National Library of Energy BETA

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. Nucleic acid detection assays

    DOE Patents [OSTI]

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

    2005-04-05

    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)

    2008-08-05

    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)

    2010-11-09

    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. 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)

    2007-12-11

    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.

    2005-03-29

    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. Composition for nucleic acid sequencing

    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)

    2008-08-26

    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.

  8. 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)

    2002-01-01

    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.

  9. Nucleic acid detection methods

    DOE Patents [OSTI]

    Smith, C.L.; Yaar, R.; Szafranski, P.; Cantor, C.R.

    1998-05-19

    The invention relates to methods for rapidly determining the sequence and/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3{prime}-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated. 18 figs.

  10. Nucleic Acid Detection Methods

    DOE Patents [OSTI]

    Smith, Cassandra L. (Boston, MA); Yaar, Ron (Brookline, MA); Szafranski, Przemyslaw (Boston, MA); Cantor, Charles R. (Boston, MA)

    1998-05-19

    The invention relates to methods for rapidly determining the sequence and/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3'-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated.

  11. Replica amplification of nucleic acid arrays

    DOE Patents [OSTI]

    Church, George M. (Brookline, MA)

    2002-01-01

    A method of producing a plurality of a nucleic acid array, comprising, in order, the steps of amplifying in situ nucleic acid molecules of a first randomly-patterned, immobilized nucleic acid array comprising a heterogeneous pool of nucleic acid molecules affixed to a support, transferring at least a subset of the nucleic acid molecules produced by such amplifying to a second support, and affixing the subset so transferred to the second support to form a second randomly-patterned, immobilized nucleic acid array, wherein the nucleic acid molecules of the second array occupy positions that correspond to those of the nucleic acid molecules from which they were amplified on the first array, so that the first array serves as a template to produce a plurality, is disclosed.

  12. Method for sequencing nucleic acid molecules

    DOE Patents [OSTI]

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

    2006-06-06

    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.

  13. Method for sequencing nucleic acid molecules

    DOE Patents [OSTI]

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

    2006-05-30

    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.

  14. 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)

    1996-01-01

    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.

  15. 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)

    1999-10-12

    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.

  16. 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.

    1996-10-01

    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.

  17. Double stranded nucleic acid biochips

    DOE Patents [OSTI]

    Chernov, Boris; Golova, Julia

    2006-05-23

    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.

  18. Chip-based sequencing nucleic acids

    DOE Patents [OSTI]

    Beer, Neil Reginald

    2014-08-26

    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.

  19. Replica amplification of nucleic acid arrays

    DOE Patents [OSTI]

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

    2010-08-31

    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.

  20. Amplification of trace amounts of nucleic acids

    DOE Patents [OSTI]

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

    2008-06-17

    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).

  1. Nucleic acid based fluorescent sensor for copper detection

    DOE Patents [OSTI]

    Lu, Yi; Liu, Juewen

    2013-04-02

    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.

  2. Method for nucleic acid isolation using supercritical fluids

    DOE Patents [OSTI]

    Nivens, D.E.; Applegate, B.M.

    1999-07-13

    A method is disclosed 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. 4 figs.

  3. 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)

    1999-01-01

    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.

  4. 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)

    2008-04-22

    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.

  5. 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

    2012-10-16

    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.

  6. 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)

    2002-01-01

    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.

  7. 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; Foote, Robert S.

    2003-12-09

    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.

  8. 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)

    2012-02-21

    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.

  9. 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.

    2014-09-02

    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.

  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)

    2008-11-11

    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; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2015-04-14

    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.

  12. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

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

    2014-02-25

    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.

  13. 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)

    2012-02-14

    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. EGVII endoglucanase and nucleic acids encoding the same

    DOE Patents [OSTI]

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

    2013-07-16

    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.

  15. 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)

    2010-10-12

    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.

  16. 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)

    2010-10-05

    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.

  17. 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)

    2008-04-01

    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.

  18. 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)

    2009-05-05

    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.

  19. Nucleic acid amplification using modular branched primers

    DOE Patents [OSTI]

    Ulanovsky, Levy (Westmont, IL)

    2001-01-01

    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.

  20. 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)

    1999-01-01

    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.

  1. 1999 Oxford University Press186187 Nucleic Acids Research, 1999, Vol. 27, No. 1 The viroid and viroid-like RNA database

    E-Print Network [OSTI]

    Perreault, Jean-Pierre

    and viroid-like RNA database Daniel A. Lafontaine, Patrick Deschênes, Frédéric Bussière, Véronique Poisson This is an online database to facilitate research on viroid, viroid-like RNAs and human hepatitis delta virus (v' of the smallest known auto-replicable RNAs. This online database is available on the World Wide Web at http

  2. Methods and compositions for efficient nucleic acid sequencing

    DOE Patents [OSTI]

    Drmanac, Radoje

    2006-07-04

    Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

  3. Methods and compositions for efficient nucleic acid sequencing

    DOE Patents [OSTI]

    Drmanac, Radoje (850 E. Greenwich Pl., Palo Alto, CA 94303)

    2002-01-01

    Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

  4. 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)

    1999-06-15

    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.

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

    DOE Patents [OSTI]

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

    1999-06-15

    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.

  6. Simple Bulk Readout of Digital Nucleic Acid Quantification Assays

    E-Print Network [OSTI]

    Morinishi, Leanna S.

    Digital assays are powerful methods that enable detection of rare cells and counting of individual nucleic acid molecules. However, digital assays are still not routinely applied, due to the cost and specific equipment ...

  7. Isolated menthone reductase and nucleic acid molecules encoding same

    DOE Patents [OSTI]

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

    2013-04-23

    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.

  8. 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 ...

  9. Kit for detecting nucleic acid sequences using competitive hybridization probes

    DOE Patents [OSTI]

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

    2001-01-01

    A kit is provided for detecting a target nucleic acid sequence in a sample, the kit comprising: a first hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the first hybridization probe including a first complexing agent for forming a binding pair with a second complexing agent; and a second hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the first hybridization probe does not selectively hybridize, the second hybridization probe including a detectable marker; a third hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the third hybridization probe including the same detectable marker as the second hybridization probe; and a fourth hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the third hybridization probe does not selectively hybridize, the fourth hybridization probe including the first complexing agent for forming a binding pair with the second complexing agent; wherein the first and second hybridization probes are capable of simultaneously hybridizing to the target sequence and the third and fourth hybridization probes are capable of simultaneously hybridizing to the target sequence, the detectable marker is not present on the first or fourth hybridization probes and the first, second, third, and fourth hybridization probes each include a competitive nucleic acid sequence which is sufficiently complementary to a third portion of the target sequence that the competitive sequences of the first, second, third, and fourth hybridization probes compete with each other to hybridize to the third portion of the target sequence.

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

    DOE Patents [OSTI]

    Nasarabadi, Shanavaz (Livermore, CA)

    2011-01-11

    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.

  11. 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

    2014-09-30

    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.

  12. 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.

    2013-06-11

    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.

  13. 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)

    2007-08-14

    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.

  14. 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

    2012-10-16

    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.

  15. 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

    2010-06-22

    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.

  16. 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)

    2010-11-02

    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.

  17. 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

    2010-04-20

    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.

  18. Universal nucleic acids sample preparation method for cells, spores and their mixture

    DOE Patents [OSTI]

    Bavykin, Sergei (Darien, IL)

    2011-01-18

    The present invention relates to a method for extracting nucleic acids from biological samples. More specifically the invention relates to a universal method for extracting nucleic acids from unidentified biological samples. An advantage of the presently invented method is its ability to effectively and efficiently extract nucleic acids from a variety of different cell types including but not limited to prokaryotic or eukaryotic cells and/or recalcitrant organisms (i.e. spores). Unlike prior art methods which are focused on extracting nucleic acids from vegetative cell or spores, the present invention effectively extracts nucleic acids from spores, multiple cell types or mixtures thereof using a single method. Important that the invented method has demonstrated an ability to extract nucleic acids from spores and vegetative bacterial cells with similar levels effectiveness. The invented method employs a multi-step protocol which erodes the cell structure of the biological sample, isolates, labels, fragments nucleic acids and purifies labeled samples from the excess of dye.

  19. 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)

    2000-01-01

    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.

  20. Highly simplified lateral flow-based nucleic acid sample preparation and passive fluid flow control

    DOE Patents [OSTI]

    Cary, Robert B.

    2015-12-08

    Highly simplified lateral flow chromatographic nucleic acid sample preparation methods, devices, and integrated systems are provided for the efficient concentration of trace samples and the removal of nucleic acid amplification inhibitors. Methods for capturing and reducing inhibitors of nucleic acid amplification reactions, such as humic acid, using polyvinylpyrrolidone treated elements of the lateral flow device are also provided. Further provided are passive fluid control methods and systems for use in lateral flow assays.

  1. 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)

    2001-01-01

    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.

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

    E-Print Network [OSTI]

    Russell, Brandon S. (Brandon Skylur)

    2014-01-01

    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 ...

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

    DOE Patents [OSTI]

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

    2008-08-05

    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.

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

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2015-04-14

    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.

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

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2014-03-04

    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.

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

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2015-08-11

    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.

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

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2014-03-25

    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; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2012-10-30

    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; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-05-16

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

    DOE Patents [OSTI]

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

    2006-02-28

    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.

  11. 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)

    2011-12-06

    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.

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

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2013-01-29

    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.

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

    DOE Patents [OSTI]

    Dunn-Coleman, Nigel; Ward, Michael

    2012-10-02

    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.

  14. 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

    2008-01-22

    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.

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

    DOE Patents [OSTI]

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

    2009-09-01

    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. 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)

    2011-06-14

    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.

  17. 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)

    2008-03-18

    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.

  18. 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)

    2008-04-01

    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.

  19. 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)

    2007-09-25

    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.

  20. Nucleic acid sequence detection using multiplexed oligonucleotide PCR

    DOE Patents [OSTI]

    Nolan, John P. (Santa Fe, NM); White, P. Scott (Los Alamos, NM)

    2006-12-26

    Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

  1. Microfluidic-based biosensors toward point-of-care detection of nucleic acids and proteins

    E-Print Network [OSTI]

    Wong, Pak Kin

    REVIEW Microfluidic-based biosensors toward point-of-care detection of nucleic acids and proteins reviews state-of-the-art microflu- idic 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

  2. 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

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

    E-Print Network [OSTI]

    Santiago, Juan G.

    Simultaneous purification and fractionation of nucleic acids and proteins from complex samples purification and fractionation of nucleic acids and proteins from complex biological samples: · Figure S-1: Images of on-chip DNA ITP zones and protein ITP zones · Figure S-2: Experimental setup and procedure

  4. Methods for point-of-care detection of nucleic acid in a sample

    DOE Patents [OSTI]

    Bearinger, Jane P.; Dugan, Lawrence C.

    2015-12-29

    Provided herein are methods and apparatus for detecting a target nucleic acid in a sample and related methods and apparatus for diagnosing a condition in an individual. The condition is associated with presence of nucleic acid produced by certain pathogens in the individual.

  5. The present invention relates to automated methods of introducing multiple nucleic acid sequences into one or more target cells.

    DOE Patents [OSTI]

    Church, George M. (Brookline, MA); Wang, Harris H. (Cambridge, MA); Isaacs, Farren J. (Brookline, MA)

    2012-04-10

    The present invention relates to automated methods of introducing multiple nucleic acid sequences into one or more target cells.

  6. A Stochastic Model of Nonenzymatic Nucleic Acid Replication: ``Elongators'' Sequester Replicators

    E-Print Network [OSTI]

    Fernando, Chrisantha

    (polymerase chain reaction) acting on nucleic acid polymers, allowing their self-replication. However), but there is no replication, because templates do not recycle by unzipping (Kovac et al. 2003). Short oligonucleotide

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

    E-Print Network [OSTI]

    Eltoukhy, Ahmed Atef

    2013-01-01

    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 ...

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

    E-Print Network [OSTI]

    Peng, Chunte Sam

    2014-01-01

    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 ...

  9. 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)

    2001-01-01

    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.

  10. 5[prime] to 3[prime] nucleic acid synthesis using 3[prime]-photoremovable protecting group

    DOE Patents [OSTI]

    Pirrung, M.C.; Shuey, S.W.; Bradley, J.C.

    1999-06-01

    The present invention relates, in general, to a method of synthesizing a nucleic acid, and, in particular, to a method of effecting 5[prime] to 3[prime] nucleic acid synthesis. The method can be used to prepare arrays of oligomers bound to a support via their 5[prime] end. The invention also relates to a method of effecting mutation analysis using such arrays. The invention further relates to compounds and compositions suitable for use in such methods.

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

    DOE Patents [OSTI]

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

    1997-04-01

    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.

  12. 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

    2006-10-03

    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.

  13. Mapping nucleic acid structure by hydroxyl radical cleavage Thomas D Tullius1,2

    E-Print Network [OSTI]

    Tullius, Thomas D.

    Mapping nucleic acid structure by hydroxyl radical cleavage Thomas D Tullius1,2 and Jason A Greenbaum2 Hydroxyl radical footprinting is a widely used method for following the folding of RNA molecules be followed simultaneously at single-nucleotide resolution. In recent work, hydroxyl radical footprinting has

  14. Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe

    E-Print Network [OSTI]

    Tan, Weihong

    Using photons to manipulate enzyme inhibition by an azobenzene-modified nucleic acid probe Youngmi and concluded the feasibility of using photon energy to temporally and spatially regulate these enzymatic reactions. Thus, we can report the development of DNA probes in the form of photon-controllable (thrombin

  15. NucleicAcids Research, 1995, Vol. 23, No. 7 1231-1238 Preparation of probe-modified RNA with

    E-Print Network [OSTI]

    Church, George M.

    NucleicAcids Research, 1995, Vol. 23, No. 7 1231-1238 Preparation of probe-modified RNA with 5, USA Received November 7, 1994; Revised and Accepted February 13, 1995 ABSTRACT We report a modified

  16. Nucleic acids encoding modified human immunodeficiency virus type 1 (HIV-1) group M consensus envelope glycoproteins

    DOE Patents [OSTI]

    Haynes, Barton F. (Durham, NC); Gao, Feng (Durham, NC); Korber, Bette T. (Los Alamos, NM); Hahn, Beatrice H. (Birmingham, AL); Shaw, George M. (Birmingham, AL); Kothe, Denise (Birmingham, AL); Li, Ying Ying (Hoover, AL); Decker, Julie (Alabaster, AL); Liao, Hua-Xin (Chapel Hill, NC)

    2011-12-06

    The present invention relates, in general, to an immunogen and, in particular, to an immunogen for inducing antibodies that neutralizes a wide spectrum of HIV primary isolates and/or to an immunogen that induces a T cell immune response. The invention also relates to a method of inducing anti-HIV antibodies, and/or to a method of inducing a T cell immune response, using such an immunogen. The invention further relates to nucleic acid sequences encoding the present immunogens.

  17. 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

    2014-01-14

    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.

  18. 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.; Mellors, J.W.; Jeang, K.T.; Wain-Hobson, S.

    1997-04-01

    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.

  19. 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)

    2001-10-30

    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.

