators' group average score was 20.7 (SD 9.9) and students' average was 18.1 (SD 8.5). A significant positive correlation (r = 0.395277, P < 0.0001) was found between the competence measured by the questionnaire and the year of graduation in the educators' group. The attitudes towards the role of ICT in dental education amongst the educators were very positive, regardless of their competence with computers, year of graduation or academic position. The results from this study indicate that there is wide diversity in computer competence amongst both students and academic staff. In addition, students' actual competence in the use of computers might not be as high as is often perceived through self-assessment and ordinal scales.

Conditional long-term survival following minimally invasive robotic mitral valve repair: a health services perspective.

PubMed

Efird, Jimmy T; Griffin, William F; Gudimella, Preeti; O'Neal, Wesley T; Davies, Stephen W; Crane, Patricia B; Anderson, Ethan J; Kindell, Linda C; Landrine, Hope; O'Neal, Jason B; Alwair, Hazaim; Kypson, Alan P; Nifong, Wiley L; Chitwood, W Randolph

2015-09-01

Conditional survival is defined as the probability of surviving an additional number of years beyond that already survived. The aim of this study was to compute conditional survival in patients who received a robotically assisted, minimally invasive mitral valve repair procedure (RMVP). Patients who received RMVP with annuloplasty band from May 2000 through April 2011 were included. A 5- and 10-year conditional survival model was computed using a multivariable product-limit method. Non-smoking men (≤65 years) who presented in sinus rhythm had a 96% probability of surviving at least 10 years if they survived their first year following surgery. In contrast, recent female smokers (>65 years) with preoperative atrial fibrillation only had an 11% probability of surviving beyond 10 years if alive after one year post-surgery. In the context of an increasingly managed healthcare environment, conditional survival provides useful information for patients needing to make important treatment decisions, physicians seeking to select patients most likely to benefit long-term following RMVP, and hospital administrators needing to comparatively assess the life-course economic value of high-tech surgical procedures.

Projected Clinical, Resource Use, and Fiscal Impacts of Implementing Low-Dose Computed Tomography Lung Cancer Screening in Medicare.

PubMed

Roth, Joshua A; Sullivan, Sean D; Goulart, Bernardo H L; Ravelo, Arliene; Sanderson, Joanna C; Ramsey, Scott D

2015-07-01

The Centers for Medicare and Medicaid Services (CMS) recently issued a national coverage determination that provides reimbursement for low-dose computed tomography (CT) lung cancer screening for enrollees age 55 to 77 years with ≥ 30-pack-year smoking history who currently smoke or quit in the last 15 years. The clinical, resource use, and fiscal impacts of this change in screening coverage policy remain uncertain. We developed a simulation model to forecast the 5-year health outcome impacts of the CMS low-dose CT screening policy in Medicare compared with no screening. The model used data from the National Lung Screening Trial, CMS enrollment statistics and reimbursement schedules, and peer-reviewed literature. Outcomes included counts of screening examinations, patient cases of lung cancer detected, stage distribution, and total and per-enrollee per-month fiscal impact. Over 5 years, we project that low-dose CT screening will result in 10.7 million more low-dose CT scans, 52,000 more lung cancers detected, and increased overall expenditure of $6.8 billion ($2.22 per Medicare enrollee per month). The most fiscally impactful factors were the average cost-per-screening episode, proportion of enrollees eligible for screening, and cost of treating stage I lung cancer. Low-dose CT screening is expected to increase lung cancer diagnoses, shift stage at diagnosis toward earlier stages, and substantially increase Medicare expenditures over a 5-year time horizon. These projections can inform planning efforts by Medicare administrators, contracted health care providers, and other stakeholders. Copyright © 2015 by American Society of Clinical Oncology.

Upper extremity pain and computer use among engineering graduate students.

PubMed

Schlossberg, Eric B; Morrow, Sandra; Llosa, Augusto E; Mamary, Edward; Dietrich, Peter; Rempel, David M

2004-09-01

The objective of this study was to investigate risk factors associated with persistent or recurrent upper extremity and neck pain among engineering graduate students. A random sample of 206 Electrical Engineering and Computer Science (EECS) graduate students at a large public university completed an online questionnaire. Approximately 60% of respondents reported upper extremity or neck pain attributed to computer use and reported a mean pain severity score of 4.5 (+/-2.2; scale 0-10). In a final logistic regression model, female gender, years of computer use, and hours of computer use per week were significantly associated with pain. The high prevalence of upper extremity pain reported by graduate students suggests a public health need to identify interventions that will reduce symptom severity and prevent impairment.

Worldwide Diversity and Occurrence of Arsenite Transporter acr3(2) Suggests an Important and Overlooked Pathway

NASA Astrophysics Data System (ADS)

Mailloux, B. J.; Wagner, P.; Foster, R.; Stolz, J. F.; Scholz, M.; Wovkulich, K.; Freyer, G. A.

2009-12-01

Arsenic is a toxic element that occurs naturally in the environment. Microorganisms have detoxification pathways that involve the expulsion of arsenite from the cytoplasm. The genes encoding these processes, including acr3(2), have been well studied in laboratory. However, comparatively less is known of detoxification genes in the environment. Here we report on the environmental diversity of acr3(2), an arsenite transporter gene, in 15 samples from a variety of habitats, including 2 marine samples from near the Amazon River plume, 2 sediment samples from California Soda Lakes (Mono and Searle), 8 groundwater samples from Bangladesh, 1 sediment sample from Union Lake, NJ, and 2 microcosm experiments using sediment from the Vineland Chemical Co Superfund site, NJ amended with acetate and arsenate. These sites were chosen to represent a variety arsenic impacted environments. Aqueous concentrations of arsenic ranged from below 13 nM to 5.6 mM (1 ppb to 422 ppm). Fifteen clone libraries were generated, and the 304 unique sequences clustered with or near Proteobacteria, Cyanobacteria , Euryarchaeota (Archaea),Acidobacteria, Thermatogae (Archaea), Planctomycetes, Bacteroidetes and Firmicutes. Thus, the acr3(2) gene appears to be highly conserved worldwide and across the domains of Archaea and Bacteria. Comparison of clone libraries, however, indicated that individual sites had distinct communities. Rarefraction analysis and CHAO1 estimation of species richness showed that even with 1406 available acr sequences from JGI and this study, the known diversity of the gene is not saturated. These results suggests that the acr3(2) gene and detoxification in general may be more important than previously thought in environmental arsenic cycling and mobilization.

Cardiac and great vessel injuries after chest trauma: our 10-year experience.

PubMed

Onan, Burak; Demirhan, Recep; Öz, Kürşad; Onan, Ismihan Selen

2011-09-01

Cardiovascular injuries after trauma present with high mortality. The aim of the study was to present our experience in cardiac and great vessel injuries after chest trauma. During the 10-year period, 104 patients with cardiac (n=94) and great vessel (n=10) injuries presented to our hospital. The demographic data, mechanism of injury, location of injury, other associated injuries, timing of surgical intervention, surgical approach, and clinical outcome were reviewed. Eighty-eight (84.6%) males presented after chest trauma. The mean age of the patients was 32.5±8.2 years (range: 12-76). Penetrating injuries (62.5%) were the most common cause of trauma. Computed tomography was performed in most cases and echocardiography was used in some stable cases. Cardiac injuries mostly included the right ventricle (58.5%). Great vessel injuries involved the subclavian vein in 6, innominate vein in 1, vena cava in 1, and descending aorta in 2 patients. Early operations after admission to the emergency were performed in 75.9% of the patients. Thoracotomy was performed in 89.5% of the patients. Operative mortality was significantly high in penetrating injuries (p=0.01). Clinicians should suspect cardiac and great vessel trauma in every patient presenting to the emergency unit after chest trauma. Computed tomography and echocardiography are beneficial in the management of chest trauma. Operative timing depends on hemodynamic status, and a multidisciplinary team approach improves the patient's prognosis.

DEVELOPMENT OF A SET OF MESH-BASED AND AGE-DEPENDENT CHINESE PHANTOMS AND APPLICATION FOR CT DOSE CALCULATIONS.

PubMed

Pi, Yifei; Liu, Tianyu; Xu, X George

2018-06-01

Phantoms for organ dose calculations are essential in radiation protection dosimetry. This article describes the development of a set of mesh-based and age-dependent phantoms for Chinese populations using reference data recommended by the Chinese government and by the International Atomic Energy Agency (IAEA). Existing mesh-based RPI adult male (RPI-AM) and RPI adult female (RPI-AF) phantoms were deformed to form new phantoms according to anatomical data for the height and weight of Chinese individuals of 5 years old male, 5 years old female, 10 years old male, 10 years old female,15 years old male, 15 years old female, adult male and adult female-named USTC-5 M, USTC-5F, USTC-10M, USTC-10F, USTC-15M, USTC-15F, USTC-AM and USTC-AF, respectively. Following procedures to ensure the accuracy, more than 120 organs/tissues in each model were adjusted to match the Chinese reference parameters and the mass errors were within 0.5%. To demonstrate the usefulness, these new set of phantoms were combined with a fully validated model of the GE LightSpeed Pro 16 multi-detector computed tomography (MDCT) scanner and the GPU-based ARCHER Monte Carlo code to compute organ doses from CT examinations. Organ doses for adult models were then compared with the data of RPI-AM and RPI-AF under the same conditions. The absorbed doses and the effective doses of RPI phantoms are found to be lower than these of the USTC adult phantoms whose body sizes are smaller. Comparisons for the doses among different ages and genders were also made. It was found that teenagers receive more radiation doses than adults do. Such Chinese-specific phantoms are clearly better suited in organ dose studies for the Chinese individuals than phantoms designed for western populations. As already demonstrated, data derived from age-specific Chinese phantoms can help CT operators and designers to optimize image quality and doses.

How Do Residents Spend Their Shift Time? A Time and Motion Study With a Particular Focus on the Use of Computers

PubMed Central

Mamykina, Lena; Vawdrey, David K.; Hripcsak, George

2016-01-01

Purpose To understand how much time residents spend using computers as compared with other activities, and what residents use computers for. Method This time and motion study was conducted in June and July 2010 at NewYork-Presbyterian/Columbia University Medical Center with seven residents (first-, second-, and third-year) on the general medicine service. An experienced observer shadowed residents during a single day shift, captured all their activities using an iPad application, and took field notes. The activities were captured using a validated taxonomy of clinical activities, expanded to describe computer-based activities with a greater level of detail. Results Residents spent 364.5 minutes (50.6%) of their shift time using computers, compared with 67.8 minutes (9.4%) interacting with patients. In addition, they spent 292.3 minutes (40.6%) talking with others in person, 186.0 minutes (25.8%) handling paper notes, 79.7 minutes (11.1%) in rounds, 80.0 minutes (11.1%) walking or waiting, and 54.0 minutes (7.5%) talking on the phone. Residents spent 685 minutes (59.6%) multitasking. Computer-based documentation activities amounted to 189.9 minutes (52.1%) of all computer-based activities time, with 128.7 minutes (35.3%) spent writing notes and 27.3 minutes (7.5%) reading notes composed by others. Conclusions The study showed residents spent considerably more time interacting with computers (over 50% of their shift time), than in direct contact with patients (less than 10% of their shift time). Some of this may be due to an increasing reliance on computing systems for access to patient data, further exacerbated by inefficiencies in the design of the electronic health record. PMID:27028026

How Do Residents Spend Their Shift Time? A Time and Motion Study With a Particular Focus on the Use of Computers.

PubMed

Mamykina, Lena; Vawdrey, David K; Hripcsak, George

2016-06-01

To understand how much time residents spend using computers compared with other activities, and what residents use computers for. This time and motion study was conducted in June and July 2010 at NewYork-Presbyterian/Columbia University Medical Center with seven residents (first-, second-, and third-year) on the general medicine service. An experienced observer shadowed residents during a single day shift, captured all their activities using an iPad application, and took field notes. The activities were captured using a validated taxonomy of clinical activities, expanded to describe computer-based activities with a greater level of detail. Residents spent 364.5 minutes (50.6%) of their shift time using computers, compared with 67.8 minutes (9.4%) interacting with patients. In addition, they spent 292.3 minutes (40.6%) talking with others in person, 186.0 minutes (25.8%) handling paper notes, 79.7 minutes (11.1%) in rounds, 80.0 minutes (11.1%) walking or waiting, and 54.0 minutes (7.5%) talking on the phone. Residents spent 685 minutes (59.6%) multitasking. Computer-based documentation activities amounted to 189.9 minutes (52.1%) of all computer-based activities time, with 128.7 minutes (35.3%) spent writing notes and 27.3 minutes (7.5%) reading notes composed by others. The study showed that residents spent considerably more time interacting with computers (over 50% of their shift time) than in direct contact with patients (less than 10% of their shift time). Some of this may be due to an increasing reliance on computing systems for access to patient data, further exacerbated by inefficiencies in the design of the electronic health record.

