Sample records for nucleic acid database

  1. Nucleic Acid Database: a Repository of Three-Dimensional Information about Nucleic Acids

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S. H.; Srinivasan, A. R.; Schneider, B.

    The Nucleic Acid Database (NDB) provides 3-D structural information about nucleic acids.  It is a relational database designed to facilitate the easy search for nucleic acid structures using any of the stored primary or derived structural features. Reports can then be created describing any properties of the selected structures and structures may be viewed in several different formats, including the mmCIF format, the NDB Atlas format, the NDB coordinate format, or the PDB coordinate format. Browsing structure images created directly from coordinates in the repository can also be done. More than 7000 structures have been released as of May 2014. This website also includes a number of specialized tools and interfaces. The NDB Project is funded by the National Institutes of Health and has been funded by the National Science Foundation and the Department of Energy in the past.

  2. Cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor L. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2007-12-11T23:59:59.000Z

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  3. Nucleic acid detection compositions

    DOE Patents [OSTI]

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann (Madison, WI); Dahlberg, James L. (Madison, WI)

    2008-08-05T23:59:59.000Z

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  4. Cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Waunakee, WI); Lyamichev, Victor I. (Madison, WI); Brow; Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2010-11-09T23:59:59.000Z

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  5. Nucleic acid detection assays

    DOE Patents [OSTI]

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann; Dahlberg, James E.

    2005-04-05T23:59:59.000Z

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  6. Nucleic acid detection kits

    DOE Patents [OSTI]

    Hall, Jeff G.; Lyamichev, Victor I.; Mast, Andrea L.; Brow, Mary Ann; Kwiatkowski, Robert W.; Vavra, Stephanie H.

    2005-03-29T23:59:59.000Z

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of nucleic acid from various viruses in a sample.

  7. Invasive cleavage of nucleic acids

    DOE Patents [OSTI]

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2002-01-01T23:59:59.000Z

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  8. Self-assembling multimeric nucleic acid constructs

    DOE Patents [OSTI]

    Cantor, Charles R. (Boston, MA); Niemeyer, Christof M. (Bremen, DE); Smith, Cassandra L. (Boston, MA); Sano, Takeshi (Boston, MA); Hnatowich, Donald J. (Brookline, MA); Rusckowski, Mary (Southborough, MA)

    1999-10-12T23:59:59.000Z

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products.

  9. Self-assembling multimeric nucleic acid constructs

    DOE Patents [OSTI]

    Cantor, Charles R. (Boston, MA); Niemeyer, Christof M. (Bremen, DE); Smith, Cassandra L. (Boston, MA); Sano, Takeshi (Boston, MA); Hnatowich, Donald J. (Brookline, MA); Rusckowski, Mary (Southborough, MA)

    1996-01-01T23:59:59.000Z

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products.

  10. Self-assembling multimeric nucleic acid constructs

    DOE Patents [OSTI]

    Cantor, C.R.; Niemeyer, C.M.; Smith, C.L.; Sano, Takeshi; Hnatowich, D.J.; Rusckowski, M.

    1996-10-01T23:59:59.000Z

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products. 5 figs.

  11. 1998 Oxford University Press42804290 Nucleic Acids Research, 1998, Vol. 26, No. 18 A database of macromolecular motions

    E-Print Network [OSTI]

    Gerstein, Mark

    to implement the database. However, the complexity and heterogeneity of the information kept in the database, are involved in many basic functions such as catalysis, regulation of activity, transport of metabolites

  12. Double stranded nucleic acid biochips

    DOE Patents [OSTI]

    Chernov, Boris; Golova, Julia

    2006-05-23T23:59:59.000Z

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  13. Chip-based sequencing nucleic acids

    DOE Patents [OSTI]

    Beer, Neil Reginald

    2014-08-26T23:59:59.000Z

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  14. Replica amplification of nucleic acid arrays

    DOE Patents [OSTI]

    Church, George M. (Brookline, MA); Mitra, Robi D. (Chestnut Hill, MA)

    2010-08-31T23:59:59.000Z

    Disclosed are improved methods of making and using immobilized arrays of nucleic acids, particularly methods for producing replicas of such arrays. Included are methods for producing high density arrays of nucleic acids and replicas of such arrays, as well as methods for preserving the resolution of arrays through rounds of replication. Also included are methods which take advantage of the availability of replicas of arrays for increased sensitivity in detection of sequences on arrays. Improved methods of sequencing nucleic acids immobilized on arrays utilizing single copies of arrays and methods taking further advantage of the availability of replicas of arrays are disclosed. The improvements lead to higher fidelity and longer read lengths of sequences immobilized on arrays. Methods are also disclosed which improve the efficiency of multiplex PCR using arrays of immobilized nucleic acids.

  15. Methods for analyzing nucleic acid sequences

    DOE Patents [OSTI]

    Korlach, Jonas (Ithaca, NY); Webb, Watt W. (Ithaca, NY); Levene, Michael (Ithaca, NY); Turner, Stephen (Ithaca, NY); Craighead, Harold G. (Ithaca, NY); Foquet, Mathieu (Ithaca, NY)

    2011-05-17T23:59:59.000Z

    The present invention is directed to a method of sequencing a target nucleic acid. The method provides a complex comprising a polymerase enzyme, a target nucleic acid molecule, and a primer, wherein the complex is immobilized on a support Fluorescent label is attached to a terminal phosphate group of the nucleotide or nucleotide analog. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The time duration of the signal from labeled nucleotides or nucleotide analogs that become incorporated is distinguished from freely diffusing labels by a longer retention in the observation volume for the nucleotides or nucleotide analogs that become incorporated than for the freely diffusing labels.

  16. Amplification of trace amounts of nucleic acids

    DOE Patents [OSTI]

    Church, George M. (Brookline, MA); Zhang, Kun (Brighton, MA)

    2008-06-17T23:59:59.000Z

    Methods of reducing background during amplification of small amounts of nucleic acids employ careful analysis of sources of low level contamination. Ultraviolet light can be used to reduce nucleic acid contaminants in reagents and equipment. "Primer-dimer" background can be reduced by judicious design of primers. We have shown clean signal-to-noise with as little as starting material as one single human cell (.about.6 picogram), E. coli cell (.about.5 femtogram) or Prochlorococcus cell (.about.3 femtogram).

  17. Nucleic acid based fluorescent sensor for copper detection

    DOE Patents [OSTI]

    Lu, Yi; Liu, Juewen

    2013-04-02T23:59:59.000Z

    A nucleic acid enzyme responsive to copper, comprising an oligonucleotide comprising a nucleotide sequence of SEQ ID NO:1, wherein the nucleic acid enzyme is not self-cleaving.

  18. Method for identifying and quantifying nucleic acid sequence aberrations

    DOE Patents [OSTI]

    Lucas, Joe N. (San Ramon, CA); Straume, Tore (Tracy, CA); Bogen, Kenneth T. (Walnut Creek, CA)

    1998-01-01T23:59:59.000Z

    A method for detecting nucleic acid sequence aberrations by detecting nucleic acid sequences having both a first and a second nucleic acid sequence type, the presence of the first and second sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. The method uses a first hybridization probe which includes a nucleic acid sequence that is complementary to a first sequence type and a first complexing agent capable of attaching to a second complexing agent and a second hybridization probe which includes a nucleic acid sequence that selectively hybridizes to the second nucleic acid sequence type over the first sequence type and includes a detectable marker for detecting the second hybridization probe.

  19. Method for nucleic acid isolation using supercritical fluids

    DOE Patents [OSTI]

    Nivens, David E. (11912 Kingsgate Rd., Knoxville, TN 37911); Applegate, Bruce M. (3700 Sutherland Ave. #Q2, Knoxville, TN 37911)

    1999-01-01T23:59:59.000Z

    A method for detecting the presence of a microorganism in an environmental sample involves contacting the sample with a supercritical fluid to isolate nucleic acid from the microorganism, then detecting the presence of a particular sequence within the isolated nucleic acid. The nucleic acid may optionally be subjected to further purification.

  20. Nucleic acid analysis using terminal-phosphate-labeled nucleotides

    DOE Patents [OSTI]

    Korlach, Jonas (Ithaca, NY); Webb, Watt W. (Ithaca, NY); Levene, Michael (Ithaca, NY); Turner, Stephen (Ithaca, NY); Craighead, Harold G. (Ithaca, NY); Foquet, Mathieu (Ithaca, NY)

    2008-04-22T23:59:59.000Z

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

  1. Detection of nucleic acids by multiple sequential invasive cleavages

    DOE Patents [OSTI]

    Hall, Jeff G; Lyamichev, Victor I; Mast, Andrea L; Brow, Mary Ann D

    2012-10-16T23:59:59.000Z

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  2. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOE Patents [OSTI]

    Ramsey, J. Michael (Knoxville, TN); Foote, Robert S. (Oak Ridge, TN)

    2002-01-01T23:59:59.000Z

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  3. Nucleic acids, compositions and uses thereof

    DOE Patents [OSTI]

    Preston, III, James F. (Micanopy, FL); Chow, Virginia (Gainesville, FL); Nong, Guang (Gainesville, FL); Rice, John D. (Gainesville, FL); St. John, Franz J. (Baltimore, MD)

    2012-02-21T23:59:59.000Z

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  4. Nucleic acid compositions and the encoding proteins

    DOE Patents [OSTI]

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02T23:59:59.000Z

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  5. Ramon Eritja Nucleic Acid Chemistry Group

    E-Print Network [OSTI]

    Ritort, Felix

    Ramon Eritja Nucleic Acid Chemistry Group Chemistry and Molecular Pharmacology Dpt. IRB Barcelona nanoparticle assemblies. #12;The DNA can be used as template for the fabrication of silver nanowires between;Preparation of thiol-functionalized arrays N N O NH S-St Bu N N O NH S-St Bu N N O NH S-St BuO DMT-O O P O N

  6. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-11-11T23:59:59.000Z

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  7. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2014-02-25T23:59:59.000Z

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  8. EGVI endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2010-10-12T23:59:59.000Z

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  9. EGVI endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2010-10-05T23:59:59.000Z

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  10. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2012-02-14T23:59:59.000Z

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  11. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2009-05-05T23:59:59.000Z

    The present invention provides an endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  12. EGVI endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-04-01T23:59:59.000Z

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  13. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2013-07-16T23:59:59.000Z

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  14. Nucleic acid amplification using modular branched primers

    DOE Patents [OSTI]

    Ulanovsky, Levy (Westmont, IL)

    2001-01-01T23:59:59.000Z

    Methods and compositions expand the options for making primers for use in amplifying nucleic acid segments. The invention eliminates the step of custom synthesis of primers for Polymerase Chain Reactions (PCR). Instead of being custom-synthesized, a primer is replaced by a combination of several oligonucleotide modules selected from a pre-synthesized library. A modular combination of just a few oligonucleotides essentially mimics the performance of a conventional, custom-made primer by matching the sequence of the priming site in the template. Each oligonucleotide module has a segment that matches one of the stretches within the priming site.

  15. Nucleic acids encoding metal uptake transporters and their uses

    DOE Patents [OSTI]

    Schroeder, Julian I. (La Jolla, CA); Antosiewicz, Danuta M. (Warsaw, PL); Schachtman, Daniel P. (Tranmere, AU); Clemens, Stephan (San Diego, CA)

    1999-01-01T23:59:59.000Z

    The invention provides LCT1 nucleic acids which encode metal ion uptake transporters. The invention also provides methods of modulating heavy metal and alkali metal uptake in plants. The methods involve producing transgenic plants comprising a recombinant expression cassette containing an LCT1 nucleic acid linked to a plant promoter.

  16. Digital MDA for enumeration of total nucleic acid contamination

    E-Print Network [OSTI]

    Quake, Stephen R.

    Digital MDA for enumeration of total nucleic acid contamination Paul C. Blainey and Stephen R; Accepted October 14, 2010 ABSTRACT Multiple displacement amplification (MDA) is an iso- thermal, sequence). Here we report digital MDA (dMDA), an ultrasensitive method for quantifying nucleic acid fragments

  17. Oligonucleoside alkyl or arylphosphonate derivatives capable of crosslinking with or cleaving nucleic acids

    DOE Patents [OSTI]

    Miller, Paul S. (Baltimore, MD); Ts'o, Paul O.P. (Lutherville, MD)

    1999-06-15T23:59:59.000Z

    A composition for inactivating a target nucleic acid which comprises an oligonucleoside alkyl or arylphosphonate analogue which is complementary to the sequence of the target nucleic acid and includes a functional group which reacts with the target nucleic acid to render the target nucleic acid inactive or nonfunctional.

  18. Nucleic Acid Conformational Changes Essential for HIV-1 Nucleocapsid Protein-mediated Inhibition of

    E-Print Network [OSTI]

    Levin, Judith G.

    and a TAR-containing acceptor RNA molecule, we find that when both nucleic acids are present, NC facilitatesNucleic Acid Conformational Changes Essential for HIV-1 Nucleocapsid Protein-mediated Inhibition) is a nucleic acid chaperone protein that has been shown to greatly facilitate the nucleic acid rearrangements

  19. Oligonucleoside alkyl or arylphosphonate derivatives capable of crosslinking with or cleaving nucleic acids

    DOE Patents [OSTI]

    Miller, P.S.; Ts'o, P.O.P.

    1999-06-15T23:59:59.000Z

    A composition for inactivating a target nucleic acid which comprises an oligonucleoside alkyl or arylphosphonate analogue which is complementary to the sequence of the target nucleic acid is provided. It includes a functional group which reacts with the target nucleic acid to render the target nucleic acid inactive or nonfunctional. 16 figs.

  20. Isolated menthone reductase and nucleic acid molecules encoding same

    DOE Patents [OSTI]

    Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L

    2013-04-23T23:59:59.000Z

    The present invention provides isolated menthone reductase proteins, isolated nucleic acid molecules encoding menthone reductase proteins, methods for expressing and isolating menthone reductase proteins, and transgenic plants expressing elevated levels of menthone reductase protein.

  1. Optimization of Encoded Hydrogel Particles for Nucleic Acid Quantification

    E-Print Network [OSTI]

    Pregibon, Daniel C.

    The accurate quantification of nucleic acids is of utmost importance for clinical diagnostics, drug discovery, and basic science research. These applications require the concurrent measurement of multiple targets while ...

  2. Polymerase chain reaction system using magnetic beads for analyzing a sample that includes nucleic acid

    DOE Patents [OSTI]

    Nasarabadi, Shanavaz (Livermore, CA)

    2011-01-11T23:59:59.000Z

    A polymerase chain reaction system for analyzing a sample containing nucleic acid includes providing magnetic beads; providing a flow channel having a polymerase chain reaction chamber, a pre polymerase chain reaction magnet position adjacent the polymerase chain reaction chamber, and a post pre polymerase magnet position adjacent the polymerase chain reaction chamber. The nucleic acid is bound to the magnetic beads. The magnetic beads with the nucleic acid flow to the pre polymerase chain reaction magnet position in the flow channel. The magnetic beads and the nucleic acid are washed with ethanol. The nucleic acid in the polymerase chain reaction chamber is amplified. The magnetic beads and the nucleic acid are separated into a waste stream containing the magnetic beads and a post polymerase chain reaction mix containing the nucleic acid. The reaction mix containing the nucleic acid flows to an analysis unit in the channel for analysis.

  3. Thermoplastic Microfluidic Device for On-Chip Purification of Nucleic Acids for Disposable

    E-Print Network [OSTI]

    Thermoplastic Microfluidic Device for On-Chip Purification of Nucleic Acids for Disposable, Brookline, Massachusetts 02446 A polymeric microfluidic device for solid-phase extraction (SPE applications. Microfluidic approaches to nucleic acid isolation have therefore received great attention

  4. Nucleic Acids Research, 2009, 112 doi:10.1093/nar/gkp675

    E-Print Network [OSTI]

    Hassibi, Arjang

    Nucleic Acids Research, 2009, 1­12 doi:10.1093/nar/gkp675 Real-time DNA microarray analysis Arjang for the analysis of complex nucleic acid samples, use the base pairing of nucleic acid molecules (3) as both uncertainty associated with tar- get analyte capturing and detection, in all practical biosensors, binding

  5. Mosaic protein and nucleic acid vaccines against hepatitis C virus

    DOE Patents [OSTI]

    Yusim, Karina; Korber, Bette T. M.; Kuiken, Carla L.; Fischer, William M.

    2013-06-11T23:59:59.000Z

    The invention relates to immunogenic compositions useful as HCV vaccines. Provided are HCV mosaic polypeptide and nucleic acid compositions which provide higher levels of T-cell epitope coverage while minimizing the occurrence of unnatural and rare epitopes compared to natural HCV polypeptides and consensus HCV sequences.

  6. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    SciTech Connect (OSTI)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2010-06-22T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  7. Cell cycle nucleic acids, polypeptides and uses thereof

    DOE Patents [OSTI]

    Gordon-Kamm, William J. (Urbandale, IA); Lowe, Keith S. (Johnston, IA); Larkins, Brian A. (Tucson, AZ); Dilkes, Brian R. (Tucson, AZ); Sun, Yuejin (Westfield, IN)

    2007-08-14T23:59:59.000Z

    The invention provides isolated nucleic acids and their encoded proteins that are involved in cell cycle regulation. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions. The present invention provides methods and compositions relating to altering cell cycle protein content, cell cycle progression, cell number and/or composition of plants.

  8. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    DOE Patents [OSTI]

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2014-09-30T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  9. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    DOE Patents [OSTI]

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2012-10-16T23:59:59.000Z

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  10. Isolated nucleic acids encoding antipathogenic polypeptides and uses thereof

    DOE Patents [OSTI]

    Altier, Daniel J.; Crane, Virginia C.; Ellanskaya, Irina; Ellanskaya, Natalia; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K.; Schepers, Eric J.; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-04-20T23:59:59.000Z

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from fungal fermentation broths. Nucleic acids that encode the antipathogenic polypeptides are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  11. Nucleic acids encoding antifungal polypeptides and uses thereof

    DOE Patents [OSTI]

    Altier, Daniel J. (Granger, IA); Ellanskaya, I. A. (Kyiv, UA); Gilliam, Jacob T. (Norwalk, IA); Hunter-Cevera, Jennie (Elliott City, MD); Presnail, James K (Avondale, PA); Schepers, Eric (Port Deposit, MD); Simmons, Carl R. (Des Moines, IA); Torok, Tamas (Richmond, CA); Yalpani, Nasser (Johnston, IA)

    2010-11-02T23:59:59.000Z

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  12. Method and apparatus for staining immobilized nucleic acids

    DOE Patents [OSTI]

    Ramsey, J. Michael (Knoxville, TN); Foote, Robert S. (Oak Ridge, TN); Jacobson, Stephen C. (Knoxville, TN)

    2000-01-01T23:59:59.000Z

    A method for staining immobilized nucleic acids includes the steps of affixing DNA probes to a solid substrate, moving target DNA material into proximity with the DNA probes, whereby the target DNA hybridized with specific ones of the DNA probes, and moving a fluorescent dye into proximity with the hybridized target DNA, whereby the fluorescent dye binds to the hybridized DNA to enable subsequent detection of fluorescence.

  13. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOE Patents [OSTI]

    Lucas, Joe N. (San Ramon, CA); Straume, Tore (Tracy, CA); Bogen, Kenneth T. (Walnut Creek, CA)

    1998-01-01T23:59:59.000Z

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

  14. Nucleic acid modifications in bacterial pathogens - impact on pathogenesis, diagnosis, and therapy

    E-Print Network [OSTI]

    Russell, Brandon S. (Brandon Skylur)

    2014-01-01T23:59:59.000Z

    Nucleic acids are subject to extensive chemical modification by all organisms. These modifications display incredible structural diversity, and some are essential for survival. Intriguingly, several of these modifications ...

  15. BGL6 .beta.-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2012-10-02T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

  16. BGL6 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2014-03-04T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

  17. BGL7 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2014-03-25T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

  18. BGL7 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2013-01-29T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

  19. BGL6 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Ward, Michael (San Francisco, CA)

    2009-09-01T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

  20. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-04-01T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  1. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2011-06-14T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  2. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2012-10-30T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  3. BGL4 .beta.-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-05-16T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  4. BGL5 .beta.-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-03-18T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl5, and the corresponding BGL5 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL5, recombinant BGL5 proteins and methods for producing the same.

  5. BGL4 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA) [Los Gatos, CA; Goedegebuur, Frits (Vlaardingen, NL) [Vlaardingen, NL; Ward, Michael (San Francisco, CA) [San Francisco, CA; Yao, Jian (Sunnyvale, CA) [Sunnyvale, CA

    2008-01-22T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  6. BGL5 .beta.-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-02-28T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl5, and the corresponding BGL5 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL5, recombinant BGL5 proteins and methods for producing the same.

  7. BGL7 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Ward, Michael (San Francisco, CA)

    2008-08-05T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

  8. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2007-09-25T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  9. BGL4 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2011-12-06T23:59:59.000Z

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  10. Nucleic acids encoding human trithorax protein

    DOE Patents [OSTI]

    Evans, Glen A. (Encinitas, CA); Djabali, Malek (Marseilles, FR); Selleri, Licia (Del Mar, CA); Parry, Pauline (San Diego, CA)

    2001-01-01T23:59:59.000Z

    In accordance with the present invention, there is provided an isolated peptide having the characteristics of human trithorax protein (as well as DNA encoding same, antisense DNA derived therefrom and antagonists therefor). The invention peptide is characterized by having a DNA binding domain comprising multiple zinc fingers and at least 40% amino acid identity with respect to the DNA binding domain of Drosophila trithorax protein and at least 70% conserved sequence with respect to the DNA binding domain of Drosophila trithorax protein, and wherein said peptide is encoded by a gene located at chromosome 11 of the human genome at q23. Also provided are methods for the treatment of subject(s) suffering from immunodeficiency, developmental abnormality, inherited disease, or cancer by administering to said subject a therapeutically effective amount of one of the above-described agents (i.e., peptide, antagonist therefor, DNA encoding said peptide or antisense DNA derived therefrom). Also provided is a method for the diagnosis, in a subject, of immunodeficiency, developmental abnormality, inherited disease, or cancer associated with disruption of chromosome 11 at q23.

  11. Structure and function of circadian clock proteins and deuterium isotope effects in nucleic acid hydrogen bonds

    E-Print Network [OSTI]

    Vakonakis, Ioannis

    2005-08-29T23:59:59.000Z

    -terminal domain. Hydrogen bonds are of paramount importance in nucleic acid structure and function. Here we show that changes in the width and anharmonicity of vibrational potential energy wells of hydrogen bonded groups can be measured in nucleic acids and can...

  12. A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry

    E-Print Network [OSTI]

    Gerstein, Mark

    uncertainties in this data set closely match numerical values reported in the recent survey of nucleic acid baseA Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry These preliminary (Rockefeller University), Richard E. Dickerson (University of California, Los Angeles), Mark Gerstein (Yale

  13. Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification 

    E-Print Network [OSTI]

    Syed, Shahida Nina

    2014-06-28T23:59:59.000Z

    Denaturation and renaturation is indispensable for the biological function of nucleic acids in many cellular processes, such as for example transcription for the synthesis of RNA and DNA replication during cell division. ...

  14. Development of polymer and lipid materials for enhanced delivery of nucleic acids and proteins

    E-Print Network [OSTI]

    Eltoukhy, Ahmed Atef

    2013-01-01T23:59:59.000Z

    The development of synthetic vectors enabling efficient intracellular delivery of macromolecular therapeutics such as nucleic acids and proteins could potentially catalyze the clinical translation of many gene and protein-based ...

  15. Two-dimensional infrared spectroscopy of nucleic acids : application to tautomerism and DNA aptamer unfolding dynamics

    E-Print Network [OSTI]

    Peng, Chunte Sam

    2014-01-01T23:59:59.000Z

    The structural dynamics of nucleic acids are intimately related to their biological functions; however, our ability to study these molecular dynamics has been largely impeded by the lack of techniques that possess both ...

  16. Plants having modified response to ethylene by transformation with an ETR nucleic acid

    DOE Patents [OSTI]

    Meyerowitz, Elliott M. (Pasadena, CA); Chang, Caren (Pasadena, CA); Bleecker, Anthony B. (Madison, WI)

    2001-01-01T23:59:59.000Z

    The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype.

  17. Studies toward biomimetic claisen condensation using nucleic acid templates and ribozyme catalysis

    E-Print Network [OSTI]

    Ryu, Youngha

    2005-08-29T23:59:59.000Z

    Many different experimental approaches were attempted to achieve carbon-carbon bond formation by nucleic acid template-directed reactions and ribozyme catalysis as potential lipid synthesizing machineries in the RNA world. A novel biomimetic...

  18. Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe

    DOE Patents [OSTI]

    Lucas, Joe N. (San Ramon, CA); Straume, Tore (Tracy, CA); Bogen, Kenneth T. (Walnut Creek, CA)

    2000-01-01T23:59:59.000Z

    A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

  19. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOE Patents [OSTI]

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1997-04-01T23:59:59.000Z

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

  20. Method for producing labeled single-stranded nucleic acid probes

    DOE Patents [OSTI]

    Dunn, John J. (Bellport, NY); Quesada, Mark A. (Middle Island, NY); Randesi, Matthew (Upton, NY)

    1999-10-19T23:59:59.000Z

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  1. DimaSense™: A Novel Nucleic Acid Detection System

    SciTech Connect (OSTI)

    Stadler, A.

    2011-05-18T23:59:59.000Z

    Recently, we developed a suite of methods for the rational design and fabrication of well-defined nanoparticle architectures, including clusters using bio-encoded nanoscale building blocks and layer-by-layer stepwise assembly on a solid support. In particular, the Nano-Assembly platform using Encoded Solid Supports (NAESS) allows for controlled interactions, purification of side products, modularity of design, and the construction of complex nanoparticle architectures. This approach offers several advantages over the current art of designing nanoparticle clusters, which include the high-yield synthesis of desired architectures, a 'plug-and-play' design allowing for the introduction of a variety of sensing modalities, and ease of scalability in high-throughput and synthesis yield. As a utility proof of concept, we implemented our unique cluster fabrication platform to design gold nanoparticle dimers which are linked via a single-stranded DNA oligonucleotide recognition motif. The design of this motif is such that binding of complementary nucleic acids results in specific, selective and rapid dimer dissociation, which can be monitored by dynamic light scattering (DLS). We demonstrated single level mismatch selectivity using this approach. The limit of detection was determined to be 1011 molecules of synthetic target RNA or DNA within 30 minutes of incubation at 33 C. This detection limit is determined by the dimer's concentration which can be probed by currently used standard DLS instruments. We also demonstrated a specific detection of target RNA in a solution containing competing 1,000-fold excess of non-complementary DNA fragments, 10% BSA, and endonucleases. Molecular diagnostic companies, RNA-based technology developers, and personalized medicine companies have applications that could benefit from using DimaSense{trademark}. The technology represents a platform which enables the simple and reasonably inexpensive design and fabrication of highly selective genetic sensors. These sensors operate with very low concentrations of target, can utilize standard instrumentation, produce detection results rapidly, and are robust enough to function in the presence of many competing genetic targets. Many current genetic target detection products/approaches/technologies rely upon methods (such as qPCR) which are more complicated, cumbersome, and costly to perform, and are not well suited to point-of-care diagnostic applications. Several clinical diagnostic applications, particularly point-of-care (POC) diagnostics for infectious diseases, are possible and appear to be a good fit for the technology. In addition, the advent of personalized medicine will create opportunities for molecular diagnostic companies with the capabilities of rapidly and quantitatively detecting nucleic acid sequences. The global POC market was {approx}$7.7B in 2010, with a recent annual growth rate of {approx}7%. A specific disease or disease-class diagnostic would need to be identified before a more meaningful sub-market value could be stated. Additional validation of the technology to show that it displays appropriate performance parameters for a commercial application on 'real world' samples is required for true commercial readiness. In addition, optimization of sensor design parameters, to effect a 10-fold increase in sensitivity, may be required to produce a commercially ready sensor system. These validation and sensor design optimization are estimated to require 3-4 months and {approx}$75k. For an unregulated product to give this sensor system a distinct competitive advantage, 2-3 years of product development and $1.5-3M are likely required. For regulated markets, time to market (through clinic) and cost would depend upon the product.

  2. Methods of staining target chromosomal DNA employing high complexity nucleic acid probes

    DOE Patents [OSTI]

    Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Ol'li-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

    2006-10-03T23:59:59.000Z

    Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

  3. Methods and kits for nucleic acid analysis using fluorescence resonance energy transfer

    DOE Patents [OSTI]

    Kwok, Pui-Yan (Clayton, MO); Chen, Xiangning (St. Louis, MO)

    1999-01-01T23:59:59.000Z

    A method for detecting the presence of a target nucleotide or sequence of nucleotides in a nucleic acid is disclosed. The method is comprised of forming an oligonucleotide labeled with two fluorophores on the nucleic acid target site. The doubly labeled oligonucleotide is formed by addition of a singly labeled dideoxynucleoside triphosphate to a singly labeled polynucleotide or by ligation of two singly labeled polynucleotides. Detection of fluorescence resonance energy transfer upon denaturation indicates the presence of the target. Kits are also provided. The method is particularly applicable to genotyping.