  20. Nucleic acid encoding DS-CAM proteins and products related thereto

    DOE Patents [OSTI]

    Korenberg, Julie R.

    2005-11-01

    In accordance with the present invention, there are provided Down Syndrome-Cell Adhesion Molecule (DS-CAM) proteins. Nucleic acid sequences encoding such proteins and assays employing same are also disclosed. The invention DS-CAM proteins can be employed in a variety of ways, for example, for the production of anti-DS-CAM antibodies thereto, in therapeutic compositions and methods employing such proteins and/or antibodies. DS-CAM proteins are also useful in bioassays to identify agonists and antagonists thereto.

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

    DOE Patents [OSTI]

    Studier, F.W.

    1995-04-18

    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.

  2. 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)

    1995-04-18

    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.

  3. volume 6 Number 4 April 1979 Nucleic Acids Research Core nucleosomes by digestion of reconstructed histone-DNA complexes

    E-Print Network [OSTI]

    Olins, Ada L.

    volume 6 Number 4 April 1979 Nucleic Acids Research Core nucleosomes by digestion of reconstructed4) and a variety of DNAs were digested with micrococcal nuclease to yield very homogeneous by circular dichroism, thermal denaturation, electron microscopy, and DNAse I digestion. Circular dichroism

  4. 1995 Oxford University Press 30093017Nucleic Acids Research, 1995, Vol. 23, No. 15 Chemical probe and missing nucleoside analysis of

    E-Print Network [OSTI]

    Tullius, Thomas D.

    © 1995 Oxford University Press 3009­3017Nucleic Acids Research, 1995, Vol. 23, No. 15 ChemicalDepartment of Microbiology, University of Texas, Austin, TX 78712, USA Received March 3, 1995; Revised and Accepted June 19, 1995 ABSTRACT The Flp protein catalyzes a site-specific recombination reaction between

  5. 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

    2013-07-23

    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.

  6. 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

    2014-04-08

    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.

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

    DOE Patents [OSTI]

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

    2011-11-15

    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.

  8. Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA

    E-Print Network [OSTI]

    Yuan-Yan Wu; Zhong-Liang Zhang; Jin-Si Zhang; Xiao-Long Zhu; Zhi-Jie Tan

    2015-07-10

    Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Cobalt Hexammine ion (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive.However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become internal binding into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit external binding to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.

  9. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOE Patents [OSTI]

    Weier, H.U.G.; Gray, J.W.

    1995-06-27

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers and probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity. 18 figs.

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

    SciTech Connect (OSTI)

    Kingsley, Mark T

    2001-03-13

    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.

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

    SciTech Connect (OSTI)

    Kingsley, Mark T.

    2001-03-13

    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.

  12. 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

  13. 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,

    2013-01-25

    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.

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

    DOE Patents [OSTI]

    Freimuth, Paul I.

    2010-04-06

    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.

  15. RegTransBase -- a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

    E-Print Network [OSTI]

    2013-01-01

    NC: The Genomes OnLine Database (GOLD) v.4: status ofNucleic Acids Res 2012, 40(Database issue):D571–D579. 3. LiuAcids Res 2007, 35(Database issue):D407–D412. Novichkov PS,

  16. 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.; Wain-Hobson, S.; Smith, R.F.; Pavlakis, G.N.

    1993-12-31

    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.

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

    DOE Patents [OSTI]

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

    2001-01-01

    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.

  18. 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)

    2001-01-01

    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.

  19. Nucleic acid biosensors

    DOE Patents [OSTI]

    Lu, Yi (Champaign, IL); Liu, Juewen (Urbana, IL)

    2009-11-03

    Sensors comprising aptazymes capable of detecting the presence and concentration of effectors, as well as methods of using such sensors, are disclosed.

  20. Nucleic acid indexing

    DOE Patents [OSTI]

    Guilfoyle, Richard A. (Madison, WI); Guo, Zhen (Bellevue, WA)

    1999-01-01

    A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

  1. Nucleic acid indexing

    DOE Patents [OSTI]

    Guilfoyle, Richard A. (Madison, WI); Guo, Zhen (Bellevue, WA)

    2001-01-01

    A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

  2. Nucleic acid isolation process

    DOE Patents [OSTI]

    Longmire, Jonathan L. (Los Alamos, NM); Lewis, Annette K. (La Jolla, CA); Hildebrand, Carl E. (Los Alamos, NM)

    1990-01-01

    A method is provided for isolating DNA from eukaryotic cell and flow sorted chromosomes. When DNA is removed from chromosome and cell structure, detergent and proteolytic digestion products remain with the DNA. These products can be removed with organic extraction, but the process steps associated with organic extraction reduce the size of DNA fragments available for experimental use. The present process removes the waste products by dialyzing a solution containing the DNA against a solution containing polyethylene glycol (PEG). The waste products dialyze into the PEG leaving isolated DNA. The remaining DNA has been prepared with fragments containing more than 160 kb. The isolated DNA has been used in conventional protocols without affect on the protocol.

  3. Nucleic acid isolation

    DOE Patents [OSTI]

    Longmire, J.L.; Lewis, A.K.; Hildebrand, C.E.

    1988-01-21

    A method is provided for isolating DNA from eukaryotic cell and flow sorted chromosomes. When DNA is removed from chromosome and cell structure, detergent and proteolytic digestion products remain with the DNA. These products can be removed with organic extraction, but the process steps associated with organic extraction reduces the size of DNA fragments available for experimental use. The present process removes the waste products by dialyzing a solution containing the DNA against a solution containing polyethylene glycol (PEG). The waste products dialyze into the PEG leaving isolated DNA. The remaining DNA has been prepared with fragments containing more than 160 kb. The isolated DNA has been used in conventional protocols without effect on the protocol.

  4. 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.

    2012-03-16

    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.

  5. 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

  6. 1997 Oxford University Press236239 Nucleic Acids Research, 1997, Vol. 25, No. 1 SCOP: a Structural Classification of Proteins

    E-Print Network [OSTI]

    : a Structural Classification of Proteins database Tim J. P. Hubbard1, Alexey G. Murzin1, Steven E. Brenner and Cyrus Chothia MRC Laboratory of Molecular Biology and 1Cambridge Centre for Protein Engineering, Hills The Structural Classification of Proteins (SCOP) data- base provides a detailed and comprehensive descrip- tion

  7. 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room NewsInformation Current HAB Packet HanfordDOEDaniel Shechtman andDarkIDDatabases Databases

  8. 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.

    2010-03-08

    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.

  9. 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)

  10. Databases for rRNA gene profiling of microbial communities

    DOE Patents [OSTI]

    Ashby, Matthew

    2013-07-02

    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.

  11. 1996 Oxford University Press 15Nucleic Acids Research, 1996, Vol. 24, No. 1 Dennis A. Benson*, Mark Boguski, David J. Lipman and James Ostell

    E-Print Network [OSTI]

    Boguski, Mark S.

    the other major public databases. An integrated retrieval system, known as Entrez, contains data from Gen automated information systems to support molecular biology and biotechnology. Its other mission, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda

  12. Published online 3 November 2007 Nucleic Acids Research, 2008, Vol. 36, Database issue D577D581 doi:10.1093/nar/gkm909

    E-Print Network [OSTI]

    Botstein, David

    experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene information for genes that have not been experimentally characterized, GO annotations from independent sources traditional experimental methods published in the scientific literature are the primary sources of evidence

  13. Published online 30 October 2008 Nucleic Acids Research, 2009, Vol. 37, Database issue D669D673 doi:10.1093/nar/gkn739

    E-Print Network [OSTI]

    concentrated mainly on viruses known to be associated with infectious diseases and oncogenesis in humans

  14. Fatty acid-producing hosts

    DOE Patents [OSTI]

    Pfleger, Brian F; Lennen, Rebecca M

    2013-12-31

    Described are hosts for overproducing a fatty acid product such as a fatty acid. The hosts include an exogenous nucleic acid encoding a thioesterase and, optionally, an exogenous nucleic acid encoding an acetyl-CoA carboxylase, wherein an acyl-CoA synthetase in the hosts are functionally delected. The hosts prefereably include the nucleic acid encoding the thioesterase at an intermediate copy number. The hosts are preferably recominantly stable and growth-competent at 37.degree. C. Methods of producing a fatty acid product comprising culturing such hosts at 37.degree. C. are also described.

  15. ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

    E-Print Network [OSTI]

    McDonald, Andrew G; Boyce, Sinead; Moss, Gerard P; Dixon, Henry B F; Tipton, Keith F

    2007-07-27

    434-D437 [http://www.ebi.ac.uk/intenz/]. 8. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M: From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, 34:D354-D357... [http://www.genome.ad.jp/]. 9. A direct link to EC x.y.z.w. . http://www.enzyme-database.org/ query.php?ec=x.y.z.wyours — you keep the copyright Submit your manuscript here: http://www.biomedcentral.com/info/publishing_adv.asp BioMedcentral Page 7 of 7...

  16. Supporting Information Selective nucleic acid capture

    E-Print Network [OSTI]

    Pierce, Niles A.

    . . . . . . . . . . . . . . . . . . . . . . . . . S10 S4.2 Absence of thermal activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . S11 S4.3 Light sources for photo-activation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . S13 S4.5 Wavelength-dependence of photo-activation and photo-reversal processes

  17. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect (OSTI)

    States, David J.

    2004-07-28

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  18. Nucleic acids encoding a cellulose binding domain

    DOE Patents [OSTI]

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

    1996-03-05

    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.

  19. Diagnostic method employing MSH2 nucleic acids

    DOE Patents [OSTI]

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

    1997-01-01

    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.

  20. Understanding Nucleic AcidIon Interactions

    E-Print Network [OSTI]

    Herschlag, Dan

    of Technology, 2628 CJ Delft, Netherlands; email: Jan.Lipfert@lmu.de 2 Department of Physics and Center for Nano Keywords ions, RNA/DNA, electrostatics, Poisson­Boltzmann, Manning condensation, Hill equation, free energy;Contents INTRODUCTION. . . . . . . . . . . . . . . . . 814 THE BASICS

  1. 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)

    1996-01-01

    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.

  2. Diagnostic method employing MSH2 nucleic acids

    DOE Patents [OSTI]

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

    1997-12-02

    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.

  3. 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)

  4. Plant fatty acid hydroxylase

    DOE Patents [OSTI]

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

    2000-01-01

    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.

  5. 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

    2013-04-30

    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.

  6. 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)

    2011-04-12

    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.

  7. Targeting nucleic acids for pancreatic cancer: disease modeling and therapy

    E-Print Network [OSTI]

    Lo, Justin Han Je

    2015-01-01

    Pancreatic cancer is responsible for nearly 40,000 deaths in the U.S. annually, with a dismal 5-year survival rate below 7%. The poor therapeutic outcomes reflect a paucity of new approaches targeting the genomic underpinnings ...

  8. Targeting unique nucleic acid structures with small molecules

    E-Print Network [OSTI]

    Tam, Victor Kin-man

    2007-01-01

    OF AMINOGLYCOSIDE RESISTANCE Bacteria utilize three mainas bacteria continuously develop new resistance mechanisms,bacteria almost immediately acquire resistance. The

  9. Pyrene Excimer Signaling Molecular Beacons for Probing Nucleic Acids

    E-Print Network [OSTI]

    Tan, Weihong

    Ville, Florida 32611-7200, Department of Chemistry, Columbia UniVersity, New York, New York 10027, and Key of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling resonance energy transfer (FRET) from the excited-state fluo- rophore to the quencher molecule, thus

  10. Rapid microfluidic thermal cycler for nucleic acid amplification

    DOE Patents [OSTI]

    Beer, Neil Reginald; Vafai, Kambiz

    2015-10-27

    A system for thermal cycling a material to be thermal cycled including a microfluidic heat exchanger; a porous medium in the microfluidic heat exchanger; a microfluidic thermal cycling chamber containing the material to be thermal cycled, the microfluidic thermal cycling chamber operatively connected to the microfluidic heat exchanger; a working fluid at first temperature; a first system for transmitting the working fluid at first temperature to the microfluidic heat exchanger; a working fluid at a second temperature, a second system for transmitting the working fluid at second temperature to the microfluidic heat exchanger; a pump for flowing the working fluid at the first temperature from the first system to the microfluidic heat exchanger and through the porous medium; and flowing the working fluid at the second temperature from the second system to the heat exchanger and through the porous medium.

  11. Rapid microfluidic thermal cycler for nucleic acid amplification

    DOE Patents [OSTI]

    Beer, Neil Reginald; Vafai, Kambiz

    2015-11-06

    A system for thermal cycling a material to be thermal cycled including a microfluidic heat exchanger; a porous medium in the microfluidic heat exchanger; a microfluidic thermal cycling chamber containing the material to be thermal cycled, the microfluidic thermal cycling chamber operatively connected to the microfluidic heat exchanger; a working fluid at first temperature; a first system for transmitting the working fluid at first temperature to the microfluidic heat exchanger; a working fluid at a second temperature, a second system for transmitting the working fluid at second temperature to the microfluidic heat exchanger; a pump for flowing the working fluid at the first temperature from the first system to the microfluidic heat exchanger and through the porous medium; and flowing the working fluid at the second temperature from the second system to the heat exchanger and through the porous medium.

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

    E-Print Network [OSTI]

    Winkle, Stephen Alan

    2012-01-01

    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

  13. Genomic nucleic acid memory storage with directed endonucleases

    E-Print Network [OSTI]

    Jakimo, Noah

    2015-01-01

    Technologies for long-term recording of cellular pathway activation are constrained by the difficultly to constantly monitor transient signaling events and expression of target genes. To overcome these limitations we ...

  14. Method for replicating an array of nucleic acid probes

    DOE Patents [OSTI]

    Cantor, C.R.; Przetakiewicz, M.; Smith, C.L.; Sano, T.

    1998-08-18

    The invention relates to the replication of probe arrays and methods for replicating arrays of probes which are useful for the large scale manufacture of diagnostic aids used to screen biological samples for specific target sequences. Arrays created using PCR technology may comprise probes with 5{prime}- and/or 3{prime}-overhangs. 16 figs.

  15. 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

  16. Quantification of false positive reduction in nucleic acid purificatio...

    Office of Scientific and Technical Information (OSTI)

    Bibtex Format Close 0 pages in this document matching the terms "" Search For Terms: Enter terms in the toolbar above to search the full text of this document for pages...

  17. Quantification of false positive reduction in nucleic acid purification on

    Office of Scientific and Technical Information (OSTI)

    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 Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTech ConnectSpeedingConnect Pulse energy measurement at

  18. Quantification of false positive reduction in nucleic acid purification on

    Office of Scientific and Technical Information (OSTI)

    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 Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTech ConnectSpeedingConnect Pulse energy measurement athemorrhagic fever DNA.

  19. Effect of Amino Acid Subsititution in Set1 on Histone H3 Methylation and Gene Silencing in Saaccharomyces Cerevisiae 

    E-Print Network [OSTI]

    Chateau, Morgan

    2008-08-24

    -1231 4. Robzyk, K., and Kassir, Y. A. (1992) Nucleic Acids Research 20, 3790 5. Huang, Y. (2002) Nucleic Acids Research 30, 1465-1482 6. Bryk, M., Banerjee, M., Murphy, M., Knudsen, K. E., Garfinkel, D. J., and Curcio, M. J. (1997) Genes...