Einstein-Home search for periodic gravitational waves in early S5 LIGO data

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

Abbott, B. P.; Abbott, R.; Adhikari, R.

This paper reports on an all-sky search for periodic gravitational waves from sources such as deformed isolated rapidly spinning neutron stars. The analysis uses 840 hours of data from 66 days of the fifth LIGO science run (S5). The data were searched for quasimonochromatic waves with frequencies f in the range from 50 to 1500 Hz, with a linear frequency drift f (measured at the solar system barycenter) in the range -f/{tau}

Sedentary patterns and media availability in European adolescents: The HELENA study.

PubMed

Rey-López, Juan P; Vicente-Rodriguez, Germán; Ortega, Francisco B; Ruiz, Jonatan R; Martinez-Gómez, David; De Henauw, Stefan; Manios, Yannis; Molnar, Denes; Polito, Angela; Verloigne, Maite; Castillo, Manuel J; Sjöström, Michael; De Bourdeaudhuij, Ilse; Moreno, Luis A

2010-07-01

To describe sedentary behaviors in adolescents and to examine the influence of media availability on TV viewing. The study assessed 3278 adolescents (1537 males and 1741 females, 12.5-17.5 years) involved in the HELENA study (2007). Adolescents reported hours of TV viewing, computer games, console, internet for study and non-study reasons, and study, as well as availability of TVs, computers and consoles. Time spent in sedentary behaviors was higher during weekends (all p<0.001). Males spent more hours on TV viewing (for > or = 15 years at weekends), playing computer games and console games while females spent more time studying and surfing for non-study reasons. During weekdays, one third of adolescents exceeded the screen time guidelines (>2h/day) based solely on TV viewing, whereas around 60% exceeded it at weekends. Having a TV or a console in the bedroom was associated with higher TV viewing (OR=2.66; 95% CI 2.23-3.18; and OR=1.92; 95% CI 1.61-2.28, respectively) whereas the presence of computer reduced it (OR=0.57; 95% CI 0.48-0.68). Adolescents living in Europe are not meeting media recommendations, especially during weekend. The absence of a TV in the adolescents' bedroom might reduce TV viewing. Further studies are needed to confirm or contrast our findings. Copyright 2010 Elsevier Inc. All rights reserved.

Emerging technology in surgical education: combining real-time augmented reality and wearable computing devices.

PubMed

Ponce, Brent A; Menendez, Mariano E; Oladeji, Lasun O; Fryberger, Charles T; Dantuluri, Phani K

2014-11-01

The authors describe the first surgical case adopting the combination of real-time augmented reality and wearable computing devices such as Google Glass (Google Inc, Mountain View, California). A 66-year-old man presented to their institution for a total shoulder replacement after 5 years of progressive right shoulder pain and decreased range of motion. Throughout the surgical procedure, Google Glass was integrated with the Virtual Interactive Presence and Augmented Reality system (University of Alabama at Birmingham, Birmingham, Alabama), enabling the local surgeon to interact with the remote surgeon within the local surgical field. Surgery was well tolerated by the patient and early surgical results were encouraging, with an improvement of shoulder pain and greater range of motion. The combination of real-time augmented reality and wearable computing devices such as Google Glass holds much promise in the field of surgery. Copyright 2014, SLACK Incorporated.

Migration of the Duraloc cup after 5 years.

PubMed

Stihsen, Christoph; Pabinger, Christof; Radl, Roman; Rehak, Peter; Windhager, Reinhard

2008-12-01

The Duraloc cup is a frequently used metal-backed, porous-coated, hemispherical, press-fit acetabular component. Published data on loosening rates are contradictory. In this study we investigated migration patterns with computer-assisted Einzel-Bild-Roentgen-Analyse (EBRA) of 67 Duraloc 100 cups. Cup migration and clinical scores were analysed over a 5-year follow-up period. Median total migration of the Duraloc 100 cup was 1.21 mm at 5 years. Seventy-five percent of implants were radiologically stable at 2 years and 90% at 4 years. One cup loosened aseptically at 60 months, requiring revision. Cup diameters > or = 54 mm migrated significantly more than cups < 54 mm in diameter (p = 0.029 at 4 years). There was a significant correlation between high polyethylene wear and further migrating cups within the first post-operative year (p = 0.035 at 12 months). Our analysis revealed significantly higher wear in males (p = 0.029 at 4 years). Radiological loosening at two years could be calculated using receiver-operating characteristic curve analysis, and 1.2 mm as an adequate threshold value (sensitivity = 100%, specificity = 89%).

Differentiation of nonneoplastic and neoplastic gallbladder polyps 1 cm or bigger with multi-detector row computed tomography.

PubMed

Park, Ko Woon; Kim, Seong Hyun; Choi, Seong Ho; Lee, Won Jae

2010-01-01

To evaluate useful computed tomographic features to differentiate nonneoplastic and neoplastic gallbladder polyps 1 cm or bigger. Thirty-one patients with 32 nonneoplastic polyps and 67 patients with 73 neoplastic polyps 1 cm or bigger underwent unenhanced and dual-phase (arterial and portal venous phases) multi-detector row computed tomography. Gallbladder polyps were diagnosed by cholecystectomy. Computed tomographic features including size (1.5 cm), surface (smooth or irregular), shape (pedunculated or sessile), accompanying wall thickening, basal indentation, perception on unenhanced images, and enhancement pattern between 2 groups were compared using univariate and multivariate analyses. On univariate analysis, age 55 years or older (P = 0.0019), size bigger than 1.5 cm (P < 0.0001), irregular surface (P = 0.0033), sessile shape (P = 0.0016), accompanying wall thickening (P = 0.0056), basal indentation (P = 0.0236), and perception on unenhanced images (P < 0.0001) were significantly more frequent in neoplastic polyps as compared with nonneoplastic polyps. On multivariate analysis, size bigger than 1.5 cm (P = 0.0260), sessile shape (P = 0.0397), and perception on unenhanced images (P < 0.0001) were statistically significant. Size bigger than 1.5 cm, sessile shape, and perception on unenhanced images are the main factors that differentiate neoplastic from nonneoplastic gallbladder polyps 1 cm or bigger.

Level II scour analysis for Bridge 9 (BARRUSO3020009) on U.S. Route 302, crossing Jail Branch, Barre, Vermont

USGS Publications Warehouse

Olson, Scott A.; Ivanoff, Michael A.

1997-01-01

skew-to-roadway. There is evidence of channel scour along the right bank from 190 feet upstream of the bridge and extending through the bridge along the right abutment. Under the bridge, the scour depth is approximately 0.5 feet below the mean thalweg depth. Scour protection measures at the site include type-3 stone fill (less than 48 inches diameter) along the right bank extending from the bridge to 192 feet upstream. Type-2 stone fill (less than 36 inches diameter) is along the right abutment and the right downstream bank to 205 feet downtream of the bridge. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour for all modelled flows ranged from 0.2 to 0.5 ft. The worst-case contraction scour occurred at the 500-year discharge. Abutment scour ranged from 4.3 to 7.5 ft. The worst-case abutment scour occurred at the 500-year discharge. Computed scour for the 100-year event does not go below the abutment footings. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Time-Constrained Functional Connectivity Analysis of Cortical Networks Underlying Phonological Decoding in Typically Developing School-Aged Children: A Magnetoencephalography Study

ERIC Educational Resources Information Center

Simos, Panagiotis G.; Rezaie, Roozbeh; Fletcher, Jack M.; Papanicolaou, Andrew C.

2013-01-01

The study investigated functional associations between left hemisphere occipitotemporal, temporoparietal, and inferior frontal regions during oral pseudoword reading in 58 school-aged children with typical reading skills (aged 10.4 [plus or minus] 1.6, range 7.5-12.5 years). Event-related neuromagnetic data were used to compute source-current…

Computer and internet use by persons after traumatic spinal cord injury.

PubMed

Goodman, Naomi; Jette, Alan M; Houlihan, Bethlyn; Williams, Steve

2008-08-01

To determine whether computer and internet use by persons post spinal cord injury (SCI) is sufficiently prevalent and broad-based to consider using this technology as a long-term treatment modality for patients who have sustained SCI. A multicenter cohort study. Twenty-six past and current U.S. regional Model Spinal Cord Injury Systems. Patients with traumatic SCI (N=2926) with follow-up interviews between 2004 and 2006, conducted at 1 or 5 years postinjury. Not applicable. Results revealed that 69.2% of participants with SCI used a computer; 94.2% of computer users accessed the internet. Among computer users, 19.1% used assistive devices for computer access. Of the internet users, 68.6% went online 5 to 7 days a week. The most frequent use for internet was e-mail (90.5%) and shopping sites (65.8%), followed by health sites (61.1%). We found no statistically significant difference in computer use by sex or level of neurologic injury, and no difference in internet use by level of neurologic injury. Computer and internet access differed significantly by age, with use decreasing as age group increased. The highest computer and internet access rates were seen among participants injured before the age of 18. Computer and internet use varied by race: 76% of white compared with 46% of black subjects were computer users (P<.001), and 95.3% of white respondents who used computers used the internet, compared with 87.6% of black respondents (P<.001). Internet use increased with education level (P<.001): eighty-six percent of participants who did not graduate from high school or receive a degree used the internet, while over 97% of those with a college or associate's degree did. While the internet holds considerable potential as a long-term treatment modality after SCI, limited access to the internet by those who are black, those injured after age 18, and those with less education does reduce its usefulness in the short term for these subgroups.

The MAGIC-5 CAD for nodule detection in low dose and thin slice lung CTs

NASA Astrophysics Data System (ADS)

Cerello, Piergiorgio; MAGIC-5 Collaboration

2010-11-01

Lung cancer is the leading cause of cancer-related mortality in developed countries. Only 10-15% of all men and women diagnosed with lung cancer live 5 years after the diagnosis. However, the 5-year survival rate for patients diagnosed in the early asymptomatic stage of the disease can reach 70%. Early-stage lung cancers can be diagnosed by detecting non-calcified small pulmonary nodules with computed tomography (CT). Computer-aided detection (CAD) could support radiologists in the analysis of the large amount of noisy images generated in screening programs, where low-dose and thin-slice settings are used. The MAGIC-5 project, funded by the Istituto Nazionale di Fisica Nucleare (INFN, Italy) and Ministero dell'Università e della Ricerca (MUR, Italy), developed a multi-method approach based on three CAD algorithms to be used in parallel with a merging of their results: the Channeler Ant Model (CAM), based on Virtual Ant Colonies, the Dot-Enhancement/Pleura Surface Normals/VBNA (DE-PSN-VBNA), and the Region Growing Volume Plateau (RGVP). Preliminary results show quite good performances, to be improved with the refining of the single algorithm and the added value of the results merging.

Computer and online health information literacy among Belgrade citizens aged 66-89 years.