  4. Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids

    SciTech Connect (OSTI)

    Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A., E-mail: alashkov83@gmail.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

    2012-05-15T23:59:59.000Z

    Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

  5. Nucleic Acids Research, 2009, 114 doi:10.1093/nar/gkn1064

    E-Print Network [OSTI]

    Shamir, Ron

    Nucleic Acids Research, 2009, 1­14 doi:10.1093/nar/gkn1064 Allegro: Analyzing expression- ulate. We present Allegro, a method for de-novo dis- covery of cis-regulatory transcriptional programs by a group of co-regulated genes. We show that Allegro is more accurate and sensitive than existing

  6. Adsorption of Nucleic Acid Components on Rutile (TiO2) Surfaces

    E-Print Network [OSTI]

    Sverjensky, Dimitri A.

    Adsorption of Nucleic Acid Components on Rutile (TiO2) Surfaces H. James Cleaves II,1 Caroline M and horizontal gene transfer. The adsorption of mono-, oligo-, and polynucleotides and their components obtained from studies of other minerals. In contrast with recent studies of nucleotide adsorption on Zn

  7. Do Electrostatic Interactions Destabilize ProteinNucleic Acid Binding? Sanbo Qin,1

    E-Print Network [OSTI]

    Weston, Ken

    interaction energies between proteins and nucleic acids are positive, meaning that electrostatic interactions as the boundary between the solute low dielectric and the solvent dielectric. We have explored an alternative choice, i.e., the van der Waals (vdW) surface, and found that the electrostatic interaction energy

  8. Nucleosides, Nucleotides, and Nucleic Acids, 25:915, 2006 Copyright C Taylor & Francis Group, LLC

    E-Print Network [OSTI]

    Stoltz, Brian M.

    Nucleosides, Nucleotides, and Nucleic Acids, 25:9­15, 2006 Copyright C Taylor & Francis Group, LLC-LABELED NUCLEOTIDE SPACER ARM ON INCORPORATION BY THERMOPHILIC DNA POLYMERASES Christopher J. Lacenere 2 Division incor- porate fluorescently labeled nucleotides sequentially was analyzed by a gel based primer

  9. 1997 Oxford University Press49945002 Nucleic Acids Research, 1997, Vol. 25, No. 24 Information analysis of Fis binding sites

    E-Print Network [OSTI]

    Schneider, Thomas D.

    © 1997 Oxford University Press4994­5002 Nucleic Acids Research, 1997, Vol. 25, No. 24 Information to fit into two successive major grooves on straight B-form DNA, suggesting that the DNA bends

  10. Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol

    DOE Patents [OSTI]

    Brown, Steven; Guss, Adam; Yang, Shihui; Karpinets, Tatiana; Lynd, Lee; Shao, Xiongjun

    2014-01-14T23:59:59.000Z

    The present invention provides isolated nucleic acid molecules which encode a mutant acetaldehyde-CoA/alcohol dehydrogenase or mutant alcohol dehydrogenase and confer enhanced tolerance to ethanol. The invention also provides related expression vectors, genetically engineered microorganisms having enhanced tolerance to ethanol, as well as methods of making and using such genetically modified microorganisms for production of biofuels based on fermentation of biomass materials.

  11. Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

    SciTech Connect (OSTI)

    Myers, G.; Foley, B.; Korber, B. [eds.] [Los Alamos National Lab., NM (United States). Theoretical Div.] [eds.; Los Alamos National Lab., NM (United States). Theoretical Div.; Mellors, J.W. [ed.] [Univ. of Pittsburgh, PA (United States)] [ed.; Univ. of Pittsburgh, PA (United States); Jeang, K.T. [ed.] [National Institutes of Health, Bethesda, MD (United States). Molecular Virology Section] [ed.; National Institutes of Health, Bethesda, MD (United States). Molecular Virology Section; Wain-Hobson, S. [Pasteur Inst., Paris (France)] [ed.] [Pasteur Inst., Paris (France); ed.

    1997-04-01T23:59:59.000Z

    This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. While this publication could take the form of a review or sequence monograph, it is not so conceived. Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.

  12. Nucleic Acid Encoding A Lectin-Derived Progenitor Cell Preservation Factor

    DOE Patents [OSTI]

    Colucci, M. Gabriella (Dugenta, IT); Chrispeels, Maarten J. (La Jolla, CA); Moore, Jeffrey G. (New York, NY)

    2001-10-30T23:59:59.000Z

    The invention relates to an isolated nucleic acid molecule that encodes a protein that is effective to preserve progenitor cells, such as hematopoietic progenitor cells. The nucleic acid comprises a sequence defined by SEQ ID NO:1, a homolog thereof, or a fragment thereof. The encoded protein has an amino acid sequence that comprises a sequence defined by SEQ ID NO:2, a homolog thereof, or a fragment thereof that contains an amino acid sequence TNNVLQVT. Methods of using the encoded protein for preserving progenitor cells in vitro, ex vivo, and in vivo are also described. The invention, therefore, include methods such as myeloablation therapies for cancer treatment wherein myeloid reconstitution is facilitated by means of the specified protein. Other therapeutic utilities are also enabled through the invention, for example, expanding progenitor cell populations ex vivo to increase chances of engraftation, improving conditions for transporting and storing progenitor cells, and facilitating gene therapy to treat and cure a broad range of life-threatening hematologic diseases.

  13. Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

    DOE Patents [OSTI]

    Studier, F. William (Stony Brook, NY)

    1995-04-18T23:59:59.000Z

    Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient.

  14. Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

    DOE Patents [OSTI]

    Studier, F.W.

    1995-04-18T23:59:59.000Z

    Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient. 2 figs.

  15. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    DOE Patents [OSTI]

    Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

    2013-07-23T23:59:59.000Z

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  16. Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes

    DOE Patents [OSTI]

    Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

    2014-04-08T23:59:59.000Z

    A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

  17. Alteration of Nucleic Acid Structure and Stability Modulates the Efficiency of Minus-Strand Transfer Mediated by the

    E-Print Network [OSTI]

    Levin, Judith G.

    Alteration of Nucleic Acid Structure and Stability Modulates the Efficiency of Minus destabilizes the highly structured complementary trans-activation response ele- ment (TAR) stem-loop (TAR DNA) at the 3 -end of ( ) SSDNA and inhibits TAR-induced self-priming, a dead- end reaction that competes

  18. Site-Selective Binding of Nanoparticles to Double-Stranded DNA via Peptide Nucleic Acid "Invasion"

    SciTech Connect (OSTI)

    Stadler, A.L.; van der Lelie, D.; Sun, D.; Maye, M. M.; Gang, O.

    2011-04-01T23:59:59.000Z

    We demonstrate a novel method for by-design placement of nano-objects along double-stranded (ds) DNA. A molecular intercalator, designed as a peptide nucleic acid (PNA)-DNA chimera, is able to invade dsDNA at the PNA-side due to the hybridization specificity between PNA and one of the duplex strands. At the same time, the single-stranded (ss) DNA tail of the chimera, allows for anchoring of nano-objects that have been functionalized with complementary ssDNA. The developed method is applied for interparticle attachment and for the fabrication of particle clusters using a dsDNA template. This method significantly broadens the molecular toolbox for constructing nanoscale systems by including the most conventional not yet utilized DNA motif, double helix DNA.

  19. Quantification of false positive reduction in nucleic acid purification on hemorrhagic fever DNA.

    SciTech Connect (OSTI)

    James, Conrad D.; Pohl, Kenneth Roy; Derzon, Mark Steven; McClain, Jaime; Achyuthan, Komandoor

    2006-11-01T23:59:59.000Z

    Columbia University has developed a sensitive highly multiplexed system for genetic identification of nucleic acid targets. The primary obstacle to implementing this technology is the high rate of false positives due to high levels of unbound reporters that remain within the system after hybridization. The ability to distinguish between free reporters and reporters bound to targets limits the use of this technology. We previously demonstrated a new electrokinetic method for binary separation of kb pair long DNA molecules and oligonucleotides. The purpose of this project 99864 is to take these previous demonstrations and further develop the technique and hardware for field use. Specifically, our objective was to implement separation in a heterogeneous sample (containing target DNA and background oligo), to perform the separation in a flow-based device, and to develop all of the components necessary for field testing a breadboard prototype system.

  20. Aptamer- and nucleic acid enzyme-based systems for simultaneous detection of multiple analytes

    DOE Patents [OSTI]

    Lu, Yi (Champaign, IL); Liu, Juewen (Albuquerque, NM)

    2011-11-15T23:59:59.000Z

    The present invention provides aptamer- and nucleic acid enzyme-based systems for simultaneously determining the presence and optionally the concentration of multiple analytes in a sample. Methods of utilizing the system and kits that include the sensor components are also provided. The system includes a first reactive polynucleotide that reacts to a first analyte; a second reactive polynucleotide that reacts to a second analyte; a third polynucleotide; a fourth polynucleotide; a first particle, coupled to the third polynucleotide; a second particle, coupled to the fourth polynucleotide; and at least one quencher, for quenching emissions of the first and second quantum dots, coupled to the first and second reactive polynucleotides. The first particle includes a quantum dot having a first emission wavelength. The second particle includes a second quantum dot having a second emission wavelength different from the first emission wavelength. The third polynucleotide and the fourth polynucleotide are different.

  1. Exhaustive Database Searching for Amino Acid Mutations in Proteomes

    SciTech Connect (OSTI)

    Hyatt, Philip Douglas [ORNL; Pan, Chongle [ORNL

    2012-01-01T23:59:59.000Z

    Amino acid mutations in proteins can be found by searching tandem mass spectra acquired in shotgun proteomics experiments against protein sequences predicted from genomes. Traditionally, unconstrained searches for amino acid mutations have been accomplished by using a sequence tagging approach that combines de novo sequencing with database searching. However, this approach is limited by the performance of de novo sequencing. The Sipros algorithm v2.0 was developed to perform unconstrained database searching using high-resolution tandem mass spectra by exhaustively enumerating all single non-isobaric mutations for every residue in a protein database. The performance of Sipros for amino acid mutation identification exceeded that of an established sequence tagging algorithm, Inspect, based on benchmarking results from a Rhodopseudomonas palustris proteomics dataset. To demonstrate the viability of the algorithm for meta-proteomics, Sipros was used to identify amino acid mutations in a natural microbial community in acid mine drainage.

  2. Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids

    SciTech Connect (OSTI)

    Nguyen, Hung T. [BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854 (United States); Pabit, Suzette A.; Meisburger, Steve P.; Pollack, Lois [School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853 (United States); Case, David A., E-mail: case@biomaps.rutgers.edu [BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, New Jersey 08854 (United States); Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854 (United States)

    2014-12-14T23:59:59.000Z

    A new method is introduced to compute X-ray solution scattering profiles from atomic models of macromolecules. The three-dimensional version of the Reference Interaction Site Model (RISM) from liquid-state statistical mechanics is employed to compute the solvent distribution around the solute, including both water and ions. X-ray scattering profiles are computed from this distribution together with the solute geometry. We describe an efficient procedure for performing this calculation employing a Lebedev grid for the angular averaging. The intensity profiles (which involve no adjustable parameters) match experiment and molecular dynamics simulations up to wide angle for two proteins (lysozyme and myoglobin) in water, as well as the small-angle profiles for a dozen biomolecules taken from the BioIsis.net database. The RISM model is especially well-suited for studies of nucleic acids in salt solution. Use of fiber-diffraction models for the structure of duplex DNA in solution yields close agreement with the observed scattering profiles in both the small and wide angle scattering (SAXS and WAXS) regimes. In addition, computed profiles of anomalous SAXS signals (for Rb{sup +} and Sr{sup 2+}) emphasize the ionic contribution to scattering and are in reasonable agreement with experiment. In cases where an absolute calibration of the experimental data at q = 0 is available, one can extract a count of the excess number of waters and ions; computed values depend on the closure that is assumed in the solution of the Ornstein–Zernike equations, with results from the Kovalenko–Hirata closure being closest to experiment for the cases studied here.

  3. 1996 Oxford University Press 47094718Nucleic Acids Research, 1996, Vol. 24, No. 23 Logitlinear models for the prediction of splice sites in

    E-Print Network [OSTI]

    Brendel, Volker

    © 1996 Oxford University Press 4709­4718Nucleic Acids Research, 1996, Vol. 24, No. 23 Logitlinear the degree of fit to some average signal pattern around known splice sites in a learning set (e.g., 3

  4. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    SciTech Connect (OSTI)

    Kingsley, Mark T.

    2001-03-13T23:59:59.000Z

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, and analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: 1) to assess the potential terrorist threat to U.S. agricultural crops, 2) to determine whether suitable assays exist to monitor that threat, and 3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  5. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    SciTech Connect (OSTI)

    Kingsley, Mark T

    2001-03-13T23:59:59.000Z

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, an d analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: (1) to assess the potential terrorist threat to U.S. agricultural crops, (2) to determine whether suitable assays exist to monitor that threat, and (3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  6. Published online 17 April 2014 Nucleic Acids Research, 2014, Vol. 42, No. 10 e83 doi: 10.1093/nar/gku250

    E-Print Network [OSTI]

    Published online 17 April 2014 Nucleic Acids Research, 2014, Vol. 42, No. 10 e83 doi: 10.1093/nar onto either magnetic beads or gold nanoparticles grafted with the com- plementary ODN, as shown variety of applications, among which is the indirect functionalization of the MPs they bind to (3

  7. Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

    ScienceCinema (OSTI)

    Patel, Kamlesh D [Ken]; SNL,

    2013-01-25T23:59:59.000Z

    Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

  8. A Highly Salt-Dependent Enthalpy Change for Escherichia coli SSB Protein-Nucleic Acid Binding Due to Ion-Protein Interactions

    E-Print Network [OSTI]

    Lohman, Timothy M.

    A Highly Salt-Dependent Enthalpy Change for Escherichia coli SSB Protein-Nucleic Acid Binding Due ReceiVed February 5, 1996X ABSTRACT: We have examined the linkage between salt concentration association constant, Kobs, decreases with increasing salt concentration at all temperatures examined

  9. Nucleic acid sequences encoding D1 and D1/D2 domains of human coxsackievirus and adenovirus receptor (CAR)

    DOE Patents [OSTI]

    Freimuth, Paul I.

    2010-04-06T23:59:59.000Z

    The invention provides recombinant human CAR (coxsackievirus and adenovirus receptor) polypeptides which bind adenovirus. Specifically, polypeptides corresponding to adenovirus binding domain D1 and the entire extracellular domain of human CAR protein comprising D1 and D2 are provided. In another aspect, the invention provides nucleic acid sequences encoding these domains and expression vectors for producing the domains and bacterial cells containing such vectors. The invention also includes an isolated fusion protein comprised of the D1 polypeptide fused to a polypeptide which facilitates folding of D1 when expressed in bacteria. The functional D1 domain finds application in a therapeutic method for treating a patient infected with a CAR D1-binding virus, and also in a method for identifying an antiviral compound which interferes with viral attachment. The invention also provides a method for specifically targeting a cell for infection by a virus which binds to D1.

  10. Production of extracellular nucleic acids by genetically altered bacteria in aquatic-environment microcosms. [Escherichia coli, Pseudomonas aeroginosa, Pseudomonas cepacia, Bradyrhizobium japonicum

    SciTech Connect (OSTI)

    Paul, J.H.; David, A.W. (Univ. of South Florida, St. Petersburg (USA))

    1989-08-01T23:59:59.000Z

    The factors which affect the production of extracellular DNA by genetically altered strains of Escherichia coli, Pseudomonas aeruginosa, Pseudomonas cepacia, and Bradyrhizobium japonicum in aquatic environments were investigated. Cellular nucleic acids were labeled in vivo by incubation with ({sup 3}H)thymidine or ({sup 3}H)adenine, and production of extracellular DNA in marine waters, artificial seawater, or minimal salts media was determined by detecting radiolabeled macromolecules in incubation filtrates. The presence or absence of the ambient microbial community had little effect on the production of extracellular DNA. Three of four organisms produced the greatest amounts of extracellular nucleic acids when incubated in low-salinity media (2% artificial seawater) rather than high-salinity media (10 to 50% artificial seawater). The greatest production of extracellular nucleic acids by P. cepacia occurred at pH 7 and 37{degree}C, suggesting that extracellular-DNA production may be a normal physiologic function of the cell. Incubation of labeled P. cepacia cells in water from Bimini Harbor, Bahamas, resulted in labeling of macromolecules of the ambient microbial population. Collectively these results indicate that (i) extracellular-DNA production by genetically altered bacteria released into aquatic environments is more strongly influenced by physicochemical factors than biotic factors, (ii) extracellular-DNA production rates are usually greater for organisms released in freshwater than marine environments, and (iii) ambient microbial populations can readily utilize materials released by these organisms.

  11. Human Retroviruses and AIDS. A compilation and analysis of nucleic acid and amino acid sequences: I--II; III--V

    SciTech Connect (OSTI)

    Myers, G.; Korber, B. [eds.] [Los Alamos National Lab., NM (United States)] [eds.; Los Alamos National Lab., NM (United States); Wain-Hobson, S. [ed.] [Laboratory of Molecular Retrovirology, Pasteur Inst.] [ed.; Laboratory of Molecular Retrovirology, Pasteur Inst.; Smith, R.F. [ed.] [Baylor Coll. of Medicine, Houston, TX (United States). Dept. of Pharmacology] [ed.; Baylor Coll. of Medicine, Houston, TX (United States). Dept. of Pharmacology; Pavlakis, G.N. [ed.] [National Cancer Inst., Frederick, MD (United States). Cancer Research Facility] [ed.; National Cancer Inst., Frederick, MD (United States). Cancer Research Facility

    1993-12-31T23:59:59.000Z

    This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (I) HIV and SIV Nucleotide Sequences; (II) Amino Acid Sequences; (III) Analyses; (IV) Related Sequences; and (V) Database Communications. Information within all the parts is updated at least twice in each year, which accounts for the modes of binding and pagination in the compendium.

  12. acids research database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  13. Nucleic acid molecules encoding isopentenyl monophosphate kinase, and methods of use

    DOE Patents [OSTI]

    Croteau, Rodney B. (Pullman, WA); Lange, Bernd M. (Pullman, WA)

    2001-01-01T23:59:59.000Z

    A cDNA encoding isopentenyl monophosphate kinase (IPK) from peppermint (Mentha x piperita) has been isolated and sequenced, and the corresponding amino acid sequence has been determined. Accordingly, an isolated DNA sequence (SEQ ID NO:1) is provided which codes for the expression of isopentenyl monophosphate kinase (SEQ ID NO:2), from peppermint (Mentha x piperita). In other aspects, replicable recombinant cloning vehicles are provided which code for isopentenyl monophosphate kinase, or for a base sequence sufficiently complementary to at least a portion of isopentenyl monophosphate kinase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding isopentenyl monophosphate kinase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant isopentenyl monophosphate kinase that may be used to facilitate its production, isolation and purification in significant amounts. Recombinant isopentenyl monophosphate kinase may be used to obtain expression or enhanced expression of isopentenyl monophosphate kinase in plants in order to enhance the production of isopentenyl monophosphate kinase, or isoprenoids derived therefrom, or may be otherwise employed for the regulation or expression of isopentenyl monophosphate kinase, or the production of its products.

  14. Nucleic and amino acid sequences relating to a novel transketolase, and methods for the expression thereof

    DOE Patents [OSTI]

    Croteau, Rodney Bruce (Pullman, WA); Wildung, Mark Raymond (Colfax, WA); Lange, Bernd Markus (Pullman, WA); McCaskill, David G. (Pullman, WA)

    2001-01-01T23:59:59.000Z

    cDNAs encoding 1-deoxyxylulose-5-phosphate synthase from peppermint (Mentha piperita) have been isolated and sequenced, and the corresponding amino acid sequences have been determined. Accordingly, isolated DNA sequences (SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7) are provided which code for the expression of 1-deoxyxylulose-5-phosphate synthase from plants. In another aspect the present invention provides for isolated, recombinant DXPS proteins, such as the proteins having the sequences set forth in SEQ ID NO:4, SEQ ID NO:6 and SEQ ID NO:8. In other aspects, replicable recombinant cloning vehicles are provided which code for plant 1-deoxyxylulose-5-phosphate synthases, or for a base sequence sufficiently complementary to at least a portion of 1-deoxyxylulose-5-phosphate synthase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding a plant 1-deoxyxylulose-5-phosphate synthase. Thus, systems and methods are provided for the recombinant expression of the aforementioned recombinant 1-deoxyxylulose-5-phosphate synthase that may be used to facilitate its production, isolation and purification in significant amounts. Recombinant 1-deoxyxylulose-5-phosphate synthase may be used to obtain expression or enhanced expression of 1-deoxyxylulose-5-phosphate synthase in plants in order to enhance the production of 1-deoxyxylulose-5-phosphate, or its derivatives such as isopentenyl diphosphate (BP), or may be otherwise employed for the regulation or expression of 1-deoxyxylulose-5-phosphate synthase, or the production of its products.

  15. acid index database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Summary: in as guestanon. Guests do not have full access to the database. Enter terms in the Search for: box and it will search all words that you enter. Searches are...

  16. Synthesis, Improved Antisense Activity and Structural Rationale for the Divergent RNA Affinities of 3;#8242;-Fluoro Hexitol Nucleic Acid (FHNA and Ara-FHNA) Modified Oligonucleotides

    SciTech Connect (OSTI)

    Egli, Martin; Pallan, Pradeep S.; Allerson, Charles R.; Prakash, Thazha P.; Berdeja, Andres; Yu, Jinghua; Lee, Sam; Watt, Andrew; Gaus, Hans; Bhat, Balkrishen; Swayze, Eric E.; Seth, Punit P. (Isis Pharm.); (Vanderbilt)

    2012-03-16T23:59:59.000Z

    The synthesis, biophysical, structural, and biological properties of both isomers of 3'-fluoro hexitol nucleic acid (FHNA and Ara-FHNA) modified oligonucleotides are reported. Synthesis of the FHNA and Ara-FHNA thymine phosphoramidites was efficiently accomplished starting from known sugar precursors. Optimal RNA affinities were observed with a 3'-fluorine atom and nucleobase in a trans-diaxial orientation. The Ara-FHNA analog with an equatorial fluorine was found to be destabilizing. However, the magnitude of destabilization was sequence-dependent. Thus, the loss of stability is sharply reduced when Ara-FHNA residues were inserted at pyrimidine-purine (Py-Pu) steps compared to placement within a stretch of pyrimidines (Py-Py). Crystal structures of A-type DNA duplexes modified with either monomer provide a rationalization for the opposing stability effects and point to a steric origin of the destabilization caused by the Ara-FHNA analog. The sequence dependent effect can be explained by the formation of an internucleotide C-F {hor_ellipsis} H-C pseudo hydrogen bond between F3' of Ara-FHNA and C8-H of the nucleobase from the 3'-adjacent adenosine that is absent at Py-Py steps. In animal experiments, FHNA-modified antisense oligonucleotides formulated in saline showed a potent downregulation of gene expression in liver tissue without producing hepatotoxicity. Our data establish FHNA as a useful modification for antisense therapeutics and also confirm the stabilizing influence of F(Py) {hor_ellipsis} H-C(Pu) pseudo hydrogen bonds in nucleic acid structures.

  17. Salt: Combining ACID and BASE in a Distributed Database Chao Xie, Chunzhi Su, Manos Kapritsos, Yang Wang,

    E-Print Network [OSTI]

    Alvisi, Lorenzo

    Salt: Combining ACID and BASE in a Distributed Database Chao Xie, Chunzhi Su, Manos Kapritsos, Yang: This paper presents Salt, a distributed database that allows developers to improve the perfor- mance and scalability of their ACID applications through the incremental adoption of the BASE approach. Salt

  18. acid adenine dinucleotide: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases Brian T potentials for N-methyl substituted nucleic acid bases guanine, adenine, cytosine,...

  19. Nucleic Acids Research, 1993, Vol. 21, No. 9 2247-2248 The nucleosome repeat length of Kluyveromyces lactis is

    E-Print Network [OSTI]

    for the production of heterologous proteins like prochymosin (7), human serum albumin (8), and human interleukin 1,B each pellet was resuspended in 125 ml TESM. After 10 minutes at room temperature, the cells were spun down, each pellet washed with 225 ml SCE (1 M sorbitol, 0.1 M citric acid, 0.06 M EDTA, pH = 5

  20. Structural Rationalization of a Large Difference in RNA Affinity Despite a Small Difference in Chemistry between Two 2'-O-Modified Nucleic Acid Analogs

    SciTech Connect (OSTI)

    Pattanayek, R.; Sethaphong, L.; Pan, C.; Prhavc, M.; Prakash, T.P.; Manoharan, M.; Egli, M. (Tennessee); (Isis Pharmaceuticals Inc.); (Alnylam Pharmaceuticals,); (Vanderbilt)

    2010-03-08T23:59:59.000Z

    Chemical modification of nucleic acids at the 2'-position of ribose has generated antisense oligonucleotides (AONs) with a range of desirable properties. Electron-withdrawing substituents such as 2'-O-[2-(methoxy)ethyl] (MOE) confer enhanced RNA affinity relative to that of DNA by conformationally preorganizing an AON for pairing with the RNA target and by improving backbone hydration. 2'-Substitution of the ribose has also been shown to increase nuclease resistance and cellular uptake via changes in lipophilicity. Interestingly, incorporation of either 2'-O-[2-(methylamino)-2-oxoethyl]- (NMA) or 2'-O-(N-methylcarbamate)-modified (NMC) residues into AONs has divergent effects on RNA affinity. Incorporation of 2'-O-NMA-T considerably improves RNA affinity while incorporation of 2'-O-NMC-T drastically reduces RNA affinity. Crystal structures at high resolution of A-form DNA duplexes containing either 2'-O-NMA-T or 2'-O-NMC-T shed light on the structural origins of the surprisingly large difference in stability given the relatively minor difference in chemistry between NMA and NMC. NMA substituents adopt an extended conformation and use either their carbonyl oxygen or amino nitrogen to trap water molecules between phosphate group and sugar. The conformational properties of NMA and the observed hydration patterns are reminiscent of those found in the structures of 2'-O-MOE-modified RNA. Conversely, the carbonyl oxygen of NMC and O2 of T are in close contact, providing evidence that an unfavorable electrostatic interaction and the absence of a stable water structure are the main reasons for the loss in thermodynamic stability as a result of incorporation of 2'-O-NMC-modified residues.

  1. GOLD: The Genomes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kyrpides, Nikos; Liolios, Dinos; Chen, Amy; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor; Bernal, Alex

    Since its inception in 1997, GOLD has continuously monitored genome sequencing projects worldwide and has provided the community with a unique centralized resource that integrates diverse information related to Archaea, Bacteria, Eukaryotic and more recently Metagenomic sequencing projects. As of September 2007, GOLD recorded 639 completed genome projects. These projects have their complete sequence deposited into the public archival sequence databases such as GenBank EMBL,and DDBJ. From the total of 639 complete and published genome projects as of 9/2007, 527 were bacterial, 47 were archaeal and 65 were eukaryotic. In addition to the complete projects, there were 2158 ongoing sequencing projects. 1328 of those were bacterial, 59 archaeal and 771 eukaryotic projects. Two types of metadata are provided by GOLD: (i) project metadata and (ii) organism/environment metadata. GOLD CARD pages for every project are available from the link of every GOLD_STAMP ID. The information in every one of these pages is organized into three tables: (a) Organism information, (b) Genome project information and (c) External links. [The Genomes On Line Database (GOLD) in 2007: Status of genomic and metagenomic projects and their associated metadata, Konstantinos Liolios, Konstantinos Mavromatis, Nektarios Tavernarakis and Nikos C. Kyrpides, Nucleic Acids Research Advance Access published online on November 2, 2007, Nucleic Acids Research, doi:10.1093/nar/gkm884]

    The basic tables in the GOLD database that can be browsed or searched include the following information:

    • Gold Stamp ID
    • Organism name
    • Domain
    • Links to information sources
    • Size and link to a map, when available
    • Chromosome number, Plas number, and GC content
    • A link for downloading the actual genome data
    • Institution that did the sequencing
    • Funding source
    • Database where information resides
    • Publication status and information

    (Specialized Interface)

  2. Energy/structure database of all proteinogenic amino acids and dipeptides without and with divalent cations

    E-Print Network [OSTI]

    Ropo, Matti; Blum, Volker

    2015-01-01T23:59:59.000Z

    We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to an overall of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building...

  3. Databases for rRNA gene profiling of microbial communities

    DOE Patents [OSTI]

    Ashby, Matthew

    2013-07-02T23:59:59.000Z

    The present invention relates to methods for performing surveys of the genetic diversity of a population. The invention also relates to methods for performing genetic analyses of a population. The invention further relates to methods for the creation of databases comprising the survey information and the databases created by these methods. The invention also relates to methods for analyzing the information to correlate the presence of nucleic acid markers with desired parameters in a sample. These methods have application in the fields of geochemical exploration, agriculture, bioremediation, environmental analysis, clinical microbiology, forensic science and medicine.