  20. `Modern' Databases Database Systems Lecture 18

    E-Print Network [OSTI]

    Alechina, Natasha

    `Modern' Databases Database Systems Lecture 18 Natasha Alechina #12;'Modern' Databases In This Lecture · 'Modern' Databases · Distributed DBs · Web-based DBs · Object Oriented DBs · Semistructured Data chapter 4 #12;'Modern' Databases Other Sorts of DB · We have looked mainly at relational databases

  1. `Modern' Databases Database Systems Lecture 18

    E-Print Network [OSTI]

    Alechina, Natasha

    1 `Modern' Databases Database Systems Lecture 18 Natasha Alechina 'Modern' Databases In This Lecture · 'Modern' Databases · Distributed DBs · Web-based DBs · Object Oriented DBs · Semistructured Data chapter 4 'Modern' Databases Other Sorts of DB · We have looked mainly at relational databases

  2. Database Help

    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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submit theCovalent Bonding Low-Cost2 DOE HQSiteoC. DoranDatabase Help Database Help

  3. Producing dicarboxylic acids using polyketide synthases

    DOE Patents [OSTI]

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

    2013-10-29

    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.

  4. Microbial Metabolism Databases of Microbial

    E-Print Network [OSTI]

    Huang, Ching-Tsan

    1 Microbial Metabolism Databases of Microbial Metabolism & Degradation Ching-Tsan Huang () Office://www.ebi.ac.uk/ http://umbbd.msi.umn.edu/index.html #12;9 http://umbbd.msi.umn.edu/meta/meta_map.html #12;10 Microbial, Energy, Lipids, Nucleotides, Amino acids, Glycans, Polyketides/Nonribosome peptides, Secondary

  5. GWIDD: Genome-wide protein docking database

    E-Print Network [OSTI]

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

    2009-11-09

    . However, none of the above resources provide single integrated and searchable pool of experimental and modeled 3D structures for all genomes for which at least one PPI is annotated. Recently developed ProtInfo PPC server (http://protinfo.compbio.washington.edu/ppc...,R.E. and Samudrala,R. (2009) Protinfo PPC: A web server for atomic level prediction of protein complexes. Nucleic Acids Res., 37, W519–W525. 22. Katchalski-Katzir,E., Shariv,I., Eisenstein,M., Friesem,A.A., Aflalo,C. and Vakser,I.A. (1992) Molecular surface...

  6. NUCLEAR STRUCTURE DATABASE

    E-Print Network [OSTI]

    Firestone, R.B.

    2010-01-01

    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. Introduction to Database Database Systems Lecture 1

    E-Print Network [OSTI]

    Alechina, Natasha

    .cs.nott.ac.uk/~nza/G51DBS #12;In this Lecture · Course Information · Databases and Database Systems · Some History bookings · Credit card details · Student records · Customer histories · Stock market prices · Discussion of information · A database management system (DBMS) is the software than controls that information · Examples

  8. The EMIME Bilingual Database 

    E-Print Network [OSTI]

    Wester, Mirjam

    2010-01-01

    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. USER'S GUIDE DATABASE SYSTEM

    E-Print Network [OSTI]

    Budny, Robert

    USER'S GUIDE TO THE MINGL DATABASE SYSTEM FOR TFTR Version 4.1 R. M. Wieland Plasma Physics blank] #12;1 Abstract The MINGL database system is an integrated set of tools which is used to collect relational databases. A flexible software tool set makes it easy to browse, select, compare and display

  10. Database Encryption Luc Bouganim

    E-Print Network [OSTI]

    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

  11. 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

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

    E-Print Network [OSTI]

    Alwes, Frederike

    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

  13. 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)

    2011-10-04

    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.

  14. 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

    2014-11-18

    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.

  15. 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.

  16. 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)

  17. Hazard Analysis Database Report

    SciTech Connect (OSTI)

    GAULT, G.W.

    1999-10-13

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

  18. ORISE: Human Subjects Research Database

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

    in support of the HSRD database: Database maintenance Federal Internet server access Software development Quality assurancequality control Project assistance Human Subjects...

  19. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Calm, J.M.

    1994-05-27

    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.

  20. Nano Databases Nano Business

    E-Print Network [OSTI]

    Xie, Xiaoliang Sunney

    Home News Nano Databases Nano Business Nano Jobs Resources Introduc on to Nanotechnology Open menu's lab. A team of interna onal researchers, led by Lieber, the Mark Hyman, Jr. Professor of Chemistry

  1. Nuclear Science References Database

    E-Print Network [OSTI]

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

    2014-07-08

    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.

  2. 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 Fuels DataEnergy Webinar:IAbout Us| DepartmentFunds Recipients |DatabasesDatabases

  3. 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.

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

    E-Print Network [OSTI]

    Grechanik, Mark

    the process of software evolution error- prone, expensive, and difficult. Currently, database deadlocksTesting 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

  5. The EPILEPSIAE database: An extensive electroencephalography database of epilepsy patients

    E-Print Network [OSTI]

    Timmer, Jens

    The EPILEPSIAE database: An extensive electroencephalography database of epilepsy patients *yz1. In this article we present the EPILEPSIAE database, which was made publicly available in 2012. We illustrate its content and scope. The EPILEPSIAE database provides long-term EEG recordings of 275 patients as well

  6. 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

  7. 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

  8. Computer Science: An Overview Database Systems

    E-Print Network [OSTI]

    Lanubile, Filippo

    .1 Database Fundamentals · 9.2 The Relational Model · 9.3 Object-Oriented Databases · 9.4 Maintaining Database of a database without changing the application software that uses it Database Models · Database model: A conceptual view of a d t bdatabase ­ Relational database model ­ Object-oriented database model Copyright

  9. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Calm, J.M.

    1992-04-30

    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, though some may be added at a later date. The database identifies sources of specific information on R-32, R-123, R-124, R- 125, R-134a, R-141b, R142b, R-143a, R-152a, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses polyalkylene glycol (PAG), ester, and other lubricants. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits.

  10. Database Security: A Historical Perspective

    E-Print Network [OSTI]

    Lesov, Paul

    2010-01-01

    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 ...

  11. Survey on indirect optical manipulation of cells, nucleic acids, and motor proteins

    E-Print Network [OSTI]

    Banerjee, Ashis

    Optical tweezers have emerged as a promising technique for manipulating biological objects. Instead of direct laser exposure, more often than not, optically-trapped beads are attached to the ends or boundaries of the objects ...

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

    DOE Patents [OSTI]

    Regan, John Frederick

    2014-09-09

    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.

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

    E-Print Network [OSTI]

    Christensen, Lane

    2006-10-26

    In ten sit y ( 10 0% ) Polymer Reaction Mn (kDa) Mw (kDa) Mw/Mn Titration % Protonated Degree of Time (#1;mol HCl) Nitrogens Branching poly(EDA/CBA) 48 h 1.6 2.0 1.26 8.2 21.9 0.37 poly(DETA/CBA) 18 h 3.3 4.8 1.47 5.0 10.1 0.72 poly(TETA/CBA) 16 h 2.3 3... 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...

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

    E-Print Network [OSTI]

    Rubloff, Gary W.

    . The thermally responsive protein gelatin is then cast on top of the chitosan film, and the gelatin gel serves regions of the gelatin thermoresist and selectively expose the underlying chitosan. Finally, molecules are conjugated to the exposed chitosan sublayer and the sacrificial gelatin layer is removed (either by treating

  15. Nucleic Acids Research, 1992, Vol. 20, No. 22 5991 -5997 Transcriptionally driven cruciform formation in vivo

    E-Print Network [OSTI]

    Mirkin, Sergei

    formation in vivo Andrey Dayn, Sergei Malkhosyan1 and Sergei M.Mirkin* Department of Genetics, University of Illinois at Chicago, 808 S.Wood Street, Chicago, IL 60612 and 'California Institute of Biological Research studied the formation of d(A-T)n cruciforms in E.coli cells by probing intracellular plasmid DNA

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

    SciTech Connect (OSTI)

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

    2013-04-23

    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.

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

    DOE Patents [OSTI]

    Waldo, Geoffrey S; Cabantous, Stephanie

    2014-04-01

    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.

  18. Nucleic Acids Research Chrysanthemum stunt viroid: primary sequence and secondary structure

    E-Print Network [OSTI]

    Haseloff, Jim

    , Australia Received 10 April 1981 ABSTRACT The sequence of the 356 nucleotide residues of chrysanthemum stunt putative negative strands of these two viroids code for functional polypeptide products. However, the two and is not encapsidated (3,4). No viroid has been shown to code for a protein product either in vivo (5) or in vitro (6

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

    DOE Patents [OSTI]

    Castro, Alonso

    2004-06-01

    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. Chitosans for delivery of nucleic acids Michael D. Buschmann, Abderrazzak Merzouki, Marc Lavertu, Marc

    E-Print Network [OSTI]

    Buschmann, Michael

    ..................................................................................................18 2.3.1. Modification on the C2 amine..................................................................................19 2.3.2. Modification on the C6 hydroxyl

  1. Y chromosome specific nucleic acid probe and method for determining the Y chromosome in situ

    DOE Patents [OSTI]

    Gray, J.W.; Weier, H.U.

    1998-11-24

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

  2. Y chromosome specific nucleic acid probe and method for identifying the Y chromosome in SITU

    DOE Patents [OSTI]

    Gray, J.W.; Weier, H.U.

    1999-03-30

    A method for producing a Y chromosome specific probe selected from highly repeating sequences on that chromosome is described. There is little or no nonspecific binding to autosomal and X chromosomes, and a very large signal is provided. Inventive primers allowing the use of PCR for both sample amplification and probe production are described, as is their use in producing large DNA chromosome painting sequences. 9 figs.

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

    DOE Patents [OSTI]

    Gray, Kevin A; Dirmeier, Reinhard

    2013-07-16

    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.

  4. Nucleic Acids Research, 2008, 112 doi:10.1093/nar/gkn432

    E-Print Network [OSTI]

    Perreault, Jean-Pierre

    differentiation and is known to contribute to the oncogenesis of certain cancers. The Pax-5 locus generates

  5. 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)

    2012-01-24

    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.

  6. Nucleic Acids Research doi:10.1093/nar/gkn465

    E-Print Network [OSTI]

    Bi, Xin

    is a histone acetyltransferase implicated in the regulation of transcriptional silencing, and ORC is the six the temperature sensitivity of the ORC mutants orc2-1 and orc5-1. Moreover, sas2D and orc2-1 have a synthetic and orc5-1 have a synthetic effect on transcriptional silencing at the HMR locus. Moreover, we demon

  7. 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

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

    E-Print Network [OSTI]

    ?r?v?stava, Nidhi

    2012-01-01

    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 ...

  9. Nucleic Acids Research, 2009, 113 doi:10.1093/nar/gkp004

    E-Print Network [OSTI]

    Monnat, Ray

    of Washington, Box 357705, Seattle, WA 98195, 2 Northwest Genome Engineering Consortium, Seattle, WA, 3 98195, 4 Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N. A3 (collectively termed mCreIs or mMsoIs) were characterized in detail by using a combination of biochemical

  10. 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,

    2012-06-27

    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 here as an alternative...

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

    SciTech Connect (OSTI)

    Pitonak, Michal; Neogrady, Pavel; Hobza, Pavel

    2009-12-18

    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.

  12. A HANDHELD MAGNETIC SENSING PLATFORM FOR ANTIGEN AND NUCLEIC ACID DETECTION

    E-Print Network [OSTI]

    Hajimiri, Ali

    Diagnostic Device. The device consists of a plug-in cartridge, circuit board, and single USB data interface cable for communication and power. (b) Disposable Cartridge. The disposable cartridge consists. The chip inside the cartridge has 48 sensor sites and 16 reference sensors. Sensor sites designated by EXP

  13. Nucleic Acids Research, 2007, 14 doi:10.1093/nar/gkm218

    E-Print Network [OSTI]

    Will, Sebastian

    , Institute of Computer Science, Bioinformatics Group, Georges-Koehler-Allee 106, 79110 Freiburg, Germany that gives a free energy value for each secondary structure (5). The structure with the lowest free energy [called the `minimum free energy (mfe) structure'] is expected to be the most stable one. Here, we

  14. 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 ...

  15. 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

    2007-03-13

    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).

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

    E-Print Network [OSTI]

    Meggers, Eric

    blocks contain just three carbons and one stereocen- ter, and are connected by phosphodiester bonds, thus useful scaffold for designing artificial duplexes with altered chemical and physical properties the evolution of life on Earth. ChemBioChem 2007, 8, 927 ­ 932 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim

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

    DOE Patents [OSTI]

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

    2012-03-13

    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.

  18. Nucleic Acids Research, 2007, 111 doi:10.1093/nar/gkm054

    E-Print Network [OSTI]

    the human genome by mining literature on chromosomal aberrations Steven Van Vooren1, *, Bernard Thienpont2 of Electrotechnical Engineering, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, B-3001 Heverlee, Belgium, 2 Center for Human Genetics, Leuven University Hospital, Herestraat 49, B-3000 Leuven, Belgium and 3 Center

  19. Nucleic Acids Research doi:10.1093/nar/gkn325

    E-Print Network [OSTI]

    of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven (Belgium) Received February 7­protein inter- actions, cis-regulatory information, gene expression data sets, sequence information and text-mining

  20. Critical Assessment of Nucleic Acid Electrostatics via Experimental and Computational Investigation of an Unfolded

    E-Print Network [OSTI]

    Herschlag, Dan

    resemble protein folding. However, RNA folding differs fundamentally from protein folding in ways that complicate the application of knowledge and intuition gained from protein folding research. In particular

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

    DOE Patents [OSTI]

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

    2011-06-07

    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.

  2. Amplification of trace amounts of nucleic acids (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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 Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefield MunicipalTechnicalInformation4563AbuseConnect Technical Report:Connect

  3. Amplification of trace amounts of nucleic acids (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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 Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefield MunicipalTechnicalInformation4563AbuseConnect Technical Report:ConnectAmplification of

  4. Replica amplification of nucleic acid arrays (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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 Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTech ConnectSpeedingConnect(Conference) |(Patent)(Conference)ConnectReplica

  5. Replica amplification of nucleic acid arrays (Patent) | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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 Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefieldSulfateSciTech ConnectSpeedingConnect(Conference) |(Patent)(Conference)ConnectReplicaReplica

  6. Lecture Notes Database Management

    E-Print Network [OSTI]

    O'Neil, Patrick

    SQL Programs. Embedded SQL means SQL statements embedded in host language (C in our case). The original idea was for end-users to access a database through SQL. Called casual users. But this is not a good idea. Takes too much concentration. Can you picture airline reservation clerk doing job with SQL

  7. 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.

  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)

    2002-01-01

    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)

    1998-01-01

    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)

    1997-01-01

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

    DOE Patents [OSTI]

    Somerville, C.; Loo, F. van de

    1997-09-16

    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. 35 figs.

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

    DOE Patents [OSTI]

    Somerville, C.; Loo, F. van de

    1998-09-01

    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. 35 figs.