PubMed

Gazibara, Tatjana; Kurtagic, Ilma; Kisic-Tepavcevic, Darija; Nurkovic, Selmina; Kovacevic, Nikolina; Gazibara, Teodora; Pekmezovic, Tatjana

2016-06-01

Computer users over 65 years of age in Serbia are rare. The purpose of this study was to (i) describe main demographic characteristics of computer users older than 65; (ii) evaluate their online health information literacy and (iii) assess factors associated with computer use in this population. Persons above 65 years of age were recruited at the Community Health Center 'Vračar' in Belgrade from November 2012 to January 2013. Data were collected after medical checkups using a questionnaire. Of 480 persons who were invited to participate 354 (73.7%) agreed to participate, while 346 filled in the questionnaire (72.1%). A total of 70 (20.2%) older persons were computer users (23.4% males vs. 17.7% females). Of those, 23.7% explored health-related web sites. The majority of older persons who do not use computers reported that they do not have a reason to use a computer (76.5%), while every third senior (30.4%) did not own a computer. Predictors of computer use were being younger [odds ratio (OR) = 2.14, 95% confidence interval (CI) 1.30-4.04; p = 0.019], having less members of household (OR = 2.97, 95% CI 1.45-6.08; p = 0.003), being more educated (OR = 3.53, 95% CI 1.88-6.63; p = 0.001), having higher income (OR = 2.31, 95% CI 1.17-4.58; p = 0.016) as well as fewer comorbidities (OR = 0.42, 95% CI 0.23-0.79; p = 0.007). Being male was independent predictor of online health information use at the level of marginal significance (OR = 4.43, 95% CI 1.93-21.00; p = 0.061). Frequency of computer and Internet use among older adults in Belgrade is similar to other populations. Patterns of Internet use as well as non-use demonstrate particular socio-cultural characteristics. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Report: EPA Needs to Improve Management Practices to Ensure a Successful Customer Technology Solutions Project

EPA Pesticide Factsheets

Report #10-P-0194, August 23, 2010. Although EPA indicated it could avoid spending more than $115.4 million over 8.5 years by consolidating the desktop computing environment, improved management practices are needed.

Impaired recognition of traffic signs in adults with dyslexia.

PubMed

Brachacki, G W; Nicolson, R I; Fawcett, A J

1995-05-01

Ten adults with dyslexia (4 women and 6 men, mean age: 26.8 years, range: 19-43 years) and 11 controls (5 women and 6 men, mean age: 20.5 years, range: 18-29 years) were tested on their ability to differentiate between real and false traffic signs. The stimuli, computer-presented color pictures, were chosen to minimize the applicability of verbal or written linguistic skills to the task. The adults with dyslexia recognized the traffic signs significantly less well than did the controls. Furthermore, whereas for the controls there was a significant correlation between traffic sign recognition and driving experience, no such correlation was found for the adults with dyslexia. The results are interpreted in terms of a deficit in implicit learning.

Technology and Learning at Home: Findings from the Evaluation of the Home Access Programme Pilot

ERIC Educational Resources Information Center

Jewitt, C.; Parashar, U.

2011-01-01

This paper examines the impact of a UK government initiative, introduced in late 2008 and closed in 2011, to provide a computer and 1 year of Internet connectivity to low-income households with children aged 5-19 years. This paper presents and discusses the findings from the evaluation of the initiative, the Home Access Programme (HAP) pilot study…

Oakton Community College Annual Budget, Fiscal Year 1998-1999, Community College District 535.

ERIC Educational Resources Information Center

Oakton Community Coll., Des Plaines, IL.

This report provides the annual budget for Oakton (Illinois) Community College's fiscal year 1998-1999. The budget contains a total of $59,751,098 in revenues and $61,697,515 in expenditures, a 5.29% increase. The deficit is due primarily to remodeling and outfitting of facilities at one of the campuses and deployment of a computing system for the…

Cosmological N-body Simulation

NASA Astrophysics Data System (ADS)

Lake, George

1994-05-01

.90ex> }}} The ``N'' in N-body calculations has doubled every year for the last two decades. To continue this trend, the UW N-body group is working on algorithms for the fast evaluation of gravitational forces on parallel computers and establishing rigorous standards for the computations. In these algorithms, the computational cost per time step is ~ 10(3) pairwise forces per particle. A new adaptive time integrator enables us to perform high quality integrations that are fully temporally and spatially adaptive. SPH--smoothed particle hydrodynamics will be added to simulate the effects of dissipating gas and magnetic fields. The importance of these calculations is two-fold. First, they determine the nonlinear consequences of theories for the structure of the Universe. Second, they are essential for the interpretation of observations. Every galaxy has six coordinates of velocity and position. Observations determine two sky coordinates and a line of sight velocity that bundles universal expansion (distance) together with a random velocity created by the mass distribution. Simulations are needed to determine the underlying structure and masses. The importance of simulations has moved from ex post facto explanation to an integral part of planning large observational programs. I will show why high quality simulations with ``large N'' are essential to accomplish our scientific goals. This year, our simulations have N >~ 10(7) . This is sufficient to tackle some niche problems, but well short of our 5 year goal--simulating The Sloan Digital Sky Survey using a few Billion particles (a Teraflop-year simulation). Extrapolating past trends, we would have to ``wait'' 7 years for this hundred-fold improvement. Like past gains, significant changes in the computational methods are required for these advances. I will describe new algorithms, algorithmic hacks and a dedicated computer to perform Billion particle simulations. Finally, I will describe research that can be enabled by Petaflop computers. This research is supported by the NASA HPCC/ESS program.

Medicine clerkships and portable computing: a national survey of internal medicine clerkship directors.

PubMed

Ferenchick, Gary; Solomon, David; Durning, Steven J

2010-01-01

Portable computers are widely used by medical trainees, but there is a lack of data on how these devices are used in clinical education programs. The objective is to define the current use of portable computing in internal medicine clerkships and to determine medicine clerkship directors' perceptions of the current value and future importance of portable computing. A 2006 national survey of institutional members of the Clerkship Directors in Internal Medicine. Eighty-three of 110 (75%) of institutional members responded. An institutional requirement for portable computing was reported by 32 schools (39%), whereas only 13 (16%) provided students with a portable computer. Between 10 and 31 institutions (12-37%) reported student use for patient care activities (i.e. order entry, writing patient notes) and only 2 to 4 institutions (2-5%) required such use. The majority of respondents (59-95%) reported portable computer use for educational activities (i.e., tracking patient problems, knowledge resource), however, only in 5 to 19 (6-23%) were such educational uses required. Fifty-six respondents (68%) reported that portable computer's "added value" for teaching and 61 (73%) reported that portable computers would be important in meeting clerkship objectives in the next 3 years. Of interest, even among the institutions requiring portable computers, only 50% recommended or required specific software. Portable computing is required at 39% of allopathic medical schools in the United States. However required portable computing for specific patient care or educational tasks is uncommon. In addition, guidance on specific software exists in only one half of school requiring portable computers, suggesting informal or unstructured uses of required portable computer's in the remaining half. The educational impact of formal institutional requirements for software versus informal "user-defined" applications is unknown.

[Preliminary evaluation of clinical effect of computer aided design and computer aided manufacture zirconia crown].

PubMed

Wang, Yu-guang; Xing, Yan-xi; Sun, Yu-chun; Zhao, Yi-jiao; Lü, Pei-jun; Wang, Yong

2013-06-01

To evaluate clinical effects of computer aided design and computer aided manufacturing (CAD/CAM) milled zirconia crown in three aspects: aesthetic, contact wear and fracture. Sixty patients were divided into two groups.In one group, 35 full contour CAD/CAM zirconia crown were made on molars of 30 patients. The manufacturing process of zirconia crown was as follow. First, the three dimensional(3-D) data of working models, antagonist impression and check records were acquired by 3-D laser scanning Dental wings S50. Then full contour zirconia crowns, which had functional occlusal contacts with antagonistic teeth, and appropriate contact with adjacent teeth were designed with Zeno-CAD(V4.2.5.5.12919) software. ZENOSTAR Zr pure zirconia material was milled in digital controlled machine WIELAND 4030 M1.In the end, the zirconia crown were completed with the method of second sintering and polishing. After clinical try-in, the crown was cemented.In the control group, thirty gold alloy full crown were made and cemented on molars of 30 patients. According to the modified U S Public Health Service Criteria(USPHS) evaluation standard, all crowns were evaluated on the same day, at three months, half a year, one year and two years following delivery. There were three aspects we were focusing on in the evaluation: aesthetic, contact wear(restoration and antagonist), and fracture. In all the prosthesis we evaluated during the 24 months, no fracture was found. Contact wear of crowns varies according to different antagonist teeth. The zirconia crowns show privilege in aesthesis, toughness and anti-wearing.However, there is contact wear on antagonistic natural teeth. Thus it is a good choice when full zirconia crowns are indicated on two antagonistic teeth in both jaws.

Association of Coronary Artery Calcium in Adults Aged 32 to 46 Years With Incident Coronary Heart Disease and Death

PubMed Central

Jacobs, David R.; Terry, James G.; Shay, Christina M.; Sidney, Stephen; Liu, Kiang; Schreiner, Pamela J.; Lewis, Cora E.; Shikany, James M.; Reis, Jared P.; Goff, David C.

2017-01-01

Importance Coronary artery calcium (CAC) is associated with coronary heart disease (CHD) and cardiovascular disease (CVD); however, prognostic data on CAC are limited in younger adults. Objective To determine if CAC in adults aged 32 to 46 years is associated with incident clinical CHD, CVD, and all-cause mortality during 12.5 years of follow-up. Design, Setting, and Participants The Coronary Artery Risk Development in Young Adults (CARDIA) Study is a prospective community-based study that recruited 5115 black and white participants aged 18 to 30 years from March 25, 1985, to June 7, 1986. The cohort has been under surveillance for 30 years, with CAC measured 15 (n = 3043), 20 (n = 3141), and 25 (n = 3189) years after recruitment. The mean follow-up period for incident events was 12.5 years, from the year 15 computed tomographic scan through August 31, 2014. Main Outcomes and Measures Incident CHD included fatal or nonfatal myocardial infarction, acute coronary syndrome without myocardial infarction, coronary revascularization, or CHD death. Incident CVD included CHD, stroke, heart failure, and peripheral arterial disease. Death included all causes. The probability of developing CAC by age 32 to 56 years was estimated using clinical risk factors measured 7 years apart between ages 18 and 38 years. Results At year 15 of the study among 3043 participants (mean [SD] age, 40.3 [3.6] years; 1383 men and 1660 women), 309 individuals (10.2%) had CAC, with a geometric mean Agatston score of 21.6 (interquartile range, 17.3-26.8). Participants were followed up for 12.5 years, with 57 incident CHD events and 108 incident CVD events observed. After adjusting for demographics, risk factors, and treatments, those with any CAC experienced a 5-fold increase in CHD events (hazard ratio [HR], 5.0; 95% CI, 2.8-8.7) and 3-fold increase in CVD events (HR, 3.0; 95% CI, 1.9-4.7). Within CAC score strata of 1-19, 20-99, and 100 or more, the HRs for CHD were 2.6 (95% CI, 1.0-5.7), 5.8 (95% CI, 2.6-12.1), and 9.8 (95% CI, 4.5-20.5), respectively. A CAC score of 100 or more had an incidence of 22.4 deaths per 100 participants (HR, 3.7; 95% CI, 1.5-10.0); of the 13 deaths in participants with a CAC score of 100 or more, 10 were adjudicated as CHD events. Risk factors for CVD in early adult life identified those above the median risk for developing CAC and, if applied, in a selective CAC screening strategy could reduce the number of people screened for CAC by 50% and the number imaged needed to find 1 person with CAC from 3.5 to 2.2. Conclusions and Relevance The presence of CAC among individuals aged between 32 and 46 years was associated with increased risk of fatal and nonfatal CHD during 12.5 years of follow-up. A CAC score of 100 or more was associated with early death. Adults younger than 50 years with any CAC, even with very low scores, identified on a computed tomographic scan are at elevated risk of clinical CHD, CVD, and death. Selective use of screening for CAC might be considered in individuals with risk factors in early adulthood to inform discussions about primary prevention. PMID:28196265

Estimation of Nasal Tip Support Using Computer-Aided Design and 3-Dimensional Printed Models

PubMed Central

Gray, Eric; Maducdoc, Marlon; Manuel, Cyrus; Wong, Brian J. F.