  4. Geochemical Rate/RNA Integration Study (GRIST): A Pilot Field Experiment for Inter-Calibration of Biogeochemistry and Nucleic Acid Measurements Final Report

    SciTech Connect (OSTI)

    Bronk, Deborah

    2007-01-08T23:59:59.000Z

    The Geochemical Rate/RNA Integration Study (GRIST) project sought to correlate biogeochemical flux rates with measurements of gene expression and mRNA abundance to demonstrate the application of molecular approaches to estimate the presence and magnitude of a suite of biogeochemical processes. The study was headed by Lee Kerkhoff of Rutgers University. In this component of the GRIST study, we characterized ambient nutrient concentrations and measured uptake rates for dissolved inorganic nitrogen (DIN, ammonium, nitrate and nitrite) and dissolved organic nitrogen (urea and dissolved free amino acids) during two diel studies at the Long-Term Ecosystem Observatory (LEO-15) on the New Jersey continental shelf.

  5. Final Scientific/Technical Report, DE-FG02-06ER64171, Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity – Subproject to Co-PI Eric E. Roden

    SciTech Connect (OSTI)

    Eric E. Roden

    2009-07-08T23:59:59.000Z

    This report summarizes research conducted in conjunction with a project entitled “Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity”, which was funded through the Integrative Studies Element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Darrell Chandler (originally at Argonne National Laboratory, now with Akonni Biosystems) was the overall PI/PD for the project. The overall project goals were to (1) apply a model iron-reducer and sulfate-reducer microarray and instrumentation systems to sediment and groundwater samples from the Scheibe et al. FRC Area 2 field site, UMTRA sediments, and other DOE contaminated sites; (2) continue development and expansion of a 16S rRNA/rDNA¬-targeted probe suite for microbial community dynamics as new sequences are obtained from DOE-relevant sites; and (3) address the fundamental molecular biology and analytical chemistry associated with the extraction, purification and analysis of functional genes and mRNA in environmental samples. Work on the UW subproject focused on conducting detailed batch and semicontinuous culture reactor experiments with uranium-contaminated FRC Area 2 sediment. The reactor experiments were designed to provide coherent geochemical and microbiological data in support of microarray analyses of microbial communities in Area 2 sediments undergoing biostimulation with ethanol. A total of four major experiments were conducted (one batch and three semicontinuous culture), three of which (the batch and two semicontinuous culture) provided samples for DNA microarray analysis. A variety of other molecular analyses (clone libraries, 16S PhyloChip, RT-PCR, and T-RFLP) were conducted on parallel samples from the various experiments in order to provide independent information on microbial community response to biostimulation.

  6. Isolated nucleic acids encoding antipathogenic polypeptides and...

    Office of Scientific and Technical Information (OSTI)

    compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes...

  7. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1996-01-01T23:59:59.000Z

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  8. Diagnostic method employing MSH2 nucleic acids

    DOE Patents [OSTI]

    Chapelle, A. de la; Vogelstein, B.; Kinzler, K.W.

    1997-12-02T23:59:59.000Z

    The human MSH2 gene, responsible for hereditary non-polyposis colorectal cancer, was identified by virtue of its homology to the MutS class of genes, which are involved in DNA mismatch repair. The sequence of cDNA clones of the human gene are provided, and the sequence of the gene can be used to demonstrate the existence of germ line mutations in hereditary non-polyposis colorectal cancer (HNPCC) kindreds, as well as in replication error{sup +}(RER{sup +}) tumor cells. 19 figs.

  9. Diagnostic method employing MSH2 nucleic acids

    DOE Patents [OSTI]

    de la Chapelle, Albert (Helsingfors, FI); Vogelstein, Bert (Baltimore, MD); Kinzler, Kenneth W. (Baltimore, MD)

    1997-01-01T23:59:59.000Z

    The human MSH2 gene, responsible for hereditary non-polyposis colorectal cancer, was identified by virtue of its homology to the MutS class of genes, which are involved in DNA mismatch repair. The sequence of cDNA clones of the human gene are provided, and the sequence of the gene can be used to demonstrate the existence of germ line mutations in hereditary non-polyposis colorectal cancer (HNPCC) kindreds, as well as in replication error.sup.+ (RER.sup.+) tumor cells.

  10. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

    1996-03-05T23:59:59.000Z

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 15 figs.

  11. acid biosensor based: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    biosensors of nucleic acids and proteins for point- of-care (POC. The merger of microfluidics and advanced biosensor technolo- gies offers new promises for POC diagnostics...

  12. acids structures applied: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Treatment of software French, James C. 5 Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications Computer Technologies and Information Sciences...

  13. MvirDB: Microbial Database of Protein Toxins, Virulence Factors and Antibiotic Resistance Genes for Bio-Defense Applications

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Zhou, C. E.; Smith, J.; Lam, M.; Zemla, M. D.; Slezak, T.

    MvirDB is a cenntralized resource (data warehouse) comprising all publicly accessible, organized sequence data for protein toxins, virulence factors, and antibiotic resistance genes. Protein entries in MvirDB are annotated using a high-throughput, fully automated computational annotation system; annotations are updated periodically to ensure that results are derived using current public database and open-source tool releases. Tools provided for using MvirDB include a web-based browser tool and BLAST interfaces. MvirDB serves researchers in the bio-defense and medical fields. (taken from page 3 of PI's paper of same title published in Nucleic Acids Research, 2007, Vol.35, Database Issue (Open Source)

  14. acid transporter specifically: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    nucleic acid concentrations from 1 nM to 5 m Zhang, David Yu 3 Long range transport of acid rain precursors MIT - DSpace Summary: A model of the long range transport of primary...

  15. Thermal and acid tolerant beta xylosidases, arabinofuranosidases, genes encoding, related organisms, and methods

    DOE Patents [OSTI]

    Thompson, David N; Thompson, Vicki S; Schaller, Kastli D; Apel, William A; Reed, David W; Lacey, Jeffrey A

    2013-04-30T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius and variations thereof are provided. Further provided are methods of at least partially degrading xylotriose, xylobiose, and/or arabinofuranose-substituted xylan using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius and variations thereof.

  16. Thermal and acid tolerant beta-xylosidases, genes encoding, related organisms, and methods

    DOE Patents [OSTI]

    Thompson, David N. (Idaho Falls, ID); Thompson, Vicki S. (Idaho Falls, ID); Schaller, Kastli D. (Ammon, ID); Apel, William A. (Jackson, WY); Lacey, Jeffrey A. (Idaho Falls, ID); Reed, David W. (Idaho Falls, ID)

    2011-04-12T23:59:59.000Z

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius and variations thereof are provided. Further provided are methods of at least partially degrading xylotriose and/or xylobiose using isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius and variations thereof.

  17. THE INTERACTIONS OF 4-NITROQUINOLINE-1-OXIDE WITH NUCLEIC ACIDS

    E-Print Network [OSTI]

    Winkle, Stephen Alan

    2012-01-01T23:59:59.000Z

    r C2 " C4 CS C6 G2 G4 G5 G6 G8 A6 A8 lS8.06 IS 8.14 IS 6. 43Dimer C2 C4 C5 C6 G2 G4 G5 G6 G8 CpG C T2 T4 T5 T6 A2 A4 A5shift was observed for G8 relative to the other guanine base

  18. Targeting unique nucleic acid structures with small molecules

    E-Print Network [OSTI]

    Tam, Victor Kin-man

    2007-01-01T23:59:59.000Z

    of mono- and disubstitued anthraquinone derivatives with anat opposite ends of the anthraquinone scaffold are employed.

  19. Scanning probe microscopy of nucleic acids and thin organic films

    E-Print Network [OSTI]

    Marat Olegovich Gallyamov

    2011-04-24T23:59:59.000Z

    We developed the models and algorithms to describe two main artefacts of AFM: (i) broadening effect and (ii) decreased heights of profiles for individual objects adsorbed on a hard substrate. It was shown how to measure elastic properties of a single adsorbed microobject. From the viewpoint of contact deformation theory we analysed mechanism of AFM visualisation of an atomic (molecular) structure of a flat surface. We tested technique of immobilisation on a substrate for free single-stranded RNA molecules in an extended state. Using AFM we visualised stages of processes of RNA release from protein coat of tobacco mosaic virus particles. The asymmetry of this process regarding two ends of a macromolecule was confirmed. The dynamics of compaction for DNA T4 molecules was traced using AFM in real time regime. The partially compacted macromolecules were clearly resolved. We detected that the partially compacted structures consisted of toroidal parts formed by different macromolecular strands. The real geometry of the compacted structures was reconstructed on the basis of systematic AFM measurements. That allowed us to calculate the amount of molecules combining each condensed DNA particle. We demonstrated clear benefits of horizontal deposition method for formation of LB films. Using AFM we achieved molecular resolution for some thin film coating and detected lattice parameters with the precision determined by the errors within a few percent. We demonstrated that the structure of the film is determined by the concurrence of several factors: by the closest packing principle for hydrocarbon tails, by the values of surface areas of polar heads at water subphase as well as by the substrate influence.

  20. SAGE-Hindawi Access to Research Journal of Nucleic Acids

    E-Print Network [OSTI]

    Borgstahl, Gloria

    Replication Protein A That Recognize G-Quadruplex DNA Aishwarya Prakash,1 Amarnath Natarajan,1 Luis A. Marky,1

  1. AminoglycosideNucleic Acid Interactions: The Case for Neomycin

    E-Print Network [OSTI]

    Stuart, Steven J.

    . . . . . . . . . . . . . . . . . . . . . . . . . . 156 3.4 Thermodynamics of Drug Binding to the DNA Triplex (ITC) . . . . . . . . . . 157 3.5 CD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161 5.2 The Common Thread that Holds Together RNA Duplex/Triplex, DNA-RNA Hybrid Duplexes, DNA

  2. Introduction to Database Database Systems Lecture 1

    E-Print Network [OSTI]

    Alechina, Natasha

    Introduction to Database Systems Database Systems Lecture 1 Natasha Alechina www.cs.nott.ac.uk/~nza/G51DBS #12;In this Lecture · Course Information · Databases and Database Systems · Some History questions · Format similar to previous years. #12;Textbook · Recommended textbooks: · `Database Systems

  3. Science Gateway Databases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Science Databases Science Database Services NERSC supports the provisioning of databases to hold large scientific datasets, as part of the science gateways effort. Data-centric...

  4. Producing dicarboxylic acids using polyketide synthases

    DOE Patents [OSTI]

    Katz, Leonard; Fortman, Jeffrey L; Keasling, Jay D

    2013-10-29T23:59:59.000Z

    The present invention provides for a polyketide synthase (PKS) capable of synthesizing a dicarboxylic acid (diacid). Such diacids include diketide-diacids and triketide-diacids. The invention includes recombinant nucleic acid encoding the PKS, and host cells comprising the PKS. The invention also includes methods for producing the diacids.

  5. DISTRIBUTED DATABASES INTRODUCTION

    E-Print Network [OSTI]

    Liu, Chengfei

    D DISTRIBUTED DATABASES INTRODUCTION The development of network and data communication tech- nology distributed database management. Naturally, the decen- tralized approach reflects the distributed aspects in the definition of a distributed database exist. First, a distributed database is distributed

  6. NUCLEAR STRUCTURE DATABASE

    E-Print Network [OSTI]

    Firestone, R.B.

    2010-01-01T23:59:59.000Z

    CALIFORNIA NUCLEAR STRUCTURE DATABASE R. B. Firestone and E.11089 NUCLEAR STRUCTURE DATABASE by R.B. Firestone and E.iii- NUCLEAR STRUCTURE DATABASE R.B Firestone and E. Browne

  7. Database Management Certificate Program

    E-Print Network [OSTI]

    Rose, Michael R.

    Database Management Certificate Program DATABASE TECHNOLOGIES 13 Today, organizations in every to obtain general data analysis and management skills or apply both Oracle and Microsoft SQL Server database capabilities of relational databases in conjunction with the new "Big Data" management frameworks for data

  8. The EMIME Bilingual Database 

    E-Print Network [OSTI]

    Wester, Mirjam

    2010-01-01T23:59:59.000Z

    This paper describes the collection of a bilingual database of Finnish/English and German/English data. In addition, the accents of the talkers in the database have been rated. English, German and Finnish listeners assessed the English, German...

  9. Hazard Analysis Database report

    SciTech Connect (OSTI)

    Niemi, B.J.

    1997-08-12T23:59:59.000Z

    This document describes and defines the Hazard Analysis Database for the Tank Waste Remediation System Final Safety Analysis Report.

  10. ORACLE CERTIFICATION Oracle Database

    E-Print Network [OSTI]

    Loudon, Catherine

    ORACLE CERTIFICATION Oracle Database Administration Certificate Program Train with the best. Get your Oracle Database Administration education from the number-one provider* of Oracle training-on, lab-based understanding of Oracle, the world's leading database platform, and long the product

  11. Database Encryption Luc Bouganim

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Database Encryption Luc Bouganim INRIA Rocquencourt Le Chesnay, FRANCE Luc.Bouganim@inria.fr Yanli GUO INRIA Rocquencourt Le Chesnay, FRANCE yanli.guo@inria.fr Related concepts and keywords Database security, Data confidentiality, Hardware Security Module Definition Database encryption refers to the use

  12. Database Description with SDM: A Semantic Database Model

    E-Print Network [OSTI]

    McLeod, Dennis

    Database Description with SDM: A Semantic Database Model MICHAEL HAMMER Massachusetts Institute of Technology and DENNIS McLEOD University of Southern California SDM is a high-level semantics-based database description and structuring formalism (database model) for databases. This database model is designed

  13. Database tool ASGARD: an open-access database of

    E-Print Network [OSTI]

    Extavour, Cassandra

    Database tool ASGARD: an open-access database of annotated transcriptomes for emerging model database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository include search term auto-completion sug- gestions based on database content, the ability to download

  14. Testing Database-Centric Applications For Causes of Database Deadlocks

    E-Print Network [OSTI]

    Grechanik, Mark

    Testing Database-Centric Applications For Causes of Database Deadlocks Mark Grechanik, B. M. Mainul--Many organizations deploy applications that use databases by sending Structured Query Language (SQL) state- ments the same databases concurrently, database deadlocks routinely occur in these databases. Testing

  15. Mutant fatty acid desaturase

    DOE Patents [OSTI]

    Shanklin, John; Cahoon, Edgar B.

    2004-02-03T23:59:59.000Z

    The present invention relates to a method for producing mutants of a fatty acid desaturase having a substantially increased activity towards fatty acid substrates with chains containing fewer than 18 carbons relative to an unmutagenized precursor desaturase having an 18 carbon atom chain length substrate specificity. The method involves inducing one or more mutations in the nucleic acid sequence encoding the precursor desaturase, transforming the mutated sequence into an unsaturated fatty acid auxotroph cell such as MH13 E. coli, culturing the cells in the absence of supplemental unsaturated fatty acids, thereby selecting for recipient cells which have received and which express a mutant fatty acid desaturase with an elevated specificity for fatty acid substrates having chain lengths of less than 18 carbon atoms. A variety of mutants having 16 or fewer carbon atom chain length substrate specificities are produced by this method. Mutant desaturases produced by this method can be introduced via expression vectors into prokaryotic and eukaryotic cells and can also be used in the production of transgenic plants which may be used to produce specific fatty acid products.

  16. 2010 Worldwide Gasification Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The 2010 Worldwide Gasification Database describes the current world gasification industry and identifies near-term planned capacity additions. The database lists gasification projects and includes information (e.g., plant location, number and type of gasifiers, syngas capacity, feedstock, and products). The database reveals that the worldwide gasification capacity has continued to grow for the past several decades and is now at 70,817 megawatts thermal (MWth) of syngas output at 144 operating plants with a total of 412 gasifiers.

  17. Using IMG: Comparative Analysis with the Integrated Microbial Genomes System

    E-Print Network [OSTI]

    2008-01-01T23:59:59.000Z

    for genome annotation: PRIAM. Nucleic Acids Research 31 (RPS-BLAST against the PRIAM database (12), as a complementBLAST computations. Computation COG PRIAM Tool Low- Maximum

  18. DIP: The Database of Interacting Proteins

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The DIP Database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. By interaction, the DIP Database creators mean that two amino acid chains were experimentally identified to bind to each other. The database lists such pairs to aid those studying a particular protein-protein interaction but also those investigating entire regulatory and signaling pathways as well as those studying the organisation and complexity of the protein interaction network at the cellular level. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. It is a relational database that can be searched by protein, sequence, motif, article information, and pathBLAST. The website also serves as an access point to a number of projects related to DIP, such as LiveDIP, The Database of Ligand-Receptor Partners (DLRP) and JDIP. Users have free and open access to DIP after login. [Taken from the DIP Guide and the DIP website] (Specialized Interface) (Registration Required)

  19. Using metabolic databases for

    E-Print Network [OSTI]

    sequences are searched routinely against databases, and the World Wide Web has made such queries simple and you have little idea what these words even mean. The SWISS-PROT database3, main- tained by Amos especially for the Web and offers the additional ability to focus on the metabolic reactions in specific

  20. NIST Standard Reference Database 17 NIST Chemical Kinetics Database

    E-Print Network [OSTI]

    NIST Standard Reference Database 17 __________________________________________________________ NIST Chemical Kinetics Database WindowsTM Version 2Q98 Users' Guide (NIST) uses its best efforts to deliver a high quality copy of the Database and to verify that the data

  1. acid amplification test: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    amplification test First Page Previous Page 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 Next Page Last Page Topic Index 1 Diagnostic Accuracy of Nucleic Acid...

  2. Beta-alanine/alpha-ketoglutarate aminotransferase for 3-hydroxypropionic acid production

    DOE Patents [OSTI]

    Jessen, Holly Jean (Chanhassen, MN); Liao, Hans H. (Eden Prairie, MN); Gort, Steven John (Apple Valley, MN); Selifonova, Olga V. (Plymouth, MN)

    2011-10-04T23:59:59.000Z

    The present disclosure provides novel beta-alanine/alpha ketoglutarate aminotransferase nucleic acid and protein sequences having increased biological activity. Also provided are cells containing such enzymes, as well as methods of their use, for example to produce malonyl semialdehyde and downstream products thereof, such as 3-hydroxypropionic acid and derivatives thereof.

  3. Beta-alanine/alpha-ketoglutarate aminotransferase for 3-hydroxypropionic acid production

    DOE Patents [OSTI]

    Jessen, Holly Jean; Liao, Hans H; Gort, Steven John; Selifonova, Olga V

    2014-11-18T23:59:59.000Z

    The present disclosure provides novel beta-alanine/alpha ketoglutarate aminotransferase nucleic acid and protein sequences having increased biological activity. Also provided are cells containing such enzymes, as well as methods of their use, for example to produce malonyl semialdehyde and downstream products thereof, such as 3-hydroxypropionic acid and derivatives thereof.

  4. Hazard Analysis Database Report

    SciTech Connect (OSTI)

    GRAMS, W.H.

    2000-12-28T23:59:59.000Z

    The Hazard Analysis Database was developed in conjunction with the hazard analysis activities conducted in accordance with DOE-STD-3009-94, Preparation Guide for U S . Department of Energy Nonreactor Nuclear Facility Safety Analysis Reports, for HNF-SD-WM-SAR-067, Tank Farms Final Safety Analysis Report (FSAR). The FSAR is part of the approved Authorization Basis (AB) for the River Protection Project (RPP). This document describes, identifies, and defines the contents and structure of the Tank Farms FSAR Hazard Analysis Database and documents the configuration control changes made to the database. The Hazard Analysis Database contains the collection of information generated during the initial hazard evaluations and the subsequent hazard and accident analysis activities. The Hazard Analysis Database supports the preparation of Chapters 3 ,4 , and 5 of the Tank Farms FSAR and the Unreviewed Safety Question (USQ) process and consists of two major, interrelated data sets: (1) Hazard Analysis Database: Data from the results of the hazard evaluations, and (2) Hazard Topography Database: Data from the system familiarization and hazard identification.

  5. Sandia National Laboratories: CREW Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    CREW Database Sandia Involves Wind-Farm Owners in Defining New Data Pathway for National Wind-Plant Reliability Database On March 19, 2014, in Computational Modeling & Simulation,...

  6. USER'S GUIDE DATABASE SYSTEM

    E-Print Network [OSTI]

    server and runs on the PPPL VAX cluster under VMS. The MINGL database system for TFTR is composed on the VAX. This document describes the overall system in terms of how the various parts interact

  7. Nuclear Science References Database

    E-Print Network [OSTI]

    B. Pritychenko; E. B?ták; B. Singh; J. Totans

    2014-07-08T23:59:59.000Z

    The Nuclear Science References (NSR) database together with its associated Web interface, is the world's only comprehensive source of easily accessible low- and intermediate-energy nuclear physics bibliographic information for more than 210,000 articles since the beginning of nuclear science. The weekly-updated NSR database provides essential support for nuclear data evaluation, compilation and research activities. The principles of the database and Web application development and maintenance are described. Examples of nuclear structure, reaction and decay applications are specifically included. The complete NSR database is freely available at the websites of the National Nuclear Data Center http://www.nndc.bnl.gov/nsr and the International Atomic Energy Agency http://www-nds.iaea.org/nsr.

  8. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Calm, J.M. [Calm (James M.), Great Falls, VA (United States)

    1994-05-27T23:59:59.000Z

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  9. Databases | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page on Delicious Rank EERE: Alternative FuelsNovember 13, 2014ContributingDOE ContractDepartment of4Databases Databases

  10. Crude Oil Analysis Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Shay, Johanna Y.

    The composition and physical properties of crude oil vary widely from one reservoir to another within an oil field, as well as from one field or region to another. Although all oils consist of hydrocarbons and their derivatives, the proportions of various types of compounds differ greatly. This makes some oils more suitable than others for specific refining processes and uses. To take advantage of this diversity, one needs access to information in a large database of crude oil analyses. The Crude Oil Analysis Database (COADB) currently satisfies this need by offering 9,056 crude oil analyses. Of these, 8,500 are United States domestic oils. The database contains results of analysis of the general properties and chemical composition, as well as the field, formation, and geographic location of the crude oil sample. [Taken from the Introduction to COAMDATA_DESC.pdf, part of the zipped software and database file at http://www.netl.doe.gov/technologies/oil-gas/Software/database.html] Save the zipped file to your PC. When opened, it will contain PDF documents and a large Excel spreadsheet. It will also contain the database in Microsoft Access 2002.

  11. The GLIMS Glacier Database: a spatio-temporal database

    E-Print Network [OSTI]

    Raup, Bruce H.

    The GLIMS Glacier Database: a spatio-temporal database implemented using Open Source tools Bruce countries #12;#12;#12;#12;#12;System components PostgreSQL (relational database) PostGIS (geospatial) GDAL (Geospatial Data Abstraction Library) Perl, PHP, Shapelib, ... #12;GLIMS Glacier Database System

  12. Database Sampling with Functional Dependencies

    E-Print Network [OSTI]

    Riera, Jesús Bisbal

    Database Sampling with Functional Dependencies Jes´us Bisbal, Jane Grimson Department of Computer there is a need to prototype the database which the applications will use when in operation. A prototype database can be built by sampling data from an existing database. Including relevant semantic information when

  13. National Ambient Radiation Database

    SciTech Connect (OSTI)

    Dziuban, J.; Sears, R.

    2003-02-25T23:59:59.000Z

    The U.S. Environmental Protection Agency (EPA) recently developed a searchable database and website for the Environmental Radiation Ambient Monitoring System (ERAMS) data. This site contains nationwide radiation monitoring data for air particulates, precipitation, drinking water, surface water and pasteurized milk. This site provides location-specific as well as national information on environmental radioactivity across several media. It provides high quality data for assessing public exposure and environmental impacts resulting from nuclear emergencies and provides baseline data during routine conditions. The database and website are accessible at www.epa.gov/enviro/. This site contains (1) a query for the general public which is easy to use--limits the amount of information provided, but includes the ability to graph the data with risk benchmarks and (2) a query for a more technical user which allows access to all of the data in the database, (3) background information on ER AMS.

  14. Databases | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels Data Center Home Page onYouTube YouTube Note: Since the YouTube| Department ofDepartment9-92JanuaryProgram Areas »Databases Databases The Fuel

  15. acid allied chemical: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    function, structure and other criteria. Proteins are classi ed into "families " in the PIR database according to the degree of similarity in amino acid sequences. If classi ed...

  16. AN OVERVIEW ON DATABASESAN OVERVIEW ON DATABASES What is a Database?What is a Database?

    E-Print Network [OSTI]

    Schweik, Charles M.

    3/22/2011 1 1 AN OVERVIEW ON DATABASESAN OVERVIEW ON DATABASES C. Schweik 2 What is a Database?What is a Database? A well organized collection of data that are related in a meaningful way. Data can be accessed, structured and shared. #12;3/22/2011 2 3 Data in Database SystemsData in Database Systems should be:should be

  17. Database Security: A Historical Perspective

    E-Print Network [OSTI]

    Lesov, Paul

    2010-01-01T23:59:59.000Z

    The importance of security in database research has greatly increased over the years as most of critical functionality of the business and military enterprises became digitized. Database is an integral part of any information system and they often hold sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing data or degrading availability of the database. Over the last 30 years the information technology environment have gone through many changes of evolution and the database research community have tried to stay a step ahead of the upcoming threats to the database security. The database research community has thoughts about these issues long before they were address by the implementations. This paper will examine the different topics pertaining to database security and see the adaption of the research to the changing environment. Some short term database research trends will be ascertained ...

  18. Science & Engineering Engineering Databases

    E-Print Network [OSTI]

    Hampton, Randy

    -present. Good for computers, electronics, biomedical, control, electrical and ocean engineering, physics9/09 DK,DS Science & Engineering Library Engineering Databases How to search the engineering initials Special features: Limit to peer-reviewed journals Compendex [Engineering Index] 1884-present

  19. The CEBAF Element Database

    SciTech Connect (OSTI)

    Theodore Larrieu, Christopher Slominski, Michele Joyce

    2011-03-01T23:59:59.000Z

    With the inauguration of the CEBAF Element Database (CED) in Fall 2010, Jefferson Lab computer scientists have taken a step toward the eventual goal of a model-driven accelerator. Once fully populated, the database will be the primary repository of information used for everything from generating lattice decks to booting control computers to building controls screens. A requirement influencing the CED design is that it provide access to not only present, but also future and past configurations of the accelerator. To accomplish this, an introspective database schema was designed that allows new elements, types, and properties to be defined on-the-fly with no changes to table structure. Used in conjunction with Oracle Workspace Manager, it allows users to query data from any time in the database history with the same tools used to query the present configuration. Users can also check-out workspaces to use as staging areas for upcoming machine configurations. All Access to the CED is through a well-documented Application Programming Interface (API) that is translated automatically from original C++ source code into native libraries for scripting languages such as perl, php, and TCL making access to the CED easy and ubiquitous.

  20. High Performance Buildings Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The High Performance Buildings Database is a shared resource for the building industry, a unique central repository of in-depth information and data on high-performance, green building projects across the United States and abroad. The database includes information on the energy use, environmental performance, design process, finances, and other aspects of each project. Members of the design and construction teams are listed, as are sources for additional information. In total, up to twelve screens of detailed information are provided for each project profile. Projects range in size from small single-family homes or tenant fit-outs within buildings to large commercial and institutional buildings and even entire campuses. The database is a data repository as well. A series of Web-based data-entry templates allows anyone to enter information about a building project into the database. Once a project has been submitted, each of the partner organizations can review the entry and choose whether or not to publish that particular project on its own Web site.

  1. March 24, 2008 Databases: Security 1 Database Security and Authorization

    E-Print Network [OSTI]

    Adam, Salah

    to control login process by the DBMS Inference control The countermeasures to statistical database security database #12;March 24, 2008 Databases: Security 3 Chapter Outline Introduction Access Control Methods Policy System-related Security levels and categories Security Threats Loss of integrity Loss

  2. REGULAR ENTRY IN ENCYCLOPEDIA OF DATABASE SYSTEMS

    E-Print Network [OSTI]

    Risch, Tore

    ://refworks.springer.com/database-systems/ DISTRIBUTED ARCHITECTURE Tore Risch, Uppsala University, Sweden, http://user.it.uu.se/~torer/ SYNONYMS Parallel database, federated database, multi-database, peer-to-peer database DEFINITION A distributed database is a database where data management is distributed over several nodes (computers) in a computer

  3. A Case for Database Filesystems

    SciTech Connect (OSTI)

    Adams, P A; Hax, J C

    2009-05-13T23:59:59.000Z

    Data intensive science is offering new challenges and opportunities for Information Technology and traditional relational databases in particular. Database filesystems offer the potential to store Level Zero data and analyze Level 1 and Level 3 data within the same database system [2]. Scientific data is typically composed of both unstructured files and scalar data. Oracle SecureFiles is a new database filesystem feature in Oracle Database 11g that is specifically engineered to deliver high performance and scalability for storing unstructured or file data inside the Oracle database. SecureFiles presents the best of both the filesystem and the database worlds for unstructured content. Data stored inside SecureFiles can be queried or written at performance levels comparable to that of traditional filesystems while retaining the advantages of the Oracle database.