  13. 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

  14. The EMIME Mandarin Bilingual Database 

    E-Print Network [OSTI]

    Wester, Mirjam; Liang, Hui

    2011-01-01

    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...

  15. DCC Briefing Paper: Database archiving 

    E-Print Network [OSTI]

    Müller, Heiko

    2009-02-02

    In a computational context, data archiving refers to the storage of electronic documents, data sets, multimedia files, and so on, for a defined period of time. Database archiving is usually seen as a subset of data archiving. Database archiving...

  16. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Calm, J.M.

    1992-11-09

    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.

  17. A Historical Database of Sociocultural Evolution

    E-Print Network [OSTI]

    Turchin, Peter; Whitehouse, Harvey; Francois, Pieter; Slingerland, Edward; Collard, Mark

    2012-01-01

    Historical Database of Sociocultural Evolution Peter TurchinThe Historical Database of Sociocultural Evolution, which weHistorical Database of Sociocultural Evolution. Cliodynamics

  18. A Noisy 10GB Provenance Database

    E-Print Network [OSTI]

    Cheah, You-Wei

    2013-01-01

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

  19. Lessons Learned Database | Department of Energy

    Office of Environmental Management (EM)

    Lessons Learned Database Lessons Learned Database The DOE Corporate Lessons Learned Database provides a central clearinghouse that allows ready access to and communication about...

  20. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1996-07-01

    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.

  1. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1999-01-01

    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.

  2. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1996-11-15

    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.

  3. 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 Fuels DataEnergy Webinar:IAbout Us| DepartmentFunds Recipients |Databases

  4. Noiseless Database Privacy Raghav Bhaskar

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    Noiseless Database Privacy Raghav Bhaskar Microsoft Research India rbhaskar@microsoft.com Abhishek as a gold standard in the field of database privacy. While this notion has the benefit of providing concrete explore is to exploit the entropy already present in the database and substitute that in the place

  5. ARTI Refrigerant Database

    SciTech Connect (OSTI)

    Cain, J.M. , Great Falls, VA )

    1993-04-30

    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.

  6. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1997-02-01

    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.

  7. ARTI refrigerant database

    SciTech Connect (OSTI)

    Calm, J.M.

    1998-08-01

    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.

  8. Construction of file database management

    SciTech Connect (OSTI)

    MERRILL,KYLE J.

    2000-03-01

    This work created a database for tracking data analysis files from multiple lab techniques and equipment stored on a central file server. Experimental details appropriate for each file type are pulled from the file header and stored in a searchable database. The database also stores specific location and self-directory structure for each data file. Queries can be run on the database according to file type, sample type or other experimental parameters. The database was constructed in Microsoft Access and Visual Basic was used for extraction of information from the file header.

  9. 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

  10. Low-Latency Multi-Datacenter Databases using Replicated Hatem A. Mahmoud, Alexander Pucher, Faisal Nawab,

    E-Print Network [OSTI]

    California at Santa Barbara, University of

    Low-Latency Multi-Datacenter Databases using Replicated Commits Hatem A. Mahmoud, Alexander Pucher to provide the same ACID transac- tional guarantees for multi-datacenter databases with fewer cross- datacenter communication trips, compared to replicated logging, by using a more efficient architecutre

  11. 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity ofkandz-cm11 Outreach Home Room News Publications Traditional Knowledge Kiosks Barrow, AlaskaDatabaseSearchTips Publications

  12. Gasification Plant 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverse (Journal Article)ForthcomingGENERALProblems I n QEstimatesPlant Databases

  13. Database Manipulation on Quantum Computers

    E-Print Network [OSTI]

    Ahmed Younes

    2007-05-29

    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

  14. 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...

  15. Energy Citations Database (ECD) - About

    Office of Scientific and Technical Information (OSTI)

    About ECD The Energy Citations Database (1943 - Present) was developed by the U.S. Department of Energy (DOE) Office of Scientific and Technical Information (OSTI) to improve...

  16. Energy Citations Database (ECD) - Widget

    Office of Scientific and Technical Information (OSTI)

    Energy Citations Database Widget You can access key features from the Department of Energy's Office of Scientific and Technical Information (DOEOSTI) by downloading the Energy...

  17. 09-Databases-Wahid.pptx

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

    Wahid Bhimji (wbhimji@lbl.gov) https:www.nersc.govusersdata- analyticsdata-management Databases and IO --- 1 --- Systems Services Tools Capabilities Transfer Processing...

  18. 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

  19. 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

    2007-01-01

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

  20. Wind turbine reliability database update.

    SciTech Connect (OSTI)

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

    2009-03-01

    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.

  1. 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

  2. Documentation for database.txt Description

    E-Print Network [OSTI]

    Gilchrist, Michael A.

    Documentation for database.txt Description: The file database.txtis a 163MB file which contains a pair-wise list of all the proteins seen in the TAP and HMS-PCI databases as well as the MIPS Complex-wise association. See Gilchrist et al. (2003) for more details. About database.txt: The database is available

  3. Investigating Database Security in a Networked Environment

    E-Print Network [OSTI]

    Wagner, Paul J.

    Investigating Database Security in a Networked Environment Matthew Giuliani Computer Science wagnerpj@uwec.edu Abstract Database and network security have traditionally been separate fields within flowing between client and database systems. Although vender specific information is available for many

  4. Meteorological database for the United States

    E-Print Network [OSTI]

    Apte, M.G.

    2011-01-01

    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

  5. Unit  045 - Non-Spatial Database Models

    E-Print Network [OSTI]

    045, CC in GIScience; Meyer, Thomas H.

    2000-01-01

    25 Unit 045 - Non-Spatial Database Models Core Curriculum -26 Unit 045 - Non-Spatial Database Models Core Curriculum -27 Unit 045 - Non-Spatial Database Models Core Curriculum -

  6. Unit 11 - Spatial Objects and Database Models

    E-Print Network [OSTI]

    Unit 11, CC in GIS; Nyerges, Timothy L.

    1990-01-01

    Spatial Objects and Database Models NCGIA Core Curriculum inSpatial Objects and Database Models NCGIA Core Curriculum inSpatial Objects and Database Models NCGIA Core Curriculum in

  7. Updating Disjunctive Databases via Model Trees

    E-Print Network [OSTI]

    Gryz, Jarek

    Updating Disjunctive Databases via Model the update problem for disjunctive databases represented by model trees. The concept of a model tree was introduced in [4] to provide a compact representation for disjunctive databases in terms of minimal models

  8. March 23, 2008 Databases: Intro. to DBs 1 Introduction to Databases

    E-Print Network [OSTI]

    Adam, Salah

    + Characteristics of database approach + Database Management System (DBMS) + Advantages of Using DBMS + Workers Involved in DBMSs + When Not to Use A DBMS + #12;March 23, 2008 Databases: Intro. to DBs 3 - Data Data Application programsUser 2 #12;March 23, 2008 Databases: Intro. to DBs 6 -- Database Approach Database DBMS

  9. Introducing a New Section—Databases

    E-Print Network [OSTI]

    Turchin, Peter

    2012-01-01

    Historical Database of Sociocultural Evolution, described inand database papers, Cliodynamics continues the publication of book reviews and review essays, as well as special features from the Social Evolution

  10. Fire Protection Database | Department of Energy

    Office of Environmental Management (EM)

    Fire Protection Database Fire Protection Database DOE O 231.1, Environment, Safety, And Health Reporting, requires the submission of an Annual Fire Protection Summary. The previous...

  11. National Residential Efficiency Measures Database - Building...

    Energy Savers [EERE]

    National Residential Efficiency Measures Database - Building America Top Innovation National Residential Efficiency Measures Database - Building America Top Innovation Image of a...

  12. Westlaw China Westlaw China English Database

    E-Print Network [OSTI]

    Po, Lai-Man

    Guide 3 Steps: 1. Enter search term(s) into the search box. 2. Choose databases by checking............................................................................................................................................................... 2 Cross-Database Search ........................................................................................................................................ 3 Search and Browse

  13. 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.

  14. Energy Citations Database (ECD) - Comments

    Office of Scientific and Technical Information (OSTI)

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

  15. 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.

  16. CSC 4480: Principles of Database Systems

    E-Print Network [OSTI]

    and technologies underlying database management systems. · Understand data models, physical data organization, data database · Database Management System (DBMS): generic program to manage databases 13 Basic Terms · Data decisions based on large volume of facts 15 Figure 1-1b Summarized data Useful information that managers can

  17. MINERVA DATABASE Guidelines for Managing Intercollegiate Classes

    E-Print Network [OSTI]

    MINERVA DATABASE Guidelines for Managing Intercollegiate Classes The database can be accessed at http://minerva.maths.ox.ac.uk/ Minerva is a shared database run by the department for tutors, TAs enter reports on the attendance and marks of their students into the database. This should be done after

  18. WMC Database Evaluation. Case Study Report

    SciTech Connect (OSTI)

    Palounek, Andrea P. T

    2015-10-29

    The WMC Database is ultimately envisioned to hold a collection of experimental data, design information, and information from computational models. This project was a first attempt at using the Database to access experimental data and extract information from it. This evaluation shows that the Database concept is sound and robust, and that the Database, once fully populated, should remain eminently usable for future researchers.

  19. Methods and compounds for chemical ligation

    DOE Patents [OSTI]

    Church, George M.; Sismour, A. Michael

    2013-07-09

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

  20. Korean Classics Indexing Project Database Korean Classics Indexing Project Database is a

    E-Print Network [OSTI]

    Po, Lai-Man

    Korean Classics Indexing Project Database · Korean Classics Indexing Project Database is a database written in Chinese · The database serves as a discovery tool to support teaching, learning and research's works shows that the Korean Database can help promote not only the research of Korean studies, but also

  1. 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.

  2. 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.

  3. Mobile Database Ouri Wolfson1

    E-Print Network [OSTI]

    Wolfson, Ouri E.

    that resides on a mobile device such as a PDA, a smart phone, or a laptop. Such devices are often limited in resources such as memory, computing power, and battery power. Key Points Due to device limitations, a mobile are usually posed by the user of the mobile device. Updates of the database may originate from the user

  4. Relational Database SQL: Querying the Relational DB

    E-Print Network [OSTI]

    Qiu, Weigang

    Standards and Dialects ISO SQL:2008 DBMS vendors offer their own extensions Oracle PostgreSQL MySQL Weigang: auto-completion and command history Weigang Qiu Relational Database & SQL #12;Relational Database SQL

  5. Proposal for a High Energy Nuclear Database

    E-Print Network [OSTI]

    Brown, David A.; Vogt, Ramona

    2005-01-01

    Proposal for a High Energy Nuclear Database XML documentsProposal for a High Energy Nuclear Database David A. Brown 1it requires the high-energy nuclear physics com- munity’s ?

  6. 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.

  7. GDB - Human Genome Database final report

    SciTech Connect (OSTI)

    Talbot, C. Conover, Jr.

    2002-01-08

    This is the DOE final report for the GDB, Human Genome Database, project at the Johns Hopkins University.

  8. 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.

  9. 1990-1996 Nucleic Acids Research, 1995, Vol. 23, No. 11 Transformation of Escherichia coli with large DNA

    E-Print Network [OSTI]

    Franks, Robert

    with exogenous DNA has played a central role in defining the molecular events that underlie genetic phenomena (1). High efficiency transformation makes the creation of representative libraries feasible when large the highest efficiencies (reviewed in 2), making it the method of choice for construction of genomic libraries

  10. The EMBO Journal vol.8 no.1 pp.1 -4, 1989 Definitions and nomenclature of nucleic acid structure

    E-Print Network [OSTI]

    Bansal, Manju

    library of helix analysis programs, HELIB (Fratini et al., 1982; Dickerson, 1985) suffers from the fact that the translations and rotations as defined are not fully independent and depend to a certain extent upon the choice development is the creation of a new and optimized library of routines for the analysis and description

  11. Mixed molecular motor traffic on nucleic acid tracks: models of transcriptional interference and regulation of gene expression

    E-Print Network [OSTI]

    Ghosh, Soumendu; Ghanti, Dipanwita; Chowdhury, Debashish

    2015-01-01

    While polymerizing a RNA molecule, a RNA polymerase (RNAP) walks step-by-step on the corresponding single-stranded DNA (ssDNA) template in a specific direction. Thus, a RNAP can be regarded as a molecular motor for which the ssDNA template serves as the track. The sites of start and stop of its walk on the DNA mark the two ends of the genetic message that it transcribes into RNA. Interference of transcription of two overlapping genes can strongly influence the levels of their expression, i.e., the overall rate of the synthesis of the corresponding full-length RNA molecules, through suppressive effect of one on the other. Here we model this process as a mixed traffic of two groups of RNAP motors that are characterized by two distinct pairs of on- and off-ramps. Each group polymerizes identical copies of a RNA while the RNAs polymerized by the two groups are different. These models, which may also be viewed as two interfering totally asymmetric simple exclusion processes, account for all modes of transcriptiona...

  12. Mixed molecular motor traffic on nucleic acid tracks: models of transcriptional interference and regulation of gene expression

    E-Print Network [OSTI]

    Bameta, Tripti; Ghanti, Dipanwita; Ghosh, Soumendu

    2015-01-01

    RNA polymerase (RNAP) is molecular machine that polymerizes a RNA molecule, a linear heteropolymer, using a single stranded DNA (ssDNA) as the corresponding template; the sequence of monomers of the RNA is dictated by that of monomers on the ssDNA template. While polymerizing a RNA, the RNAP walks step-by-step on the ssDNA template in a specific direction. Thus, a RNAP can be regarded also as a molecular motor and the sites of start and stop of its walk on the DNA mark the two ends of the genetic message that it transcribes into RNA. Interference of transcription of two overlapping genes is believed to regulate the levels of their expression, i.e., the overall rate of the corresponding RNA synthesis, through suppressive effect of one on the other. Here we model this process as a mixed traffic of two groups of RNAP motors that are characterized by two distinct pairs of start and stop sites. Each group polymerizes identical copies of a RNA while the RNAs polymerized by the two groups are different. These models...

  13. 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 ...

  14. Nucleic Acids Research, Vol. 19, No. 18 4949-4953 Direct introduction and transient expression of capped and

    E-Print Network [OSTI]

    Kirkegaard, Karla

    with lithium acetate (9) or by converting them to spheroplasts by enzyme treatment (10- 13). Recently

  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)

    1999-01-19

    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 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

  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

    2010-01-01

    activation. Immunity 28, Hacker, H. , and Karin, M. (2006).Sci STKE 2006, re13. Hacker, H. , Mischak, H. , Miethke,Embo J 17, 6230-6240. Hacker, H. , Redecke, V. , Blagoev,

  18. 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

    2015-02-05

    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.

  19. 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

    2015-01-01

    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.

  20. Deep Sky Astronomical Image Database Project at NERSC

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

    Deep Sky Astronomical Image Database Deep Sky Astronomical Image Database Key Challenges: Develop, store, analyze, and make available an astronomical image database of...

  1. Fact Sheet: Energy Storage Database (October 2012) | Department...

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

    Energy Storage Database (October 2012) Fact Sheet: Energy Storage Database (October 2012) DOE and Sandia National Laboratories are developing a database of energy storage projects...