2016-01-01

IMPORTANCE Palpation of the nasal tip is an essential component of the preoperative rhinoplasty examination. Measuring tip support is challenging, and the forces that correspond to ideal tip support are unknown. OBJECTIVE To identify the integrated reaction force and the minimum and ideal mechanical properties associated with nasal tip support. DESIGN, SETTING, AND PARTICIPANTS Three-dimensional (3-D) printed anatomic silicone nasal models were created using a computed tomographic scan and computer-aided design software. From this model, 3-D printing and casting methods were used to create 5 anatomically correct nasal models of varying constitutive Young moduli (0.042, 0.086, 0.098, 0.252, and 0.302 MPa) from silicone. Thirty rhinoplasty surgeons who attended a regional rhinoplasty course evaluated the reaction force (nasal tip recoil) of each model by palpation and selected the model that satisfied their requirements for minimum and ideal tip support. Data were collected from May 3 to 4, 2014. RESULTS Of the 30 respondents, 4 surgeons had been in practice for 1 to 5 years; 9 surgeons, 6 to 15 years; 7 surgeons, 16 to 25 years; and 10 surgeons, 26 or more years. Seventeen surgeons considered themselves in the advanced to expert skill competency levels. Logistic regression estimated the minimum threshold for the Young moduli for adequate and ideal tip support to be 0.096 and 0.154 MPa, respectively. Logistic regression estimated the thresholds for the reaction force associated with the absolute minimum and ideal requirements for good tip recoil to be 0.26 to 4.74 N and 0.37 to 7.19 N during 1- to 8-mm displacement, respectively. CONCLUSIONS AND RELEVANCE This study presents a method to estimate clinically relevant nasal tip reaction forces, which serve as a proxy for nasal tip support. This information will become increasingly important in computational modeling of nasal tip mechanics and ultimately will enhance surgical planning for rhinoplasty. LEVEL OF EVIDENCE NA. PMID:27124818

System Engineering Concept Demonstration, Technology Assessments. Volume 5

DTIC Science & Technology

1992-12-01

MacUser Editor’s Choice Award for the most significant hardware/software product for the Macintosh for the year. Ivan Mimica, founder and CEO of...industry has typed for decades, the devices that are really, to borrow the phrase Apple computer founder Steve Jobs, "the computer for the rest of us.ŕ...43. 3 Ibid. 4 Ibid. 76 android is also displayed, indicating to the group that Liza is participating."’ Liza represents a set of rules that are active

Bibliography on the Distribution, Properties, and Uses of Zeolites from Sedimentary Deposits, 1998-2002

USGS Publications Warehouse

Sheppard, Richard A.

2003-01-01

This bibliography is an alphabetical listing by author of about 1,500 publications and formal releases, including patents and selected abstracts, from the world literature on the distribution, properties, and uses of zeolites from sedimentary deposits for the period 1998-2002. The bibliography is available on a 3.5-inch floppy diskette, which was prepared on a MacintoshTM computer using EndNoteTM software. Computer searches of the bibliography can be made by author, year, title, journal, publisher, and keywords.

Video control system for a drilling in furniture workpiece

NASA Astrophysics Data System (ADS)

Khmelev, V. L.; Satarov, R. N.; Zavyalova, K. V.

2018-05-01

During last 5 years, Russian industry has being starting to be a robotic, therefore scientific groups got new tasks. One of new tasks is machine vision systems, which should solve problem of automatic quality control. This type of systems has a cost of several thousand dollars each. The price is impossible for regional small business. In this article, we describe principle and algorithm of cheap video control system, which one uses web-cameras and notebook or desktop computer as a computing unit.

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

DOE PAGES

Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken; ...

2016-11-29

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic genemore » clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.« less

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes

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

Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic genemore » clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery.« less

High performance computing and communications: Advancing the frontiers of information technology

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

NONE

1997-12-31

This report, which supplements the President`s Fiscal Year 1997 Budget, describes the interagency High Performance Computing and Communications (HPCC) Program. The HPCC Program will celebrate its fifth anniversary in October 1996 with an impressive array of accomplishments to its credit. Over its five-year history, the HPCC Program has focused on developing high performance computing and communications technologies that can be applied to computation-intensive applications. Major highlights for FY 1996: (1) High performance computing systems enable practical solutions to complex problems with accuracies not possible five years ago; (2) HPCC-funded research in very large scale networking techniques has been instrumental inmore » the evolution of the Internet, which continues exponential growth in size, speed, and availability of information; (3) The combination of hardware capability measured in gigaflop/s, networking technology measured in gigabit/s, and new computational science techniques for modeling phenomena has demonstrated that very large scale accurate scientific calculations can be executed across heterogeneous parallel processing systems located thousands of miles apart; (4) Federal investments in HPCC software R and D support researchers who pioneered the development of parallel languages and compilers, high performance mathematical, engineering, and scientific libraries, and software tools--technologies that allow scientists to use powerful parallel systems to focus on Federal agency mission applications; and (5) HPCC support for virtual environments has enabled the development of immersive technologies, where researchers can explore and manipulate multi-dimensional scientific and engineering problems. Educational programs fostered by the HPCC Program have brought into classrooms new science and engineering curricula designed to teach computational science. This document contains a small sample of the significant HPCC Program accomplishments in FY 1996.« less

Turin before the city: Earth Science and Audiovisual Art for scientific storytelling and communication

NASA Astrophysics Data System (ADS)

Lombardo, Vincenzo; Giardino, Marco

2017-04-01

The multimedia product "Turin before the city" is an audiovisual reconstruction of the geomorphologic, climatic and environmental setting of the pre-urban settlement area on which the town of Turin stands today. Through geological and geomorphologic evidences in the Piemonte region, we describe the evolution of plains and reliefs from 2 million years ago until the birth of Augusta Taurinorum (now Turin), about 2000 years ago. From its initial configuration within a local sea (Padan gulf) to the recent continental areas, which form the western end of the Po plain. This history leads to the formation of the main elements that characterize the history of the settlement: the hill, which determines the settlement, the mountains, with their defensive climate, the plains and rivers, which accept the settlement and provide energy, irrigation, and transportation, respectively. Data collected during previous geological and climatic studies allow summarize the history of the area in four main chapters, numbered from the ancient one: (1) from 5 to 2.5 million years ago; (2) from 2.5-million to 700.000 years ago; (3) from 700.000 to 10.000 years ago; (4) from 10.000 to 4.000 years ago. The representation of paleogeographic and paleoenvironmental contexts was achieved through a computer graphics movie displayed on twelve screens all around an inner court of a middle age palace. The movie is an expression of Disney's Fantasia version of Wagners Gesamtkunstwerk ("total work of art"), in which the computer animation and the original music were both integral in conveying the artistic installation. 3D Digital Elevation Models and elaboration from aerial views were integrated with originally conceived CGI (Computer Generated Imagery) scenes. The 5-minute movie shows the setting of the Turin Hill from the sea, the evolution of the Quaternary glaciers, and fluvial processes where will arise Turin. The four chapters above were set in a 24-hour duration and several climatic conditions to achieve a dramatic sense of the settlement evolution, through a careful design of light-conditions, colors, music, and sound effects. Subtitles helped the tracking of the scientific explanation of the animated scenes. The immersive setting was achieved through 12 virtual cameras that explored the computer graphics environment, full of details for grasping the visitors. The storytelling proceeds as follows. 1) The marine environment is illustrated through an exploration of the deep inland sea, characterized by the presence of cetaceans, and introductory music. 2) Within a subtropical coastal environment, we illustrate the Turin hill in the full light of the afternoon, with a fresh music overture. 3) There comes the alluvial fans modelled by river carving the Alps at sunset. 4) Climatic change around 1.8 million years ago allows onset of the Susa Valley glaciers, during a nocturne visual environment and music, soon followed by the dawn of damp and temperate periods, with a fresh celebration music comment. 5) The "Villafranchian" continental environment and River Po migration in the mist and dramatic music just preceded the great ending, with an overview of the Alpine chain that dominated the Turin settlement in the pre-urban era.

Clinical application of quantitative computed tomography in osteogenesis imperfecta-suspected cat.

PubMed

Won, Sungjun; Chung, Woo-Jo; Yoon, Junghee

2017-09-30

One-year-old male Persian cat presented with multiple fractures and no known traumatic history. Marked decrease of bone radiopacity and thin cortices of all long bones were identified on radiography. Tentative diagnosis was osteogenesis imperfecta, a congenital disorder characterized by fragile bone. To determine bone mineral density (BMD), quantitative computed tomography (QCT) was performed. The QCT results revealed a mean trabecular BMD of vertebral bodies of 149.9 ± 86.5 mg/cm 3 . After bisphosphonate therapy, BMD of the same site increased significantly (218.5 ± 117.1 mg/cm 3 , p ＜ 0.05). QCT was a useful diagnostic tool to diagnose osteopenia and quantify response to medical treatment.

Italian regional health system structure and expected cancer survival.

PubMed

Vercelli, Marina; Lillini, Roberto; Quaglia, Alberto; Capocaccia, Riccardo

2014-01-01

Few studies deal with the association of socioeconomic and health system resource variables with cancer survival at the Italian regional level, where the greatest number of decisions about social and health policies and resource allocations are taken. The present study aimed to describe the causal relationships between socioeconomic and health system resource factors and regional cancer survival and to compute the expected cancer survival at provincial, regional and area levels. Age-standardized relative survival at 5 years from diagnosis of cases incident in 1995-1998 and followed up to 2004 were derived by gender for 11 sites from the Italian Association of Cancer Registries data bank. The socioeconomic and health system resource variables, describing at a regional level the macro-economy, demography, labor market, and health resources for 1995-2005, came from the Health for All database. A principal components factor analysis was applied to the socioeconomic and health system resource variables. For every site, linear regression models were computed considering the relative survival at 5 years as a dependent variable and the principal components factor analysis factors as independent variables. The factors described the socioeconomic and health-related features of the regional systems and were causally related to the characteristics of the patient taken in charge. The models built by the factors allowed computation of the expected relative survival at 5 years with very good concordance with those observed at regional, macro-regional and national levels. In the regions without any cancer registry, survival was coherent with that of neighboring regions with similar socioeconomic and health system resources characteristics. The models highlighted the causal correlations between socioeconomic and health system resources and cancer survival, suggesting that they could be good evaluation tools for the efficiency of the resources allocation and use.

Why computational models are better than verbal theories: the case of nonword repetition.

PubMed

Jones, Gary; Gobet, Fernand; Freudenthal, Daniel; Watson, Sarah E; Pine, Julian M

2014-03-01

Tests of nonword repetition (NWR) have often been used to examine children's phonological knowledge and word learning abilities. However, theories of NWR primarily explain performance either in terms of phonological working memory or long-term knowledge, with little consideration of how these processes interact. One theoretical account that focuses specifically on the interaction between short-term and long-term memory is the chunking hypothesis. Chunking occurs because of repeated exposure to meaningful stimulus items, resulting in the items becoming grouped (or chunked); once chunked, the items can be represented in short-term memory using one chunk rather than one chunk per item. We tested several predictions of the chunking hypothesis by presenting 5-6-year-old children with three tests of NWR that were either high, medium, or low in wordlikeness. The results did not show strong support for the chunking hypothesis, suggesting that chunking fails to fully explain children's NWR behavior. However, simulations using a computational implementation of chunking (namely CLASSIC, or Chunking Lexical And Sub-lexical Sequences In Children) show that, when the linguistic input to 5-6-year-old children is estimated in a reasonable way, the children's data are matched across all three NWR tests. These results have three implications for the field: (a) a chunking account can explain key NWR phenomena in 5-6-year-old children; (b) tests of chunking accounts require a detailed specification both of the chunking mechanism itself and of the input on which the chunking mechanism operates; and (c) verbal theories emphasizing the role of long-term knowledge (such as chunking) are not precise enough to make detailed predictions about experimental data, but computational implementations of the theories can bridge the gap. © 2013 John Wiley & Sons Ltd.

Increased Incidence of Visual Field Abnormalities as Determined by Frequency Doubling Technology Perimetry in High Computer Users Among Japanese Workers: A Retrospective Cohort Study.