  4. The EMIME Mandarin Bilingual Database 

    E-Print Network [OSTI]

    Wester, Mirjam; Liang, Hui

    2011-01-01T23:59:59.000Z

    This paper describes the collection of a bilingual database of Mandarin/English data. In addition, the accents of the talkers in the database have been rated. English and Mandarin listeners assessed the English and Mandarin talkers' degree...

  5. DAPS: Database of Aligned Protein Structures

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Mallick, Parag; Rice, Danny; Eisenberg, David

    How is DAPS constructed? We begin with the set of all chains from the current release of the PDB. An all on all search is done on the list to find pairs that have the same fold acoording to both the FSSP and CATH databases and clustered into groups by a representative structure (representative structures have less than 25% sequence identity to each other). For each protein pair, regions aligned by the DALI program are extracted from the corresponding FSSP file, or recomputed using DALI-lite. In domain DAPS, only regions that are called "domains" by CATH are included in the alignment. The amino acid type, secondary structure type, and solvent accessibility are extracted from the DSSP file and written pairwise into the database. DAPS is updated with updates of CATH.[Taken from http://nihserver.mbi.ucla.edu/DAPS/daps_help.html

  6. R&D Accomplishments Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    recent accomplishments, including the latest Nobel Laureates associated with DOE. Database * Selected documents about noted accomplishments * Documents and individual pages...

  7. A Noisy 10GB Provenance Database

    E-Print Network [OSTI]

    Cheah, You-Wei

    2013-01-01T23:59:59.000Z

    Workload The provenance database is generated from theperformance of the provenance database generation process tox-axis). Figure 4 shows the database being populated with

  8. Observational Mishaps - a Database

    E-Print Network [OSTI]

    Kaspar von Braun; Kristin Chiboucas; Denise Hurley-Keller

    1999-06-11T23:59:59.000Z

    We present a World-Wide-Web-accessible database of astronomical images which suffer from a variety of observational problems, ranging from common occurences, such as dust grains on filters and/or the dewar window, to more exotic phenomena, such as loss of primary mirror support due to the deflation of the support airbags. Apart from its educational usefulness, the purpose of this database is to assist astronomers in diagnosing and treating errant images at the telescope, thus saving valuable telescope time. Every observational mishap contained in this on-line catalog is presented in the form of a GIF image, a brief explanation of the problem, and, when possible, a suggestion for improving the image quality.

  9. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Calm, J.M.

    1992-11-09T23:59:59.000Z

    The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R- 717 (ammonia), ethers, and others as well as azeotropic and zeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents on compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. A computerized version is available that includes retrieval software.

  10. REALALGEBRAIC GEOMETRY AND CONSTRAINT DATABASES

    E-Print Network [OSTI]

    Antwerpen, Universiteit

    of tuples. Fig. 13.1 shows an instance of a relational database that contains the two relations Beer and Pub. This database contains tourist information about beers and the pubs where they are served. It also contains, the attributes of Beer are Name, Pub, City and Postal code. The complete schema of the relational database of Fig

  11. DATABASE FOR PREMATURE CONCRETE DETERIORATION

    E-Print Network [OSTI]

    Texas at Austin, University of

    0-4085-P3 DATABASE FOR PREMATURE CONCRETE DETERIORATION Author: Kevin J. Folliard Project 0. This product presents the architecture for a database to collect relevant information on materials and mixture in developing and populating various materials- and structures-specific databases for both new concrete

  12. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M. [Calm (James M.), Great Falls, VA (United States)

    1999-01-01T23:59:59.000Z

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilities access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  13. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1996-11-15T23:59:59.000Z

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  14. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1996-07-01T23:59:59.000Z

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

  15. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M. [Calm (James M.), Great Falls, VA (United States)] [Calm (James M.), Great Falls, VA (United States)

    1996-04-15T23:59:59.000Z

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates. Citations in this report are divided into the following topics: thermophysical properties; materials compatibility; lubricants and tribology; application data; safety; test and analysis methods; impacts; regulatory actions; substitute refrigerants; identification; absorption and adsorption; research programs; and miscellaneous documents. Information is also presented on ordering instructions for the computerized version.

  16. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Cain, J.M. [Calm (James M.), Great Falls, VA (United States)

    1993-04-30T23:59:59.000Z

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents to accelerate availability of the information and will be completed or replaced in future updates.

  17. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M. [Calm (James M.), Great Falls, VA (United States)

    1998-08-01T23:59:59.000Z

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufactures and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on many refrigerants including propane, ammonia, water, carbon dioxide, propylene, ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

  18. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1997-02-01T23:59:59.000Z

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alterative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on various refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

  19. volume 17 Number 12 1989 Nucleic Acids Research The 5S RNA gene minichromosome of Euplotes

    E-Print Network [OSTI]

    Olins, Ada L.

    extract and 1.33 g/L anhydrous sodium acetate. Algae were harvested and resuspended in Pringsheim solution boiled wheat seeds in Carolina Spring-water. Large-scale cultures of Euplotes were grown in trays

  20. Type I Interferon is Not Just for Viruses: Cytosolic Sensing of Bacterial Nucleic Acids

    E-Print Network [OSTI]

    Monroe, Kathryn McGee

    2011-01-01T23:59:59.000Z

    in the recognition of Helicobacter pylori. Gastroenterologypneumophila, Helicobacter pylori, Francisella tularensis,the focus of Chapter 3. Helicobacter pylori is another gram-

  1. Relations between intraruminal protein and nucleic acid synthesis and forms of urinary nitrogen excreted by sheep

    E-Print Network [OSTI]

    Razzaque, Md. Abdur

    1967-01-01T23:59:59.000Z

    alcohol. The samples were coils. cted in duplicates. An attempt was made to determine the volume of the rumen digesta and its passage out of the reticulo-rumen by usi. ng polyethylene glycol. An appropriate amount of polyethylene glycol (2 gm... procedure for poly- ethylene glycol it was not possible to determine the volume of the rumen digesta and rate of passage out of the reticulo-rumen. Fasting Animals At the end of all experimer. . tal feeding and collection periods, the rumens of two...

  2. DOI: 10.1002/cbic.200600435 Duplex Formation of the Simplified Nucleic Acid

    E-Print Network [OSTI]

    Meggers, Eric

    ) with a stripped-down acyclic backbone can form stable duplexes.[8,9] The propylene glycol nucleotide building sequence and the painstaking separation of anomeric mixtures, this is not the case for GNA. Propylene (GNA) has an acyclic backbone of propylene glycol nucleosides that are connected by phosphodiester

  3. Stable nitrogen isotope measurements of marine bacterial proteins and nucleic acids: tracers of microbial activity

    E-Print Network [OSTI]

    Kovacs, Jeffrey Paul

    1996-01-01T23:59:59.000Z

    Stable nitrogen isotopes ([]15N) can trace elemental cycling in aquatic ecosystems if the enzyme mediated fractionations associated with nutrient uptake and assimilation are negligible or consistently predictable. In this study, bacterial proteins...

  4. Nucleic acids encoding phloem small RNA-binding proteins and transgenic plants comprising them

    DOE Patents [OSTI]

    Lucas, William J.; Yoo, Byung-Chun; Lough, Tony J.; Varkonyi-Gasic, Erika

    2007-03-13T23:59:59.000Z

    The present invention provides a polynucleotide sequence encoding a component of the protein machinery involved in small RNA trafficking, Cucurbita maxima phloem small RNA-binding protein (CmPSRB 1), and the corresponding polypeptide sequence. The invention also provides genetic constructs and transgenic plants comprising the polynucleotide sequence encoding a phloem small RNA-binding protein to alter (e.g., prevent, reduce or elevate) non-cell autonomous signaling events in the plants involving small RNA metabolism. These signaling events are involved in a broad spectrum of plant physiological and biochemical processes, including, for example, systemic resistance to pathogens, responses to environmental stresses, e.g., heat, drought, salinity, and systemic gene silencing (e.g., viral infections).

  5. Cellulases, nucleic acids encoding them and methods for making and using them

    DOE Patents [OSTI]

    Blum, David; Gemsch Cuenca, Joslin; Dycaico, Mark

    2013-04-23T23:59:59.000Z

    This invention relates to molecular and cellular biology and biochemistry. In one aspect, the invention provides polypeptides having cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or .beta.-glucosidase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides cellulase activity, e.g., endoglucanase, cellobiohydrolase, mannanase and/or .beta.-glucosidase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts.

  6. Cellulolytic enzymes, nucleic acids encoding them and methods for making and using them

    DOE Patents [OSTI]

    Gray, Kevin A. (San Diego, CA); Zhao, Lishan (Emeryville, CA); Cayouette, Michelle H. (San Diego, CA)

    2012-01-24T23:59:59.000Z

    The invention provides polypeptides having any cellulolytic activity, e.g., a cellulase activity, a endoglucanase, a cellobiohydrolase, a beta-glucosidase, a xylanase, a mannanse, a .beta.-xylosidase, an arabinofuranosidase, and/or an oligomerase activity, polynucleotides encoding these polypeptides, and methods of making and using these polynucleotides and polypeptides. In one aspect, the invention is directed to polypeptides having any cellulolytic activity, e.g., a cellulase activity, e.g., endoglucanase, cellobiohydrolase, beta-glucosidase, xylanase, mannanse, .beta.-xylosidase, arabinofuranosidase, and/or oligomerase activity, including thermostable and thermotolerant activity, and polynucleotides encoding these enzymes, and making and using these polynucleotides and polypeptides. In one aspect, the invention provides polypeptides having an oligomerase activity, e.g., enzymes that convert recalcitrant soluble oligomers to fermentable sugars in the saccharification of biomass. The polypeptides of the invention can be used in a variety of pharmaceutical, agricultural, food and feed processing and industrial contexts. The invention also provides compositions or products of manufacture comprising mixtures of enzymes comprising at least one enzyme of this invention.

  7. Identification and analysis of hepatitis C virus NS3 helicase inhibitors using nucleic acid binding assays

    E-Print Network [OSTI]

    Mukherjee, Sourav; Hanson, Alica M.; Shadrick, William R.; Ndjomou, Jean; Sweeney, Noreena L.; Hernadez, John J.; Bartczak, Diana; Li, Kelin; Frankowski, Kevin J.; Heck, Julie A.; Arnold, Leggy A.; Schoenen, Frank; Frick, David N,

    2012-06-27T23:59:59.000Z

    Typical assays used to discover and analyze small molecules that inhibit the hepatitis C virus (HCV) NS3 helicase yield few hits and are often confounded by compound interference. Oligonucleotide binding assays are examined ...

  8. Nucleic Acids Research doi:10.1093/nar/gkn305

    E-Print Network [OSTI]

    Lin, Guohui

    server for rapidly generating accurate 3D protein structures using only assigned nuclear magnetic no NOE and/or J-coupling data to perform its calculations. CS23D accepts chemical shift files in either. Tests conducted on more than 100 proteins from the BioMagResBank indicate that CS23D converges (i

  9. Nucleic acid encoding a self-assembling split-fluorescent protein system

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2014-04-01T23:59:59.000Z

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  10. Production of extracellular nucleic acids by genetically altered bacteria in aquatic-environment microcosms

    SciTech Connect (OSTI)

    Paul, J.H.; David, A.W.

    1989-01-01T23:59:59.000Z

    Factors which affect the production of extracellular DNA by genetically altered strains of Escherichia coli, Pseudomonas aeruginosa, Pseudomonas cepacia, and Bradyrhizobium japonicum in aquatic environments were investigated. The presence or absence of the ambient microbial community had little effect on the production of extracellular DNA. Results indicate the extracellular-DNA production by genetically altered bacteria released into aquatic environments is more strongly influenced by physiochemical factors than biotic factors; extracellular-DNA production rates are usually greater for organisms released in freshwater than marine environments; and ambient microbial populations can readily utilize materials released by these organisms.

  11. Nucleic acid encoding a self-assembling split-fluorescent protein system

    DOE Patents [OSTI]

    Waldo, Geoffrey S. (Santa Fe, NM); Cabantous, Stephanie (Los Alamos, NM)

    2011-06-07T23:59:59.000Z

    The invention provides a protein labeling and detection system based on self-complementing fragments of fluorescent and chromophoric proteins. The system of the invention is exemplified with various combinations of self-complementing fragments derived from Aequorea victoria Green Fluorescent Protein (GFP), which are used to detect and quantify protein solubility in multiple assay formats, both in vitro and in vivo.

  12. Response of DNA repair and replication systems to exocyclic nucleic acid base damage

    E-Print Network [OSTI]

    ?r?v?stava, Nidhi

    2012-01-01T23:59:59.000Z

    Genomes experience an often hostile environment that creates a vast array of damages that can give rise to myriad biological outcomes. Fortunately, cells are equipped with networks such as direct reversal, base excision ...

  13. Nucleic Acids Research, 2008, 19 doi:10.1093/nar/gkn836

    E-Print Network [OSTI]

    Dekker, Nynke

    and 2 Institute of Biotechnology and Department of Biological and Environmental Sciences, Viikki active mode. INTRODUCTION Template-directed polymerization of nucleotides (NTPs) is an essential process in all living entities. Accordingly, enzymes catalyzing these processes operate in both cel- lular

  14. Progress Report No. AT(11-1)-3083-6 RE: Nucleic Acids and Protein...

    Office of Scientific and Technical Information (OSTI)

    Chiu, N., Chiu, A. & Suyama, Y. (1974). J. Mol. Biol. (In the ress). 4. Elder, K.T. & Smith, A.E. (1973). Proc. Natl. Acad. Sci. U.S.A . 70, .. 1 2823-2826. ' 5. Gillespie, D. &...

  15. BGL7 beta-glucosidase and nucleic acids encoding the same

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel (Los Gatos, CA); Ward, Michael (San Francisco, CA)

    2012-03-13T23:59:59.000Z

    The present invention provides BGL7 polypeptides with the biological activity of a .beta.-glucosidase and a method of producing a recombinant enzyme having .beta.-glucosidase activity.

  16. Xylanases, nucleic acids encoding them and methods for making and using them

    DOE Patents [OSTI]

    Gray, Kevin A; Dirmeier, Reinhard

    2013-07-16T23:59:59.000Z

    The invention relates to enzymes having xylanase, mannanase and/or glucanase activity, e.g., catalyzing hydrolysis of internal .beta.-1,4-xylosidic linkages or endo-.beta.-1,4-glucanase linkages; and/or degrading a linear polysaccharide beta-1,4-xylan into xylose. Thus, the invention provides methods and processes for breaking down hemicellulose, which is a major component of the cell wall of plants, including methods and processes for hydrolyzing hemicelluloses in any plant or wood or wood product, wood waste, paper pulp, paper product or paper waste or byproduct. In addition, methods of designing new xylanases, mannanases and/or glucanases and methods of use thereof are also provided. The xylanases, mannanases and/or glucanases have increased activity and stability at increased pH and temperature.

  17. Reducible Poly(amido ethylenimine)s for Nucleic Acid Delivery

    E-Print Network [OSTI]

    Christensen, Lane

    2006-10-26T23:59:59.000Z

    is reduced 1 2 4 8 16 32 64 -50 -25 0 25 50 EDA/CBA DETA/CBA TETA/CBA n = 5 ? SEM w/DTT w/w Z e t a P o t e n t i a l ( m V ) Bioconjugate Chemistry (2006) 17; 1233-1240. 1 2 3 4 5 6 7 8 9 10 11 12 13 14... in fluorescence #1; Due to reducible disulfide bonds? 12 0 50 250 500 1.0?10 07 1.0?10 08 1.0?10 09 1.0?10 10 SS-PAED bPEI mM BSO R L U / m g P r o t e i n Effect on the Presence of GSH Inhibitor DL -Buthionine Sulfoxamine (BSO) ? BSO decreases intracellular GSH...

  18. Nucleic Acids Research, 2014 1 doi: 10.1093/nar/gku645

    E-Print Network [OSTI]

    Mühlemann, Oliver

    -independent interaction between SMG6 and UPF1 is essential for human NMD Pamela Nicholson1 , Christoph Josi1 , Hitomi be degraded by different routes that all require phosphorylated UPF1 (P-UPF1) as a starting point to be recruited to non- sense mRNAs via an interaction with P-UPF1, leading to eventual mRNA degradation

  19. Method for the detection of specific nucleic acid sequences by polymerase nucleotide incorporation

    DOE Patents [OSTI]

    Castro, Alonso

    2004-06-01T23:59:59.000Z

    A method for rapid and efficient detection of a target DNA or RNA sequence is provided. A primer having a 3'-hydroxyl group at one end and having a sequence of nucleotides sufficiently homologous with an identifying sequence of nucleotides in the target DNA is selected. The primer is hybridized to the identifying sequence of nucleotides on the DNA or RNA sequence and a reporter molecule is synthesized on the target sequence by progressively binding complementary nucleotides to the primer, where the complementary nucleotides include nucleotides labeled with a fluorophore. Fluorescence emitted by fluorophores on single reporter molecules is detected to identify the target DNA or RNA sequence.

  20. Structure-based model for light-harvesting properties of nucleic acid nanostructures

    E-Print Network [OSTI]

    Pan, Keyao

    Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary ...

  1. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes

    E-Print Network [OSTI]

    Richardson, David

    is the addition and full optimization of all hydrogen atoms, bothpolar and nonpolar.The results are reported. The all-atom contact analysis (7) featured on the MOLPROBITY site provides a simple but powerful system uses the information from both hydro- gen bonding and all-atom steric compatibility to fully

  2. An unprecedented nucleic acid capture mechanism for excision of DNA damage

    SciTech Connect (OSTI)

    Rubinson, Emily H.; Prakasha Gowda, A.S.; Spratt, Thomas E.; Gold, Barry; Eichmanbrand, Brandt F. (Pitt); (Vanderbilt); (Penn)

    2010-11-18T23:59:59.000Z

    DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation, providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.

  3. Thermo-Biolithography: A Technique for Patterning Nucleic Acids and Proteins

    E-Print Network [OSTI]

    Rubloff, Gary W.

    fluorescent protein (using tyrosinase-initiated conjugation). Because gelatin can be applied and removed under

  4. STRUCTURAL EFFECTS ON THE CIRCULAR DICHROISM OF ETHIDIUM-NUCLEIC ACID COMPLEXES

    E-Print Network [OSTI]

    Dahl, Kenneth Steven

    2013-01-01T23:59:59.000Z

    trup et al. (1978) examined dye binding with pdC- dG-dC-dG (2 dC-dG sites), pdC-dC-dG-dG (l dC-dG site), pdG-dG-dC-dC,1 dC-dG Site). For dye plus pdC-dG-dC-dG, both dC-dG sites

  5. Simultaneous purification and fractionation of nucleic acids and proteins from complex

    E-Print Network [OSTI]

    Santiago, Juan G.

    . Santiago1 * 1 Department of Mechanical Engineering, 2 Department of Chemical Engineering, Stanford, Sterling Heights, MI). We captured images using a 1300 × 1030, 12-bit, interline CCD camera (MicroMAX-1300Y

  6. Disposable and removable nucleic acid extraction and purification cartridges for automated flow-through systems

    DOE Patents [OSTI]

    Regan, John Frederick

    2014-09-09T23:59:59.000Z

    Removable cartridges are used on automated flow-through systems for the purpose of extracting and purifying genetic material from complex matrices. Different types of cartridges are paired with specific automated protocols to concentrate, extract, and purifying pathogenic or human genetic material. Their flow-through nature allows large quantities sample to be processed. Matrices may be filtered using size exclusion and/or affinity filters to concentrate the pathogen of interest. Lysed material is ultimately passed through a filter to remove the insoluble material before the soluble genetic material is delivered past a silica-like membrane that binds the genetic material, where it is washed, dried, and eluted. Cartridges are inserted into the housing areas of flow-through automated instruments, which are equipped with sensors to ensure proper placement and usage of the cartridges. Properly inserted cartridges create fluid- and air-tight seals with the flow lines of an automated instrument.

  7. Three- and four-body nonadditivities in nucleic acid tetramers: a CCSD(T) study

    SciTech Connect (OSTI)

    Pitonak, Michal; Neogrady, Pavel; Hobza, Pavel

    2009-12-18T23:59:59.000Z

    Three- and four-body nonadditivities in the uracil tetramer (in DNA-like geometry) and the GC step (in crystal geometry) were investigated at various levels of the wave-function theory: HF, MP2, MP3, L-CCD, CCSD and CCSD(T). All of the calculations were performed using the 6-31G**(0.25,0.15) basis set, whereas the HF, MP2 and the MP3 nonadditivities were, for the sake of comparison, also determined with the much larger aug-cc-pVDZ basis set. The HF and MP2 levels do not provide reliable values for many-body terms, making it necessary to go beyond the MP2 level. The benchmark CCSD(T) three- and four-body nonadditivities are reasonably well reproduced at the MP3 level, and almost quantitative agreement is obtained (fortuitously) either on the L-CCD level or as an average of the MP3 and the CCSD results. Reliable values of many-body terms (especially their higher-order correlation contributions) are obtained already when the rather small 6-31G**(0.25,0.15) basis set is used. The four-body term is much smaller when compared to the three-body terms, but it is definitely not negligible, e.g. in the case of the GC step it represents about 16% of all of the three- and four-body terms. While investigating the geometry dependence of many-body terms for the GG step at the MP3/6-31G**(0.25,0.15) level, we found that it is necessary to include at least three-body terms in the determination of optimal geometry parameters.

  8. Use of plant fatty acyl hydroxylases to produce hydroxylated fatty acids and derivatives in plants

    DOE Patents [OSTI]

    Somerville, Chris (Portola Valley, CA); van de Loo, Frank (Lexington, KY)

    2002-01-01T23:59:59.000Z

    The present invention relates to the identification of nucleic acid sequences and constructs, and methods related thereto, and the use of these sequences and constructs to produce genetically modified plants for the purpose of altering the composition of plant oils, waxes and related compounds.

  9. Use of plant fatty acyl hydroxylases to produce hydroxylated fatty acids and derivatives in plants

    DOE Patents [OSTI]

    Somerville, Chris (Portola Valley, CA); van de Loo, Frank (Lexington, KY)

    1998-01-01T23:59:59.000Z

    The present invention relates to the identification of nucleic acid sequences and constructs, and methods related thereto, and the use of these sequences and constructs to produce genetically modified plants for the purpose of altering the composition of plant oils, waxes and related compounds.

  10. Use of plant fatty acyl hydroxylases to produce hydroxylated fatty acids and derivatives in plants

    DOE Patents [OSTI]

    Somerville, Chris (Portola Valley, CA); van de Loo, Frank (Lexington, KY)

    1997-01-01T23:59:59.000Z

    The present invention relates to the identification of nucleic acid sequences and constructs, and methods related thereto, and the use of these sequences and constructs to produce genetically modified plants for the purpose of altering the composition of plant oils, waxes and related compounds.

  11. The SUPERFAMILY database in 2007: families and functions

    E-Print Network [OSTI]

    Gough, Julian

    of the protein domains in amino acid sequences. The classification of these domains is built on the Structural Classification of Proteins (SCOP) database (2) which groups domains of 40 known structure hierarchically the community. Underlying the assignments is an expert curated library of profile hidden Markov models (HMMs) (5

  12. National Residential Efficiency Measures Database Webinar Slides...

    Energy Savers [EERE]

    National Residential Efficiency Measures Database Webinar Slides National Residential Efficiency Measures Database Webinar Slides Presentation slides for the Building Technologies...

  13. ARM Publications Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisiting the TWP TWP Related Links Facilities andPastWrittenDatabaseSearchTips

  14. Database Manipulation on Quantum Computers

    E-Print Network [OSTI]

    Ahmed Younes

    2007-05-29T23:59:59.000Z

    Manipulating a database system on a quantum computer is an essential aim to benefit from the promising speed-up of quantum computers over classical computers in areas that take a vast amount of storage and processing time such as in databases. In this paper, the basic operations for manipulating the data in a quantum database will be defined, e.g. INSERT, UPDATE, DELETE, SELECT, backing up and restoring a database file. This gives the ability to perform the data processing that usually takes a long processing time on a classical database system, in a simultaneous way on a quantum computer. Defining a quantum version of more advanced concepts used in database systems, e.g. the referential integrity and the relational algebra, is a normal extension to this work

  15. Biological & Environmental Research Abstracts Database

    Office of Scientific and Technical Information (OSTI)

    Welcome to the Administrative section of the Biological and Environmental Research Abstracts Database. Please logon. Logon Name: Password: Logon CommentsEmail Us * Security...

  16. Energy Citations Database (ECD) - Architecture

    Office of Scientific and Technical Information (OSTI)

    Search Architecture - What Is under the hood? The Energy Citations Database makes searchable over two million bibliographic citations for energy and energy related STI from the...

  17. Ribosomal Database Project II

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Ribosomal Database Project (RDP) provides ribosome related data and services to the scientific community, including online data analysis and aligned and annotated Bacterial small-subunit 16S rRNA sequences. As of March 2008, RDP Release 10 is available and currently (August 2009) contains 1,074,075 aligned 16S rRNA sequences. Data that can be downloaded include zipped GenBank and FASTA alignment files, a histogram (in Excel) of the number of RDP sequences spanning each base position, data in the Functional Gene Pipeline Repository, and various user submitted data. The RDP-II website also provides numerous analysis tools.[From the RDP-II home page at http://rdp.cme.msu.edu/index.jsp

  18. The rice kinase database. A phylogenomic database for the rice kinome.

    E-Print Network [OSTI]

    Dardick, Christopher; Chen, Johann; Richter, Todd; Ouyang, Shu; Ronald, Pamela

    2007-01-01T23:59:59.000Z

    Bioinformatics The Rice Kinase Database.A Phylogenomic Database for the Rice Kinome 1[OA]created a phylogenomic database (http://rkd.ucdavis.edu) to

  19. Wind turbine reliability database update.

    SciTech Connect (OSTI)

    Peters, Valerie A.; Hill, Roger Ray; Stinebaugh, Jennifer A.; Veers, Paul S.

    2009-03-01T23:59:59.000Z

    This report documents the status of the Sandia National Laboratories' Wind Plant Reliability Database. Included in this report are updates on the form and contents of the Database, which stems from a fivestep process of data partnerships, data definition and transfer, data formatting and normalization, analysis, and reporting. Selected observations are also reported.

  20. Vienna Database Library Version 1.0

    E-Print Network [OSTI]

    Neumaier, Arnold

    Vienna Database Library Version 1.0 Reference Manual Hermann Schichl University of Vienna.2.14 #12;CONTENTS 1 Contents 1 Introduction 1 2 Vienna Database Library Module Index 3 3 Vienna Database Library Hierarchical Index 3 4 Vienna Database Library Compound Index 5 5 Vienna Database Library File

  1. Database Hints for Readex's AccessUN

    E-Print Network [OSTI]

    Stowell, Michael

    Database Hints for Readex's AccessUN Direct Link to Database: http://infoweb.newsbank.com/?db=UNAD Database Scope Readex's AccessUN database provides an index to United Nations documents from the six main Council, Secretariat and International Court of Justice. This database covers documents from 1946

  2. Chapter 20Chapter 20 Physical Database

    E-Print Network [OSTI]

    Yang, Jing

    1 Chapter 20Chapter 20 Physical Database Design and Tuning Copyright © 2011 Pearson Education, Inc. Publishing as Pearson Addison-Wesley 1. Physical Database Design in Relational Databases (1) Factors that Influence Physical Database Design: A. Analyzing the database queries and transactionsA. Analyzing

  3. Site specific incorporation of heavy atom-containing unnatural amino acids into proteins for structure determination

    DOE Patents [OSTI]

    Xie, Jianming (San Diego, CA); Wang, Lei (San Diego, CA); Wu, Ning (Boston, MA); Schultz, Peter G. (La Jolla, CA)

    2008-07-15T23:59:59.000Z

    Translation systems and other compositions including orthogonal aminoacyl tRNA-synthetases that preferentially charge an orthogonal tRNA with an iodinated or brominated amino acid are provided. Nucleic acids encoding such synthetases are also described, as are methods and kits for producing proteins including heavy atom-containing amino acids, e.g., brominated or iodinated amino acids. Methods of determining the structure of a protein, e.g., a protein into which a heavy atom has been site-specifically incorporated through use of an orthogonal tRNA/aminoacyl tRNA-synthetase pair, are also described.