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

    E-Print Network [OSTI]

    Lowe, Heather Ann

    2013-01-01

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

  3. HEXEvent: a database of Human EXon splicing Events

    E-Print Network [OSTI]

    Busch, A.; Hertel, K. J

    2012-01-01

    The UCSC Genome Browser database: extensions and updatesa comparative relational database of alternative splicing.and Transcript Diversity database. Genomics, 93, 213–220.

  4. SUN Attribute Database: Discovering, Annotating, and Recognizing Scene Attributes

    E-Print Network [OSTI]

    Hays, James

    SUN Attribute Database: Discovering, Annotating, and Recognizing Scene Attributes Genevieve attributes. Next, we build the "SUN attribute database" on top of the diverse SUN categorical database. Our

  5. INCREMENTAL HORIZONTAL FRAGMENTATION OF DATABASE CLASS OBJECTS

    E-Print Network [OSTI]

    Ezeife, Christie

    INCREMENTAL HORIZONTAL FRAGMENTATION OF DATABASE CLASS OBJECTS C.I. Ezeife School of Computer-orientd databases, Incremental horizontal fragmentation, Distribution Abstract: Horizontal fragments of a class in an object-oriented database system contain subsets of the class extent or instance objects. These fragments

  6. Temporal Databases Status and Research Directions

    E-Print Network [OSTI]

    Snodgrass, Richard T.

    is a personal, subjective, and necessarily incomplete history of the field over the last 4,000 years. I attempt these databases several thousand years and look up the (then current) grain harvest. Oral histories, e.g., Homer transaction time, recording a history of updates made to the database. Such a database supports rollback

  7. Comprehensive Database on Concrete Creep and Shrinkage

    E-Print Network [OSTI]

    ://iti.northwestern.edu. Evolution of Databases A vast number of creep and shrinkage experiments have been carried out aroundComprehensive 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

  8. Supporting Database Provenance under Schema Evolution

    E-Print Network [OSTI]

    Zaniolo, Carlo

    Supporting Database Provenance under Schema Evolution Shi Gao and Carlo Zaniolo University of California, Los Angeles {gaoshi, zaniolo}@cs.ucla.edu Abstract. Database schema upgrades are common in modern to explain the provenance of contents generated by the database conversion that is part of such upgrades

  9. Answering Historical Queries in Databases using Relevance

    E-Print Network [OSTI]

    Bertossi, Leopoldo

    consider the problem of answering queries about the evolution of the database along a sequence Reiter's proposal [14, 16] to specify the database evolution in the situation calculus, a first.e. in the whole evolution of the database, that a given property holds''? or ``Has a given property been true

  10. 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 evolution that are addressed in the title: -- Evolution towards object databases: Here we address

  11. Database System Concepts Silberschatz, Korth and Sudarshan

    E-Print Network [OSTI]

    Dragan, Feodor F.

    Database System Concepts ©Silberschatz, Korth and Sudarshan See www.db-book.com for conditions on re-use ©Silberschatz, Korth and SudarshanDatabase System Concepts Chapter 8: Application Design andChapter 8: Application Design and DevelopmentDevelopment #12;©Silberschatz, Korth and Sudarshan8.2Database

  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. 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

  14. IMPLEMENTING RELATIONSHIPS IN AN OBJECTORIENTED DATABASE

    E-Print Network [OSTI]

    Doherty, Michael

    OF RHODE ISLAND 1992 i #12; Abstract Semantic database models have shown the importance and utility of arbi­ trary user­defined relationships to define the semantics of database information. Object­oriented models on that model. The data definition language is automat­ ically mapped to a database implementation which

  15. Modelling Lexical Databases with Formal Concept Analysis

    E-Print Network [OSTI]

    Priss, Uta

    . The primary lexical database used in this paper is Roget's International Thesaurus [Roget 1962 and formal ontologies. We are using the following relational database versions of Roget's Thesaurus: ­ RIT11: a relational database version of Roget's Thesaurus [Roget 1911] which was compiled by the second author based

  16. 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

  17. Database specification for the Worldwide Port System (WPS) Regional Integrated Cargo Database (ICDB)

    SciTech Connect (OSTI)

    Faby, E.Z.; Fluker, J.; Hancock, B.R.; Grubb, J.W.; Russell, D.L. [Univ. of Tennessee, Knoxville, TN (United States)] [Univ. of Tennessee, Knoxville, TN (United States); Loftis, J.P.; Shipe, P.C.; Truett, L.F. [Oak Ridge National Lab., TN (United States)] [Oak Ridge National Lab., TN (United States)

    1994-03-01

    This Database Specification for the Worldwide Port System (WPS) Regional Integrated Cargo Database (ICDB) describes the database organization and storage allocation, provides the detailed data model of the logical and physical designs, and provides information for the construction of parts of the database such as tables, data elements, and associated dictionaries and diagrams.

  18. 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

  19. NIST Standard Reference Database 1A NIST/EPA/NIH Mass Spectral Database (NIST 11) and

    E-Print Network [OSTI]

    NIST Standard Reference Database 1A NIST/EPA/NIH Mass Spectral Database (NIST 11) and NIST Mass 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. © 1987, 1988, 1990, 1992, 1994, 1995, 1996, 1997

  20. 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

  1. A DATABASE INTEGRATION SYSTEM BASED ON GLOBAL VIEW GENERATION

    E-Print Network [OSTI]

    Lawrence, Ramon

    A DATABASE INTEGRATION SYSTEM BASED ON GLOBAL VIEW GENERATION Uchang Park Duksung Women: database, integration, view, heterogeneity. Abstract: Database integration is a common and growing challenge with the proliferation of database systems, data warehouses, data marts, and other OLAP systems

  2. 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

  3. THE PROTEIN NON-FOLDING PROBLEM: AMINO ACID DETERMINANTS OF INTRINSIC ORDER AND DISORDER

    E-Print Network [OSTI]

    Obradovic, Zoran

    THE PROTEIN NON-FOLDING PROBLEM: AMINO ACID DETERMINANTS OF INTRINSIC ORDER AND DISORDER R with 52,688 putatively disordered residues. For the four disordered databases, the amino acid compositions that the first set be called order-promoting and the second set disorder-promoting. Also, 265 amino acid

  4. Enhancing the DNA Patent Database

    SciTech Connect (OSTI)

    Walters, LeRoy B.

    2008-02-18

    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.

  5. PDS: A Performance Database Server

    DOE Public Access Gateway for Energy & Science Beta (PAGES Beta)

    Berry, Michael W.; Dongarra, Jack J.; Larose, Brian H.; Letsche, Todd A.

    1994-01-01

    The process of gathering, archiving, and distributing computer benchmark data is a cumbersome task usually performed by computer users and vendors with little coordination. Most important, there is no publicly available central depository of performance data for all ranges of machines from personal computers to supercomputers. We present an Internet-accessible performance database server (PDS) that can be used to extract current benchmark data and literature. As an extension to the X-Windows-based user interface (Xnetlib) to the Netlib archival system, PDS provides an on-line catalog of public domain computer benchmarks such as the LINPACK benchmark, Perfect benchmarks, and the NAS parallelmore »benchmarks. PDS does not reformat or present the benchmark data in any way that conflicts with the original methodology of any particular benchmark; it is thereby devoid of any subjective interpretations of machine performance. We believe that all branches (research laboratories, academia, and industry) of the general computing community can use this facility to archive performance metrics and make them readily available to the public. PDS can provide a more manageable approach to the development and support of a large dynamic database of published performance metrics.« less

  6. The Dartmouth Stellar Evolution Database

    E-Print Network [OSTI]

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

    2008-04-28

    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.

  7. Nuclear Concrete Materials Database Phase I Development

    SciTech Connect (OSTI)

    Ren, Weiju; Naus, Dan J

    2012-05-01

    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.

  8. Human retroviruses and AIDS 1994

    SciTech Connect (OSTI)

    Myers, G.; Korber, B.; Wain-Hobson, S.; Jeang, Kuan-Teh; Henderson, L.E.; Pavlakis, G.N.

    1995-01-01

    This compendium, including accompanying floppy diskettes, is 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 it comprises: (I) Nucleic Acid Alignments and Sequences; (II) Amino Acid Alignments; (III) Analysis; (IV) Related Sequences; (V) Database communications.

  9. National Residential Efficiency Measures Database Unveiled (text...

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

    technical activities, including the database project we're discussing today and the BEopt software development efforts. During today's webinar, Dave will outline the current...

  10. Transmission/Nepa Database | Open Energy Information

    Open Energy Info (EERE)

    Nepa Database < Transmission Jump to: navigation, search NepaHeader.png Transmission Dashboard Permitting Atlas Compare States Arizona California Colorado Idaho Montana Nevada New...

  11. 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

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

    Energy Savers [EERE]

    binar20100324openpvquniby.pdf Solar Energy - Capturing and Using Power and Heat from the Sun Building America Webinar: National Residential Efficiency Measures Database Unveiled...

  13. Basic energy properties of electrolytic solutions database. ...

    Office of Scientific and Technical Information (OSTI)

    Basic energy properties of electrolytic solutions database. Viscosity, thermal conductivity, density, enthalpy Citation Details In-Document Search Title: Basic energy properties...

  14. HANFORD NUCLEAR CRITICALITY SAFETY PROGRAM DATABASE

    SciTech Connect (OSTI)

    TOFFER, H.

    2005-05-02

    The Hanford Database is a useful information retrieval tool for a criticality safety practitioner. The database contains nuclear criticality literature screened for parameter studies. The entries, characterized with a value index, are segregated into 16 major and six minor categories. A majority of the screened entries have abstracts and a limited number are connected to the Office of Scientific and Technology Information (OSTI) database of full-size documents. Simple and complex searches of the data can be accomplished very rapidly and the end-product of the searches could be a full-size document. The paper contains a description of the database, user instructions, and a number of examples.

  15. 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.

  16. Catalog of databases and reports

    SciTech Connect (OSTI)

    Burtis, M.D.

    1997-04-01

    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.

  17. A procedure for automatically linking a geographical database and a pavement attribute database 

    E-Print Network [OSTI]

    Lehmann, Erwin August

    1996-01-01

    operational PMS packages display information in a tabular format, a Geographical Information System (GIS) displays information graphically. Therefore, linking a PMS attribute database to a GIS spatial database can improve and enhance its functionality...

  18. Parallel Database Systems: The Future of High Performance Database Processing1

    E-Print Network [OSTI]

    Cafarella, Michael J.

    . 94105-2403 dewitt @ cs.wisc.edu Gray @ SFbay.enet.dec.com January 1992 Abstract: Parallel database

  19. 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

  20. Hydroxycarboxylic acids and salts

    SciTech Connect (OSTI)

    Kiely, Donald E; Hash, Kirk R; Kramer-Presta, Kylie; Smith, Tyler N

    2015-02-24

    Compositions which inhibit corrosion and alter the physical properties of concrete (admixtures) are prepared from salt mixtures of hydroxycarboxylic acids, carboxylic acids, and nitric acid. The salt mixtures are prepared by neutralizing acid product mixtures from the oxidation of polyols using nitric acid and oxygen as the oxidizing agents. Nitric acid is removed from the hydroxycarboxylic acids by evaporation and diffusion dialysis.

  1. 1 Files and Databases mass storage

    E-Print Network [OSTI]

    Verschelde, Jan

    Outline 1 Files and Databases mass storage hash functions 2 Dictionaries logical key values nested Jan Verschelde, 28 January 2015 Intro to Computer Science (MCS 260) mass storage and dictionaries L-7 28 January 2015 1 / 32 #12;mass storage dictionaries in Python 1 Files and Databases mass storage

  2. Quantum search of an unstructured database

    E-Print Network [OSTI]

    Bogus?aw Broda

    2015-07-10

    A simple model of circuit implementation of the standard Grover algorithm for quantum search of an unstructured real classical database is proposed. The Grover iteration utilizes an appropriately defined oracle, which contains a kind of quantumly accessible classical memory storing the database.

  3. 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

  4. REGULAR ENTRY IN ENCYCLOPEDIA OF DATABASE SYSTEMS

    E-Print Network [OSTI]

    Risch, Tore

    network. In a central DBMS the data is managed by one node whereas in a distributed DBMS the data is managed by several nodes. A distributed DBMS is a database manager consisting of several nodes distributed in the network. In a regular distributed DBMS it is up to the database administrator to manually specify how data

  5. 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

  6. DATA QUALITY IN GENOME DATABASES (Research Paper)

    E-Print Network [OSTI]

    Freytag, Johann-Christoph

    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

  7. DISTRIBUTED DATABASE SYSTEMS M. Tamer zsu

    E-Print Network [OSTI]

    Özsu, M. Tamer

    a database that is distributed across the nodes of a computer network and makes this distribution transparent of consistent and atomic execution against the database. Transparency: Extension of data independence at every site where it executes. The name comes from the fact that two rounds of messages are exchanged

  8. Quantifying the consistency of scientific databases

    E-Print Network [OSTI]

    Šubelj, Lovro; Boshkoska, Biljana Mileva; Kastrin, Andrej; Levnaji?, Zoran

    2015-01-01

    Science is a social process with far-reaching impact on our modern society. In the recent years, for the first time we are able to scientifically study the science itself. This is enabled by massive amounts of data on scientific publications that is increasingly becoming available. The data is contained in several databases such as Web of Science or PubMed, maintained by various public and private entities. Unfortunately, these databases are not always consistent, which considerably hinders this study. Relying on the powerful framework of complex networks, we conduct a systematic analysis of the consistency among six major scientific databases. We found that identifying a single "best" database is far from easy. Nevertheless, our results indicate appreciable differences in mutual consistency of different databases, which we interpret as recipes for future bibliometric studies.

  9. 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

  10. Copyright Y. Daniel Liang, 2005 Database Concept and Design

    E-Print Network [OSTI]

    Liang, Y. Daniel

    to interact with the database system, as shown in Figure 1.1. Database Management System (DBMS) Application Programs System Users Application Users database Figure 1.1 A database system consists of data, DBMS. The software that stores and manages data is known as database management system, or DBMS. DBMS is usually

  11. An Approach to Evolving Database Dependent Systems (Extended Abstract)

    E-Print Network [OSTI]

    Perry, Dewayne E.

    -58113-545 -9/02/05...$5.00 ficient and slow evolution of database schemas and software that uses the databasesAn Approach to Evolving Database Dependent Systems (Extended Abstract) Mark Grechanika to relational databases using such standards as Universal Data Access (UDA) and Open Database Connec~vity (ODBC

  12. VDBL (Vienna Database Library) Version 1.0

    E-Print Network [OSTI]

    Schichl, Hermann

    VDBL (Vienna Database Library) Version 1.0 Reference Manual Hermann Schichl University of Vienna #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 6 5 Vienna Database Library File

  13. 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.

  14. Development of an OCS Cementing Operational Guidelines Database 

    E-Print Network [OSTI]

    Bell, Matthew G.

    2014-08-20

    the goals of the database, identifying its users, and selecting an appropriate database management system. The main goal of the database is to present specific design, testing, and operational procedures to ensure optimized cement seal effectiveness...