PubMed

Nakano, Tadashi; Hayashi, Takeshi; Nakagawa, Toru; Honda, Toru; Owada, Satoshi; Endo, Hitoshi; Tatemichi, Masayuki

2018-04-05

This retrospective cohort study primarily aimed to investigate the possible association of computer use with visual field abnormalities (VFA) among Japanese workers. The study included 2,377 workers (mean age 45.7 [standard deviation, 8.3] years; 2,229 men and 148 women) who initially exhibited no VFA during frequency doubling technology perimetry (FDT) testing. Subjects then underwent annual follow-up FDT testing for 7 years, and VFA were determined using a FDT-test protocol (FDT-VFA). Subjects with FDT-VFA were examined by ophthalmologists. Baseline data about the mean duration of computer use during a 5-year period and refractive errors were obtained via self-administered questionnaire and evaluations for refractive errors (use of eyeglasses or contact lenses), respectively. A Cox proportional hazard analysis demonstrated that heavy computer users (>8 hr/day) had a significantly increased risk of FDT-VFA (hazard ratio [HR] 2.85; 95% confidence interval [CI], 1.26-6.48) relative to light users (<4 hr/day), and this association was strengthened among subjects with refractive errors (HR 4.48; 95% CI, 1.87-10.74). The computer usage history also significantly correlated with FDT-VFA among subject with refractive errors (P < 0.05), and 73.1% of subjects with FDT-VFA and refractive errors were diagnosed with glaucoma or ocular hypertension. The incidence of FDT-VFA appears to be increased among Japanese workers who are heavy computer users, particularly if they have refractive errors. Further investigations of epidemiology and causality are warranted.

The prevalence of, and factors associated with, paying for sex among men resident in Britain: findings from the third National Survey of Sexual Attitudes and Lifestyles (Natsal-3)

PubMed Central

Jones, Kyle G; Johnson, Anne M; Wellings, Kaye; Sonnenberg, Pam; Field, Nigel; Tanton, Clare; Erens, Bob; Clifton, Soazig; Datta, Jessica; Mitchell, Kirstin R; Prah, Phillip; Mercer, Catherine H

2015-01-01

Objectives Men who pay for sex (MPS) are considered a bridging population for sexually transmitted infections (STI). However, the extent, characteristics and role of MPS in transmission is poorly understood. We investigate these questions using data from Britain's third National Survey of Sexual Attitudes and Lifestyles (Natsal-3). Methods We performed complex survey analyses of data from 6293 men aged 16–74 years resident in Britain who completed Natsal-3, a probability sample survey undertaken during 2010–2012, using computer-assisted personal interviewing and computer-assisted self-interview. Results 11.0% (95% CI10.1% to 11.9%) of all men reported ever paying for sex. Among MPS, 18.4% (95% CI 18.2% to 18.7%) of their lifetime sexual partners were paid. 3.6% (95% CI 3.1% to 4.2%) of men had paid for sex in the past 5 years. Partners of MPS constitute 14.7% of all reported partners and MPS report 15.6% of all reported STI diagnoses in the past 5 years. Paying for sex in the past 5 years was strongly associated with reporting larger numbers of sexual partners (adjusted OR, AOR for 5+ partners, past 5 years, 31.50, 95% CI 18.69 to 53.09). After adjusting for partner numbers, paying for sex remained strongly associated with reporting new foreign partners outside the UK (AOR 7.96; 95% CI 4.97 to 12.73) and STI diagnosis/es (AOR 2.34; 95% CI 1.44 to 3.81), all in the past 5 years. Among men ever paying for sex, 62.6% (95% CI 58.3% to 66.8%) reported paying for sex outside the UK, most often in Europe and Asia. Conclusions MPS in Britain remain at greater risk of STI acquisition and onward transmission than men who do not. They report high numbers of partners, but the minority are paid partners. They are an important core group in STI transmission. PMID:25404706

A web-based system for neural network based classification in temporomandibular joint osteoarthritis.

PubMed

de Dumast, Priscille; Mirabel, Clément; Cevidanes, Lucia; Ruellas, Antonio; Yatabe, Marilia; Ioshida, Marcos; Ribera, Nina Tubau; Michoud, Loic; Gomes, Liliane; Huang, Chao; Zhu, Hongtu; Muniz, Luciana; Shoukri, Brandon; Paniagua, Beatriz; Styner, Martin; Pieper, Steve; Budin, Francois; Vimort, Jean-Baptiste; Pascal, Laura; Prieto, Juan Carlos

2018-07-01

The purpose of this study is to describe the methodological innovations of a web-based system for storage, integration and computation of biomedical data, using a training imaging dataset to remotely compute a deep neural network classifier of temporomandibular joint osteoarthritis (TMJOA). This study imaging dataset consisted of three-dimensional (3D) surface meshes of mandibular condyles constructed from cone beam computed tomography (CBCT) scans. The training dataset consisted of 259 condyles, 105 from control subjects and 154 from patients with diagnosis of TMJ OA. For the image analysis classification, 34 right and left condyles from 17 patients (39.9 ± 11.7 years), who experienced signs and symptoms of the disease for less than 5 years, were included as the testing dataset. For the integrative statistical model of clinical, biological and imaging markers, the sample consisted of the same 17 test OA subjects and 17 age and sex matched control subjects (39.4 ± 15.4 years), who did not show any sign or symptom of OA. For these 34 subjects, a standardized clinical questionnaire, blood and saliva samples were also collected. The technological methodologies in this study include a deep neural network classifier of 3D condylar morphology (ShapeVariationAnalyzer, SVA), and a flexible web-based system for data storage, computation and integration (DSCI) of high dimensional imaging, clinical, and biological data. The DSCI system trained and tested the neural network, indicating 5 stages of structural degenerative changes in condylar morphology in the TMJ with 91% close agreement between the clinician consensus and the SVA classifier. The DSCI remotely ran with a novel application of a statistical analysis, the Multivariate Functional Shape Data Analysis, that computed high dimensional correlations between shape 3D coordinates, clinical pain levels and levels of biological markers, and then graphically displayed the computation results. The findings of this study demonstrate a comprehensive phenotypic characterization of TMJ health and disease at clinical, imaging and biological levels, using novel flexible and versatile open-source tools for a web-based system that provides advanced shape statistical analysis and a neural network based classification of temporomandibular joint osteoarthritis. Published by Elsevier Ltd.

High Resolution Nature Runs and the Big Data Challenge

NASA Technical Reports Server (NTRS)

Webster, W. Phillip; Duffy, Daniel Q.

2015-01-01

NASA's Global Modeling and Assimilation Office at Goddard Space Flight Center is undertaking a series of very computationally intensive Nature Runs and a downscaled reanalysis. The nature runs use the GEOS-5 as an Atmospheric General Circulation Model (AGCM) while the reanalysis uses the GEOS-5 in Data Assimilation mode. This paper will present computational challenges from three runs, two of which are AGCM and one is downscaled reanalysis using the full DAS. The nature runs will be completed at two surface grid resolutions, 7 and 3 kilometers and 72 vertical levels. The 7 km run spanned 2 years (2005-2006) and produced 4 PB of data while the 3 km run will span one year and generate 4 BP of data. The downscaled reanalysis (MERRA-II Modern-Era Reanalysis for Research and Applications) will cover 15 years and generate 1 PB of data. Our efforts to address the big data challenges of climate science, we are moving toward a notion of Climate Analytics-as-a-Service (CAaaS), a specialization of the concept of business process-as-a-service that is an evolving extension of IaaS, PaaS, and SaaS enabled by cloud computing. In this presentation, we will describe two projects that demonstrate this shift. MERRA Analytic Services (MERRA/AS) is an example of cloud-enabled CAaaS. MERRA/AS enables MapReduce analytics over MERRA reanalysis data collection by bringing together the high-performance computing, scalable data management, and a domain-specific climate data services API. NASA's High-Performance Science Cloud (HPSC) is an example of the type of compute-storage fabric required to support CAaaS. The HPSC comprises a high speed Infinib and network, high performance file systems and object storage, and a virtual system environments specific for data intensive, science applications. These technologies are providing a new tier in the data and analytic services stack that helps connect earthbound, enterprise-level data and computational resources to new customers and new mobility-driven applications and modes of work. In our experience, CAaaS lowers the barriers and risk to organizational change, fosters innovation and experimentation, and provides the agility required to meet our customers' increasing and changing needs

Flow characteristics at U.S. Geological Survey streamgages in the conterminous United States

USGS Publications Warehouse

Wolock, David

2003-01-01

This dataset represents point locations and flow characteristics for current (as of November 20, 2001) and historical U.S. Geological Survey (USGS) streamgages in the conterminous United States. The flow characteristics were computed from the daily streamflow data recorded at each streamgage for the period of record. The attributes associated with each streamgage include: Station number Station name Station latitude (decimal degrees in North American Datum of 1983, NAD 83) Station longitude (decimal degrees in NAD 83) First date (year, month, day) of streamflow data Last date (year, month, day) of streamflow data Number of days of streamflow data Minimum and maximum daily flow for the period of record (cubic feet per second) Percentiles (1, 5, 10, 20, 25, 50, 75, 80, 90, 95, 99) of daily flow for the period of record (cubic feet per second) Average and standard deviation of daily flow for the period of record (cubic feet per second) Mean annual base-flow index (BFI: see supplemental information) computed for the period of record (fraction, ranging from 0 to 1) Year-to-year standard deviation of the annual base-flow index computed for the period of record (fraction) Number of years of data used to compute the base-flow index (years) Reported drainage area (square miles) Reported contributing drainage area (square miles) National Water Information System (NWIS)-Web page URL for streamgage Hydrologic Unit Code (HUC, 8 digit) Hydrologic landscape region (HLR) River Reach File 1 (RF1) segment identification number (E2RF1##) Station numbers, names, locations, and drainage areas were acquired through the National Water Information System (NWIS)-Web (http://water.usgs.gov/nwis) on November 20, 2001. The streamflow data used to compute flow characteristics were copied from the Water server (water.usgs.gov:/www/htdocs/nwisweb/data1/discharge/) on November 2, 2001. The missing value indicator for all attributes is -99. Some streamflow characteristics are missing for: (1) streamgages measuring flow subject to tidal effects, which cause flow to reverse directions, (2) streamgages with site information but no streamflow data at the time the data were retrieved, and (3) streamgages with record length too short to compute the base-flow index.

Sex- and age-related differences in mid-thigh composition and muscle quality determined by computed tomography in middle-aged and elderly Japanese.

PubMed

Kasai, Takehiro; Ishiguro, Naoki; Matsui, Yasumoto; Harada, Atsushi; Takemura, Marie; Yuki, Atsumu; Kato, Yuki; Otsuka, Rei; Ando, Fujiko; Shimokata, Hiroshi

2015-06-01

Sex- and age-related differences in mid-thigh composition and muscle quality remain unclear. The present study aimed to clarify these differences using computed tomography in middle-aged and elderly Japanese. A total of 2310 participants (age 40-89 years), who were randomly selected from the local residents, underwent computed tomography examination of the right mid-thigh. Thigh circumference and cross-sectional areas of the thigh, muscle, quadriceps, non-quadriceps, fat, and bone were measured. Knee extension strength and muscle quality index (knee extension strength/quadriceps cross-sectional area) were also assessed. Sex- and age-related differences in these indices were analyzed. The thigh cross-sectional area in men and women decreased by 0.6% and 0.5%/year, respectively, because of a decrease in muscle cross-sectional area (men 75.2%, women 40.6%), fat cross-sectional area (men 24.4%, women 59.6%) and bone cross-sectional area (men 0.5%, women -0.2%). Muscle cross-sectional area in men and women decreased by 0.6% and 0.4%/year, respectively, because of a decrease in quadriceps cross-sectional area (men 65.6%, women 81.6%) and non-quadriceps cross-sectional area (men 34.4%, women 18.4%). Muscle quality in men and women decreased by 0.4% and 0.3%/year, respectively. Thigh cross-sectional area decreased with age mainly because of a decrease in muscle cross-sectional area in men and fat cross-sectional area in women. The rate of decrease in muscle cross-sectional area was 1.5-fold higher in men than in women. Muscle cross-sectional area decreased with age mainly because of a decrease in quadriceps cross-sectional area, especially in women. Decrease in muscle quality with age was similar in both sexes. © 2014 Japan Geriatrics Society.

Ground Source Heat Pump Computational Results

DOE Data Explorer

James Menart

2013-07-31

This data submission includes simulation results for ground loop heat pump systems located in 6 different cities across the United States. The cities are Boston, MA, Dayton, OH, Omaha, NE, Orlando, FL, Sacramento, CA, and St. Paul, MN. These results were obtained from the two-dimensional geothermal computer code called GEO2D. GEO2D was written as part of this DOE funded grant. The results included in this submission for each of the 6 cities listed above are: 1) specific information on the building being heated or cooled by the ground loop geothermal system, 2) some extreme values for the building heating and cooling loads during the year, 3) the inputs required to carry out the simulation, 4) a plot of the hourly building heating and cooling loads throughout the year, 5) a plot of the fluid temperature exiting the ground loop for a 20 year period, 6) a plot of the heat exchange between the ground loop and the ground for a 20 year period, and 7) ground and ground loop temperature contour plots at different times of the year for the 20 year period.