  4. IMPROVING DATABASE DESIGN TEACHING IN SECONDARY EDUCATION

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Review Copy IMPROVING DATABASE DESIGN TEACHING IN SECONDARY EDUCATION: ACTION RESEARCH Education, University of Patras, 26500, Patras, GREECE. Abstract Database design and use has educational interest for utilitarian and learning reasons. Database technology has significant economic impact

  5. Intelligent Transportation Systems Deployment Statistics Database

    E-Print Network [OSTI]

    Intelligent Transportation Systems Deployment Statistics Database Oak Ridge National Laboratory direction. In addition, through the ITS Deployment Tracking web site, the database supports other users in 2010. Users can also download the entire 2010 deployment tracking database through the website

  6. Meteorological database for the United States

    E-Print Network [OSTI]

    Apte, M.G.

    2011-01-01T23:59:59.000Z

    to Indoor Air Meteorological Database for the United StatesUC-402 Meteorological Database for the United States M.G.Abstract A meteorological database has been developed to aid

  7. Sandia Energy - Sandia Wind Turbine Loads Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Sandia Wind Turbine Loads Database Home Stationary Power Energy Conversion Efficiency Wind Energy Resources Wind Software Downloads Sandia Wind Turbine Loads Database Sandia Wind...

  8. Hydrogen Storage Materials Database Demonstration Webinar (Text...

    Broader source: Energy.gov (indexed) [DOE]

    Database Demonstration Webinar (Text Version) Hydrogen Storage Materials Database Demonstration Webinar (Text Version) Below is the text version of the webinar titled "Hydrogen...

  9. Sandia National Laboratories: national reliability database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    national reliability database Third Annual Continuous Reliability Enhancement for Wind (CREW) Database Report Now Available On October 17, 2013, in Energy, News, News & Events,...

  10. SIX GOING ON SEVEN Database Dictionary

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    SIX GOING ON SEVEN Database Dictionary This database dictionary provides a brief explanation of measure naming schemes and mapping used to align the Northwest Power and...

  11. Buildings Performance Database Analysis Tools | Department of...

    Broader source: Energy.gov (indexed) [DOE]

    Performance Database Analysis Tools The Buildings Performance Database offers several analysis tools for exploring building data and forecasting financial and energy savings,...

  12. Marine and Hydrokinetic Technology Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    DOE’s Marine and Hydrokinetic Technology Database provides up-to-date information on marine and hydrokinetic renewable energy, both in the U.S. and around the world. The database includes wave, tidal, current, and ocean thermal energy, and contains information on the various energy conversion technologies, companies active in the field, and development of projects in the water. Depending on the needs of the user, the database can present a snapshot of projects in a given region, assess the progress of a certain technology type, or provide a comprehensive view of the entire marine and hydrokinetic energy industry. Results are displayed as a list of technologies, companies, or projects. Data can be filtered by a number of criteria, including country/region, technology type, generation capacity, and technology or project stage. The database was updated in 2009 to include ocean thermal energy technologies, companies, and projects.

  13. ORISE: Human Subjects Research Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Human Subjects Research Database Section 10, Part 745 of the Code of Federal Regulations and U.S. Department of Energy (DOE) Orders 443.1 and 481.1 require the maintenance of...

  14. Rice Glycosyltransferase (GT) Phylogenomic Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Ronald, Pamela

    The Ronald Laboratory staff at the University of California-Davis has a primary research focus on the genes of the rice plant. They study the role that genetics plays in the way rice plants respond to their environment. They created the Rice GT Database in order to integrate functional genomic information for putative rice Glycosyltransferases (GTs). This database contains information on nearly 800 putative rice GTs (gene models) identified by sequence similarity searches based on the Carbohydrate Active enZymes (CAZy) database. The Rice GT Database provides a platform to display user-selected functional genomic data on a phylogenetic tree. This includes sequence information, mutant line information, expression data, etc. An interactive chromosomal map shows the position of all rice GTs, and links to rice annotation databases are included. The format is intended to "facilitate the comparison of closely related GTs within different families, as well as perform global comparisons between sets of related families." [From http://ricephylogenomics.ucdavis.edu/cellwalls/gt/genInfo.shtml] See also the primary paper discussing this work: Peijian Cao, Laura E. Bartley, Ki-Hong Jung and Pamela C. Ronalda. Construction of a Rice Glycosyltransferase Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases. Molecular Plant, 2008, 1(5): 858-877.

  15. Protein sequence databases Rolf Apweiler1,

    E-Print Network [OSTI]

    Information NREF non-redundant reference databases PDB Protein Data Bank PIR Protein Information Resource PIR

  16. Benchmarking Database Systems A Systematic Approach

    E-Print Network [OSTI]

    Liblit, Ben

    Benchmarking Database Systems A Systematic Approach Dina Bitton David J. DeWitt Carolyn Turbyfill-81ER10920. #12;ABSTRACT This paper describes a customized database and a comprehensive set of queries that can be used for sys- tematic benchmarking of relational database systems. Designing this database

  17. Compression Aware Physical Database Design

    E-Print Network [OSTI]

    Kimura, Hideaki; Syamala, Manoj

    2011-01-01T23:59:59.000Z

    Modern RDBMSs support the ability to compress data using methods such as null suppression and dictionary encoding. Data compression offers the promise of significantly reducing storage requirements and improving I/O performance for decision support queries. However, compression can also slow down update and query performance due to the CPU costs of compression and decompression. In this paper, we study how data compression affects choice of appropriate physical database design, such as indexes, for a given workload. We observe that approaches that decouple the decision of whether or not to choose an index from whether or not to compress the index can result in poor solutions. Thus, we focus on the novel problem of integrating compression into physical database design in a scalable manner. We have implemented our techniques by modifying Microsoft SQL Server and the Database Engine Tuning Advisor (DTA) physical design tool. Our techniques are general and are potentially applicable to DBMSs that support other co...

  18. National Residential Efficiency Measures Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The National Residential Efficiency Measures Database is a publicly available, centralized resource of residential building retrofit measures and costs for the U.S. building industry. With support from the U.S. Department of Energy, NREL developed this tool to help users determine the most cost-effective retrofit measures for improving energy efficiency of existing homes. Software developers who require residential retrofit performance and cost data for applications that evaluate residential efficiency measures are the primary audience for this database. In addition, home performance contractors and manufacturers of residential materials and equipment may find this information useful. The database offers the following types of retrofit measures: 1) Appliances, 2) Domestic Hot Water, 3) Enclosure, 4) Heating, Ventilating, and Air Conditioning (HVAC), 5) Lighting, 6) Miscellaneous.

  19. DOE Global Energy Storage Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The DOE International Energy Storage Database has more than 400 documented energy storage projects from 34 countries around the world. The database provides free, up-to-date information on grid-connected energy storage projects and relevant state and federal policies. More than 50 energy storage technologies are represented worldwide, including multiple battery technologies, compressed air energy storage, flywheels, gravel energy storage, hydrogen energy storage, pumped hydroelectric, superconducting magnetic energy storage, and thermal energy storage. The policy section of the database shows 18 federal and state policies addressing grid-connected energy storage, from rules and regulations to tariffs and other financial incentives. It is funded through DOE’s Sandia National Laboratories, and has been operating since January 2012.

  20. Methods and compounds for chemical ligation

    DOE Patents [OSTI]

    Church, George M.; Sismour, A. Michael

    2013-07-09T23:59:59.000Z

    Compositions and methods for chemical ligation are provided. Methods for nucleic acid sequencing, nucleic acid assembly and nucleic acid synthesis are also provided.

  1. Workload-Aware Database Monitoring and Consolidation

    E-Print Network [OSTI]

    Curino, Carlo

    In most enterprises, databases are deployed on dedicated database servers. Often, these servers are underutilized much of the time. For example, in traces from almost 200 production servers from different organizations, ...

  2. Webinar: NREL's Fuel Cell Contaminant Database

    Broader source: Energy.gov [DOE]

    Video recording and text version of the webinar titled "NREL's Fuel Cell Contaminant Database," originally presented on May 27, 2014.

  3. Buildings Performance Database Recommend Data Fields | Department...

    Broader source: Energy.gov (indexed) [DOE]

    Renewable Energy. bpdrecommendeddatafields.pdf More Documents & Publications BEDES Beta Data Preparation Process for the Buildings Performance Database Commercial Building...

  4. Webinar: Hydrogen Storage Materials Database Demonstration

    Broader source: Energy.gov [DOE]

    Video recording and text version of the webinar, Hydrogen Storage Materials Database Demonstration, originally presented on December 13, 2011.

  5. 1991-2005 National Solar Radiation Database

    SciTech Connect (OSTI)

    Wilcox, S.

    2007-05-01T23:59:59.000Z

    This fact sheet provides an overview of the purpose, benefit, and features of the newly updated National Solar Radiation Database.

  6. Search Log Analysis of the ARTstor Cultural Heritage Image Database

    E-Print Network [OSTI]

    Lowe, Heather Ann

    2013-01-01T23:59:59.000Z

    Patterns in a Digital Image Database. Information RetrievalCultural Heritage Image Database A thesis submitted inCultural Heritage Image Database by Heather Ann Lowe Master

  7. The Majorana Parts Tracking Database

    E-Print Network [OSTI]

    Abgrall, N; Avignone, F T; Bertrand, F E; Brudanin, V; Busch, M; Byram, D; Caldwell, A S; Chan, Y-D; Christofferson, C D; Combs, D C; Cuesta, C; Detwiler, J A; Doe, P J; Efremenko, Yu; Egorov, V; Ejiri, H; Elliott, S R; Esterline, J; Fast, J E; Finnerty, P; Fraenkle, F M; Galindo-Uribarri, A; Giovanetti, G K; Goett, J; Green, M P; Gruszko, J; Guiseppe, V E; Gusev, K; Hallin, A L; Hazama, R; Hegai, A; Henning, R; Hoppe, E W; Howard, S; Howe, M A; Keeter, K J; Kidd, M F; Kochetov, O; Kouzes, R T; LaFerriere, B D; Leon, J Diaz; Leviner, L E; Loach, J C; MacMullin, J; Martin, R D; Meijer, S J; Mertens, S; Miller, M L; Mizouni, L; Nomachi, M; Orrell, J L; O'Shaughnessy, C; Overman, N R; Petersburg, R; Phillips, D G; Poon, A W P; Pushkin, K; Radford, D C; Rager, J; Rielage, K; Robertson, R G H; Romero-Romero, E; Ronquest, M C; Shanks, B; Shima, T; Shirchenko, M; Snavely, K J; Snyder, N; Soin, A; Suriano, A M; Tedeschi, D; Thompson, J; Timkin, V; Tornow, W; Trimble, J E; Varner, R L; Vasilyev, S; Vetter, K; Vorren, K; White, B R; Wilkerson, J F; Wiseman, C; Xu, W; Yakushev, E; Young, A R; Yu, C -H; Zhitnikov, I

    2015-01-01T23:59:59.000Z

    The Majorana Demonstrator is an ultra-low background physics experiment searching for the neutrinoless double beta decay of $^{76}$Ge. The Majorana Parts Tracking Database is used to record the history of components used in the construction of the Demonstrator. The tracking implementation takes a novel approach based on the schema-free database technology CouchDB. Transportation, storage, and processes undergone by parts such as machining or cleaning are linked to part records. Tracking parts provides a great logistics benefit and an important quality assurance reference during construction. In addition, the location history of parts provides an estimate of their exposure to cosmic radiation. A web application for data entry and a radiation exposure calculator have been developed as tools for achieving the extreme radio-purity required for this rare decay search.

  8. The Majorana Parts Tracking Database

    E-Print Network [OSTI]

    The Majorana Collaboration; N. Abgrall; E. Aguayo; F. T. Avignone III; A. S. Barabash; F. E. Bertrand; V. Brudanin; M. Busch; D. Byram; A. S. Caldwell; Y-D. Chan; C. D. Christofferson; D. C. Combs; C. Cuesta; J. A. Detwiler; P. J. Doe; Yu. Efremenko; V. Egorov; H. Ejiri; S. R. Elliott; J. Esterline; J. E. Fast; P. Finnerty; F. M. Fraenkle; A. Galindo-Uribarri; G. K. Giovanetti; J. Goett; M. P. Green; J. Gruszko; V. E. Guiseppe; K. Gusev; A. L. Hallin; R. Hazama; A. Hegai; R. Henning; E. W. Hoppe; S. Howard; M. A. Howe; K. J. Keeter; M. F. Kidd; O. Kochetov; S. I. Konovalov; R. T. Kouzes; B. D. LaFerriere; J. Diaz Leon; L. E. Leviner; J. C. Loach; J. MacMullin; R. D. Martin; S. J. Meijer; S. Mertens; M. L. Miller; L. Mizouni; M. Nomachi; J. L. Orrell; C. O'Shaughnessy; N. R. Overman; R. Petersburg; D. G. Phillips II; A. W. P. Poon; K. Pushkin; D. C. Radford; J. Rager; K. Rielage; R. G. H. Robertson; E. Romero-Romero; M. C. Ronquest; B. Shanks; T. Shima; M. Shirchenko; K. J. Snavely; N. Snyder; A. Soin; A. M. Suriano; D. Tedeschi; J. Thompson; V. Timkin; W. Tornow; J. E. Trimble; R. L. Varner; S. Vasilyev; K. Vetter; K. Vorren; B. R. White; J. F. Wilkerson; C. Wiseman; W. Xu; E. Yakushev; A. R. Young; C. -H. Yu; V. Yumatov; I. Zhitnikov

    2015-02-05T23:59:59.000Z

    The Majorana Demonstrator is an ultra-low background physics experiment searching for the neutrinoless double beta decay of $^{76}$Ge. The Majorana Parts Tracking Database is used to record the history of components used in the construction of the Demonstrator. The tracking implementation takes a novel approach based on the schema-free database technology CouchDB. Transportation, storage, and processes undergone by parts such as machining or cleaning are linked to part records. Tracking parts provides a great logistics benefit and an important quality assurance reference during construction. In addition, the location history of parts provides an estimate of their exposure to cosmic radiation. A web application for data entry and a radiation exposure calculator have been developed as tools for achieving the extreme radio-purity required for this rare decay search.

  9. GRAPHDB -a database of Axel Kohnert

    E-Print Network [OSTI]

    Laue, Reinhard

    GRAPHDB - a database of graphs March 2003 Axel Kohnert University of Bayreuth http://btm2xg ADMIN DBUSER ¡£¢ DB ¤ ¥ GRAPHVIEWER ¦ GRAPHSERVER #12;A: The Database Part I. THE MASTER TABLE #12;B: The client access to the database There are several web pages which allow the search

  10. Comprehensive Database on Concrete Creep and Shrinkage

    E-Print Network [OSTI]

    Comprehensive Database on Concrete Creep and Shrinkage Zdenek P. Bazant and Guang-Hua Li Structural Database on Concrete Creep and Shrinkage Zdenek P. Bazant1 and Guang-Hua Li2 Abstract: As a sequel to the first large database created at Northwestern University in 1978, the paper presents a further

  11. Computer Note A Prototype Object Database for

    E-Print Network [OSTI]

    Neigel, Joseph E.

    Computer Note A Prototype Object Database for Mitochondrial DNA Variation J. E. NEIGEL AND P preserved. We hope to prevent further loss by establishing a community database for population genetic surveys. We explored the feasibility of a population genetics database by developing a prototype

  12. DATABASE AUTHENTICATION BY DISTORTION FREE WATERMARKING

    E-Print Network [OSTI]

    Cortesi, Tino

    DATABASE AUTHENTICATION BY DISTORTION FREE WATERMARKING Sukriti Bhattacharya and Agostino Cortesi@dsi.unive.it, cortesi@unive.it Keywords: Database watermarking, ZAW, Public key watermark, Abstract interpretation the verification of integrity of the relational databases by using a public zero distortion authentication

  13. 8, 76577702, 2008 A new database of

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    ACPD 8, 7657­7702, 2008 A new database of trace gases and aerosols B. Hassler et al. Title Page.0 License. Atmospheric Chemistry and Physics Discussions Technical Note: A new global database of trace­7702, 2008 A new database of trace gases and aerosols B. Hassler et al. Title Page Abstract Introduction

  14. Stockpile Dismantlement Database Training Materials

    SciTech Connect (OSTI)

    Not Available

    1993-11-01T23:59:59.000Z

    This document, the Stockpile Dismantlement Database (SDDB) training materials is designed to familiarize the user with the SDDB windowing system and the data entry steps for Component Characterization for Disposition. The foundation of information required for every part is depicted by using numbered graphic and text steps. The individual entering data is lead step by step through generic and specific examples. These training materials are intended to be supplements to individual on-the-job training.

  15. Databases

    E-Print Network [OSTI]

    Mcgregor, D.; Cockshott, P.; Wilson, J.; US Patent 6169990 British Patent, Volume BP 9604522.4 Academic Press [More Details

    Mcgregor,D. Cockshott,P. Wilson,J. US Patent 6169990 British Patent, Volume BP 9604522.4 Academic Press

  16. Databases

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645 3,625govInstrumentstdmadapInactiveVisitingContract Management Fermi SitePARTOfficeOctoberDanielDTN Data

  17. Distributed DatabasesDistributed Databases Based on material provided by:Based on material provided by

    E-Print Network [OSTI]

    /References ?? A Database Management SystemA Database Management System (DBMS) is a software package designed(DBMS Databases, 2001 5 Why Use a DBMS?Why Use a DBMS? ?? Data IndependenceData Independence ?? Efficient Access data #12;J.J.Bunn, Distributed Databases, 2001 9 Concurrency ControlConcurrency Control ?? Good DBMS

  18. Artemis Chado database -practical guide Annotation in the database version of Artemis

    E-Print Network [OSTI]

    Maizels, Rick

    -1- Artemis Chado database - practical guide Annotation in the database version of Artemis 1 directory for the backup files and optionally save this setting between sessions. Wait for the `Database and File Manager' to be loaded. Click on `Launch Artemis'. #12;-2- Artemis Chado database - practical guide

  19. The USC CreativeIT Database: A Multimodal Database of Theatrical Improvisation

    E-Print Network [OSTI]

    Busso, Carlos

    The USC CreativeIT Database: A Multimodal Database of Theatrical Improvisation Angeliki Metallinou' creativity. The USC CreativeIT database provides a novel bridge between the study of theatrical improvisation and human expressive behavior in dyadic interaction. The theoretical design of the database is based

  20. NIST Standard Reference Database 88 NIST/TRC Ideal Gas Database

    E-Print Network [OSTI]

    Magee, Joseph W.

    #12;NIST Standard Reference Database 88 NIST/TRC Ideal Gas Database Version 2.0 Users' Guide Data of the database and to verify that the data contained therein have been selected on the basis of sound scientific that may result from errors or omissions in the database. COPYRIGHT (C) 2006 copyright by the U

  1. CIS 330: Database Management Systems Course Number & Title (A.1) CIS 330: Database Management Systems

    E-Print Network [OSTI]

    Plotkin, Joshua B.

    CIS 330: Database Management Systems Course Number & Title (A.1) CIS 330: Database Management & Johannes Gehrke, Database Management Systems (third edition), McGraw Hill. Additional materials as handouts, e.g., research papers Catalog Description (A.5a) Introduction to database management systems

  2. Overview of selected molecular biological databases

    SciTech Connect (OSTI)

    Rayl, K.D.; Gaasterland, T.

    1994-11-01T23:59:59.000Z

    This paper presents an overview of the purpose, content, and design of a subset of the currently available biological databases, with an emphasis on protein databases. Databases included in this summary are 3D-ALI, Berlin RNA databank, Blocks, DSSP, EMBL Nucleotide Database, EMP, ENZYME, FSSP, GDB, GenBank, HSSP, LiMB, PDB, PIR, PKCDD, ProSite, and SWISS-PROT. The goal is to provide a starting point for researchers who wish to take advantage of the myriad available databases. Rather than providing a complete explanation of each database, we present its content and form by explaining the details of typical entries. Pointers to more complete ``user guides`` are included, along with general information on where to search for a new database.

  3. This overview covers: Connecting to a Chado Database

    E-Print Network [OSTI]

    Maizels, Rick

    This overview covers: · Connecting to a Chado Database · Reading From the Database · iBatis Database Mapping · Gene Representation · Gene Building · Gene merging and splitting · Transfer Annotation Tool · Writing To The Database · Opening the Standalone Gene Builder · Community Annotation · Writing

  4. Development of a Series of National Coalbed Methane Databases

    E-Print Network [OSTI]

    Mohaghegh, Shahab

    . · Offer in one set public literature, reservoir characteristics and production data available. · Are easy Asset ­ Scattered Public Data Motivations #12;Information in Hand · CBM - Literature Database · CBM - Reservoir Characteristics Database · CBM - Production Database #12;CBM - Literature Database · SPE Papers

  5. V-036: EMC Smarts Network Configuration Manager Database Authenticatio...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    36: EMC Smarts Network Configuration Manager Database Authentication Bypass Vulnerability V-036: EMC Smarts Network Configuration Manager Database Authentication Bypass...

  6. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18T23:59:59.000Z

    Final Report on Award No. DE-FG0201ER63171 Principal Investigator: LeRoy B. Walters February 18, 2008 This project successfully completed its goal of surveying and reporting on the DNA patenting and licensing policies at 30 major U.S. academic institutions. The report of survey results was published in the January 2006 issue of Nature Biotechnology under the title “The Licensing of DNA Patents by US Academic Institutions: An Empirical Survey.” Lori Pressman was the lead author on this feature article. A PDF reprint of the article will be submitted to our Program Officer under separate cover. The project team has continued to update the DNA Patent Database on a weekly basis since the conclusion of the project. The database can be accessed at dnapatents.georgetown.edu. This database provides a valuable research tool for academic researchers, policymakers, and citizens. A report entitled Reaping the Benefits of Genomic and Proteomic Research: Intellectual Property Rights, Innovation, and Public Health was published in 2006 by the Committee on Intellectual Property Rights in Genomic and Protein Research and Innovation, Board on Science, Technology, and Economic Policy at the National Academies. The report was edited by Stephen A. Merrill and Anne-Marie Mazza. This report employed and then adapted the methodology developed by our research project and quoted our findings at several points. (The full report can be viewed online at the following URL: http://www.nap.edu/openbook.php?record_id=11487&page=R1). My colleagues and I are grateful for the research support of the ELSI program at the U.S. Department of Energy.

  7. CS 525: Advanced Database Organization Study of relational, semantic, and object-oriented data models and interfaces. Database management system

    E-Print Network [OSTI]

    Heller, Barbara

    CS 525: Advanced Database Organization Objectives Study of relational, semantic, and object-oriented data models and interfaces. Database management system techniques for query optimization, concurrency History of database management. Goals of database system development. Relational systems Data models

  8. Thermodynamics and Enzymatic Polymerization of Artificial Metallo-Nucleic Acids AND Investigation of Duplex Formation between GAN and RNA

    E-Print Network [OSTI]

    Kim, Eun Kyong

    2011-01-01T23:59:59.000Z

    cells on a Varian Cary 500 UV-Vis spectrophotometer equipped with a Peltiercell on a Varian Cary 500 UV-Vis spectrophotometer equipped with a Peltier

  9. Electrical Detection of Nucleic Acid Amplification Using an On-Chip Quasi-Reference Electrode and a PVC REFET

    E-Print Network [OSTI]

    Bashir, Rashid

    and a PVC REFET Eric Salm,, Yu Zhong,,§ Bobby Reddy, Jr.,,§ Carlos Duarte-Guevara,,§ Vikhram Swaminathan that utilizes a platinum QRE to establish a pH-sensitive fluid gate potential and a PVC membrane REFET to enable

  10. Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins and Nucleic Acids in Solution

    E-Print Network [OSTI]

    Levitt, Michael

    Calibration and Testing of a Water Model for Simulation of the Molecular Dynamics of Proteins important in biological macromolecules, where fewer experimental results are available for calibration. Our

  11. Electronic structure and spectroscopy of nucleic acid bases: Ionization energies, ionization-induced structural changes, and photoelectron spectra

    SciTech Connect (OSTI)

    Bravaya, Ksenia B.; Kostko, Oleg; Dolgikh, Stanislav; Landau, Arie; Ahmed, Musahid; Krylov, Anna I.

    2010-08-02T23:59:59.000Z

    We report high-level ab initio calculations and single-photon ionization mass spectrometry study of ionization of adenine (A), thymine (T), cytosine (C) and guanine (G). For thymine and adenine, only the lowest-energy tautomers were considered, whereas for cytosine and guanine we characterized five lowest-energy tautomeric forms. The first adiabatic and several vertical ionization energies were computed using equation-of-motion coupled-cluster method for ionization potentials with single and double substitutions. Equilibrium structures of the cationic ground states were characterized by DFT with the {omega}B97X-D functional. The ionization-induced geometry changes of the bases are consistent with the shapes of the corresponding molecular orbitals. For the lowest-energy tautomers, the magnitude of the structural relaxation decreases in the following series G > C > A > T, the respective relaxation energies being 0.41, 0.32, 0.25 and 0.20 eV. The computed adiabatic ionization energies (8.13, 8.89, 8.51-8.67 and 7.75-7.87 eV for A,T,C and G, respectively) agree well with the onsets of the photoionization efficiency (PIE) curves (8.20 {+-} 0.05, 8.95 {+-} 0.05, 8.60 {+-} 0.05 and 7.75 {+-} 0.05 eV). Vibrational progressions for the S{sub 0}-D{sub 0} vibronic bands computed within double-harmonic approximation with Duschinsky rotations are compared with previously reported experimental photoelectron spectra.

  12. Discrimination of Alternative Spliced Isoforms by Real-Time PCR Using Locked Nucleic Acid (LNA) Substituted Primer

    E-Print Network [OSTI]

    Wan, Guoqiang

    Determination of quantitative expression levels of alternatively spliced isoforms provides an important approach to the understanding of the functional significance of each isoform. Real-time PCR using exon junction ...

  13. 2001 Oxford University Press Nucleic Acids Research, 2001, Vol. 29, No. 22 46634673 Importance of the conserved nucleotides around the

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    of the conserved nucleotides around the tRNA-like structure of Escherichia coli transfer- messenger RNA for protein nucleotide stretches 16­20 and 333­335 seriously impair protein tagging with only minor changes nucleotides next to the tRNA-like portion is proposed. Overall, the highly conserved nucleotides around the t

  14. Nucleic Acids Research, 1994, Vol. 22, No. 11 1981 -1987 Interaction between the first and last nucleotides of

    E-Print Network [OSTI]

    Chanfreau, Guillaume

    nucleotides of pre-mRNA introns is a determinant of 3' splice site selection in S.cerevisiae Guillaume be reactivated by a G to C substitution of the last intron nucleotide. These results demonstrate that the inter- action between the first and last intron nucleotides is a conserved feature of nuclear pre-mRNA splicing

  15. Array of nucleic acid probes on biological chips for diagnosis of HIV and methods of using the same

    DOE Patents [OSTI]

    Chee, Mark (Palo Alto, CA); Gingeras, Thomas R. (Santa Clara, CA); Fodor, Stephen P. A. (Palo Alto, CA); Hubble, Earl A. (Mountain View, CA); Morris, MacDonald S. (San Jose, CA)

    1999-01-19T23:59:59.000Z

    The invention provides an array of oligonucleotide probes immobilized on a solid support for analysis of a target sequence from a human immunodeficiency virus. The array comprises at least four sets of oligonucleotide probes 9 to 21 nucleotides in length. A first probe set has a probe corresponding to each nucleotide in a reference sequence from a human immunodeficiency virus. A probe is related to its corresponding nucleotide by being exactly complementary to a subsequence of the reference sequence that includes the corresponding nucleotide. Thus, each probe has a position, designated an interrogation position, that is occupied by a complementary nucleotide to the corresponding nucleotide. The three additional probe sets each have a corresponding probe for each probe in the first probe set. Thus, for each nucleotide in the reference sequence, there are four corresponding probes, one from each of the probe sets. The three corresponding probes in the three additional probe sets are identical to the corresponding probe from the first probe or a subsequence thereof that includes the interrogation position, except that the interrogation position is occupied by a different nucleotide in each of the four corresponding probes.