  15. 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

  16. The volatile compound BinBase mass spectral database

    E-Print Network [OSTI]

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

    2011-01-01

    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.

  17. 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

  18. Unit 10 - Spatial Databases as Models of Reality

    E-Print Network [OSTI]

    Unit 10, CC in GIS; Nyerges, Timothy L.

    1990-01-01

    data. 4. What is a database model, and why is it importantAttributes Attribute value Database model Layers D. DATABASEnot an official DCDSTF term Database model is a conceptual

  19. 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)...

  20. Motivate Homeowner Action With Updated DOE Incentives Database...

    Energy Savers [EERE]

    Database Motivate Homeowner Action With Updated DOE Incentives Database Is customer motivation a barrier to marketing upgrades in your community? You can find ideas for incentives...

  1. DOE Facility Database - Datasets - OpenEI Datasets

    Open Energy Info (EERE)

    DOE Facility Database Data and Resources DOE Facility DatabaseCSV Preview Download Research and Develo... User Facilities Additional Info Field Value Author U.S. Office of...

  2. T-614: Cisco Unified Communications Manager Database Security...

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

    14: Cisco Unified Communications Manager Database Security Vulnerability T-614: Cisco Unified Communications Manager Database Security Vulnerability May 3, 2011 - 7:37am Addthis...

  3. Standard Energy Efficiency Database Platform - 2013 BTO Peer...

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

    Database Platform - 2013 BTO Peer Review Standard Energy Efficiency Database Platform - 2013 BTO Peer Review commlbldgs09prindle040313.pdf More Documents & Publications Buildings...

  4. It's All About the Data: How the Building Performance Database...

    Energy Savers [EERE]

    the Data: How the Building Performance Database is Informing Decisions on Energy Efficiency It's All About the Data: How the Building Performance Database is Informing...

  5. Fault-tolerant distributed transactions for partitioned OLTP databases

    E-Print Network [OSTI]

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

    2012-01-01

    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 ...

  6. 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...

  7. A Welsh speech database: preliminary results. 

    E-Print Network [OSTI]

    Williams, Briony

    1999-01-01

    A speech database for Welsh was recorded in a studio from read text by a few speakers. The purpose is to investigate the acoustic characteristics of Welsh speech sounds and prosody. It can also serve as a resource ...

  8. Deductive Databases: Achievements and Future Directions

    E-Print Network [OSTI]

    Zaniolo, Carlo

    demands that are not answered by conventional DBMS, such as the following: · The need to deal wigh complex to examine a database of medical histories to test a variety of hypotheses about possible causes of diseases

  9. A database of circumstellar OH masers

    E-Print Network [OSTI]

    Engels, D

    2015-01-01

    We present a new database of circumstellar OH masers at 1612, 1665, and 1667 MHz in the Milky Way galaxy. The database (version 2.4) contains 13655 observations and 2341 different stars detected in at least one transition. Detections at 1612\\,MHz are considered to be complete until the end of 2014 as long as they were published in refereed papers. Detections of the main lines (1665 and 1667 MHz) and non-detections in all transitions are included only if published after 1983. The database contains flux densities and velocities of the two strongest maser peaks, the expansion velocity of the shell, and the radial velocity of the star. Links are provided for about 100 stars ($database is possible over the Web (www.hs.uni-hamburg.de/maserdb), allowing cone searches for individual sources and lists of sources. A general search is possible in...

  10. Enabling Geographical Queries to a Botanical Database 

    E-Print Network [OSTI]

    Sato, Go

    2011-11-25

    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. 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...

  12. Proposal for a High Energy Nuclear Database

    E-Print Network [OSTI]

    Brown, David A.; Vogt, Ramona

    2005-01-01

    Proposal for a High Energy Nuclear Database David A. Brown 1it requires the high-energy nuclear physics com- munity’s ?compilations of high-energy nuclear data for applications

  13. An online climate database for Texas 

    E-Print Network [OSTI]

    Nordeen, Michele Lynn

    2000-01-01

    A climate database for the state of Texas has been created from daily observations made at 1336 stations throughout Texas. These stations consist of both fest-order stations and local cooperative weather stations. The ...

  14. Towards Privacy Preserving of Forensic DNA Databases 

    E-Print Network [OSTI]

    Liu, Sanmin

    2012-02-14

    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...

  15. Session title: Distributed and intelligent databases

    SciTech Connect (OSTI)

    Argos, P.; Mewes, H.W.; Frishman, D.

    1996-12-31

    This session focuses on the recent advances in the delivery of information to the biological community concerning genome sequencing and related information. New approaches include interconnecting existing databases, knowledge-based expert systems, interface languages and multiserver management.

  16. 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

  17. 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

  18. DYNAMIC DATABASE INTEGRATION IN A JDBC DRIVER Terrence Mason

    E-Print Network [OSTI]

    Lawrence, Ramon

    -lawrence@uiowa.edu Keywords: integration, database, schema, metadata, annotation, evolution, dynamic, JDBC, conceptualDYNAMIC DATABASE INTEGRATION IN A JDBC DRIVER Terrence Mason Iowa Database and Emerging Iowa Database and Emerging Applications Laboratory, Computer Science University of Iowa Email: ramon

  19. Automating Database Schema Evolution in Information System Upgrades

    E-Print Network [OSTI]

    Zaniolo, Carlo

    Automating Database Schema Evolution in Information System Upgrades Carlo Curino Hyun J. Moon Carlo, and down-time currently created by the database schema evolution process is the source of incessant prob and historical queries for database archives under schema evolution. Keywords Schema Evolution, Database Design

  20. Predictive Database Schema Evolution Hassina BOUNIF, Stefano SPACCAPIETRA

    E-Print Network [OSTI]

    Madiraju, Praveen

    Predictive Database Schema Evolution Hassina BOUNIF, Stefano SPACCAPIETRA Database Laboratory (LBD.spaccapietra@epfl.ch Abstract: This paper proposes a new approach for organizing the evolution of existing database system and easy-to-evolve database schema. Evolution algorithms are tailored to choose the best evolution

  1. Single Database Private Information Retrieval with Logarithmic Communication

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    Single Database Private Information Retrieval with Logarithmic Communication Yan-Cheng Chang of single database private information retrieval, and present schemes with only logarithmic server database private information retrieval (1dPIR) is a cryptographic protocol between a database server, who

  2. 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

  3. 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

  4. 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

  5. Single Database Private Information Retrieval with Logarithmic Communication

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    Single Database Private Information Retrieval with Logarithmic Communication Yan­Cheng Chang of single database private information retrieval, and present schemes with only logarithmic server Single database private information retrieval (1dPIR) is a cryptographic protocol between a database

  6. Private Database Queries Using Somewhat Homomorphic Craig Gentry

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    Private Database Queries Using Somewhat Homomorphic Encryption Dan Boneh Craig Gentry Shai Halevi Frank Wang David J. Wu Abstract In a private database query system, a client issues queries to a database and obtains the results with- out learning anything else about the database and without the server

  7. 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 3: SQLChapter 3: SQL #12;©Silberschatz, Korth and Sudarshan3.2Database System of the Database Joined Relations** #12;©Silberschatz, Korth and Sudarshan3.3Database System Concepts, 5th Edition

  8. I. Course Particulars Number & Title ICS 434 ADVANCED DATABASE SYSTEMS

    E-Print Network [OSTI]

    Adam, Salah

    Description Advanced data models: object-oriented model, and object-relational model, conceptual database. Course Objectives 1. To learn advanced data modeling techniques. 2. To learn how modern database systems an automated database design tool to design complex database systems. 2. Apply object-relational data model

  9. Querying RDF Data from a Graph Database Perspective

    E-Print Network [OSTI]

    Baeza-Yates, Ricardo

    }@dcc.uchile.cl Agenda · Motivations, Problem and Proposal · Database Models · Graph Database Models · RDF as data model of data model with inherent graph structure. · Database models and query languages should support its that a query language for RDF should provide. Database Models Data structures Operators and Query Language

  10. MAC, material accounting database user guide

    SciTech Connect (OSTI)

    Russell, V.K.

    1994-09-22

    The K Basins Material Accounting (MAC) database system user guide describes the user features and functions, and the document is structured like the database menus. This document presents the MAC database system user instructions which explain how to record the movements and configuration of canisters and materials within the K Basins on the computer, the mechanics of handling encapsulation tracking, and administrative functions associated with the system. This document includes the user instructions, which also serve as the software requirements specification for the system implemented on the microcomputer. This includes suggested user keystrokes, examples of screens displayed by the system, and reports generated by the system. It shows how the system is organized, via menus and screens. It does not explain system design nor provide programmer instructions.

  11. Acid Violence in Pakistan

    E-Print Network [OSTI]

    Zia, Taiba

    2013-01-01

    Jordan. “Acid Attacks: Bangladesh’s Efforts to Stop thesubcontinent, especially in Bangladesh and Pakistan, and inon acid crimes in Bangladesh, for instance). Reliable data

  12. Online interaction database: What have we learned

    E-Print Network [OSTI]

    Zadezensky, I.; de Castro, W.; Meyer, J.; Butterweck, V.; Derendorf, H.

    2006-10-25

    ?[Citrus?Reference?Book] 1Center?for?Food?and?Drug?Interaction?Research?and?Education,?University?of?Florida,?Gainesville,?FL Online?Database?For?Grapefruit?Juice?Drug?Interactions:?What?Have?We?Learned?? I.?Zadezensky1,?W.V.?de?Castro1,??J.?Meyer1,?V...?[Citrus?Reference?Book] 1Center?for?Food?and?Drug?Interaction?Research?and?Education,?University?of?Florida,?Gainesville,?FL Online?Database?For?Grapefruit?Juice?Drug?Interactions:?What?Have?We?Learned?? I.?Zadezensky1,?W.V.?de?Castro1,??J.?Meyer1,?V...

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

    SciTech Connect (OSTI)

    Wang, Jy-An John

    2010-08-01

    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.

  14. 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

  15. Using Delay to Defend Against Database Extraction

    E-Print Network [OSTI]

    Cafarella, Michael J.

    a business in competition. This attacker could attempt to hack into the provider's system ­ such attacks, the "crown jewels" of their business are the data that they have organized. If someone could copy their entire database, it would be a competitive catastrophe. Yet, a data provider is in the business

  16. World Gasification Database Now Available from DOE

    Broader source: Energy.gov [DOE]

    A database just released by the U.S. Department of Energy documents the worldwide growth of gasification, the expected technology of choice for future coal-based plants that produce power, fuels, and/or chemicals with near-zero emissions.

  17. Hypercat : A Database for extragalactic astronomy

    E-Print Network [OSTI]

    Ph. Prugniel; G. Maubon

    1999-10-01

    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.

  18. Qunits: queried units in database search

    E-Print Network [OSTI]

    Nandi, Arnab

    2009-01-01

    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...

  19. Databases of problems using LATEX Mark Hickman

    E-Print Network [OSTI]

    Hickman, Mark

    of Canterbury mark.hickman@canterbury.ac.nz Version 1.3 1 OVERVIEW This document describes the package problems. This package allows the management of a database of problems (with optional solutions) within LATEX equation is given by $$ \\pder[2]{u}{t^2} = c^2 \\, \\pder[2]{u}{x^2} \\label{wave} $$ where $c

  20. 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

  1. Case for Staged Database Systems Stavros Harizopoulos

    E-Print Network [OSTI]

    increasing demands performance, high­end DBMS employ parallel processing techniques coupled with plethora­ lithic approach DBMS software lead complex difficult to extend designs. paper introduces a staged design high­per­ formance, evolvable DBMS that tune maintain. propose break the database system into modules

  2. SQL and Java Database Systems Lecture 19

    E-Print Network [OSTI]

    Alechina, Natasha

    1 SQL and Java Database Systems Lecture 19 Natasha Alechina SQL and Java In this Lecture · SQL in Java · SQL from within other Languages · SQL, Java, and JDBC · For More Information · Sun Java tutorial: http://java.sun.com/docs/books/tutorial/jdbc · Connolly and Begg 29.7 SQL and Java SQL and Other

  3. SQL and Java Database Systems Lecture 19

    E-Print Network [OSTI]

    Alechina, Natasha

    SQL and Java Database Systems Lecture 19 Natasha Alechina #12;SQL and Java In this Lecture · SQL in Java · SQL from within other Languages · SQL, Java, and JDBC · For More Information · Sun Java tutorial: http://java.sun.com/docs/books/tutorial/jdbc · Connolly and Begg 29.7 #12;SQL and Java SQL and Other

  4. SQL Data Definition Database Systems Lecture 5

    E-Print Network [OSTI]

    Alechina, Natasha

    SQL Data Definition Database Systems Lecture 5 Natasha Alechina #12;SQL Data Definition In This Lecture · SQL · The SQL language · SQL, the relational model, and E/R diagrams · CREATE TABLE · Columns.6. #12;SQL Data Definition SQL · Originally `Sequel' - Structured English query Language, part of an IBM

  5. SQL Data Definition Database Systems Lecture 5

    E-Print Network [OSTI]

    Alechina, Natasha

    1 SQL Data Definition Database Systems Lecture 5 Natasha Alechina SQL Data Definition In This Lecture · SQL · The SQL language · SQL, the relational model, and E/R diagrams · CREATE TABLE · Columns.6. SQL Data Definition SQL · Originally `Sequel' - Structured English query Language, part of an IBM

  6. 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

  7. 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.

  8. CP'96 Page 1 Constraint Databases

    E-Print Network [OSTI]

    Goldin, Dina Q.

    CP'96 Page 1 Constraint Databases: a lecture in honor of Paris C. Kanellakis Dina Q. Goldin Brown University CP'96 Page 2 Here went the group photo from CP'95 taken from Paris' memorial page http://www.cs.brown.edu/people/pck #12;CP'96 Page 3 Paris C. Kanellakis: professor, Brown University, 1981-1995 here went the Paris

  9. 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

  10. 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 be implemented in a GIS, in a computer-assisted design (CAD) system coupled with a DBMS, in a universal server

  11. Asphaltene damage in matrix acidizing 

    E-Print Network [OSTI]

    Hinojosa, Roberto Antonio

    1996-01-01

    were acidized with three stage treatments of 15% hydrochloric acid (HCl), 12% HCL-3% hydrofluoric acid (HF) and 15% HCL. No additives were used in the acid. Comparisons were made between cores acidized with a variety of saturating fluids. Petrographic...

  12. SEMANTIC WEB APPROACH TO DATABASE INTEGRATION IN THE LIFE SCIENCES

    E-Print Network [OSTI]

    Gerstein, Mark

    of the Human Genome Project (HGP) [1] together with the popularity of the Web (or World Wide Web) [2] has made the inception of HGP, a multitude of Web accessible biological databases have emerged. These databases differ

  13. DB-PABP: a database of polyanion-binding proteins

    E-Print Network [OSTI]

    Fang, Jianwen; Dong, Yinghua; Slamat-Miller, Nazila; Middaugh, C. Russell

    2007-10-04

    scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http...

  14. Evaluation of Functional Data Models for Database Design and Use 

    E-Print Network [OSTI]

    Kulkarni, Krishnarao Gururao

    1983-01-01

    The problems of design, operation, and maintenance of databases using the three most popular database management systems (Hierarchical, CQDASYL/DBTG, and Relational) are well known. Users wishing to use these systems ...