Level II scour analysis for Bridge 49 (BENNCYHUNT0049) on Hunt Street, crossing the Walloomsac River, Bennington, Vermont

USGS Publications Warehouse

Olson, Scott A.; Medalie, Laura

1997-01-01

2 stone fill also protects the channel banks upstream and downstream of the bridge for a minimum distance of 17 feet from the respective bridge faces. Additional details describing conditions at the site are included in the Level II Summary and Appendices D and E. Scour depths and recommended rock rip-rap sizes were computed using the general guidelines described in Hydraulic Engineering Circular 18 (Richardson and others, 1995). Total scour at a highway crossing is comprised of three components: 1) long-term streambed degradation; 2) contraction scour (due to accelerated flow caused by a reduction in flow area at a bridge) and; 3) local scour (caused by accelerated flow around piers and abutments). Total scour is the sum of the three components. Equations are available to compute depths for contraction and local scour and a summary of the results of these computations follows. Contraction scour computed for all modelled flows ranged from 0.9 to 5.0 ft. The worst-case contraction scour occurred at the 500-year discharge. Computed left abutment scour ranged from 15.3 to 16.5 ft. with the worst-case scour occurring at the incipient roadway-overtopping discharge. Computed right abutment scour ranged from 6.0 to 8.7 ft. with the worst-case scour occurring at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Launch Site Computer Simulation and its Application to Processes

NASA Technical Reports Server (NTRS)

Sham, Michael D.

1995-01-01

This paper provides an overview of computer simulation, the Lockheed developed STS Processing Model, and the application of computer simulation to a wide range of processes. The STS Processing Model is an icon driven model that uses commercial off the shelf software and a Macintosh personal computer. While it usually takes one year to process and launch 8 space shuttles, with the STS Processing Model this process is computer simulated in about 5 minutes. Facilities, orbiters, or ground support equipment can be added or deleted and the impact on launch rate, facility utilization, or other factors measured as desired. This same computer simulation technology can be used to simulate manufacturing, engineering, commercial, or business processes. The technology does not require an 'army' of software engineers to develop and operate, but instead can be used by the layman with only a minimal amount of training. Instead of making changes to a process and realizing the results after the fact, with computer simulation, changes can be made and processes perfected before they are implemented.

Application of a sediment-transport model to estimate bridge scour at selected sites in Colorado, 1991-93

USGS Publications Warehouse

Vaill, J.E.

1995-01-01

A bridge-scour study by the U.S. Geological Survey, in cooperation with the Colorado Department of Transportation, was begun in 1991 to evaluate bridges in the State for potential scour during floods. A part of that study was to apply a computer model for sediment-transport routing to simulate channel aggradation or degradation and pier scour during floods at three bridge sites in Colorado. Stream-channel reaches upstream and downstream from the bridges were simulated using the Bridge Stream Tube model for Alluvial River Simulation (BRI-STARS). Synthetic flood hydrographs for the 500-year floods were developed for Surveyor Creek near Platner and for the Rio Grande at Wagon Wheel Gap. A part of the recorded mean daily hydrograph for the peak flow of record was used for the Yampa River near Maybell. The recorded hydrograph for the peak flow of record exceeded the computed 500-year-flood magnitude for this stream by about 22 percent. Bed-material particle-size distributions were determined from samples collected at Surveyor Creek and the Rio Grande. Existing data were used for the Yampa River. The model was used to compute a sediment-inflow hydrograph using particle-size data collected and a specified sediment-transport equation at each site. Particle sizes ranged from less than 0.5 to 16 millimeters for Surveyor Creek, less than 4 to 128 millimeters for the Yampa River, and 22.5 to 150 millimeters for the Rio Grande. Computed scour at the peak steamflows ranged from -2.32 feet at Surveyor Creek near Platner to +0.63 foot at the Rio Grande at Wagon Wheel Gap. Pier- scour depths computed at the peak streamflows ranged from 4.46 feet at the Rio Grande at Wagon Wheel Gap to 5.94 feet at the Yampa River near Maybell. The number of streamtubes used in the model varied at each site.

Eddy Resolving Global Ocean Prediction including Tides

DTIC Science & Technology

2013-09-30

atlantic meridional overturning circulation in the subpolar North Atlantic . Journal of Geophysical Research vol 118, doi:10.1002/jgrc,20065. [published, refereed] ...global ocean circulation model was examined using results from years 2005-2009 of a seven and a half year 1/12.5° global simulation that resolves...internal tides, along with barotropic tides and the eddying general circulation . We examined tidal amplitudes computed using 18 183-day windows that

A Randomized Controlled Trial of an Early-intervention, Computer-Based Literacy Program to Boost Phonological Skills in 4- to 6-year-old Children

ERIC Educational Resources Information Center

O'Callaghan, Paul; McIvor, Aimee; McVeigh, Claire; Rushe, Teresa

2016-01-01

Background: Many school-based interventions are being delivered in the absence of evidence of effectiveness (Snowling & Hulme, 2011, "Br. J. Educ. Psychol., 81," 1). Aims: This study sought to address this oversight by evaluating the effectiveness of the commonly used the Lexia Reading Core5 intervention, with 4- to 6-year-old pupils…

42 CFR Appendix A to Part 5 - Criteria for Designation of Areas Having Shortages of Primary Medical Care Professional(s)

Code of Federal Regulations, 2013 CFR

2013-10-01

... internees per year to the number of FTE primary care physicians serving the institution is at least 1,000:1... year). (The number of FTE primary care physicians is computed as in part I, section B, paragraph 3... care physicians, as follows: Group 1—Institutions with 500 or more inmates and no physicians. Group 2...

42 CFR Appendix A to Part 5 - Criteria for Designation of Areas Having Shortages of Primary Medical Care Professional(s)

Code of Federal Regulations, 2014 CFR

2014-10-01

... internees per year to the number of FTE primary care physicians serving the institution is at least 1,000:1... year). (The number of FTE primary care physicians is computed as in part I, section B, paragraph 3... care physicians, as follows: Group 1—Institutions with 500 or more inmates and no physicians. Group 2...

42 CFR Appendix A to Part 5 - Criteria for Designation of Areas Having Shortages of Primary Medical Care Professional(s)

Code of Federal Regulations, 2012 CFR

2012-10-01

... internees per year to the number of FTE primary care physicians serving the institution is at least 1,000:1... year). (The number of FTE primary care physicians is computed as in part I, section B, paragraph 3... care physicians, as follows: Group 1—Institutions with 500 or more inmates and no physicians. Group 2...

Effects of dry period length on production, cash flows and greenhouse gas emissions of the dairy herd: A dynamic stochastic simulation model

PubMed Central

van Middelaar, Corina E.; Mostert, Pim F.; van Knegsel, Ariëtte T. M.; Kemp, Bas; de Boer, Imke J. M.; Hogeveen, Henk

2017-01-01

Shortening or omitting the dry period of dairy cows improves metabolic health in early lactation and reduces management transitions for dairy cows. The success of implementation of these strategies depends on their impact on milk yield and farm profitability. Insight in these impacts is valuable for informed decision-making by farmers. The aim of this study was to investigate how shortening or omitting the dry period of dairy cows affects production and cash flows at the herd level, and greenhouse gas emissions per unit of milk, using a dynamic stochastic simulation model. The effects of dry period length on milk yield and calving interval assumed in this model were derived from actual performance of commercial dairy cows over multiple lactations. The model simulated lactations, and calving and culling events of individual cows for herds of 100 cows. Herds were simulated for 5 years with a dry period of 56 (conventional), 28 or 0 days (n = 50 herds each). Partial cash flows were computed from revenues from sold milk, calves, and culled cows, and costs from feed and rearing youngstock. Greenhouse gas emissions were computed using a life cycle approach. A dry period of 28 days reduced milk production of the herd by 3.0% in years 2 through 5, compared with a dry period of 56 days. A dry period of 0 days reduced milk production by 3.5% in years 3 through 5, after a dip in milk production of 6.9% in year 2. On average, dry periods of 28 and 0 days reduced partial cash flows by €1,249 and €1,632 per herd per year, and increased greenhouse gas emissions by 0.7% and 0.5%, respectively. Considering the potential for enhancing cow welfare, these negative impacts of shortening or omitting the dry period seem justifiable, and they might even be offset by improved health. PMID:29077739

Effects of dry period length on production, cash flows and greenhouse gas emissions of the dairy herd: A dynamic stochastic simulation model.

PubMed

Kok, Akke; van Middelaar, Corina E; Mostert, Pim F; van Knegsel, Ariëtte T M; Kemp, Bas; de Boer, Imke J M; Hogeveen, Henk

2017-01-01

Shortening or omitting the dry period of dairy cows improves metabolic health in early lactation and reduces management transitions for dairy cows. The success of implementation of these strategies depends on their impact on milk yield and farm profitability. Insight in these impacts is valuable for informed decision-making by farmers. The aim of this study was to investigate how shortening or omitting the dry period of dairy cows affects production and cash flows at the herd level, and greenhouse gas emissions per unit of milk, using a dynamic stochastic simulation model. The effects of dry period length on milk yield and calving interval assumed in this model were derived from actual performance of commercial dairy cows over multiple lactations. The model simulated lactations, and calving and culling events of individual cows for herds of 100 cows. Herds were simulated for 5 years with a dry period of 56 (conventional), 28 or 0 days (n = 50 herds each). Partial cash flows were computed from revenues from sold milk, calves, and culled cows, and costs from feed and rearing youngstock. Greenhouse gas emissions were computed using a life cycle approach. A dry period of 28 days reduced milk production of the herd by 3.0% in years 2 through 5, compared with a dry period of 56 days. A dry period of 0 days reduced milk production by 3.5% in years 3 through 5, after a dip in milk production of 6.9% in year 2. On average, dry periods of 28 and 0 days reduced partial cash flows by €1,249 and €1,632 per herd per year, and increased greenhouse gas emissions by 0.7% and 0.5%, respectively. Considering the potential for enhancing cow welfare, these negative impacts of shortening or omitting the dry period seem justifiable, and they might even be offset by improved health.

Travel costs associated with flood closures of state highways near Centralia/Chehalis, Washington.

DOT National Transportation Integrated Search

2014-09-01

This report discusses the travel costs associated with the closure of roads in the greater : Centralia/Chehalis, Washington region due to 100-year flood conditions starting on the Chehalis River. The costs : were computed for roadway closures on I-5,...

Changes in television viewing and computers/videogames use among high school students in Southern Brazil between 2001 and 2011.

PubMed

Silva, Kelly Samara; da Silva Lopes, Adair; Dumith, Samuel Carvalho; Garcia, Leandro Martin Totaro; Bezerra, Jorge; Nahas, Markus Vinicius

2014-02-01

To compare the prevalence of television (TV) watching and of computer/videogame use among high school students (15-19 years) from Southern Brazil between 2001 and 2011 and to identify associated socio-demographic factors. Panel studies were conducted with high school students in the state of Santa Catarina, Brazil, in 2001 (n = 5,028) and 2011 (n = 6,529). TV watching and computer/videogame use were collected using questionnaires. Prevalence of ≥2 h/day of TV watching dropped from 76.8 to 61.5 % and ≥2 h/day of computer/videogame use increased from 37.9 to 60.6 %. In both surveys, those aged 15-16 and those who did not work had higher likelihoods of being exposed to ≥2 h/day of TV watching. Boys, those with higher family income, and those who were living in urban areas had higher likelihoods of ≥2 h/day of computer/videogame use. Older age, studying at night and not working were protective factors to these behaviors. After a decade, there was a decrease in the prevalence of TV viewing and an increase in computer/videogame use. Socio-demographic factors were differently associated with these behaviors.

Effect of once-yearly zoledronic acid on the spine and hip as measured by quantitative computed tomography: results of the HORIZON Pivotal Fracture Trial

PubMed Central

Lang, T.; Boonen, S.; Cummings, S.; Delmas, P. D.; Cauley, J. A.; Horowitz, Z.; Kerzberg, E.; Bianchi, G.; Kendler, D.; Leung, P.; Man, Z.; Mesenbrink, P.; Eriksen, E. F.; Black, D. M.