  16. Volume 15 Number 19 1987 Nucleic Acids Research Deduced prducts of C4-dkarboxylate tranort regultory genes of Rukobium kgminowsaum

    E-Print Network [OSTI]

    Ausubel, Frederick M.

    of the dctD gene poduct (DctD)was strongly conserved with N-terminal domains of theproducts of several

  17. Activation of nucleic acid-sensing Toll-like receptors requires cleavage by endolysosomal proteases: a mechanism to avoid autoimmunity

    E-Print Network [OSTI]

    Ewald, Sarah Elisabeth

    2010-01-01T23:59:59.000Z

    receptor DC: dendritic cell pDC: plasmacytoid dendritic celltaken up by plasmacytoid DCs (pDC) and elicit large amountsare also components of the pDC-MyD88 signaling complex (

  18. Volume 4 Number 6 June 1977 Nucleic Acids Research Conformational states of chromatin v bodies induced by urea

    E-Print Network [OSTI]

    Olins, Ada L.

    and 7 M urea. Companion studies on the conformation of the inner histone "heterotypic tetramer" also pairs. The inner histone "heterotypic tetramer" (one each of H4, H3, H2A, and H2B, devoid of DNA/ml solution A^o =3.5 (12). The heterotypic tetramer was fractionated from HI and H5 by layering 0.5 ml

  19. The Dartmouth Stellar Evolution Database

    E-Print Network [OSTI]

    Aaron Dotter; Brian Chaboyer; Darko Jevremovic; Veselin Kostov; E. Baron; J. W. Ferguson

    2008-04-28T23:59:59.000Z

    The ever-expanding depth and quality of photometric and spectroscopic observations of stellar populations increase the need for theoretical models in regions of age-composition parameter space that are largely unexplored at present. Stellar evolution models that employ the most advanced physics and cover a wide range of compositions are needed to extract the most information from current observations of both resolved and unresolved stellar populations. The Dartmouth Stellar Evolution Database is a collection of stellar evolution tracks and isochrones that spans a range of [Fe/H] from -2.5 to +0.5, [alpha/Fe] from -0.2 to +0.8 (for [Fe/H] 0), and initial He mass fractions from Y=0.245 to 0.40. Stellar evolution tracks were computed for masses between 0.1 and 4 Msun, allowing isochrones to be generated for ages as young as 250 Myr. For the range in masses where the core He flash occurs, separate He-burning tracks were computed starting from the zero age horizontal branch. The tracks and isochrones have been transformed to the observational plane in a variety of photometric systems including standard UBV(RI)c, Stromgren uvby, SDSS ugriz, 2MASS JHKs, and HST ACS-WFC and WFPC2. The Dartmouth Stellar Evolution Database is accessible through a website at http://stellar.dartmouth.edu/~models/ where all tracks, isochrones, and additional files can be downloaded.

  20. Nuclear Concrete Materials Database Phase I Development

    SciTech Connect (OSTI)

    Ren, Weiju [ORNL; Naus, Dan J [ORNL

    2012-05-01T23:59:59.000Z

    The FY 2011 accomplishments in Phase I development of the Nuclear Concrete Materials Database to support the Light Water Reactor Sustainability Program are summarized. The database has been developed using the ORNL materials database infrastructure established for the Gen IV Materials Handbook to achieve cost reduction and development efficiency. In this Phase I development, the database has been successfully designed and constructed to manage documents in the Portable Document Format generated from the Structural Materials Handbook that contains nuclear concrete materials data and related information. The completion of the Phase I database has established a solid foundation for Phase II development, in which a digital database will be designed and constructed to manage nuclear concrete materials data in various digitized formats to facilitate electronic and mathematical processing for analysis, modeling, and design applications.

  1. Concurrency control in heterogeneous distributed database systems

    E-Print Network [OSTI]

    Rahman, Md. Rezaur

    1992-01-01T23:59:59.000Z

    APPROACHES IN HDDBS . III. A Approaches Requiring Local DBMS Modihcations 17 19 III. B Approaches Without Local DBMS Modifications 22 IV A NEW APPROACH TO HDDBS CONCURRENCY CONTROL 30 IV. A The Concurrency Control Scheme 30 CIIA PTER Page IV. B... related to Database Systems in general which will be used consistently throughout this thesis. A Database system (DBS) consists of a set of dutiibiises (DB) which contain the data of interest and software, the database msnageinent system (DBMS), which...

  2. Graphical visualization of implemented storage databases

    SciTech Connect (OSTI)

    Fischer, C.; Hamp, H.P. [Admintec GmbH, Pforzheim (Germany)

    1993-12-31T23:59:59.000Z

    The PC-program LANUC, developed from Admintec, supports a decentralized or centralized storage management of radioactive waste. It gives the storekeeper a graphical view of a storage area and its contents which are otherwise only represented in lists and databases. The storekeeper can plan any movements within the storage area and once they are confirmed, the data in the database are automatically altered. Any implemented database can be represented by simulating a human operator with a program.

  3. Top Resources | Commercial Buildings Resource Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Home Programs & Offices Consumer Information Commercial Buildings Resource Database Resources to support the adoption of energy-saving building technologies Search form Search...

  4. COSC6340: Database Systems Instructor: Carlos Ordonez

    E-Print Network [OSTI]

    Ordonez, Carlos

    available. Topics include the following. Database design: ER model, relational model and algebra, indexing data structures, query optimizer, concurrency control, transaction processing, recovery. Advanced

  5. A Database Index to Large Biological Sequences

    E-Print Network [OSTI]

    Hunt, E.

    Hunt,E. Atkinson,M.P. Irving,R.W. Proceedings of the 27th Conference on Very Large Databases pp 139-148 Morgan Kaufmann

  6. DEPOT database: Reference manual and user's guide

    SciTech Connect (OSTI)

    Clancey, P.; Logg, C.

    1991-03-01T23:59:59.000Z

    DEPOT has been developed to provide tracking for the Stanford Linear Collider (SLC) control system equipment. For each piece of equipment entered into the database, complete location, service, maintenance, modification, certification, and radiation exposure histories can be maintained. To facilitate data entry accuracy, efficiency, and consistency, barcoding technology has been used extensively. DEPOT has been an important tool in improving the reliability of the microsystems controlling SLC. This document describes the components of the DEPOT database, the elements in the database records, and the use of the supporting programs for entering data, searching the database, and producing reports from the information.

  7. Sandia Wind Turbine Loads Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Sandia Wind Turbine Loads Database is divided into six files, each corresponding to approximately 16 years of simulation. The files are text files with data in columnar format. The 424MB zipped file containing six data files can be downloaded by the public. The files simulate 10-minute maximum loads for the NREL 5MW wind turbine. The details of the loads simulations can be found in the paper: “Decades of Wind Turbine Loads Simulations”, M. Barone, J. Paquette, B. Resor, and L. Manuel, AIAA2012-1288 (3.69MB PDF). Note that the site-average wind speed is 10 m/s (class I-B), not the 8.5 m/s reported in the paper.

  8. Catalog of databases and reports

    SciTech Connect (OSTI)

    Burtis, M.D. [comp.

    1997-04-01T23:59:59.000Z

    This catalog provides information about the many reports and materials made available by the US Department of Energy`s (DOE`s) Global Change Research Program (GCRP) and the Carbon Dioxide Information Analysis Center (CDIAC). The catalog is divided into nine sections plus the author and title indexes: Section A--US Department of Energy Global Change Research Program Research Plans and Summaries; Section B--US Department of Energy Global Change Research Program Technical Reports; Section C--US Department of Energy Atmospheric Radiation Measurement (ARM) Program Reports; Section D--Other US Department of Energy Reports; Section E--CDIAC Reports; Section F--CDIAC Numeric Data and Computer Model Distribution; Section G--Other Databases Distributed by CDIAC; Section H--US Department of Agriculture Reports on Response of Vegetation to Carbon Dioxide; and Section I--Other Publications.

  9. Nuclear Databases: National Resource Nuclear databases consists of carefully organized scientific

    E-Print Network [OSTI]

    Ohta, Shigemi

    Nuclear Databases: National Resource Nuclear databases consists of carefully organized scientific information that has been gathered over 50 years of low-energy nuclear physics research worldwide. These powerful databases have enormous value and they represent a genuine national resource. Six core nuclear

  10. U.S. LIFE CYCLE INVENTORY DATABASE Goals of the U.S. LCI Database Project

    E-Print Network [OSTI]

    U.S. LIFE CYCLE INVENTORY DATABASE ROADMAP rsed e #12;Goals of the U.S. LCI Database Project. Vision Statement The U.S. Life Cycle Inventory Database will be the recognized source of U.S.-based, quality, transparent life cycle inventory data and will become an integral part of the rapidly expanding

  11. Database, Spatial Spatial databases are the foundation for computer-based applications involving spatially

    E-Print Network [OSTI]

    managed using a particular type of software called a database management system (DBMS) that allows, leading to spatio-temporal databases when geometric evolutions are supported. Spatial databases can be implemented in a GIS, in a computer-assisted design (CAD) system coupled with a DBMS, in a universal server

  12. Database Management Systems 3ed, R. Ramakrishnan and J. Gehrke 1 Database Management Systems

    E-Print Network [OSTI]

    Li, Yanjun "Lisa"

    What Is a DBMS? A database is a collection of data. Models real-world enterprise, e.g. university System (DBMS) is a software package designed to store and manage databases. #12;Database Management Systems 3ed, R. Ramakrishnan and J. Gehrke 3 Why we need DBMS Huge amount of data is available. Users need

  13. Database Transposition for Constrained (Closed) Pattern Mining

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Database Transposition for Constrained (Closed) Pattern Mining Baptiste Jeudy1 and Fran¸cois Rioult-Normandie, France. francois.rioult@info.unicaen.fr Abstract. Recently, different works proposed a new way to mine). In this case, mining the "transposed" database runs through a smaller search space, and the Ga- lois connection

  14. Novanet Libcasts BASIC Searching an EBSCO database

    E-Print Network [OSTI]

    Brownstone, Rob

    interface. Dal Libraries Database Search Screen with PsycINFO as search term. Click search. Open Database First let's consider our search terms. In advanced search you can combine search words in a variety some terms. TV, violence and children are three terms we can use to begin our search. Place an asterisk

  15. AIAA 033726 Preliminary DNS Database of

    E-Print Network [OSTI]

    Martín, Pino

    technology. In a high-speed boundary layer, the ki- netic energy is substantial and the dissipation dueAIAA 03­3726 Preliminary DNS Database of Hypersonic Turbulent Boundary Layers M. Pino Martin­4344 #12;Preliminary DNS Database of Hypersonic Turbulent Boundary Layers M. Pino Martin Department

  16. Publication Kind Codes in STN Patent Databases

    E-Print Network [OSTI]

    Hoffmann, Armin

    Publication Kind Codes in STN Patent Databases Dokumentenart-Codes in STN-Patentdatenbanken Imprint Abstracts (CAPLUS), Chemical Abstracts (CAPLUS), Derwent World Patents Index (DWPI), and Derwent World Patents Index (DWPI)und INPADOCDB INPADOCDB international patent databases, together with a short

  17. Evolution towards, in, and beyond Object Databases

    E-Print Network [OSTI]

    Scholl, Marc H.

    Evolution towards, in, and beyond Object Databases Marc H. Scholl and Markus Tresch Faculty ``evolution'' in the database arena. This paper tries to categorize some of these into a unique framework of ``external services'' to enrich DBMS functionalities. The following are presented in more detail: first, we

  18. DRAFT Chapter 1 Introduction to spatial databases

    E-Print Network [OSTI]

    Shekhar, Shashi

    . Today, data is housed in and managed via a database management system (DBMS). Databases and the software which manages them (DBMS) are the silent success story of the information age. They have slowly role of a DBMS has been that of a simple but e#11;ective warehouse of business and accounting data

  19. NUCLEAR THERMODYNAMIC DATABASE MOX-TDB

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    NUCLEAR THERMODYNAMIC DATABASE « MOX-TDB » Ba-Fe-La-O-Pu-Ru-Sr-U-Zr + Ar-H Version 2006-01 6 rue du hal-00160137,version1-5Jul2007 #12;MOX-TDB Nuclear Thermodynamic Database Version 2006-01 developed examined and rechecked before final conclusions are drawn. hal-00160137,version1-5Jul2007 #12;MOX

  20. Documentation for database.txt Description

    E-Print Network [OSTI]

    Gilchrist, Michael A.

    . The database should also be importable into standard statistical programs such as SAS, R, or SPlus. Reference querying. Instead we recommend that researchers write their own Perl program for database querying Gilchrist, M.A., L.A. Salter,and A.Wagner. 2003. A statistical framework for combining and interpreting

  1. DATA QUALITY IN GENOME DATABASES (Research Paper)

    E-Print Network [OSTI]

    Weske, Mathias

    DATA QUALITY IN GENOME DATABASES (Research Paper) Heiko Müller Humboldt University Berlin, Germany@dbis.informatik.hu-berlin.de Abstract: Genome databases store data about molecular biological entities such as genes, proteins, diseases is their importance in the process of drug discovery. Genome data is analyzed and interpreted to gain so-called leads

  2. Environmental release summary (ERS) database CY 1997

    SciTech Connect (OSTI)

    Gleckler, B.P.

    1998-07-01T23:59:59.000Z

    This report discusses the Environmental Release Summary (ERS) database. The current needs of the Effluent and Environmental database is continually modified to fulfill monitoring (EEM) program (managed by Waste Management Federal Services of Hanford, Incorporated, Air and Water Services Organization). Changes are made to accurately calculate current releases, to affect how past releases are calculated. This document serves as a snap-shot of the database and software for the CY-1997 data and releases. This document contains all of the relevant data for calculating radioactive-airborne and liquid effluent. The ERS database is the official repository for the CY-1997 ERS release reports and the settings used to generate those reports. As part of the Tri-Party Agreement, FDH is committed to provide a hard copy of the ERS database for Washington State Department of Ecology, upon request. This document also serves as that hard copy for the last complete calendar year.

  3. Evolution of the Configuration Database Design

    SciTech Connect (OSTI)

    Salnikov, A

    2006-04-19T23:59:59.000Z

    The BABAR experiment at SLAC successfully collects physics data since 1999. One of the major parts of its on-line system is the configuration database which provides other parts of the system with the configuration data necessary for data taking. Originally the configuration database was implemented in the Objectivity/DB ODBMS. Recently BABAR performed a successful migration of its event store from Objectivity/DB to ROOT and this prompted a complete phase-out of the Objectivity/DB in all other BABAR databases. It required the complete redesign of the configuration database to hide any implementation details and to support multiple storage technologies. In this paper we describe the process of the migration of the configuration database, its new design, implementation strategy and details.

  4. Remote Access to Large Spatial Databases Egemen Tanin

    E-Print Network [OSTI]

    Samet, Hanan

    --Spatial databases and GIS This work was supported in part by the National Sci- ence Foundation under Grants EIA-99Remote Access to Large Spatial Databases Egemen Tanin Frantisek Brabec Hanan Samet Computer--Client/server, Distributed applications, Distributed databases; H.2.8 [Database Management]: Database Applications

  5. Ris-R-1301(EN) Database on Wind Characteristics

    E-Print Network [OSTI]

    Risø-R-1301(EN) Database on Wind Characteristics Contents of Database Bank Gunner C. Larsen Risø XVII, Database on Wind Characteristics - Contents of the database Abstract The main objective of IEA R&D Wind Annex XVII - Database on Wind Characteristics - is to provide wind energy planners and designers

  6. Collod-Broud & Boileau The Marfan Mutation Database

    E-Print Network [OSTI]

    Paris-Sud XI, Université de

    Collod-Béroud & Boileau The Marfan Mutation Database Gwenaëlle Collod-Béroud1 and Catherine Boileau created, in 1995, a mutation database named "UMD-FBN1". The database follows the guidelines on mutation databases of the Hugo Mutation Database Initiative and gives access to a software package that provides

  7. National Spill Test Technology Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Sheesley, David [Western Research Institute

    Western Research Institute established, and ACRC continues to maintain, the National Spill Technology database to provide support to the Liquified Gaseous Fuels Spill Test Facility (now called the National HAZMAT Spill Center) as directed by Congress in Section 118(n) of the Superfund Amendments and Reauthorization Act of 1986 (SARA). The Albany County Research Corporation (ACRC) was established to make publicly funded data developed from research projects available to benefit public safety. The founders since 1987 have been investigating the behavior of toxic chemicals that are deliberately or accidentally spilled, educating emergency response organizations, and maintaining funding to conduct the research at the DOEÆs HAZMAT Spill Center (HSC) located on the Nevada Test Site. ACRC also supports DOE in collaborative research and development efforts mandated by Congress in the Clean Air Act Amendments. The data files are results of spill tests conducted at various times by the Silicones Environmental Health and Safety Council (SEHSC) and DOE, ANSUL, Dow Chemical, the Center for Chemical Process Safety (CCPS) and DOE, Lawrence Livermore National Laboratory (LLNL), OSHA, and DOT; DuPont, and the Western Research Institute (WRI), Desert Research Institute (DRI), and EPA. Each test data page contains one executable file for each test in the test series as well as a file named DOC.EXE that contains information documenting the test series. These executable files are actually self-extracting zip files that, when executed, create one or more comma separated value (CSV) text files containing the actual test data or other test information.

  8. The volatile compound BinBase mass spectral database

    E-Print Network [OSTI]

    Skogerson, Kirsten; Wohlgemuth, Gert; Barupal, Dinesh K; Fiehn, Oliver

    2011-01-01T23:59:59.000Z

    B, Eriksson R: SuperScent-a database of flavors and scents.Sayaed AM: The Pherobase: Database of Insect Pheromones andA public study design database for metabolomics projects.

  9. DATE A DAtabase of TIM Barrel 2.1 Introduction......................................................................................

    E-Print Network [OSTI]

    Babu, M. Madan

    24 DATE ­ A DAtabase of TIM Barrel Enzymes 2.1 Introduction...................................................................................... 2.2 Objective and salient features of the database .................................... 2.2.1 Choice on the database............................................... 2.4 Features

  10. Proposed database model and file structures for arthropod collection management

    E-Print Network [OSTI]

    Mathis, Wayne N.

    Proposed database model and file structures for arthropod collection management Ronald A for taxonomic analysis or behavioral, physiological, and ecological information. The database model described how specific computerization projects can be related to each other. The proposed database model

  11. Database Structure and Visualization Software for Microbial Physiology Data INTRODUCTION

    E-Print Network [OSTI]

    Database Structure and Visualization Software for Microbial Physiology Data INTRODUCTION Nicholas includes database input. Other related information can be entered through the website. The relational structure of the database is responsible for associating related data · A structured query is sent

  12. Visiting Database Programmer/Application Developer School of Chemical Sciences

    E-Print Network [OSTI]

    Zimmerman, Steven C.

    Visiting Database Programmer/Application Developer School of Chemical Sciences University professional as Visiting Database Programmer/Application Developer. This position reports to the Information administrative database environment (specifically Oracle and SQL Server). This is a visiting position, but may

  13. SPATIAL DATABASE MODELING WITH PICTOGRAMMIC LANGUAGES Yvan Bdard, Suzie Larrive

    E-Print Network [OSTI]

    SPATIAL DATABASE MODELING WITH PICTOGRAMMIC LANGUAGES Yvan Bédard, Suzie Larrivée Dept of Geomatics Sciences Centre for Research in Geomatics Canada NSERC Industrial Research Chair in Geospatial Databases language extension, Spatial data modeling, Perceptory pictograms. DEFINITION "Spatial databases" consist

  14. A report on the investigation of the Cefas monitoring database

    E-Print Network [OSTI]

    A report on the investigation of the Cefas monitoring database for incidences of high activities of the Cefas monitoring database for incidences of high activities in mollusc samples The Centre. Cefas' monitoring database ................................................... 3 4. Data Analysis

  15. EERE Project Management Center Database PIA, The Office of Energy...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Project Management Center Database PIA, The Office of Energy Efficiency and Renewable Energy (EERE) EERE Project Management Center Database PIA, The Office of Energy Efficiency and...

  16. Fault-tolerant distributed transactions for partitioned OLTP databases

    E-Print Network [OSTI]

    Jones, Evan P. C. (Evan Philip Charles), 1981-

    2012-01-01T23:59:59.000Z

    This thesis presents Dtxn, a fault-tolerant distributed transaction system designed specifically for building online transaction processing (OLTP) databases. Databases have traditionally been designed as general purpose ...

  17. EM Develops Database for Efficient Solutions to Nuclear Cleanup...

    Broader source: Energy.gov (indexed) [DOE]

    illustrate the benefits of the database. EM also shared the database with the UK's Nuclear Decommissioning Authority and the Canadian Nuclear Laboratories to identify remote...

  18. An Infrared Spectral Database for Detection of Gases Emitted...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Database for Detection of Gases Emitted by Biomass Burning. An Infrared Spectral Database for Detection of Gases Emitted by Biomass Burning. Abstract: We report the construction of...

  19. Database (Report) of U.S. CHP Installations Incorporating Thermal...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Database (Report) of U.S. CHP Installations Incorporating Thermal Energy Storage (TES) andor Turbine Inlet Cooling (TIC), 2004 Database (Report) of U.S. CHP Installations...

  20. Regional Geology: GIS Database for Alternative Host Rocks and...

    Energy Savers [EERE]

    Regional Geology: GIS Database for Alternative Host Rocks and Potential Siting Guidelines Regional Geology: GIS Database for Alternative Host Rocks and Potential Siting Guidelines...

  1. Heat Flow Database Expansion for NGDS Data Development, Collection...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Heat Flow Database Expansion for NGDS Data Development, Collection and Maintenance (SMU) Heat Flow Database Expansion for NGDS Data Development, Collection and Maintenance (SMU)...

  2. automated database mediation: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of database approach + Database Management System (DBMS) + Advantages of Using DBMS + Workers Adam, Salah 239 Mediated Homogenization Quantum Physics (arXiv) Summary:...

  3. AVTA: 2012 Chevrolet Volt PHEV Downloadable Dynamometer Database...

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    Chevrolet Volt PHEV Downloadable Dynamometer Database Reports AVTA: 2012 Chevrolet Volt PHEV Downloadable Dynamometer Database Reports The Vehicle Technologies Office's Advanced...

  4. AVTA: 2012 Toyota Prius PHEV Downloadable Dynamometer Database...

    Energy Savers [EERE]

    Toyota Prius PHEV Downloadable Dynamometer Database Reports AVTA: 2012 Toyota Prius PHEV Downloadable Dynamometer Database Reports The Vehicle Technologies Office's Advanced...

  5. Instructions on Entering Publications into the APS Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    Methods to enter user publications into the APS publication database The APS Publications Database is a searchable compendium of information on results from research at the APS,...

  6. 6.893 Database Systems, Fall 2004

    E-Print Network [OSTI]

    Madden, Samuel R. (Samuel Ross), 1976-

    This course is designed to introduce graduate students to the foundations of database systems, focusing on basics such as the relational algebra and data model, query optimization, query processing, and transactions. This ...

  7. The Proteomics Identifications database: 2010 update

    E-Print Network [OSTI]

    Vizcaino, Juan Antonio

    The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 ...

  8. Towards Privacy Preserving of Forensic DNA Databases

    E-Print Network [OSTI]

    Liu, Sanmin

    2012-02-14T23:59:59.000Z

    Protecting privacy of individuals is critical for forensic genetics. In a kinship/identity testing, related DNA profiles between user's query and the DNA database need to be extracted. However, unrelated profiles cannot be revealed to each other...

  9. GWIDD: Genome-wide protein docking database

    E-Print Network [OSTI]

    Kundrotas, Petras J.; Zhu, Zhengwei; Vasker, Ilya A.

    2009-11-09T23:59:59.000Z

    Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein–protein interactions on the genome scale...

  10. Enabling Geographical Queries to a Botanical Database 

    E-Print Network [OSTI]

    Sato, Go

    2011-11-25T23:59:59.000Z

    Conservation of the lowland savanna ecosystem in Belize Project (Defra 17-022) has created a database of savanna plant collections in the country. Some of the collections have accurate positional coordinates measured by GPS devices while the others...

  11. The LBNL Water Heater Retail Price Database

    E-Print Network [OSTI]

    Lekov, Alex; Glover, Julie; Lutz, Jim

    2000-01-01T23:59:59.000Z

    Olson, and Stuart Chaitkin (LBNL). We also want to thank ourand Mithra Moezzi, also of LBNL. This work was supported byLBNL – 44749 The LBNL Water Heater Retail Price Database

  12. Energy Citations Database (ECD) - Widget Code

    Office of Scientific and Technical Information (OSTI)

    script>

  13. Energy Citations Database (ECD) - Alerts Comments

    Office of Scientific and Technical Information (OSTI)

    Alerts Comments If you have a question about Energy Citations Database Alerts, we recommend you check frequently asked questions. If your question still has not been answered or if...

  14. Energy Citations Database (ECD) - Alerts Help

    Office of Scientific and Technical Information (OSTI)

    After you submit your new e-mail address, an e-mail will be sent to your existing Energy Citations Database Alerts e-mail address requesting that you confirm the change of...

  15. A High Energy Nuclear Database Proposal

    E-Print Network [OSTI]

    David A. Brown; Ramona Vogt

    2005-10-13T23:59:59.000Z

    We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interace. This database will be searchable and cross-indexed with relevant publications, including published detector descriptions. Since this database will be a community resource, it requires the high-energy nuclear physics community's financial and manpower support. This database should eventually contain all published data from the Bevalac, AGS and SPS to RHIC and LHC energies, proton-proton to nucleus-nucleus collisions as well as other relevant systems and all measured observables. Such a database would have tremendous scientific payoff as it makes systematic studies easier and allows simpler benchmarking of theoretical models to a broad range of old and new experiments. Furthermore, there is a growing need for compilations of high-energy nuclear data for applications including stockpile stewardship, technology development for intertial confinement fusion and target and source development for upcoming facilities such as the Next Linear Collider. To enhance the utility of this database, we propose periodically performing evaluations of the data and summarizing the results in topical reviews.

  16. Development of the downhole dynamometer database

    SciTech Connect (OSTI)

    Waggoner, J.R.; Mansure, A.

    1997-02-01T23:59:59.000Z

    The Downhole Dynamometer Database is a compilation of test data collected with a set of five downhole tools built by Albert Engineering under contract to Sandia National Laboratories. The downhole dynamometer tools are memory tools deployed in the sucker rod string with sensors to measure pressure, temperature, load, and acceleration. The acceleration data is processed to yield position, so that a load vs. position dynagraph can be generated using data collected downhole. With five tools in the hole at one time, all measured data and computed dynagraphs from five different positions in the rod string are available. The purpose of the Database is to provide industry with a complete and high quality measurement of downhole sucker rod pumping dynamics. To facilitate use of the database, Sandia has developed a Microsoft Windows-based interface that functions as a visualizer and browser to the more than 40 MBytes of data. The interface also includes a data export feature to allow users to extract data from the database for use in their own programs. This paper includes a description of the downhole dynamometer tools, data collection program, database content, and a few illustrations of the data contained in the downhole dynamometer database.

  17. Ris-R-1472(EN) Database on Wind Characteristics

    E-Print Network [OSTI]

    Risø-R-1472(EN) Database on Wind Characteristics Contents of Database Bank, revision I Gunner C on Wind Characteristics Contents of the database, revision I Abstract The main objective of IEA R&D Wind Annex XVII - Database on Wind Characteristics - has been to provide wind energy planners, designers

  18. Database System Concepts, 5th Ed. Silberschatz, Korth and Sudarshan

    E-Print Network [OSTI]

    Dragan, Feodor F.

    Concepts - 5th Edition, May 23, 2005 Database Management System (DBMS) DBMS contains information about

  19. MARS CLIMATE DATABASE v5.1 USER MANUAL

    E-Print Network [OSTI]

    Spiga, Aymeric

    MARS CLIMATE DATABASE v5.1 USER MANUAL (ESTEC Contract 11369/95/NL/JG "Mars Climate Database for version 5.1 of the Mars Climate Database (MCD) de- veloped by LMD (Paris), AOPP (Oxford), Dept. Physics and the Centre National d'Etudes Spatiales. This is a database of atmospheric statistics compiled from Global Cli

  20. October 6, 1997 ITER L-Mode Con nement Database

    E-Print Network [OSTI]

    October 6, 1997 ITER L-Mode Con nement Database S.M. Kaye and the ITER Con nement Database Working Group Abstract This paper describes the content of an L-mode database that has been compiled with data, and Tore-Supra. The database consists of a total of 2938 entries, 1881 of which are in the L-phase while

  1. Data Preparation Process for the Buildings Performance Database

    E-Print Network [OSTI]

    LBNL-6724E Data Preparation Process for the Buildings Performance Database Claudine Y. Custodio Performance Database (BPD) includes empirically measured data from a variety of data sources with varying data quality within the database and to ensure that all database entries have sufficient data

  2. A Database of Invariant Rings Gregor Kemper, Elmar K

    E-Print Network [OSTI]

    Malle, Gunter

    A Database of Invariant Rings Gregor Kemper, Elmar K Ë? ording, Gunter Malle, B. Heinrich Matzat, Denis Vogel, and Gabor Wiese CONTENTS 1. Introduction 2. Concepts of the Database 3. An Example Session/8­2 (``Invariantentheorie endlicher Gruppen''). We announce the creation of a database of invariant rings. This database

  3. Database System Concepts, 5th Ed. Silberschatz, Korth and Sudarshan

    E-Print Network [OSTI]

    Dragan, Feodor F.

    Database System Concepts, 5th Ed. ©Silberschatz, Korth and Sudarshan See www.db-book.com for conditions on re-use Chapter 7: Relational Database DesignChapter 7: Relational Database Design #12;©Silberschatz, Korth and Sudarshan7.2Database System Concepts - 5th Edition, Oct 5, 2006 Chapter 7: Relational

  4. March 23, 2008 Databases: Practical DB Design 1 Practical Database Design

    E-Print Network [OSTI]

    Adam, Salah

    approach towards development of information system, called, Information System Development Life Cycle. #12 of Information Systems in Organizations + Why Organizations Use DB Systems + Information System Life Cycle System Life Cycle ... Database DBMS Users Users #12;March 23, 2008 Databases: Practical DB Design 8

  5. A Common Database Interface (DBI) R-Databases Special Interest Group

    E-Print Network [OSTI]

    Bain, Mike

    ) and database management systems (DBMS). The interface defines a small set of classes and methods similar;2 Introduction The database interface (DBI) separates the connectivity to the DBMS into a "front-end" and a "back-end". Applications use only the exposed "front-end" API. The facilities that communicate with specific DBMS (Oracle

  6. Insights from the downhole dynamometer database

    SciTech Connect (OSTI)

    Waggoner, J.R.