  15. U.S. Life Cycle Inventory Database Roadmap (Brochure) | Department...

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

    U.S. Life Cycle Inventory Database Roadmap (Brochure) U.S. Life Cycle Inventory Database Roadmap (Brochure) Life cycle inventory data are the primary inputs for conducting life...

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

    E-Print Network [OSTI]

    Soltren, José Hiram

    2009-01-01

    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, ...

  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. Spinal palpation: The challenges of information retrieval using available databases

    E-Print Network [OSTI]

    2003-01-01

    Databases Linda S. Murphy, MLIS, Sibylle Reinsch, PhD, Wadieto: Linda S. Murphy, MLIS Susan Samueli Center for

  19. 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.

  20. Stout: Cloudy's Atomic and Molecular Database

    E-Print Network [OSTI]

    Lykins, M L; Kisielius, R; Chatzikos, M; Porter, R L; van Hoof, P A M; Williams, R J R; Keenan, F P; Stancil, P C

    2015-01-01

    We describe a new atomic and molecular database we developed for use in the spectral synthesis code Cloudy. The design of Stout is driven by the data needs of Cloudy, which simulates molecular, atomic, and ionized gas with kinetic temperatures 2.8 K data are stored in a format as close as possible to the original data sources. Few data sources include the full range of data we need. We describe how we fill in the gaps in the data or extrapolate rates beyond their tabulated range. We tabulate data sources both for the atomic spectroscopic parameters and for collision data for the next release of Cloudy. This is not intended as a review of the current status of atomic data, but rather a description of the features of the database which we will build ...

  1. Estimating Pedestrian Accident Exposure: Approaches to a Statewide Pedestrian Exposure Database

    E-Print Network [OSTI]

    Greene-Roesel, Ryan; Diogenes, Mara Chagas; Ragland, David R

    2007-01-01

    Pedestrian Exposure Database, March 23, 2007 Federal TransitNational Transit Database. http://www.ntdprogram.gov/Implementation of a National Database of Air Passenger

  2. 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

    2006-01-01

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

  3. Federated Web-accessible Clinical Data Management within an Extensible NeuroImaging Database

    E-Print Network [OSTI]

    2010-01-01

    Achieving evolvable web-database bioscience applicationsThe Human Clinical Imaging Database (HID) and Toolkit.The database schema is constructed to support the storage of

  4. A KNOWLEDGE BASED SYSTEM FOR PROVIDING INTELLIGENT ACCESS TO A PETROLEUM USER DATABASE

    E-Print Network [OSTI]

    Rosenberg, Steven

    2011-01-01

    INTELLIGENT ACCESS TO A PETROLEUM USER DATABASE StevenINTELLIGENT ACCESS TO A PETROLEUM USER DATABASE StevenINTELLIGENT ACCESS TO A PETROLEUM USER DATABASE Steven

  5. Gasification world database 2007. Current industry status

    SciTech Connect (OSTI)

    NONE

    2007-10-15

    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.

  6. 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

    1996-07-22

    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.

  7. 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

  8. Bridging Relational Database History and the Web: the XML Approach

    E-Print Network [OSTI]

    Zaniolo, Carlo

    Bridging Relational Database History and the Web: the XML Approach Fusheng Wang Integrated Data and queries, and make it easy to pub- lish database history to the Web. In this paper, we focus on the problem of preserving, publishing, and querying ef- ficiently the history of a relational database. Past research

  9. Efficient Temporal Coalescing Query Support in Relational Database Systems

    E-Print Network [OSTI]

    Zaniolo, Carlo

    demand for temporal databases have only in- creased with time; unfortunately, DBMS vendors and standard by the lessons learned from the very history of temporal databases, where past proposals failed to gain much temporal query models with current DBMS engines [5]. Even if temporal database and query model can be well

  10. SCDBR: An Automated Reasoner for Database (Extended Abstract)

    E-Print Network [OSTI]

    Bertossi, Leopoldo

    . In general, theories of action and change, such as the specification of the evolution of a database, includeSCDBR: An Automated Reasoner for Database Updates (Extended Abstract) Leopoldo Bertossi, Marcelo In this paper we describe SCDBR, a system that automates reasoning with specifications of database updates

  11. Meta Object Management and its Application to Database Evolution ?

    E-Print Network [OSTI]

    Scholl, Marc H.

    Meta Object Management and its Application to Database Evolution ? Markus Tresch and Marc H. Scholl evolution, that is, realizing incremental changes to the database schema and their propagation to data objects, and how this approach can be used to build a complete tool for database evolution. 1 Introduction

  12. Efficien and Scalable Data Evolution with Column Oriented Databases

    E-Print Network [OSTI]

    Chen, Yi

    Efficien and Scalable Data Evolution with Column Oriented Databases Ziyang Liu1 , Bin He2 , Hui@us.ibm.com, hhsiao@almaden.ibm.com, yi@asu.edu ABSTRACT Database evolution is the process of updating the schema of a database or data warehouse (schema evolution) and e- volving the data to the updated schema (data evolution

  13. Requirements Ontology and Multirepresentation Strategy for Database Schema Evolution 1

    E-Print Network [OSTI]

    Pottinger, Rachel

    Requirements Ontology and Multirepresentation Strategy for Database Schema Evolution 1 Hassina important utilization field of ontology related to database schemas and which is schema evolution topic and which is related to information systems. That is database schema evolution, an important, complex

  14. Modularization of the DADAISM Ada Database System Architecture

    E-Print Network [OSTI]

    Keller, Arthur M.

    implemen­ tation paradigm is necessary to handle the evolution of database systems over the next fewPage 1 Modularization of the DADAISM Ada Database System Architecture Arthur M. Keller Gio Wiederhold Stanford University Draft of May 21, 1991 Abstract. We describe a new database management system

  15. CODS: Evolving Data Efficiently and Scalably in Column Oriented Databases

    E-Print Network [OSTI]

    Chen, Yi

    evolution is the process of updating the schema of a database or data warehouse (schema evolution) and evolving the data to the updated schema (data evolution). Database evolution is often necessitated processing, evolving the data during a database evolution through SQL queries is shown to be prohibitively

  16. Modularization of the DADAISM Ada Database System Architecture

    E-Print Network [OSTI]

    Keller, Arthur M.

    implemen- tation paradigm is necessary to handle the evolution of database systems over the next fewPage 1 Modularization of the DADAISM Ada Database System Architecture Arthur M. Keller Gio Wiederhold Stanford University Draft of May 21, 1991 Abstract. We describe a new database management system

  17. Dynamic Functional DependenciesandDatabaseAging VICTOR VIANU

    E-Print Network [OSTI]

    Madiraju, Praveen

    of dynamic constraints on database evolution. Both static and dynamic constraints are used in conjunction future evolution of the database is briefly discussedusing the notions of survivability and survivability in the real world concerns the laws that govern their evolution in time. Many database models capture

  18. Temporal Conditions and Integrity Constraints in Active Database Systems \\Lambda

    E-Print Network [OSTI]

    Wolfson, Ouri E.

    to specify conditions that involve both, events and database states, and their evolution over time. BasicallyTemporal Conditions and Integrity Constraints in Active Database Systems \\Lambda A. Prasad Sistla, for specifying conditions and events in the rules for active database sys­ tem. This language permits

  19. The SUPERFAMILY database in 2007: families and functions

    E-Print Network [OSTI]

    -level functional annotation. The SUPERFAMILY database can be used for general protein evolution and superfamilyThe SUPERFAMILY database in 2007: families and functions Derek Wilson*, Martin Madera1 , Christine The SUPERFAMILY database provides protein domain assignments, at the SCOP `superfamily' level, for the predicted

  20. Development of the Global Earthquake Model's neotectonic fault database

    E-Print Network [OSTI]

    New Hampshire, University of

    Development of the Global Earthquake Model's neotectonic fault database Annemarie Christophersen1 database and a unique graphical interface for the compilation of new fault data. A key design principle is that of an electronic field notebook for capturing observations a geologist would make about a fault. The database

  1. Efficient Consistency Proofs for Generalized Queries on a Committed Database

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    Efficient Consistency Proofs for Generalized Queries on a Committed Database Rafail Ostrovsky UCLA@csail.mit.edu July 20, 2004 Abstract A consistent query protocol (CQP) allows a database owner to publish a very short string c which commits her and everybody else to a particular database D, so that any copy

  2. Secure Database Commitments and Universal Arguments of Quasi Knowledge

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    Secure Database Commitments and Universal Arguments of Quasi Knowledge Melissa Chase Microsoft@dia.unisa.it Abstract In this work we focus on a simple database commitment functionality where besides the standard) of the proposed functionality. The first result of this submission consists in defining "secure" database

  3. THE DESIGN AND IMPLEMENTATION OF A DATA LEVEL DATABASE

    E-Print Network [OSTI]

    Yoo, S. J. Ben

    THE DESIGN AND IMPLEMENTATION OF A DATA LEVEL DATABASE INFERENCE DETECTION SYSTEM Raymond W. Yip and Karl N. Levitt Abstract: Inference is a way to subvert access control mechanisms of database systems. Most existing work on inference detection relies on analyzing func- tional dependencies in the database

  4. 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

  5. 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, Korth and Sudarshan12.2Database System Concepts - 5th Edition, Oct 4, 2006 Chapter 12: Indexing Multiple-Key Access #12;©Silberschatz, Korth and Sudarshan12.3Database System Concepts - 5th Edition, Oct 4

  6. 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

  7. 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

  8. SPIN Funding Database Instruction Book Useful Links & Contacts................................................................................................................................1

    E-Print Network [OSTI]

    Hill, Wendell T.

    SPIN Funding Database Instruction Book Contents Useful Links & Contacts .....................................................................................................................................23 InfoEd SPIN Funding Database Useful Links & Contacts To Create an Account - http are on the University of Maryland network, you do not need an account to search the database ­ only if you want

  9. Image database clustering with SVM-based class personalization

    E-Print Network [OSTI]

    Le Saux, Bertrand

    Image database clustering with SVM-based class personalization Bertrand Le Saux and Nozha Boujemaa present in this paper a robust approach to organize image databases: the Adaptive Robust Competition (ARC). This algorithm relies on a non-supervised database categorization, coupled with a selection of prototypes in each

  10. Efficient Consistency Proofs for Generalized Queries on a Committed Database

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    Efficient Consistency Proofs for Generalized Queries on a Committed Database #3; Rafail Ostrovsky asmith@csail.mit.edu July 20, 2004 Abstract A consistent query protocol (CQP) allows a database owner to publish a very short string c which commits her and everybody else to a particular database D, so that any

  11. 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

  12. PRTAD: A DATABASE FOR PROTEIN RESIDUE TORSION ANGLE DISTRIBUTIONS

    E-Print Network [OSTI]

    PRTAD: A DATABASE FOR PROTEIN RESIDUE TORSION ANGLE DISTRIBUTIONS By Xiaoyong Sun Di Wu Robert­0436 Phone: 612-624-6066 Fax: 612-626-7370 URL: http://www.ima.umn.edu #12;PRTAD: A Database for Protein@iastate.edu Abstract PRTAD is a dedicated database and structural bioinformatics system for protein analysis

  13. VDBL (Vienna Database Library) Version 1.2

    E-Print Network [OSTI]

    Schichl, Hermann

    VDBL (Vienna Database Library) Version 1.2 Reference Manual Hermann Schichl University of Vienna Documentation 20 10 File Documentation 190 1 Introduction The Vienna Database Library (VDBL) is a in-memory database developed with generic programming in mind. It uses STL containers like map and vector to organize

  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, 2006 #12;©Silberschatz, Korth and Sudarshan11.2Database System Concepts - 5th Edition Chapter 11-Dictionary Storage #12;©Silberschatz, Korth and Sudarshan11.3Database System Concepts - 5th Edition Classification

  15. Conceptual Modelling of Database Applications Using an Extended ER Model

    E-Print Network [OSTI]

    Gogolla, Martin - Fachbereich 3

    Conceptual Modelling of Database Applications Using an Extended ER Model Data and Knowledge is divided into the modelling of admissible database state evolutions by means of temporal integrity184/1) #12; H.2.1 [Database Management] Logical Design -- Data models; Schema and subschema. H.2

  16. DEMIDS: A Misuse Detection System for Database Systems

    E-Print Network [OSTI]

    Yoo, S. J. Ben

    information stored in database systems DBS, existing security models are insu cient to prevent misuseDEMIDS: A Misuse Detection System for Database Systems Christina Yip Chung, Michael Gertz, Karl the information stored in the database system against misuse, they are seldom used by security o cers because

  17. IMPLEMENTING RELATIONSHIPS IN AN OBJECT-ORIENTED DATABASE

    E-Print Network [OSTI]

    Doherty, Michael

    OF RHODE ISLAND 1992 i #12;Abstract Semantic database models have shown the importance and utility of arbi- trary user-de ned relationships to de ne the semantics of database information. Object-oriented models on that model. The data de nition language is automat- ically mapped to a database implementation which

  18. The Feasibility of Outsourced Database Search in the Plain Model

    E-Print Network [OSTI]

    International Association for Cryptologic Research (IACR)

    The Feasibility of Outsourced Database Search in the Plain Model Carmit Hazay Hila Zarosim Abstract. In this paper, we focus on the outsourced database search problem which is highly motivated in the context of delegatable computing since it offers storage alternatives for massive databases, that may contain

  19. Performance Modelling of Database Contention using Queueing Petri Nets

    E-Print Network [OSTI]

    Knottenbelt, William J.

    Performance Modelling of Database Contention using Queueing Petri Nets David Coulden Rasha Osman Petri Net model of table-level database locking. We show that this model predicts mean response times modelling, database locking. 1. INTRODUCTION The data landscape has changed dramatically in size

  20. Jeroen Weijers Universitt Tbingen1 A Database Coprocessor for Haskell

    E-Print Network [OSTI]

    Grust, Torsten

    into SQL Runtime Heap Database System Input Data Haskell Program Result 2 Dienstag, 7. September 2010 #12;Jeroen Weijers Universität Tübingen Haskell turns into SQL Runtime Heap Database System Input Data SQL into SQL Runtime Heap Database System Input Data SQL Queries Result 2 Dienstag, 7. September 2010 #12

  1. Conference and Journal Publications in Database Systems and Theory

    E-Print Network [OSTI]

    Zhou, Yuanyuan

    Conference and Journal Publications in Database Systems and Theory This document rates the conferences and journal publications in the database area with respect to quality and impact. As in many other with strong interactions but often distinct publication venues. We therefore discuss separately the database

  2. TECHNICAL NOTE Open Access Searching the protein structure database for

    E-Print Network [OSTI]

    Powers, Robert

    TECHNICAL NOTE Open Access Searching the protein structure database for ligand-binding site RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence

  3. The CEBAF Element Database and Related Operational Software

    SciTech Connect (OSTI)

    Larrieu, Theodore; Slominski, Christopher; Keesee, Marie; Turner, Dennison; Joyce, Michele

    2015-09-01

    The newly commissioned 12GeV CEBAF accelerator relies on a flexible, scalable and comprehensive database to define the accelerator. This database delivers the configuration for CEBAF operational tools, including hardware checkout, the downloadable optics model, control screens, and much more. The presentation will describe the flexible design of the CEBAF Element Database (CED), its features and assorted use case examples.