2016-01-01

Summary Changes in bone mineral density and bone strength following treatment with zoledronic acid (ZOL) were measured by quantitative computed analysis (QCT) or dual-energy X-ray absorptiometry (DXA). ZOL treatment increased spine and hip BMD vs placebo, assessed by QCT and DXA. Changes in trabecular bone resulted in increased bone strength. Introduction To investigate bone mineral density (BMD) changes in trabecular and cortical bone, estimated by quantitative computed analysis (QCT) or dual-energy X-ray absorptiometry (DXA), and whether zoledronic acid 5 mg (ZOL) affects bone strength. Methods In 233 women from a randomized, controlled trial of once-yearly ZOL, lumbar spine, total hip, femoral neck, and trochanter were assessed by DXA and QCT (baseline, Month 36). Mean percentage changes from baseline and between-treatment differences (ZOL vs placebo, t-test) were evaluated. Results Mean between-treatment differences for lumbar spine BMD were significant by DXA (7.0%, p<0.01) and QCT (5.7%, p<0.0001). Between-treatment differences were significant for trabecular spine (p=0.0017) [non-parametric test], trabecular trochanter (10.7%, p<0.0001), total hip (10.8%, p<0.0001), and compressive strength indices at femoral neck (8.6%, p=0.0001), and trochanter (14.1%, p<0.0001). Conclusions Once-yearly ZOL increased hip and spine BMD vs placebo, assessed by QCT vs DXA. Changes in trabecular bone resulted in increased indices of compressive strength. PMID:19802508

Sustained Effects of Sirolimus on Lung Function and Cystic Lung Lesions in Lymphangioleiomyomatosis

PubMed Central

Yao, Jianhua; Jones, Amanda M.; Julien-Williams, Patricia; Stylianou, Mario; Moss, Joel

2014-01-01

Rationale: Sirolimus therapy stabilizes lung function and reduces the size of chylous effusions and lymphangioleiomyomas in patients with lymphangioleiomyomatosis. Objectives: To determine whether sirolimus has beneficial effects on lung function, cystic areas, and adjacent lung parenchyma; whether these effects are sustained; and whether sirolimus is well tolerated by patients. Methods: Lung function decline over time, lung volume occupied by cysts (cyst score), and lung tissue texture in the vicinity of the cysts were quantified with a computer-aided diagnosis system in 38 patients. Then we compared cyst scores from the last study on sirolimus with studies done on sirolimus therapy. In 12 patients, we evaluated rates of change in lung function and cyst scores off and on sirolimus. Measurements and Main Results: Sirolimus reduced yearly declines in FEV1 (−2.3 ± 0.1 vs. 1.0 ± 0.3% predicted; P < 0.001) and diffusing capacity of carbon monoxide (−2.6 ± 0.1 vs. 0.9 ± 0.2% predicted; P < 0.001). Cyst scores 1.2 ± 0.8 years (30.5 ± 11.9%) and 2.5 ± 2 years (29.7 ± 12.1%) after initiating sirolimus were not significantly different from pretreatment values (28.4 ± 12.5%). In 12 patients followed for 5 years, a significant reduction in rates of yearly decline in FEV1 (−1.4 ± 0.2 vs. 0.3 ± 0.4% predicted; P = 0.025) was observed. Analyses of 104 computed tomography scans showed a nonsignificant (P = 0.23) reduction in yearly rates of change of cyst scores (1.8 ± 0.2 vs. 0.3 ± 0.3%; P = 0.23) and lung texture features. Despite adverse events, most patients were able to continue sirolimus therapy. Conclusions: Sirolimus therapy slowed down lung function decline and increase in cystic lesions. Most patients were able to tolerate sirolimus therapy. PMID:25329516

Short-term outcome of 1,465 computer-navigated primary total knee replacements 2005–2008

PubMed Central

2011-01-01

Background and purpose Improvement of positioning and alignment by the use of computer-assisted surgery (CAS) might improve longevity and function in total knee replacements, but there is little evidence. In this study, we evaluated the short-term results of computer-navigated knee replacements based on data from the Norwegian Arthroplasty Register. Patients and methods Primary total knee replacements without patella resurfacing, reported to the Norwegian Arthroplasty Register during the years 2005–2008, were evaluated. The 5 most common implants and the 3 most common navigation systems were selected. Cemented, uncemented, and hybrid knees were included. With the risk of revision for any cause as the primary endpoint and intraoperative complications and operating time as secondary outcomes, 1,465 computer-navigated knee replacements (CAS) and 8,214 conventionally operated knee replacements (CON) were compared. Kaplan-Meier survival analysis and Cox regression analysis with adjustment for age, sex, prosthesis brand, fixation method, previous knee surgery, preoperative diagnosis, and ASA category were used. Results Kaplan-Meier estimated survival at 2 years was 98% (95% CI: 97.5–98.3) in the CON group and 96% (95% CI: 95.0–97.8) in the CAS group. The adjusted Cox regression analysis showed a higher risk of revision in the CAS group (RR = 1.7, 95% CI: 1.1–2.5; p = 0.02). The LCS Complete knee had a higher risk of revision with CAS than with CON (RR = 2.1, 95% CI: 1.3–3.4; p = 0.004)). The differences were not statistically significant for the other prosthesis brands. Mean operating time was 15 min longer in the CAS group. Interpretation With the introduction of computer-navigated knee replacement surgery in Norway, the short-term risk of revision has increased for computer-navigated replacement with the LCS Complete. The mechanisms of failure of these implantations should be explored in greater depth, and in this study we have not been able to draw conclusions regarding causation. PMID:21504309

Use of information and communication technology among dental students and registrars at the faculty of dental sciences, University of Lagos.

PubMed

Butali, A; Adeyemo, W L; Akinshipo, A O; Fashina, A; Savage, K O

2011-01-01

The aim of this study was to investigate the use of information technology amongst dental students, dental nursing students and resident doctors in training at the faculty of dental Surgery University of Lagos. A structured questionnaire was distributed to 58 clinical dental students in 4 th and 5 th years of training in the 2010/2011 academic year, 36 dental nursing students and 63 resident doctors undergoing specialist training. All participants have access to the computers, 2.5% within the University and 31% at home and internet cafes and about 50% have the basic skills required. A significant difference was observed between the resident doctors and clinical dental students (P = 0.003), between resident doctors and dental nursing students (P = 0.0001) when the use of computer for study was compared. Over 95% of participants have access to internet and about 50% of them use the internet for their studies. A significant difference (P = 0.005) was observed between clinical dental students and dental nursing students that use the internet and word processing. The resident doctors used the computers for multimedia and MedLine search tools more than clinical dental students (P = 0.004) and dental nursing students (0.0006). The findings of the study show that dental students and resident doctors in training have the requisite knowledge to operate the computer for use in their study and personal activities.

Three-dimensional cone-beam computed tomography analysis of enlargement of the pharyngeal airway by the Herbst appliance.

PubMed

Iwasaki, Tomonori; Takemoto, Yoshihiko; Inada, Emi; Sato, Hideo; Saitoh, Issei; Kakuno, Eriko; Kanomi, Ryuzo; Yamasaki, Youichi

2014-12-01

Pharyngeal airway size is increasingly recognized as an important factor in obstructive sleep apnea. However, few studies have examined the changes of pharyngeal airway form after dental procedures for treating obstructive sleep apnea during growth. The purpose of this study was to evaluate the effect of the Herbst appliance on the 3-dimensional form of the pharyngeal airway using cone-beam computed tomography. Twenty-four Class II subjects (ANB, ≥5°; 11 boys; mean age, 11.6 years) who required Herbst therapy with edgewise treatment had cone-beam computed tomography images taken before and after Herbst treatment. Twenty Class I control subjects (9 boys; mean age, 11.5 years) received edgewise treatment only. The volume, depth, and width of the pharyngeal airway were compared between the groups using measurements from 3-dimensional cone-beam computed tomography images of the entire pharyngeal airway. The increase of the oropharyngeal airway volume in the Herbst group (5000.2 mm(3)) was significantly greater than that of the control group (2451.6 mm(3)). Similarly, the increase of the laryngopharyngeal airway volume in the Herbst group (1941.8 mm(3)) was significantly greater than that of the control group (1060.1 mm(3)). The Herbst appliance enlarges the oropharyngeal and laryngopharyngeal airways. These results may provide a useful assessment of obstructive sleep apnea treatment during growth. Copyright © 2014 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Two-year evaluation indicates zirconia bridges acceptable alternative to PFMs.

PubMed

Perry, Ronald D; Kugel, Gerard; Sharma, Shradha; Ferreira, Susana; Magnuson, Britta

2012-01-01

The aim of this in-vivo study was to evaluate the 2-year clinical performance of zirconia computer-aided design/computer-aided manufacturing (CAD/CAM)-generated bridges. A total of 16 three- or four-unit Lava zirconia bridges were done on 15 subjects. The bridges were cemented using RelyX™ Unicem Self-Adhesive Universal Resin Cement. Evaluation was done at 6-month, 1-year, and 2-year recall visits. Evaluation criteria were color stability and matching, marginal integrity, marginal discoloration, incidence of caries, changes in restoration-tooth interface, changes in surface texture, postoperative sensitivity, maintenance of periodontal health, changes in proximal and opposing teeth, and maintenance of anatomic form. In each of these parameters, the bridges were rated in one of three possible categories: "A" (alpha)--ideal; "B" (bravo)--acceptable; and "C" (charlie)--unacceptable. After 2 years, 100% of the bridges were rated "A" for color stability and matching, marginal discoloration, incidence of caries, changes in restoration-tooth interface, changes in surface texture, postoperative sensitivity, and change in proximal or opposing teeth. In the parameter of marginal integrity, 6.25% of the bridges were rated "B;" the remaining 93.75% were rated "A." Maintenance of periodontal health was rated "B" for 6.25% of the bridges and "A" for 93.75%. At 2 years, 12.5% of the bridges rated "C" in maintenance of anatomic form and 87.5% rated "A." The overall clinical outcome was that the CAD/CAM-generated zirconia bridges were clinically acceptable.

Large-Eddy Simulation of Aeroacoustic Applications

NASA Technical Reports Server (NTRS)

Pruett, C. David; Sochacki, James S.

1999-01-01

This report summarizes work accomplished under a one-year NASA grant from NASA Langley Research Center (LaRC). The effort culminates three years of NASA-supported research under three consecutive one-year grants. The period of support was April 6, 1998, through April 5, 1999. By request, the grant period was extended at no-cost until October 6, 1999. Its predecessors have been directed toward adapting the numerical tool of large-eddy simulation (LES) to aeroacoustic applications, with particular focus on noise suppression in subsonic round jets. In LES, the filtered Navier-Stokes equations are solved numerically on a relatively coarse computational grid. Residual stresses, generated by scales of motion too small to be resolved on the coarse grid, are modeled. Although most LES incorporate spatial filtering, time-domain filtering affords certain conceptual and computational advantages, particularly for aeroacoustic applications. Consequently, this work has focused on the development of subgrid-scale (SGS) models that incorporate time-domain filters.

Do Changes in the Production Process Affect the Outcome of Ceramic Liners: A 3-Year Follow-Up Study.

PubMed

Schmidt-Braekling, Tom; Renner, Lisa; Mintz, Douglas N; Waldstein, Wenzel; Endo, Yoshimi; Boettner, Friedrich

2017-04-01

In 2011, the current liner was withdrawn from the market because of the potential risk for liner fracture secondary to increased pressures used to assemble the metal locking ring. The present study provides a short-term follow-up of patients with this implant. We retrospectively evaluated 63 consecutive hips in 53 patients operated by a single surgeon using a recalled ceramic-on-ceramic bearing. There were 30 women and 23 men with an average age of 50.6 years (range 20.3-63.5 years). The mean follow-up was 36.8 months. Six hips in 6 patients were revised (9.5%) because of a liner-fracture during the follow-up period. All liner fractures were identified on computer tomography imaging. Nine patients had self-reported episodes of squeaking (14.3%). All 6 patients that underwent revision surgery for liner fracture described squeaking before revision. There were no revisions for other causes. Two of the revised patients had a subsequent dislocation (33%). The recalled ceramic liner lots have an increased liner fracture rate. Patients with mechanical symptoms or squeaking should undergo computer tomography to rule out liner facture. Copyright © 2016 Elsevier Inc. All rights reserved.