    1997-03-01T23:59:59.000Z

    The Downhole Dynamometer Database is a compilation of test data collected with a set of five downhole tools built by Albert Engineering under contract to Sandia National Laboratories. The downhole dynamometer tools are memory tools deployed in the sucker rod string with sensors to measure pressure, temperature, load, and acceleration. The acceleration data is processed to yield position, so that a load vs. position dynagraph can be generated using data collected downhole. With five tools in the hole at one time, all measured data and computed dynagraphs from five different positions in the rod string are available. The purpose of the Database is to provide industry with a complete and high quality measurement of downhole sucker rod pumping dynamics. To facilitate use of the database, Sandia has developed a Microsoft Windows-based interface that functions as a visualizer and browser to the more than 40 MBytes of data. The interface also includes a data export feature to allow users to extract data from the database for use in their own programs. Following a brief description of the downhole dynamometer tools, data collection program, and database content, this paper will illustrate a few of the interesting and unique insights gained from the downhole data.

  7. ITER L-Mode Confinement Database

    SciTech Connect (OSTI)

    S.M. Kaye and the ITER Confinement Database Working Group

    1997-10-01T23:59:59.000Z

    This paper describes the content of an L-mode database that has been compiled with data from Alcator C-Mod, ASDEX, DIII, DIII-D, FTU, JET, JFT-2M, JT-60, PBX-M, PDX, T-10, TEXTOR, TFTR, and Tore-Supra. The database consists of a total of 2938 entries, 1881 of which are in the L-phase while 922 are ohmically heated (OH) only. Each entry contains up to 95 descriptive parameters, including global and kinetic information, machine conditioning, and configuration. The paper presents a description of the database and the variables contained therein, and it also presents global and thermal scalings along with predictions for ITER. The L-mode thermal confinement time scaling was determined from a subset of 1312 entries for which the thermal confinement time scaling was provided.

  8. Feature Level Clustering of Large Biometric Database

    E-Print Network [OSTI]

    Mehrotra, Hunny; Radhika, V Bhawani; Majhi, Banshidhar; Gupta, Phalguni

    2010-01-01T23:59:59.000Z

    This paper proposes an efficient technique for partitioning large biometric database during identification. In this technique feature vector which comprises of global and local descriptors extracted from offline signature are used by fuzzy clustering technique to partition the database. As biometric features posses no natural order of sorting, thus it is difficult to index them alphabetically or numerically. Hence, some supervised criteria is required to partition the search space. At the time of identification the fuzziness criterion is introduced to find the nearest clusters for declaring the identity of query sample. The system is tested using bin-miss rate and performs better in comparison to traditional k-means approach.

  9. The JANA Calibrations and Conditions Database API

    SciTech Connect (OSTI)

    David Lawrence

    2010-07-01T23:59:59.000Z

    Calibrations and conditions databases can be accessed from within the JANA Event Processing framework through the API defined in its JCalibration base class. The API is designed to support everything from databases, to web services to flat files for the backend. A Web Service backend using the gSOAP toolkit has been implemented which is particularly interesting since it addresses many modern cybersecurity issues including support for SSL. The API allows constants to be retrieved through a single line of C++ code with most of the context, including the transport mechanism, being implied by the run currently being analyzed and the environment relieving developers from implementing such details.

  10. Lessons Learned From Developing Reactor Pressure Vessel Steel Embrittlement Database

    SciTech Connect (OSTI)

    Wang, Jy-An John [ORNL

    2010-08-01T23:59:59.000Z

    Materials behaviors caused by neutron irradiation under fission and/or fusion environments can be little understood without practical examination. Easily accessible material information system with large material database using effective computers is necessary for design of nuclear materials and analyses or simulations of the phenomena. The developed Embrittlement Data Base (EDB) at ORNL is this comprehensive collection of data. EDB database contains power reactor pressure vessel surveillance data, the material test reactor data, foreign reactor data (through bilateral agreements authorized by NRC), and the fracture toughness data. The lessons learned from building EDB program and the associated database management activity regarding Material Database Design Methodology, Architecture and the Embedded QA Protocol are described in this report. The development of IAEA International Database on Reactor Pressure Vessel Materials (IDRPVM) and the comparison of EDB database and IAEA IDRPVM database are provided in the report. The recommended database QA protocol and database infrastructure are also stated in the report.

  11. Exam revision Database Systems Lecture 18

    E-Print Network [OSTI]

    Alechina, Natasha

    revision Example (coursework 5) · {Film} {Certificate} is a non-trivial functional dependency · {Cinema(A,B,C), candidate keys (A,B) and (A,C), fd B C. #12;Exam revision Example (coursework 5) · Relation ListingExam revision Database Systems Lecture 18 Natasha Alechina #12;Exam revision In This Lecture · Exam

  12. Exam revision Database Systems Lecture 18

    E-Print Network [OSTI]

    Alechina, Natasha

    ,B) and (A,C), fd B C. #12;3 Exam revision Example (coursework 5) · Relation Listing is not in 2NF because1 Exam revision Database Systems Lecture 18 Natasha Alechina Exam revision In This Lecture · Exam format · Main topics · How to revise Exam revision Exam format · Answer three questions out of five

  13. Identifying Relevant Databases for Multidatabase Mining

    E-Print Network [OSTI]

    Liu, Huan

    Identifying Relevant Databases for Multidatabase Mining Huan Liu, Hongjun Lu, Jun Yao Department,luhj,yaojung@iscs.nus.edu.sg Abstract. Various tools and systems for knowledge discovery and data mining are developed and available is where we should start mining. In this paper, breaking away from the conventional data mining assumption

  14. A Methodology Database System Performance Evaluation

    E-Print Network [OSTI]

    Liblit, Ben

    A Methodology for Database System Performance Evaluation Haran Boral Computer Science Department Technion - Israel Institute of Technology David J. DeWitt Computer Sciences Department University82-01870 and the Department of Energy under contract #DE-AC02-81ER10920. #12;ABSTRACT This paper

  15. Interactive Database Access with Statistics and Graphics

    E-Print Network [OSTI]

    Princeton Plasma Physics Laboratory

    DbAccess The Manual Interactive Database Access with Statistics and Graphics Version 2.1.1 D. M and graphical needs of NSTX Physicists. Flexible views and joins are possible, including options for complex SQL General Atomics (GA Plot Objects) adds extensive graphical and interactive capabilities (and documentation

  16. Qunits: queried units in database search

    E-Print Network [OSTI]

    Nandi, Arnab

    2009-01-01T23:59:59.000Z

    Keyword search against structured databases has become a popular topic of investigation, since many users find structured queries too hard to express, and enjoy the freedom of a ``Google-like'' query box into which search terms can be entered. Attempts to address this problem face a fundamental dilemma. Database querying is based on the logic of predicate evaluation, with a precisely defined answer set for a given query. On the other hand, in an information retrieval approach, ranked query results have long been accepted as far superior to results based on boolean query evaluation. As a consequence, when keyword queries are attempted against databases, relatively ad-hoc ranking mechanisms are invented (if ranking is used at all), and there is little leverage from the large body of IR literature regarding how to rank query results. Our proposal is to create a clear separation between ranking and database querying. This divides the problem into two parts, and allows us to address these separately. The first tas...

  17. Learning Bayesian Networks for Relational Databases

    E-Print Network [OSTI]

    Glymour, Clark

    Learning Bayesian Networks for Relational Databases Oliver Schulte School of Computing Science > 3.0. Multi-billion dollar industry, $15+ bill in 2006. IBM, Microsoft, Oracle, SAP. Much interest. Defining model selection scores. Computing sufficient statistics. Work in Progress. Anomaly Detection

  18. CEBAF Large Acceptance Spectrometer (CLAS) Physics Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    A username and password are required to access and search the entire database. However, the Overview page provides links to detailed data pages for each of the experiments available for public access. There are many experiments with data that the public can freely access.

  19. Hypercat : A Database for extragalactic astronomy

    E-Print Network [OSTI]

    Ph. Prugniel; G. Maubon

    1999-10-01T23:59:59.000Z

    The Hypercat Database is developed at Observatoire de Lyon and is distributed on the WEB through different mirrors in Europe. The goal of Hypercat is to gather data necessary for studying the evolution of galaxies (dynamics and stellar contains) and particularly for providing a z=0 reference for these studies.

  20. Temporal Databases Status and Research Directions

    E-Print Network [OSTI]

    Snodgrass, Richard T.

    the other excellent papers in temporal databases. My goal is to characterize the evolution of this field relations when a DBMS can support multiple kinds of time. SIGMOD RECORD, Vol. 19, No. 4, December 1990 83-attribute-time-value quadruples) and implementation of the first historical DBMS, the Time Oriented Data

  1. Capturing Database Transformations for Big Data Analytics

    E-Print Network [OSTI]

    Ordonez, Carlos

    of Houston DBMS #12;Organization · Introduction · Classification · Program · Case Study · Conclusions DBMS Transformations to Build Data Sets for Data Mining, Data & Knowledge Engineering (DKE), 2014, Elsevier. DBMS #12 for this project might remain in the database, using resources. DBMS #12;Motivation: Saving Work · Different users

  2. A Database in Every Sensor Nicolas Tsiftes

    E-Print Network [OSTI]

    Dunkels, Adam

    a database management system (DBMS), provid- ing a rich query interface to the flash storage of the node, we present Antelope, a complete DBMS for resource-constrained sen- sor devices, and a new flash indexing method called Max- Heap. Antelope, which to the best of our knowledge is the first DBMS

  3. Knowledge Discovery in Spatial Databases Martin Ester

    E-Print Network [OSTI]

    Ester, Martin

    and their interactions with each other. Most companies, governmental agencies and scientific organizations use DBMS with ex­ isting DBMS. Thus, the second goal is to propose methods of efficiently supporting spatial data mining algorithms by a DBMS. Our approach centers around a new set of database primitives for mining

  4. GERSVIEW: A New Database for Web Mapping

    E-Print Network [OSTI]

    Gilbes, Fernando

    GERSVIEW: A New Database for Web Mapping William J. Hernández, M.S. Graduate Student Department structure Develop an ArcIMS Web Mapping Interface Present spatial data created by the Geological and Environmental Remote Sensing Laboratory (GERS) Projects via ArcIMS. Create GERSVIEW home web page (launch site

  5. GERSVIEW: A New Database for Web Mapping

    E-Print Network [OSTI]

    Gilbes, Fernando

    GERSVIEW: A New Database for Web Mapping William J. Hernández, M.S. Graduate Student DepartmentIMS Web Mapping Interface Present spatial data created by the Geological and Environmental Remote Sensing Laboratory (GERS) Projects via ArcIMS. Create GERSVIEW home web page (launch site) #12;ArcIMS ArcIMS 9

  6. Database System Concepts Silberschatz, Korth and Sudarshan

    E-Print Network [OSTI]

    Dragan, Feodor F.

    : Application Design and Development User Interfaces and Tools Web Interfaces to Databases Web Fundamentals Servlets and JSP Building Large Web Applications Triggers Authorization in SQL Application Security #12 user interfaces Report generators Data analysis tools (see Chapter 18) Many interfaces are Web

  7. 1. Integrated Database 2. Boundary Analysis

    E-Print Network [OSTI]

    or gathered in the course of work under National Science Foundation grants Data Management Plans #12;Database" Soum Properties of herd Herding Households Survey Animal measures Grazing territory Pastures Migratory/Economic/ Social (existing national data) Subwatershed Data to be collected Survey Survey #12;GIS as an Integrative

  8. General Database Statistics Using Entropy Maximization

    E-Print Network [OSTI]

    Suciu, Dan

    (z) Estimate: q(y) :- R(x, y), S(y, z) Fig. 1. An example of a Statistical Program and a query, q whoseGeneral Database Statistics Using Entropy Maximization Raghav Kaushik1 , Christopher R´e2 , and Dan engines. The key object of our study is a statistical program, which is a set of pairs (v, d), where v

  9. Bioinformatics The Maize Genetics and Genomics Database.

    E-Print Network [OSTI]

    Brendel, Volker

    relationships; and to provide an array of computational tools that address biological questions in an easyBioinformatics The Maize Genetics and Genomics Database. The Community Resource for Access, Development and Cell Biology (C.J.L., V.B.), and Department of Statistics (V.B.), Iowa State University, Ames

  10. Community Connections Database (CCDB)Community Connections Database (CCDB) Instructions for Students (CSL-4S)Instructions for Students (CSL-4S)

    E-Print Network [OSTI]

    Community Connections Database (CCDB)Community Connections Database (CCDB) Instructions for Students (CSL-4S)Instructions for Students (CSL-4S) The Community Connections Database (CCDB) allows Connections Database (CCDB) allows students to search for community service learning opportunities

  11. Query execution in column-oriented database systems

    E-Print Network [OSTI]

    Abadi, Daniel J

    2008-01-01T23:59:59.000Z

    There are two obvious ways to map a two-dimension relational database table onto a one-dimensional storage interface: store the table row-by-row, or store the table column-by-column. Historically, database system implementations ...

  12. CUCS00400 Automatic Classification of Text Databases Through Query Probing

    E-Print Network [OSTI]

    and focused results than when searching a more general text database. Other services (e.g., Copernic 3://www.searchengineguide.com/ 3 http://www.copernic.com/ 1 #12; databases with queries to determine an approximation

  13. Query-based database policy assurance using semantic web technologies

    E-Print Network [OSTI]

    Soltren, José Hiram

    2009-01-01T23:59:59.000Z

    In this thesis, we present a novel approach to database security which looks at queries instead of the database tables themselves. In doing so, we use a number of Semantic Web technologies to define rules, translate queries, ...

  14. Optimizing database-backed applications with query synthesis

    E-Print Network [OSTI]

    Cheung, Alvin K.

    Object-relational mapping libraries are a popular way for applications to interact with databases because they provide transparent access to the database using the same language as the application. Unfortunately, using ...

  15. Fear and desire in systems design : negotiating database usefulness

    E-Print Network [OSTI]

    Agrawal, Tanu

    2008-01-01T23:59:59.000Z

    Databases are ubiquitous. They are used for a host of functions including coordination, decision making, and memory archiving. Despite their importance and ubiquity, databases continue to frustrate us, often departing from ...

  16. Building a database of 3D scenes from user annotations

    E-Print Network [OSTI]

    Russell, Bryan C.

    In this paper, we wish to build a high quality database of images depicting scenes, along with their real-world three-dimensional (3D) coordinates. Such a database is useful for a variety of applications, including training ...

  17. March 23, 2008 Databases: Information Systems 1 Information Systems

    E-Print Network [OSTI]

    Adam, Salah

    March 23, 2008 Databases: Information Systems 1 Information Systems #12;March 23, 2008 Databases: Information Systems 2 Objectives What is an Information System (IS) + Classification of Information Systems + Evolution of Information Systems + Information System Management + Performance Requirements of ISs + #12

  18. A database for the study of marine mammal behavior: Gap analysis, data standardization, and future directions

    E-Print Network [OSTI]

    Shaffer, S A; Costa, Daniel P

    2006-01-01T23:59:59.000Z

    directly for copies of the database and bib- liography. RCommunication _____________ A Database for the Study ofAbstract—A relational database that contained published

  19. THERMODYNAMIC TABLES FOR NUCLEAR WASTE ISOLATION, V.1: AQUEOUS SOLUTIONS DATABASE

    E-Print Network [OSTI]

    Phillips, S.L.; Hale, F.V.; Silvester, L.F.

    2008-01-01T23:59:59.000Z

    Vol. I. Aq~leous Solutions Database D L S.1,. Philiips, F.V.Vol 1. Aqueous Solutions Database Sidney L. Phillips, FrankDatabase ..

  20. Prolactin messenger ribonucleic acid concentrations throughout the ovine estrous cycle: Assessment relative to prolactin serum and pituitary amounts

    SciTech Connect (OSTI)

    Landefeld, T.; Roulia, V.; Bagnell, T.; Ballard, T.; Levitan, I. (Univ. of Michigan, Ann Arbor (USA))

    1991-01-01T23:59:59.000Z

    Prolactin (PRL) mRNA concentrations were assessed by nucleic acid hybridization assays in pituitaries of ewes representing the defined stages of the ovine estrous cycle. Concomitantly, pituitary and serum PRL concentrations were measured in these ewes using radioimmunoassays. It was observed that PRL serum, pituitary and mRNA concentrations tended to increase near the time of the gonadotropin preovulatory surge, particularly between 24 hrs before behavioral estrus to 5 hours after estrus. However, the changes in PRL mRNA, serum and pituitary concentrations were shown not to be statistically significant. These data suggest that PRL production during the sheep estrous cycle is maintained without dramatic changes in synthesis or secretion.

  1. Rocky Mountain Basins Produced Water Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Historical records for produced water data were collected from multiple sources, including Amoco, British Petroleum, Anadarko Petroleum Corporation, United States Geological Survey (USGS), Wyoming Oil and Gas Commission (WOGC), Denver Earth Resources Library (DERL), Bill Barrett Corporation, Stone Energy, and other operators. In addition, 86 new samples were collected during the summers of 2003 and 2004 from the following areas: Waltman-Cave Gulch, Pinedale, Tablerock and Wild Rose. Samples were tested for standard seven component "Stiff analyses", and strontium and oxygen isotopes. 16,035 analyses were winnowed to 8028 unique records for 3276 wells after a data screening process was completed. [Copied from the Readme document in the zipped file available at http://www.netl.doe.gov/technologies/oil-gas/Software/database.html] Save the Zipped file to your PC. When opened, it will contain four versions of the database: ACCESS, EXCEL, DBF, and CSV formats. The information consists of detailed water analyses from basins in the Rocky Mountain region.

  2. A Survey of Single-Database PIR: Techniques and Applications

    E-Print Network [OSTI]

    Ostrovsky, Rafail

    A Survey of Single-Database PIR: Techniques and Applications Rafail Ostrovsky William E. Skeith III Abstract In this paper we survey the notion of Single-Database Private Information Re- trieval (PIR). The first Single-Database PIR was constructed in 1997 by Kushilevitz and Ostrovsky and since then Single

  3. A Survey of SingleDatabase PIR: Techniques and Applications #

    E-Print Network [OSTI]

    A Survey of Single­Database PIR: Techniques and Applications # Rafail Ostrovsky + William E. Skeith (PIR). The first Single­Database PIR was constructed in 1997 by Kushilevitz and Ostrovsky and since then Single­Database PIR has emerged as an important cryp­ tographic primitive. For example, Single

  4. A Survey of SingleDatabase PIR: Techniques and Applications

    E-Print Network [OSTI]

    Ostrovsky, Rafail

    A Survey of Single­Database PIR: Techniques and Applications Rafail Ostrovsky # William E. Skeith (PIR). The first Single­Database PIR was constructed in 1997 by Kushilevitz and Ostrovsky and since then Single­Database PIR has emerged as an important cryp­ tographic primitive. For example, Single

  5. Data Quality of Native XML Databases in the Healthcare Domain

    E-Print Network [OSTI]

    North, Siobhán

    .0 [Database Management]: Security, integrity and protection; K.6.4 [System Management]: Quality assurance; J.3 are not foolproof. This report reviews work on data quality in both database and management research areas support database systems provide in giving a measure of the quality of the data they hold. This inducts

  6. Ris-R-1473(EN) Database on Wind Characteristics

    E-Print Network [OSTI]

    Risø-R-1473(EN) Database on Wind Characteristics Analyses of Wind Turbine Design Loads Gunner C R&D Wind Annex XVII - Database on Wind #12;IEA Annex XVII, Database on Wind Characteristics Analyses of W Characteristics - has been to provide wind energy planners, designers and researchers, as well

  7. LESSONS LEARNED AND BEST PRACTICES DATABASE USER MANUAL

    E-Print Network [OSTI]

    LESSONS LEARNED AND BEST PRACTICES DATABASE USER MANUAL OIA-OCA-0002, Rev. 0 Effective Date: June Lessons Learned and Best Practices Database User Manual RECORD OF REVISION Revision Number Date Approved.............................................................. 26 #12;OIA-OCA-0002, Rev. 0 Page 4 of 26 Lessons Learned and Best Practices Database User Manual 1

  8. Managing and Querying Transaction-time Databases under Schema Evolution

    E-Print Network [OSTI]

    Zaniolo, Carlo

    Managing and Querying Transaction-time Databases under Schema Evolution Hyun J. Moon UCLA hjmoon of a relational database in XML, whereby the evolution of the schema and its underly- ing database are given is that schema evolution is transparent to the user: she writes queries against the current schema while

  9. Database System Concepts, 5th Ed. Silberschatz, Korth and Sudarshan

    E-Print Network [OSTI]

    Dragan, Feodor F.

    Database System Concepts, 5th Ed. ©Silberschatz, Korth and Sudarshan See www and Sudarshan2.2Database System Concepts - 5th Edition, Oct 5, 2006 Chapter 2: Relational ModelChapter 2: Relational Model Structure of Relational Databases Fundamental Relational-Algebra-Operations Additional

  10. Database Managament IS&M Option Mark Levene

    E-Print Network [OSTI]

    Levene, Mark

    Database Managament IS&M Option Mark Levene Email: m.levene@dcs.bbk.ac.uk Web: http://www.dcs.bbk.ac.uk/~mark/ Lecture Plan 1. Introduction to Databases 2. Data Modelling with the Entity-Relationship Model 3 and Referential Integrity 4. Querying a Relational Database (a) Querying a Single Table (b) Aggregating

  11. SPIKE: a database of highly curated human signaling pathways

    E-Print Network [OSTI]

    Avraham, Karen

    SPIKE: a database of highly curated human signaling pathways Arnon Paz1 , Zippora Brownstein1 Knowledge Engine; http:// www.cs.tau.ac.il/spike/) is a database for achieving this goal, containing highly on the nature of each interaction. To make database population and pathway comprehension straightforward

  12. Faculty Database User Instructions Spectral Fusion Designs Page 1

    E-Print Network [OSTI]

    Chu, Xi

    Faculty Database User Instructions Spectral Fusion Designs Page 1 Faculty, Staff, and Student Instructions Introduction The Faculty Database is a tool created by Spectral Fusion Designs (SFD faculty, staff, or graduate students must be added to the Faculty Database by departmental administrators

  13. Database System Concepts, 5th Ed. Silberschatz, Korth and Sudarshan

    E-Print Network [OSTI]

    Dragan, Feodor F.

    Database System Concepts, 5th Ed. ©Silberschatz, Korth and Sudarshan See www.2Database System Concepts, 5th Edition, Oct 5. 2006 Chapter 4: Advanced SQLChapter 4: Advanced SQL SQL Data Constructs** Recursive Queries** Advanced SQL Features** #12;©Silberschatz, Korth and Sudarshan4.3Database

  14. Database System Concepts, 5th Ed. Silberschatz, Korth and Sudarshan

    E-Print Network [OSTI]

    Dragan, Feodor F.

    Database System Concepts, 5th Ed. ©Silberschatz, Korth and Sudarshan See www;©Silberschatz, Korth and Sudarshan6.2Database System Concepts - 5th Edition, Oct 5, 2006 Chapter 6: Entity Design Issues Weak Entity Sets Extended E-R Features Design of the Bank Database Reduction to Relation

  15. Calculating Very Rough Market Share Using the Canadian Business Database

    E-Print Network [OSTI]

    Thompson, Michael

    Calculating Very Rough Market Share Using the Canadian Business Database If you cannot find market market share using the company information provided in the Canadian Business Database (CBD), an online - it should be considered a last resort for this information. STEP 1: ACCESS THE CANADIAN BUSINESS DATABASE 1a

  16. Biodiversity Database Developer/Programmer Academy of Natural Sciences, Philadelphia

    E-Print Network [OSTI]

    Plotkin, Joshua B.

    Biodiversity Database Developer/Programmer Academy of Natural Sciences, Philadelphia (Position of Philadelphia seeks a database programmer who can develop desktop and web-based solutions for managing specimen), paleontology (fossils) and general invertebrates. Current databases hold more than 1 million records in various

  17. Database Connects Public to University of Nebraska Research

    E-Print Network [OSTI]

    Nebraska-Lincoln, University of

    Database Connects Public to University of Nebraska Research By Steve Ress There's a wealth of water easier. An easily accessible and searchable database sponsored by the University of Nebraska Rachael Herpel, outreach and education specialist at the UNL Water Center. The database can be found

  18. Database Research: Achievements and Opportunities Into the 21st Century

    E-Print Network [OSTI]

    Ullman, Jeffrey D.

    Database Research: Achievements and Opportunities Into the 21st Century Avi Silberschatz, Mike Stonebraker, Jeff Ullman, editors Report of an NSF Workshop on the Future of Database Systems Research, May 26--27, 1995 1 1 Introduction In February of 1990, a group of database researchers met to examine the prospects

  19. The Geometry of Uncertainty in Moving Objects Databases

    E-Print Network [OSTI]

    Wolfson, Ouri E.

    The Geometry of Uncertainty in Moving Objects Databases Goce Trajcevski1 , Ouri Wolfson1@arl.mil Abstract. This work addresses the problem of querying moving ob- jects databases. which capture- ing, constructing, and querying a trajectories database. We propose to model a trajectory as a 3D

  20. December 6, 1995 A MODEL FOR MATERIALS DATABASES

    E-Print Network [OSTI]

    Wiederhold, Gio

    believe are the most closely related to future development of materials database management. Broadly advanced materials are unsuitable. 5. Interfaces provided by existing database management systemsDecember 6, 1995 A MODEL FOR MATERIALS DATABASES Gio Wiederhold Laie Caindec John McCarthy Ken

  1. REALTIME DATABASE SYSTEMS: ARCHITECTURE AND TECHNIQUES

    E-Print Network [OSTI]

    Ramamritham, Krithi

    monitoring 175 13.3 ECA rule extended with temporal attributes 178 13.4 Response time in a real­time system using ECA paradigm. 182 14.1 A Real Time Database System 188 14.2 Maximum Age (MA) and Unapplied Update (UU) 192 14.3 Inter­arrival distribution of the stock price updates of G.E. on 94/1/3. 194 14

  2. Accelerating semantic graph databases on commodity clusters

    SciTech Connect (OSTI)

    Morari, Alessandro; Castellana, Vito G.; Haglin, David J.; Feo, John T.; Weaver, Jesse R.; Tumeo, Antonino; Villa, Oreste

    2013-10-06T23:59:59.000Z

    We are developing a full software system for accelerating semantic graph databases on commodity cluster that scales to hundreds of nodes while maintaining constant query throughput. Our framework comprises a SPARQL to C++ compiler, a library of parallel graph methods and a custom multithreaded runtime layer, which provides a Partitioned Global Address Space (PGAS) programming model with fork/join parallelism and automatic load balancing over a commodity clusters. We present preliminary results for the compiler and for the runtime.

  3. Preparing a public database of radio sources

    E-Print Network [OSTI]

    H. Andernach; S. A. Trushkin; A. G. Gubanov; O. V. Verkhodanov; V. B. Titov; A. Micol

    1996-07-22T23:59:59.000Z

    We have collected the largest existing set of radio source lists in machine-readable form: 320 tables with 1.75 million records. Only a minor fraction of these is accessible via public databases. We describe our plans to make this huge amount of heterogeneous data accessible in a homogeneous way via the World Wide Web, with reliable cross-identifications, and searchable by various observables.

  4. Gasification world database 2007. Current industry status

    SciTech Connect (OSTI)

    NONE

    2007-10-15T23:59:59.000Z

    Information on trends and drivers affecting the growth of the gasification industry is provided based on information in the USDOE NETL world gasification database (available on the www.netl.doe.gov website). Sectors cover syngas production in 2007, growth planned through 2010, recent industry changes, and beyond 2010 - strong growth anticipated in the United States. A list of gasification-based power plant projects, coal-to-liquid projects and coal-to-SNG projects under consideration in the USA is given.

  5. Mining Bug Databases for Unidentified Software Vulnerabilities

    SciTech Connect (OSTI)

    Dumidu Wijayasekara; Milos Manic; Jason Wright; Miles McQueen

    2012-06-01T23:59:59.000Z

    Identifying software vulnerabilities is becoming more important as critical and sensitive systems increasingly rely on complex software systems. It has been suggested in previous work that some bugs are only identified as vulnerabilities long after the bug has been made public. These vulnerabilities are known as hidden impact vulnerabilities. This paper discusses the feasibility and necessity to mine common publicly available bug databases for vulnerabilities that are yet to be identified. We present bug database analysis of two well known and frequently used software packages, namely Linux kernel and MySQL. It is shown that for both Linux and MySQL, a significant portion of vulnerabilities that were discovered for the time period from January 2006 to April 2011 were hidden impact vulnerabilities. It is also shown that the percentage of hidden impact vulnerabilities has increased in the last two years, for both software packages. We then propose an improved hidden impact vulnerability identification methodology based on text mining bug databases, and conclude by discussing a few potential problems faced by such a classifier.