  4. Online Energy Estimation of Relational Operations in Database Systems

    E-Print Network [OSTI]

    Tu, Yicheng

    1 Online Energy Estimation of Relational Operations in Database Systems Zichen Xu # , Yi-Cheng Tu known to consume a large amount of energy. As databases are one of the major applications in a data center, building energy-aware database systems has become an active research topic recently

  5. Database Managament IS&M Option Mark Levene

    E-Print Network [OSTI]

    Levene, Mark

    Book Stores · The Invisible Web Initial Definition of a Database. A database is an organised collection Relation ISBN LOCATION QUANTITY LOAN 0-8053-0249-2 Science 1 0 0-201-52878-9 Main 3 2 0-07-044754-3 Main 1Database Managament IS&M Option Mark Levene Email: m.levene@dcs.bbk.ac.uk Web: http

  6. A DISTORTION FREE WATERMARK FRAMEWORK FOR RELATIONAL DATABASES

    E-Print Network [OSTI]

    Cortesi, Tino

    Interpretation. Abstract: In this paper we introduce a distortion free invisible watermarking technique in pieces to parties specialized in mining it, e.g. sales patterns database, oil drilling data, financial as required in some applications. The first well-known database watermarking scheme for relational databases

  7. Database-Aware Semantically-Smart Storage Muthian Sivathanu

    E-Print Network [OSTI]

    Arpaci-Dusseau, Andrea

    the differ- ences when building database-aware storage. We find that semantically-smart disk systems can to require changes for semantically smart storage. To build database-aware storage, we investigate twoDatabase-Aware Semantically-Smart Storage Muthian Sivathanu , Lakshmi N. Bairavasundaram , Andrea C

  8. Score Region Algebra: Building a Transparent XML-IR Database

    E-Print Network [OSTI]

    Hiemstra, Djoerd

    imple- mented the algebra operators in a prototype system on top of a low-level database kernel algebra framework on top of any low-level physical database engine or existing RDBMS, allowing a more sysScore Region Algebra: Building a Transparent XML-IR Database Vojkan Mihajlovi´c Henk Ernst Blok

  9. Oracle Database DBFS Hierarchical Storage Overview

    SciTech Connect (OSTI)

    Rivenes, A

    2011-07-25

    The National Ignition Facility (NIF) at the Lawrence Livermore National Laboratory creates large numbers of images during each shot cycle for the analysis of optics, target inspection and target diagnostics. These images must be readily accessible once they are created and available for the 30 year lifetime of the facility. The Livermore Computing Center (LC) runs a High Performance Storage System (HPSS) that is capable of storing NIF's estimated 1 petabyte of diagnostic images at a fraction of what it would cost NIF to operate its own automated tape library. With Oracle 11g Release 2 database, it is now possible to create an application transparent, hierarchical storage system using the LC's HPSS. Using the Oracle DBMS-LOB and DBMS-DBFS-HS packages a SecureFile LOB can now be archived to storage outside of the database and accessed seamlessly through a DBFS 'link'. NIF has chosen to use this technology to implement a hierarchical store for its image based SecureFile LOBs. Using a modified external store and DBFS links, files are written to and read from a disk 'staging area' using Oracle's backup utility. Database external procedure calls invoke OS based scripts to manage a staging area and the transfer of the backup files between the staging area and the Lab's HPSS.

  10. RUNNING HEAD: THE FOSSIL CALIBRATION DATABASE Title: The Fossil Calibration Database, A New Resource for Divergence Dating

    E-Print Network [OSTI]

    Benton, Michael

    1 RUNNING HEAD: THE FOSSIL CALIBRATION DATABASE Title: The Fossil Calibration Database, A New Street NW, Washington, DC, 20059, USA; 19 Centre of Evolutionary and Ecological Studies, Marine Evolution continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http

  11. 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/

  12. Ceramic Technology Project database: September 1990 summary report

    SciTech Connect (OSTI)

    Keyes, B.L.P.

    1992-06-01

    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.

  13. Formic Acid Mechanical,

    E-Print Network [OSTI]

    Lee, Tonghun

    that make building block chemicals. Ethanol is blended with gasoline, reducing our dependence on petroleum for high valued products, including: Aspartic acid Glucaric acid Glycerol Sorbitol Some companies already

  14. Plant fatty acid hydroxylases

    DOE Patents [OSTI]

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

    2001-01-01

    This invention relates to plant fatty acyl hydroxylases. Methods to use conserved amino acid or nucleotide sequences to obtain plant fatty acyl hydroxylases are described. Also described is the use of cDNA clones encoding a plant hydroxylase to produce a family of hydroxylated fatty acids in transgenic plants. In addition, the use of genes encoding fatty acid hydroxylases or desaturases to alter the level of lipid fatty acid unsaturation in transgenic plants is described.

  15. 1997 Oxford University Press 33893402Nucleic Acids Research, 1997, Vol. 25, No. 17 Gapped BLAST and PSI-BLAST: a new generation of

    E-Print Network [OSTI]

    Batzoglou, Serafim

    for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA, Alejandro A. Schäffer1, Jinghui Zhang, Zheng Zhang2, Webb Miller2 and David J. Lipman National Center, 1Laboratory of Genetic Disease Research, National Human Genome Research Institute, National

  16. 732741 Nucleic Acids Research, 2008, Vol. 36, No. 3 Published online 15 December 2007 doi:10.1093/nar/gkm1096

    E-Print Network [OSTI]

    Elliot, Marie A.

    J. Haiser1 , Fedor V. Karginov2 , Gregory J. Hannon2 and Marie A. Elliot1, * 1 Department of Biology

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

    E-Print Network [OSTI]

    onto either magnetic beads or gold nanoparticles grafted with the com- plementary ODN, as shown proteins Christel Le Bon1 , Eduardo Antonio Della Pia2 , Fabrice Giusti1 , No´emie Lloret2 , Manuela) are specially designed amphi- pathic polymers that stabilize membrane proteins (MPs) in aqueous solutions

  18. Published online 21 May 2009 Nucleic Acids Research, 2009, Vol. 37, No. 12 e87 doi:10.1093/nar/gkp408

    E-Print Network [OSTI]

    and (iii) high-throughput virtual screening of this library to select aptamers with binding affinity to a desired small molecule. We developed a set of criteria that allows one to select a sequence with potential/gkp408 In silico selection of RNA aptamers Yaroslav Chushak1, * and Morley O. Stone2 1 Biotechnology HPC

  19. 1020 Nucleic Acids Research, 2008, Vol. 36, No. 1 Published online 2 November 2007 doi:10.1093/nar/gkm915

    E-Print Network [OSTI]

    Redfield, Rosemary J. "Rosie"

    to understanding the physiological role of DNA uptake. We have isolated mutations in H. influenzae sxy that greatly translational efficiency of sxy while independently triggering the sugar starva- tion regulator (CRP activation signals that energy supplies are limited. INTRODUCTION Natural competence, the ability to take up

  20. Published online 15 December 2014 Nucleic Acids Research, 2015, Vol. 43, No. 4 e22 doi: 10.1093/nar/gku1250

    E-Print Network [OSTI]

    Petrov, Dmitri

    , France, 3 Genomics, Bioinformatics and Evolution Group, Institut de Biotecnologia i de Biomedicina - IBB

  1. Published online 26 March 2015 Nucleic Acids Research, 2015, Vol. 43, No. 8 41634178 doi: 10.1093/nar/gkv247

    E-Print Network [OSTI]

    Pikaard, Craig

    compositions in plants. In all eukaryotes examined to date, AC40 and AC19 subunits are common to Pol I (a.k.a. Pol A) and Pol III (a.k.a. Pol C) and are encoded by single genes. Surprisingly, A. thaliana

  2. 9034 Chem. Commun., 2010, 46, 90349036 This journal is c The Royal Society of Chemistry 2010 Sustained release of nucleic acids from polymeric nanoparticles using

    E-Print Network [OSTI]

    are produced by precipitating a water-in-oil microemulsion in supercritical CO2. The microemulsion consists biodegradable polymers using supercritical carbon dioxide (SC-CO2) as an anti-solvent can be successfully used of the fluid and thereby solubility of the polymer and drug. SC-CO2 is also non-tox

  3. Volume 15 Number 11 1987 Nucleic Acids Research Characterization of a cDNA clone coding for a sea urchin histone H2A variant related to the

    E-Print Network [OSTI]

    Ernst, Susan G.

    Miller, Carol A.Brenner', Catherine Nocente-McGrath, Susan Francis and Robert Mclsaac Department urchin histone H2A variant related to the H2A.F/Z histone protein in vertebrates Susan G.Ernst*, Heidi

  4. Montana 310 Permit Database | Open Energy Information

    Open Energy Info (EERE)

    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 QA:QAsource History ViewMayo, Maryland: Energy ResourcesDec(Pritchett, 2004)Michigan: EnergyNew0 Permit Database Jump

  5. International Forest Policy Database | Open Energy Information

    Open Energy Info (EERE)

    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 QA:QAsource History View NewTexas: Energy ResourcesOrder at 8, 13Renewable Power JumpForest Policy Database Jump to:

  6. NAMA Database Wiki | Open Energy Information

    Open Energy Info (EERE)

    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 QA:QA J-E-1 SECTION J APPENDIX ECoop Inc Jump to: navigation,Mereg GmbHMontebalitoMtMxEnergyDatabase Wiki Jump to:

  7. NEPA Database | OpenEI Community

    Open Energy Info (EERE)

    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 QA:QA J-E-1 SECTION J APPENDIX ECoop Inc Jump to: navigation,Mereg GmbHMontebalitoMtMxEnergyDatabaseNEO CorporationNEPA

  8. DOE Research and Development Accomplishments Database Browse

    Office of Scientific and Technical Information (OSTI)

    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 Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantity of NaturalDukeWakefield Municipal GasAdministration Medal01Technical Information--Scientific andOfficeBlogDatabase

  9. Coal Power Plant Database | Open Energy Information

    Open Energy Info (EERE)

    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 QA:QA J-E-1 SECTION J APPENDIX ECoopButtePower Ventures Jump to: navigation, searchClover Hill HighPower Plant Database

  10. Environment/Health/Safety (EHS): 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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would like submitKansasCommunities EnergyU.S.Engineering Metal(2)Environment,1.Databases

  11. Lessons Learned Database | Department of Energy

    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: Alternative Fuels Data Center Homesum_a_epg0_fpd_mmcf_m.xls" ,"Available from WebQuantityBonneville Power Administration would likeUniverseIMPACTThousand CubicResourcelogo and-E C H N ILessons Learned Database Lessons

  12. Database Fundamentals: 2File: N_drive:\\jhu\\class\\1995\\db-fund.ppt 1994, 1995 Robert Robbins What is a Database?

    E-Print Network [OSTI]

    Database Fundamentals: 2File: N_drive:\\jhu\\class\\1995\\db-fund.ppt © 1994, 1995 Robert Robbins What is a Database? General: · A database is any collection of related data. Restrictive: · A database world. The portion of the real world relevant to the database is sometimes referred to as the universe

  13. Microorganisms for producing organic acids

    DOE Patents [OSTI]

    Pfleger, Brian Frederick; Begemann, Matthew Brett

    2014-09-30

    Organic acid-producing microorganisms and methods of using same. The organic acid-producing microorganisms comprise modifications that reduce or ablate AcsA activity or AcsA homolog activity. The modifications increase tolerance of the microorganisms to such organic acids as 3-hydroxypropionic acid, acrylic acid, propionic acid, lactic acid, and others. Further modifications to the microorganisms increase production of such organic acids as 3-hydroxypropionic acid, lactate, and others. Methods of producing such organic acids as 3-hydroxypropionic acid, lactate, and others with the modified microorganisms are provided. Methods of using acsA or homologs thereof as counter-selectable markers are also provided.

  14. ProQuest Databases This is a collection of databases covering a wide range of disciplines. Most of the databases available in this collection

    E-Print Network [OSTI]

    Po, Lai-Man

    to view the list of all databases or to change selection of databases. 1. Enter search terms. Check box(es) to limit search. Optional. 2. Click to start searching #12;2 Advanced Search 1. Enter search term(s). 2. Select an operator to combine terms*. 3. Select the field to search. 4. Click to start searching. Check

  15. Calibration of the MACHO Photometry Database

    E-Print Network [OSTI]

    C. Alcock; R. A. Allsman; D. R. Alves; T. S. Axelrod; A. C. Becker; D. P. Bennett; K. H. Cook; A. J. Drake; K. C. Freeman; K. Griest; M. J. Lehner; S. L. Marshall; D. Minniti; B. A. Peterson; M. R. Pratt; C. A. Nelson; P. J. Quinn; C. W. Stubbs; W. Sutherland; A. B. Tomaney; D. L. Welch

    1999-09-14

    The MACHO Project is a microlensing survey that monitors the brightnesses of 60 million stars in the Large Magellanic Cloud (LMC), Small Magellanic Cloud, and Galactic bulge. Our database presently contains about 80 billion photometric measurements, a significant fraction of all astronomical photometry. We describe the calibration of MACHO two-color photometry and transformation to the standard Kron-Cousins V and R system. Calibrated MACHO photometry may be properly compared with all other observations on the Kron-Cousins standard system, enhancing the astrophysical value of these data. For 9 million stars in the LMC bar, independent photometric measurements of 20,000 stars with V photometry with published photometric sequences and new Hubble Space Telescope observations shows agreement. The current calibration zero-point uncertainty for the remainder of the MACHO photometry database is estimated to be +- 0.10 mag in V or R and +-0.04 mag in (V-R). We describe the first application of calibrated MACHO photometry data: the construction of a color-magnitude diagram used to calculate our experimental sensitivity to detect microlensing in the LMC.

  16. Current status of the CATS database

    E-Print Network [OSTI]

    O. V. Verkhodanov; S. A. Trushkin; H. Andernach; V. N. Chernenkov

    2007-05-21

    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.

  17. Using XML to Build Efficient Transaction-Time Temporal Database Systems on Relational Databases

    E-Print Network [OSTI]

    Zaniolo, Carlo

    (virtual) representations of the database history, (b) XQuery to express powerful temporal queries with time [1, 2]; unfortunately, DBMS vendors and standard groups have not moved aggressively to extend, we propose a very useful generalization of this idea, by showing that the evolution history of a rela

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

    E-Print Network [OSTI]

    ) provides a holistic evaluation meth- odology and a consistent framework for making better- informed- ingful results. The U.S. LCI Database (www.nrel.gov/ lci) was initiated in 2003 to fulfill the need, product purchases, process performance, and educa- tion systems. The use of LCA for product and service

  19. Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm

    E-Print Network [OSTI]

    Kind, T; Fiehn, O

    2006-01-01

    literature: the Chemical Abstracts Service (CAS) database. ADatabase name Chemical Abstracts (CAS) Beilstein Database (

  20. Search for: All records | SciTech Connect

    Office of Scientific and Technical Information (OSTI)

    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...