Home-Based Risk of Falling Assessment Test Using a Closed-Loop Balance Model.

PubMed

Ayena, Johannes C; Zaibi, Helmi; Otis, Martin J-D; Menelas, Bob-Antoine J

2016-12-01

The aim of this study is to improve and facilitate the methods used to assess risk of falling at home among older people through the computation of a risk of falling in real time in daily activities. In order to increase a real time computation of the risk of falling, a closed-loop balance model is proposed and compared with One-Leg Standing Test (OLST). This balance model allows studying the postural response of a person having an unpredictable perturbation. Twenty-nine volunteers participated in this study for evaluating the effectiveness of the proposed system which includes seventeen elder participants: ten healthy elderly ( 68.4 ±5.5 years), seven Parkinson's disease (PD) subjects ( 66.28 ±8.9 years), and twelve healthy young adults ( 28.27 ±3.74 years). Our work suggests that there is a relationship between OLST score and the risk of falling based on center of pressure measurement with four low cost force sensors located inside an instrumented insole, which could be predicted using our suggested closed-loop balance model. For long term monitoring at home, this system could be included in a medical electronic record and could be useful as a diagnostic aid tool.

Migration of the Duraloc cup after 5 years

PubMed Central

Stihsen, Christoph; Pabinger, Christof; Radl, Roman; Rehak, Peter

2007-01-01

The Duraloc cup is a frequently used metal-backed, porous-coated, hemispherical, press-fit acetabular component. Published data on loosening rates are contradictory. In this study we investigated migration patterns with computer-assisted Einzel-Bild-Roentgen-Analyse (EBRA) of 67 Duraloc 100 cups. Cup migration and clinical scores were analysed over a 5-year follow-up period. Median total migration of the Duraloc 100 cup was 1.21 mm at 5 years. Seventy-five percent of implants were radiologically stable at 2 years and 90% at 4 years. One cup loosened aseptically at 60 months, requiring revision. Cup diameters ≥54 mm migrated significantly more than cups <54 mm in diameter (p = 0.029 at 4 years). There was a significant correlation between high polyethylene wear and further migrating cups within the first post-operative year (p = 0.035 at 12 months). Our analysis revealed significantly higher wear in males (p = 0.029 at 4 years). Radiological loosening at two years could be calculated using receiver-operating characteristic curve analysis, and 1.2 mm as an adequate threshold value (sensitivity = 100%, specificity = 89%). PMID:17609953

Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design.

PubMed

Yuan, Shuguang; Chan, H C Stephen; Hu, Zhenquan

2017-06-01

Web browsers have long been recognized as potential platforms for remote macromolecule visualization. However, the difficulty in transferring large-scale data to clients and the lack of native support for hardware-accelerated applications in the local browser undermine the feasibility of such utilities. With the introduction of WebGL and HTML5 technologies in recent years, it is now possible to exploit the power of a graphics-processing unit (GPU) from a browser without any third-party plugin. Many new tools have been developed for biological molecule visualization and modern drug discovery. In contrast to traditional offline tools, real-time computing, interactive data analysis, and cross-platform analyses feature WebGL- and HTML5-based tools, facilitating biological research in a more efficient and user-friendly way. Copyright © 2017 Elsevier Ltd. All rights reserved.

Quantification of biological tissue and construction of patient equivalent phantom (skull and chest) for infants (1-5 years old)

NASA Astrophysics Data System (ADS)

Alves, A. F.; Pina, D. R.; Bacchim Neto, F. A.; Ribeiro, S. M.; Miranda, J. R. A.

2014-03-01

Our main purpose in this study was to quantify biological tissue in computed tomography (CT) examinations with the aim of developing a skull and a chest patient equivalent phantom (PEP), both specific to infants, aged between 1 and 5 years old. This type of phantom is widely used in the development of optimization procedures for radiographic techniques, especially in computed radiography (CR) systems. In order to classify and quantify the biological tissue, we used a computational algorithm developed in Matlab ®. The algorithm performed a histogram of each CT slice followed by a Gaussian fitting of each tissue type. The algorithm determined the mean thickness for the biological tissues (bone, soft, fat, and lung) and also converted them into the corresponding thicknesses of the simulator material (aluminum, PMMA, and air). We retrospectively analyzed 148 CT examinations of infant patients, 56 for skull exams and 92 were for chest. The results provided sufficient data to construct a phantom to simulate the infant chest and skull in the posterior-anterior or anterior-posterior (PA/AP) view. Both patient equivalent phantoms developed in this study can be used to assess physical variables such as noise power spectrum (NPS) and signal to noise ratio (SNR) or perform dosimetric control specific to pediatric protocols.

Level II scour analysis for Bridge 71 (WODSTH00050071) on Town Highway 5, crossing Kedron Brook, Woodstock, Vermont

USGS Publications Warehouse

Olson, S.A.; Ayotte, J.D.

1997-01-01

Contraction scour for all modelled flows ranged from 0.0 to 2.5 ft. The worst-case contraction scour occurred at the incipient roadway-overtopping discharge, which was less than the 100-year discharge. The contraction scour depths do not take the concrete channel bed under the bridge into account. Abutment scour ranged from 8.7 to 18.2 ft. The worstcase abutment scour occurred at the 500-year discharge. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scouredstreambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A cross-section of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particlesize distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Level II scour analysis for Bridge 25 (ROYATH00550025) on Town Highway 55, crossing Broad Brook, Royalton, Vermont

USGS Publications Warehouse

Burns, Ronda L.; Weber, Matthew A.

1997-01-01

Contraction scour for all modelled flows ranged from 0.6 to 1.5 ft. The worst-case contraction scour occurred at the incipient-overtopping discharge which was less than the 100-year discharge. Abutment scour ranged from 3.5 to 8.9 ft. The worst-case abutment scour occurred at the incipient road-overtopping discharge for the left abutment and at the 100-year discharge for the right abutment. Additional information on scour depths and depths to armoring are included in the section titled “Scour Results”. Scoured-streambed elevations, based on the calculated scour depths, are presented in tables 1 and 2. A crosssection of the scour computed at the bridge is presented in figure 8. Scour depths were calculated assuming an infinite depth of erosive material and a homogeneous particle-size distribution. It is generally accepted that the Froehlich equation (abutment scour) gives “excessively conservative estimates of scour depths” (Richardson and others, 1995, p. 47). Usually, computed scour depths are evaluated in combination with other information including (but not limited to) historical performance during flood events, the geomorphic stability assessment, existing scour protection measures, and the results of the hydraulic analyses. Therefore, scour depths adopted by VTAOT may differ from the computed values documented herein.

Bone Mass in Boys with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Calarge, Chadi A.; Schlechte, Janet A.

2017-01-01

To examine bone mass in children and adolescents with autism spectrum disorders (ASD). Risperidone-treated 5 to 17 year-old males underwent anthropometric and bone measurements, using dual-energy X-ray absorptiometry and peripheral quantitative computed tomography. Multivariable linear regression analysis models examined whether skeletal outcomes…

Snore related signals processing in a private cloud computing system.

PubMed

Qian, Kun; Guo, Jian; Xu, Huijie; Zhu, Zhaomeng; Zhang, Gongxuan

2014-09-01

Snore related signals (SRS) have been demonstrated to carry important information about the obstruction site and degree in the upper airway of Obstructive Sleep Apnea-Hypopnea Syndrome (OSAHS) patients in recent years. To make this acoustic signal analysis method more accurate and robust, big SRS data processing is inevitable. As an emerging concept and technology, cloud computing has motivated numerous researchers and engineers to exploit applications both in academic and industry field, which could have an ability to implement a huge blue print in biomedical engineering. Considering the security and transferring requirement of biomedical data, we designed a system based on private cloud computing to process SRS. Then we set the comparable experiments of processing a 5-hour audio recording of an OSAHS patient by a personal computer, a server and a private cloud computing system to demonstrate the efficiency of the infrastructure we proposed.

Fifty-year flood-inundation maps for Nacaome, Honduras

USGS Publications Warehouse

Kresch, David L.; Mastin, M.C.; Olsen, T.D.

2002-01-01

After the devastating floods caused by Hurricane Mitch in 1998, maps of the areas and depths of 50-year-flood inundation at 15 municipalities in Honduras were prepared as a tool for agencies involved in reconstruction and planning. This report, which is one in a series of 15, presents maps of areas in the municipality of Nacaome that would be inundated by 50-year floods on Rio Nacaome, Rio Grande, and Rio Guacirope. Geographic Information System (GIS) coverages of the flood inundation are available on a computer in the municipality of Nacaome as part of the Municipal GIS project and on the Internet at the Flood Hazard Mapping Web page (http://mitchnts1.cr.usgs.gov/projects/floodhazard.html). These coverages allow users to view the flood inundation in much more detail than is possible using the maps in this report. Water-surface elevations for 50-year-floods on Rio Nacaome, Rio Grande, and Rio Guacirope at Nacaome were computed using HEC-RAS, a one-dimensional, steady-flow, step-backwater computer program. The channel and floodplain cross sections used in HEC-RAS were developed from an airborne light-detection-and-ranging (LIDAR) topographic survey of the area and ground surveys at two bridges. The estimated 50-year-flood discharge for Rio Nacaome at Nacaome, 5,040 cubic meters per second, was computed as the drainage-area-adjusted weighted average of two independently estimated 50-year-flood discharges for the gaging station Rio Nacaome en Las Mercedes, located about 13 kilometers upstream from Nacaome. One of the discharges, 4,549 cubic meters per second, was estimated from a frequency analysis of the 16 years of peak-discharge record for the gage, and the other, 1,922 cubic meters per second, was estimated from a regression equation that relates the 50-year-flood discharge to drainage area and mean annual precipitation. The weighted-average of the two discharges is 3,770 cubic meters per second. The 50-year-flood discharges for Rio Grande, 3,890 cubic meters per second, and Rio Guacirope, 1,080 cubic meters per second, were also computed by adjusting the weighted-average 50-year-flood discharge for the Rio Nacaome en Las Mercedes gaging station for the difference in drainage areas between the gage and these river reaches.

A Child Development Centre (C.D.C.) Based on the World of Work and Everyday Life: A Case of Quality Education Provision for 2.5-5 Year Old Children.

ERIC Educational Resources Information Center

Frangos, Christos

1993-01-01

Outlines the organization and activities of the Child Development Centre (CDC) of Aristotle University in Thessaloniki, which operates as a model preschool and kindergarten for over 300 similar institutions throughout Greece. The CDC utilizes art, music, visits to workplaces, movement activities, foreign languages and customs, computers,and free…

Evaluation of brain perfusion in Alzheimer disease with perfusion computed tomography and comparison to elderly patient without dementia.

PubMed

Yildirim, Tülin; Karakurum Göksel, Başak; Demir, Şenay; Tokmak, Naime; Tan, Meliha

2016-04-19

The aim of this study was to evaluate perfusion computed tomography (PCT) findings in patients with Alzheimer disease and to compare them with those of patients without dementia. PCT was performed in 35 patients: 20 with Alzheimer disease (mean age, 69.7 ± 5.5 years) and 15 control subjects (mean age, 67.5 ± 3.5 years). Control subjects were elderly individuals with no cognitive problems who were admitted with headaches. All PCT examinations were performed on a 4-slice CT unit. The PCT analysis software program was used to calculate regional cerebral blood flow (rCBF), regional cerebral blood volume (rCBV), regional time-to-peak (rTTP) values in the bilateral frontal, temporal, and occipital cortices, and bilateral lentiform nucleus. rCBF values in the bilateral frontal and temporal cortices and bilateral lentiform nucleus were significantly lower in the patients with Alzheimer disease than in the control subjects. There were no significant differences in rCBV values between Alzheimer disease and the control group. rTTP values in all cortical areas and bilateral lentiform nucleus were significantly higher in the patients with Alzheimer disease than in the control subjects. PCT is a rapid and reliable imaging modality for evaluating brain perfusion in Alzheimer disease.