  6. SQL SERVER DATABASE ADMINISTRATION An eleven-week in-depth program covering database administration using Microsoft SQL Server 2012

    E-Print Network [OSTI]

    Schaefer, Marcus

    SQL SERVER DATABASE ADMINISTRATION PROGRAM An eleven-week in-depth program covering database administration using Microsoft SQL Server® 2012 DePaul University's SQL Server Database Administration Program Server technologies. The program focuses on teaching IT professionals the knowledge for implementing

  7. SQL SERVER DATABASE ADMINISTRATION An eleven-week in-depth program covering database administration using Microsoft SQL Server 2008

    E-Print Network [OSTI]

    Schaefer, Marcus

    SQL SERVER DATABASE ADMINISTRATION PROGRAM An eleven-week in-depth program covering database administration using Microsoft SQL Server® 2008 DePaul University's SQL Server Database Administration Program Server technologies. The program focuses on teaching IT professionals the knowledge for implementing

  8. Ceramic Technology Project database: September 1990 summary report

    SciTech Connect (OSTI)

    Keyes, B.L.P.

    1992-06-01T23:59:59.000Z

    Data generated within the Ceramic Technology Project (CTP) represent a valuable resource for both research and industry. The CTP database was created to provide easy access to this information in electronic and hardcopy forms by using a computerized database and by issuing periodic hardcopy reports on the database contents. This report is the sixth in a series of semiannual database summaries and covers recent additions to the database, including joined brazed specimen test data. It covers 1 SiC, 34 SiN, 10 whisker-reinforced SiN, 2 zirconia-toughened aluminas, 8 zirconias, and 34 joints.

  9. MTBreg: The Database of Conditionally Regulated Proteins in Mycobacterium Tuberculosis

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Kaufman, Markus; Pal, Debnath; Eisenberg, David

    Proteins up- and down- regulated in Mycobacterium tuberculosis grown under conditions mimicking infection are included in this database. It also includes information on proteins that are regulated by selected transcription factors or other regulatory proteins. The literature data provided here is complimentary to the databases provided by Michael Strong that include recent TB computational functional linkages and the Prolinks Database by Peter Bowers. The experimental condition, the experimental dataset and a literature reference will be displayed, including links to the computationally linked proteins in the Prolinks Database and the entry in the Mycobacterium tuberculosis Structural Genomics Database.[Copied from information at http://www.doe-mbi.ucla.edu/Services/MTBreg/

  10. Service Description Unit Rate in $ Invoice Description Database Administration (1 to 600 MB) MB/Month 0.550 DATABASE 1-600 MB/MO

    E-Print Network [OSTI]

    Service Description Unit Rate in $ Invoice Description Database Administration (1 to 600 MB) MB/Month 0.550 DATABASE 1-600 MB/MO Database Administration (601 to 950 MB) MB/Month 0.290 DATABASE 601-950 MB/MO Database Administration (951 to 3,000 MB) MB/Month 0.200 DATABASE 951-3,000 MB/MO Database

  11. Service Description Unit Rate in $ Invoice Description Database Administration (1 to 600 MB) MB/Month 0.500 DATABASE 1-600 MB/MO

    E-Print Network [OSTI]

    Service Description Unit Rate in $ Invoice Description Database Administration (1 to 600 MB) MB/Month 0.500 DATABASE 1-600 MB/MO Database Administration (601 to 950 MB) MB/Month 0.265 DATABASE 601-950 MB/MO Database Administration (951 to 3,000 MB) MB/Month 0.175 DATABASE 951-3,000 MB/MO Database

  12. Query optimization in nested relational databases

    E-Print Network [OSTI]

    Rathakrishnan, Balaji

    1992-01-01T23:59:59.000Z

    120 75 Fig. 5. Example for nest 20 this does not apply to nests involving multiple attributes [5]. 3. An unnest operator is an inverse of the nest operator. That is, p[&'](~[&'= &](ff)) = & 4. A nest operator is not always an inverse... IV THE EXTENDED RECURSIVE ALGEBRA . A. The algebra 1 2 3 4 16 16 16 16 18 20 22 24 24 27 28 29 29 34 39 43 44 44 CHAPTER Page V QUERY OPTIMIZATION IN RELATIONAL DATABASES . . 54 A. Steps in query processing . B. Algebraic...

  13. LM FIMS Database | Department of Energy

    Office of Energy Efficiency and Renewable Energy (EERE) Indexed Site

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative Fuels Data Center Home Page on Google Bookmark EERE: Alternative Fuels DataDepartment of Energy Your Density Isn't YourTransport(FactDepartment ofLetter Report:40PM toLED Lighting5-15 LM 05-15FIMS Database LM

  14. Sandia Energy - Sandia Wind Turbine Loads Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    AFDC Printable Version Share this resource Send a link to EERE: Alternative Fuels Data Center Home Page to someone by E-mail Share EERE: Alternative Fuels Data Center Home Page on Facebook Tweet about EERE: Alternative Fuels Data Center Home Page on Twitter Bookmark EERE: Alternative1 First Use of Energy for All Purposes (Fuel and Nonfuel), 2002; Level: National5Sales for4,645U.S. DOE Office of ScienceandMesa del Sol Home Distribution GridDocuments HomeDatabase onSandia Wind Energy in the

  15. Current status of the CATS database

    E-Print Network [OSTI]

    O. V. Verkhodanov; S. A. Trushkin; H. Andernach; V. N. Chernenkov

    2007-05-21T23:59:59.000Z

    We describe the current status of CATS, a publicly accessible database (web-server http://cats.sao.ru) allowing one to search in hundreds of catalogs of astronomical objects discovered all along the electromagnetic spectrum. Our emphasis is mainly laid on catalogs of radio continuum sources observed from 30 to 15000 MHz, secondly on catalogs of objects such as radio and active stars, planetary nebulae, HII regions, supernova remnants (SNR), pulsars, nearby galaxies, AGN and quasars. CATS also includes the catalogs from the largest extragalactic surveys, like NVSS, FIRST, WENSS, VLSS, TXS, GB6, SUMSS, IRAS, 2MASS, SDSS, ROSAT, PGC, MCG, etc. In 2004 CATS comprised a total of $\\sim10^9$ records from over 400 catalogs in the radio, IR, optical and X-ray windows, including most of RATAN--600 catalogs. CATS is being expanded and updated, both with newly published catalogs as well as older ones which we have created in electronic form for the first time. We describe the principles of organization of the database of astrophysical catalogs and the main functions of CATS.

  16. Parallel Database Systems: The Future of High Performance Database Processing1

    E-Print Network [OSTI]

    Scheuermann, Peter

    systems are beginning to displace traditional mainframe computers for the largest database and transaction to double while processor speeds were predicted to increase by much larger factors. Consequently, critics by the Defense Advanced Research Projects Agency under contract N00039-86-C-0578, by the National Science

  17. Argonne Geothermal Geochemical Database v2.0

    SciTech Connect (OSTI)

    Harto, Christopher

    2013-05-22T23:59:59.000Z

    A database of geochemical data from potential geothermal sources aggregated from multiple sources as of March 2010. The database contains fields for the location, depth, temperature, pH, total dissolved solids concentration, chemical composition, and date of sampling. A separate tab contains data on non-condensible gas compositions. The database contains records for over 50,000 wells, although many entries are incomplete. Current versions of source documentation are listed in the dataset.

  18. Argonne Geothermal Geochemical Database v2.0

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Harto, Christopher

    A database of geochemical data from potential geothermal sources aggregated from multiple sources as of March 2010. The database contains fields for the location, depth, temperature, pH, total dissolved solids concentration, chemical composition, and date of sampling. A separate tab contains data on non-condensible gas compositions. The database contains records for over 50,000 wells, although many entries are incomplete. Current versions of source documentation are listed in the dataset.

  19. arti refrigerant database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    textbooks: Database Systems Alechina, Natasha 86 Energy Savings from Floating Head Pressure in Ammonia Refrigeration Systems Texas A&M University - TxSpace Summary:...

  20. Fast and accurate database searches with MS-GF+Percolator. |...

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    spectrometrybased proteomics, researches commonly employ so called database search engines. Additionally, postprocessors like Percolator have been used on the results from such...

  1. Standard Energy Efficiency Database Platform - 2013 BTO Peer...

    Broader source: Energy.gov (indexed) [DOE]

    Buildings Performance Database - 2013 BTO Peer Review Commercial Buildings Integration Program Overview - 2013 BTO Peer Review Future Funding: Effective Models for...

  2. Wind-Wildlife Impacts Literature Database (WILD)(Fact Sheet)...

    Office of Scientific and Technical Information (OSTI)

    Impacts Literature Database (WILD), developed and maintained by the National Wind Technology Center (NWTC) at the National Renewable Energy Laboratory (NREL), is...

  3. Tank Characterization Database (TCD) Data Dictionary: Version 4.0

    SciTech Connect (OSTI)

    NONE

    1996-04-01T23:59:59.000Z

    This document is the data dictionary for the tank characterization database (TCD) system and contains information on the data model and SYBASE{reg_sign} database structure. The first two parts of this document are subject areas based on the two different areas of the (TCD) database: sample analysis and waste inventory. Within each subject area is an alphabetical list of all the database tables contained in the subject area. Within each table defintiion is a brief description of the table and alist of field names and attributes. The third part, Field Descriptions, lists all field names in the data base alphabetically.

  4. Motivate Homeowner Action With Updated DOE Incentives Database...

    Broader source: Energy.gov (indexed) [DOE]

    database includes a search tool that filters incentives and policies by type, state, technology, implementing sector, and eligible sector. DSIRE's latest improvements include:...

  5. NOAA Atlas NESDIS 66 WORLD OCEAN DATABASE 2009

    E-Print Network [OSTI]

    NOAA Atlas NESDIS 66 WORLD OCEAN DATABASE 2009 Timothy P. Boyer John I. Antonov Olga K. Baranova ......................................................................................... 28 1.1.8. Application software interfaces

  6. Practical security for multi-user web application databases

    E-Print Network [OSTI]

    Redfield, Catherine M. S

    2012-01-01T23:59:59.000Z

    Online web applications are continuously vulnerable to attacks on their users' data. Outside adversaries can gain unauthorized access by exploiting unknown vulnerabilities; curious or malicious database administrators can ...

  7. anatomical database generation: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    of emotional speech databases. Ellen Douglas-Cowie; Nick Campbell; Roddy Cowie; Peter Roach 2003-01-01 16 In Proceedings of the International Conference on Logic Programming,...

  8. FOA aimed at growing expansive database of Renewable Energy and...

    Open Energy Info (EERE)

    FOA aimed at growing expansive database of Renewable Energy and Energy Efficiency Incentives and Policies Home > Groups > Utility Rate Graham7781's picture Submitted by...

  9. associations database published: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    database, integration of federated systems, and the use of "external services" to enrich DBMS functionalities. The following are presented in more detail: first, we describe the...

  10. autism genetic database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  11. anticancer compounds database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  12. artichoke est database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  13. africa research database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  14. art internet database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  15. arabidopsis hormone database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  16. association database published: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    database, integration of federated systems, and the use of "external services" to enrich DBMS functionalities. The following are presented in more detail: first, we describe the...

  17. assessment databases measurements: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  18. atlas conditions database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  19. aerospace database published: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  20. anchoring proteins database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  1. area database rogad: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  2. antimicrobial peptide database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  3. adans database specification: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  4. adverse reactions database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  5. areva global database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    sensitive data. The security of the data depends on physical security, OS security and DBMS security. Database security can be compromised by obtaining sensitive data, changing...

  6. Extracting Database Information from E-mail Messages

    E-Print Network [OSTI]

    Cooper, R.L.

    Cooper,R.L. Ali,S. 20th British National Conference on Databases, July 2003 pp 271-279 LNCS, Springer

  7. Instructions on Entering Publications into the APS Database

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and the APS of publications resulting from work conducted here. The APS Publications Database is the official record of publications derived from research at, or produced by...

  8. Distributed Online Conditions Database of the BaBar Experiment

    SciTech Connect (OSTI)

    Khan, A.; /Brunel U.; Gaponenko, I.A.; Brown, D.N.; /LBL, Berkeley

    2011-11-21T23:59:59.000Z

    This paper presents CDB - The distributed Conditions Database of the BaBar Experiment. CDB is the second major iteration of the database deployed in BaBar for production use as of October 2002. It replaced the original version of the database used through the first three years of the data taking. The new design and its implementation aims to improve the performance and scalability of the original database and addresses the emerging challenges of the distributed data production and analysis system of the Experiment.

  9. Database for Regional Geology, Phase 1- A Tool for informing...

    Office of Environmental Management (EM)

    Geology: GIS Database for Alternative Host Rocks and Potential Siting Guidelines Evaluation Of Used Fuel Disposition In Clay-Bearing Rock Oil Shale Research in the United States...

  10. Webinar: What Can We Learn from Hydrogen Safety Event Databases?

    Broader source: Energy.gov [DOE]

    Video recording of the Fuel Cell Technologies Office webinar, What Can We Learn from Hydrogen Safety Event Databases, originally presented on September 10, 2013.

  11. aspergillus genome database: Topics by E-print Network

    Broader source: All U.S. Department of Energy (DOE) Office Webpages (Extended Search)

    and avoid outdated data. Heiko Mller 11 Integrative database analysis in structural genomics CiteSeer Summary: Abstract (2 sentences) An important aspect of structural genomics...

  12. The Tariff Analysis Project: A Database and Analysis Platform...

    Open Energy Info (EERE)

    search Tool Summary LAUNCH TOOL Name: The Tariff Analysis Project: A Database and Analysis Platform for Electricity Tariffs Focus Area: Renewable Energy Topics: Policy...

  13. About the Data in Buildings Performance Database | Department...

    Broader source: Energy.gov (indexed) [DOE]

    Database The BPD is currently the largest publically available source of building energy performance data and contains information about the buildings location, use, and...

  14. Los Alamos National Laboratory 4D Database

    SciTech Connect (OSTI)

    Atencio, Julian J.

    2014-05-02T23:59:59.000Z

    4D is an integrated development platform - a single product comprised of the components you need to create and distribute professional applications. You get a graphical design environment, SQL database, a programming language, integrated PHP execution, HTTP server, application server, executable generator, and much more. 4D offers multi-platform development and deployment, meaning whatever you create on a Mac can be used on Windows, and vice-versa. Beyond productive development, 4D is renowned for its great flexibility in maintenance and modification of existing applications, and its extreme ease of implementation in its numerous deployment options. Your professional application can be put into production more quickly, at a lower cost, and will always be instantly scalable. 4D makes it easy, whether you're looking to create a classic desktop application, a client-server system, a distributed solution for Web or mobile clients - or all of the above!

  15. Renewal Strings for Cleaning Astronomical Databases

    E-Print Network [OSTI]

    Storkey, Amos J; Williams, Christopher K I; Mann, Robert G

    2014-01-01T23:59:59.000Z

    Large astronomical databases obtained from sky surveys such as the SuperCOSMOS Sky Surveys (SSS) invariably suffer from a small number of spurious records coming from artefactual effects of the telescope, satellites and junk objects in orbit around earth and physical defects on the photographic plate or CCD. Though relatively small in number these spurious records present a significant problem in many situations where they can become a large proportion of the records potentially of interest to a given astronomer. In this paper we focus on the four most common causes of unwanted records in the SSS: satellite or aeroplane tracks, scratches fibres and other linear phenomena introduced to the plate, circular halos around bright stars due to internal reflections within the telescope and diffraction spikes near to bright stars. Accurate and robust techniques are needed for locating and flagging such spurious objects. We have developed renewal strings, a probabilistic technique combining the Hough transform, renewal...

  16. Multi databases in Health Care Networks

    E-Print Network [OSTI]

    Salih, Nadir K; Sun, Mingrui

    2011-01-01T23:59:59.000Z

    E-Health is a relatively recent term for healthcare practice supported by electronic processes and communication, dating back to at least 1999. E-Health is greatly impacting on information distribution and availability within the health services, hospitals and to the public. E-health was introduced as the death of telemedicine, because - in the context of a broad availability of medical information systems that can interconnect and communicate - telemedicine will no longer exist as a specific field. The same could also be said for any other traditional field in medical informatics, including information systems and electronic patient records. E-health presents itself as a common name for all such technological fields. In this paper we focuses in multi database by determined some sites and distributed it in Homogenous way. This will be followed by an illustrative example as related works. Finally, the paper concludes with general remarks and a statement of further work.

  17. Final Report: Efficient Databases for MPC Microdata

    SciTech Connect (OSTI)

    Michael A. Bender; Martin Farach-Colton; Bradley C. Kuszmaul

    2011-08-31T23:59:59.000Z

    The purpose of this grant was to develop the theory and practice of high-performance databases for massive streamed datasets. Over the last three years, we have developed fast indexing technology, that is, technology for rapidly ingesting data and storing that data so that it can be efficiently queried and analyzed. During this project we developed the technology so that high-bandwidth data streams can be indexed and queried efficiently. Our technology has been proven to work data sets composed of tens of billions of rows when the data streams arrives at over 40,000 rows per second. We achieved these numbers even on a single disk driven by two cores. Our work comprised (1) new write-optimized data structures with better asymptotic complexity than traditional structures, (2) implementation, and (3) benchmarking. We furthermore developed a prototype of TokuFS, a middleware layer that can handle microdata I/O packaged up in an MPI-IO abstraction.

  18. Prokaryotic Genomes from Microbes Online Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    Alm, Eric J.; Huang, Katherine H.; Price, Morgan N.; Koche, Richard P.; Keller, Keith; Dubchak, Inna L.; Arkin, Adam P.

    To describe the potential functions of genes, MicrobesOnline includes protein family analyses (from InterPro and COG), metabolic maps (from KEGG), links to research papers (from UniProt and PubMed), and operon predictions for every genome. To examine each gene's evolutionary history, MicrobesOnline includes precomputed phylogenetic trees for all the gene families. It displays gene trees with genomic context or it compares the gene tree to the species tree. The tools provided with MicrobesOnline allow users to: compute customized motifs, sequence alignments, and phylogenetic trees change expression patterns in metabolic maps annotate genes in various ways The database contains more than 430 genomes. A browse tree tool and a genome browser are available, along with specialized search capabilities. (Specialized Interface)

  19. Biomass Feedstock Composition and Property Database

    DOE Data Explorer [Office of Scientific and Technical Information (OSTI)]

    The Office of Energy Efficiency and Renewable Energy's Biomass Program works with industry, academia and national laboratory partners on a balanced portfolio of research in biomass feedstocks and conversion technologies. Through research, development, and demonstration efforts geared at the development of integrated biorefineries, the Biomass Program is helping transform the nation's renewable and abundant biomass resources into cost competitive, high performance biofuels, bioproducts, and biopower.(From the Biomass Program's home page at http://www1.eere.energy.gov/biomass/) The Biomass Feedstock Composition and Property Database allows the user to choose from more than 150 types of biomass samples. The specialized interface then guides the user through choices within the sample (such as "Ash" as a choice in the "Hardwood" sample and displays tables based on choice of composition properties, structure properties, elemental properties, extractive properties, etc.

  20. Published online 14 May 2008 Nucleic Acids Research, 2008, Vol. 36, Web Server issue W97W103 doi:10.1093/nar/gkn280

    E-Print Network [OSTI]

    Lee, Doheon

    algorithms by statistical analysis with the pub- lished experimental data and derived a new efficient method Genomics Research Center, KRIBB, Daejeon 305-806, 2 Department of Bio and Brain Engineering, KAIST, Daejeon and FASTA algo- rithms and checking the folding secondary structure energy of siRNAs. To do this, we

  1. Published online 11 August 2009 Nucleic Acids Research, 2009, Vol. 37, No. 18 61616173 doi:10.1093/nar/gkp597

    E-Print Network [OSTI]

    Glover, Mark

    . N. M. Glover1, * 1 Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7 whom correspondence should be addressed. Tel: +1 780 492 2136; Fax: +1 780 492 0886; Email: mark.glover

  2. W238W244 Nucleic Acids Research, 2007, Vol. 35, Web Server issue doi:10.1093/nar/gkm308

    E-Print Network [OSTI]

    Stormo, Gary

    to biological processes or to disease states, the determination of the transcriptional regulation of these co a comprehensive, user-friendly web application suite termed the Promoter Analysis Pipeline (PAP). PAP is available of the genetic program. Aberrant regulation at different stages of these processes may result in differential

  3. A New Heat Shock Protein That Binds Nucleic Acids* (Received for publication, August 20, 1998, and in revised form, September 28, 1998)

    E-Print Network [OSTI]

    Bardwell, James

    production of a number of proteins termed heat shock proteins (Hsps).1 Although heat shock pro- teins were Hsp15-P2 (5 - TCTTGCAGGATCCAGTTATTCACT-3 ), and Taq polymerase (Strat- agene). The PCR product g, 4 °C). All further steps were performed at 4 °C. The cell pellet was resuspended in cold buffer

  4. Published online 21 April 2009 Nucleic Acids Research, 2009, Vol. 37, No. 10 31253133 doi:10.1093/nar/gkp250

    E-Print Network [OSTI]

    Vologodskii, Alexander

    reactions of break- ing and rejoining DNA strands can be performed without consumption of external energy without energy consumption as well. The energy is required, however, to shift a system away from topoisomerases Alexander Vologodskii* Department of Chemistry, New York University, New York, NY 10003, USA

  5. A FLEXIBLE FRAMEWORK FOR WEB INTERFACES TO IMAGE DATABASES: SUPPORTING USER-DEFINED ONTOLOGIES AND LINKS TO EXTERNAL DATABASES

    E-Print Network [OSTI]

    Kammen, Daniel M.

    A FLEXIBLE FRAMEWORK FOR WEB INTERFACES TO IMAGE DATABASES: SUPPORTING USER-DEFINED ONTOLOGIES. Ontology languages tend to emphasize flexibility and expressiveness rather than simplicity. Despite this

  6. CHIANTI-AN ATOMIC DATABASE FOR EMISSION LINES. XII. VERSION 7 OF THE DATABASE

    SciTech Connect (OSTI)

    Landi, E. [Department of Atmospheric, Oceanic and Space Sciences, University of Michigan, Ann Arbor, MI 48109 (United States); Del Zanna, G.; Mason, H. E. [Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA (United Kingdom); Young, P. R. [College of Science, George Mason University, 4400 University Drive, Fairfax, VA, 22030 (United States); Dere, K. P. [School of Physics, Astronomy and Computational Sciences, MS 6A2, George Mason University, 4400 University Drive, Fairfax, VA 22030 (United States)

    2012-01-10T23:59:59.000Z

    The CHIANTI spectral code consists of an atomic database and a suite of computer programs to calculate the optically thin spectrum of astrophysical objects and carry out spectroscopic plasma diagnostics. The database includes atomic energy levels, wavelengths, radiative transition probabilities, collision excitation rate coefficients, and ionization and recombination rate coefficients, as well as data to calculate free-free, free-bound, and two-photon continuum emission. Version 7 has been released, which includes several new ions, significant updates to existing ions, as well as Chianti-Py, the implementation of CHIANTI software in the Python programming language. All data and programs are freely available at http://www.chiantidatabase.org, while the Python interface to CHIANTI can be found at http://chiantipy.sourceforge.net.

  7. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

    E-Print Network [OSTI]

    Novichkov, Pavel S.

    2010-01-01T23:59:59.000Z

    motifs by comparative genomics. Nucleic Acids Res. , 28,M.S. (2009) Comparative genomics of regulation of fatty acidcomparative and functional genomics. Nucleic Acids Res. ,

  8. Single Database Private Information Retrieval with Logarithmic Communication

    E-Print Network [OSTI]

    ]. Historically, the first 1dPIR scheme was proposed in [KO97], with its security based on the hardness database private information retrieval (1dPIR) is a cryptographic protocol between a database server, who (as otherwise the problem becomes trivial). In addition to its numerous applications [A01], 1dPIR

  9. Single Database Private Information Retrieval Implies Oblivious Transfer

    E-Print Network [OSTI]

    Ostrovsky, Rafail

    Tal Malkinz Rafail Ostrovskyx Abstract A Single-Database Private Information Retrieval PIR- munication complexity. We call a PIR protocol non-trivial if its total communication is strictly less than the size of the database. Non-trivial PIR is an important cryp- tographic primitive with many applications

  10. Preserving Access Privacy Over Large Databases Femi Olumofin

    E-Print Network [OSTI]

    Goldberg, Ian

    . The security of many such systems, such as Tor, relies on a model where the adversary does not have a global. Private information retrieval (PIR) schemes are designed to prevent an adversary controlling the database-of-the-art PIR schemes have a high computational overhead that makes them expensive for querying large databases

  11. Single Database Private Information Retrieval with Logarithmic Communication

    E-Print Network [OSTI]

    ]. Historically, the first 1dPIR scheme was proposed in [KO97], with its security based on the hardness Single database private information retrieval (1dPIR) is a cryptographic protocol between a database to the user (as otherwise the problem becomes trivial). In addition to its numerous applications [A01], 1dPIR

  12. SANDBOX: A VIRTUAL REALITY INTERFACE TO SCIENTIFIC DATABASES ANDREW JOHNSON

    E-Print Network [OSTI]

    Johnson, Andrew

    SANDBOX: A VIRTUAL REALITY INTERFACE TO SCIENTIFIC DATABASES by ANDREW JOHNSON DISSERTATION: Adviser Date #12; c COPYRIGHT BY ANDREW JOHNSON 1994 All Rights Reserved #12;Dedication I dedicate; Narendra Goel, John Norman, and Don Strebel for their insight into the FIFE database; and Larry Cathey

  13. Efficient Mining of Partial Periodic Patterns in Time Series Database

    E-Print Network [OSTI]

    Dong, Guozhu

    Efficient Mining of Partial Periodic Patterns in Time Series Database In ICDE 99 Jiawei Han \\Lambda peri­ odic patterns in time­series databases, is an interesting data mining problem. Previous studies several algorithms for efficient mining of par­ tial periodic patterns, by exploring some interesting

  14. Abduction with Negation as Failure for Active Databases and Agents

    E-Print Network [OSTI]

    Toni, Francesca

    Abduction with Negation as Failure for Active Databases and Agents Fariba Sadri and Francesca Toni suggested abductive logic programming as a suitable formalism to represent active databases and intelligent agents. In particular, abducibles and integrity constaints in abductive logic pro- grams can be used

  15. Fuzzy Queries in Multimedia Database Systems Ronald Fagin

    E-Print Network [OSTI]

    Fagin, Ron

    Fuzzy Queries in Multimedia Database Systems Ronald Fagin IBM Almaden Research Center Sati Jose, CA differencesbetween multimedia databases (which may contain complicated objects, such as images), and traditional typos of queries. Wr example, in a multimedia databaseit is reasonable and natural to ask for images

  16. An Adaptive Policy for Improved Timeliness in Secure Database Systems

    E-Print Network [OSTI]

    Son, Sang H.

    An Adaptive Policy for Improved Timeliness in Secure Database Systems Sang H. Son * , Rasikan David. Multilevel security requirements introduce a new dimension to transaction processing in real­time database Timeliness, concurrency control, two­phase locking, non­interference, security, miss percentage 1

  17. Efficient Bulk Deletes in Relational Databases A. Gartner 1

    E-Print Network [OSTI]

    Kemper, Alfons

    , archiving is studied as part of the SAP Terabyte project in cooperation with the University of Passau dramatically in the last couple of years. This trend can be observed even though most database systems have become easier to use and database system administra- tors have gained more and more experience in using

  18. Medical Multimedia and Multimodality Databases Systems Peter L. Stanchev

    E-Print Network [OSTI]

    Stanchev, Peter

    multimedia systems, Medical images, Databases 1. INTRODCTION Recent advances in computer technologyMedical Multimedia and Multimodality Databases Systems Peter L. Stanchev Kettering University, Michigan, 48202 USA fotouhi@cs.wayne.edu ABSTRACT In this paper we make a review of some medical

  19. Preserving con dentiality when sharing medical database the Cellsecu system

    E-Print Network [OSTI]

    Chen, Sheng-Wei

    , with the rapid advances in the computerization of medical data, the question of protecting medical recordsPreserving con dentiality when sharing medical database the Cellsecu system Yu-Cheng Chiang y that contains sensitive information in medical database by automatically removing, generalizing, and expanding

  20. DBDOC: Querying and Browsing Databases and Interrelated Documents

    E-Print Network [OSTI]

    Ordonez, Carlos

    ]: Database Administra- tion--Data warehouse and repository General Terms Management, Documentation, Design 1 to describe this structured data. Managing semi- structured sources, such as documents, text files, web pagesDBDOC: Querying and Browsing Databases and Interrelated Documents Carlos Garcia-Alvarado University