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Sample records for cambridge structural database

  1. The Cambridge Structural Database.

    Science.gov (United States)

    Groom, Colin R; Bruno, Ian J; Lightfoot, Matthew P; Ward, Suzanna C

    2016-04-01

    The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.

  2. The Cambridge Structural Database.

    Science.gov (United States)

    Groom, Colin R; Bruno, Ian J; Lightfoot, Matthew P; Ward, Suzanna C

    2016-04-01

    The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface. PMID:27048719

  3. The Cambridge Structural Database in retrospect and prospect.

    Science.gov (United States)

    Groom, Colin R; Allen, Frank H

    2014-01-13

    The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal-organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700,000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. Nearly 40,000 new structures are added each year. As X-ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self-financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC's funding model in relation to open access and open data paradigms.

  4. The Cambridge Structural Database in retrospect and prospect.

    Science.gov (United States)

    Groom, Colin R; Allen, Frank H

    2014-01-13

    The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal-organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700,000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. Nearly 40,000 new structures are added each year. As X-ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self-financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC's funding model in relation to open access and open data paradigms. PMID:24382699

  5. Applications of the Cambridge Structural Database in chemical education.

    Science.gov (United States)

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

  6. Applications of the Cambridge Structural Database in chemical education.

    Science.gov (United States)

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

  7. WebCSD: the online portal to the Cambridge Structural Database

    OpenAIRE

    Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

    2010-01-01

    WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer.

  8. The Cambridge Structural Database: a quarter of a million crystal structures and rising.

    Science.gov (United States)

    Allen, Frank H

    2002-06-01

    The Cambridge Structural Database (CSD) now contains data for more than a quarter of a million small-molecule crystal structures. The information content of the CSD, together with methods for data acquisition, processing and validation, are summarized, with particular emphasis on the chemical information added by CSD editors. Nearly 80% of new structural data arrives electronically, mostly in CIF format, and the CCDC acts as the official crystal structure data depository for 51 major journals. The CCDC now maintains both a CIF archive (more than 73,000 CIFs dating from 1996), as well as the distributed binary CSD archive; the availability of data in both archives is discussed. A statistical survey of the CSD is also presented and projections concerning future accession rates indicate that the CSD will contain at least 500,000 crystal structures by the year 2010.

  9. Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

    Science.gov (United States)

    Allen, Frank H; Motherwell, W D Samuel

    2002-06-01

    The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

  10. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

    Science.gov (United States)

    Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

    2011-01-01

    Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

  11. Fiftieth Anniversary of the Cambridge Structural Database and Thirty Years of Its Use in Croatia

    Directory of Open Access Journals (Sweden)

    Kojić-Prodić B.

    2015-07-01

    Full Text Available This article is dedicated to the memory of Dr. F. H. Allen and the 50th anniversary of the Cambridge Crystallographic Data Centre (CCDC; the world-renowned centre for deposition and control of crystallographic data including atomic coordinates that define the three-dimensional structures of organic molecules and metal complexes containing organic ligands. The mission exposed at the web site (http://www.ccdc.cam.ac.uk is clearly stated: “The Cambridge Crystallographic Data Centre (CCDC is dedicated to the advancement of chemistry and crystallography for the public benefit through providing high quality information, software and services.” The Cambridge Structural Database (CSD, one among the first established electronic databases, nowadays is one of the most significant crystallographic databases in the world. In the International Year of Crystallography 2014, the CSD announced in December over 750,000 deposited structures. The use of the extensive and rapidly growing database needs support of sophisticated and efficient software for checking, searching, analysing, and visualising structural data. The seminal role of the CSD in researches related to crystallography, chemistry, materials science, solid state physics and chemistry, (biotechnology, life sciences, and pharmacology is widely known. The important issues of the CCDC are the accuracy of deposited data and development of software for checking the data. Therefore, the Crystallographic Information File (CIF is introduced as the standard text file format for representing crystallographic information. Among the most important software for users is ConQuest, which enables searching all the CSD information fields, and the web implementation WebCSD software. Mercury is available for visualisation of crystal structures and crystal morphology including intra- and intermolecular interactions with graph-set notations of hydrogen bonds, and analysis of geometrical parameters. The CCDC gives even

  12. Characteristic Conformation of Mosher’s Amide Elucidated Using the Cambridge Structural Database

    Directory of Open Access Journals (Sweden)

    Akio Ichikawa

    2015-07-01

    Full Text Available Conformations of the crystalline 3,3,3-trifluoro-2-methoxy-2-phenylpropanamide derivatives (MTPA amides deposited in the Cambridge Structural Database (CSD were examined statistically as Racid-enantiomers. The majority of dihedral angles (48/58, ca. 83% of the amide carbonyl groups and the trifluoromethyl groups ranged from –30° to 0° with an average angle θ1 of −13°. The other conformational properties were also clarified: (1 one of the fluorine atoms was antiperiplanar (ap to the amide carbonyl group, forming a staggered conformation; (2 the MTPA amides prepared from primary amines showed a Z form in amide moieties; (3 in the case of the MTPA amide prepared from a primary amine possessing secondary alkyl groups (i.e., Mosher-type MTPA amide, the dihedral angles between the methine groups and the carbonyl groups were syn and indicative of a moderate conformational flexibility; (4 the phenyl plane was inclined from the O–Cchiral bond of the methoxy moiety with an average dihedral angle θ2 of +21°; (5 the methyl group of the methoxy moiety was ap to the ipso-carbon atom of the phenyl group.

  13. Characteristic conformation of Mosher's amide elucidated using the cambridge structural database.

    Science.gov (United States)

    Ichikawa, Akio; Ono, Hiroshi; Mikata, Yuji

    2015-07-16

    Conformations of the crystalline 3,3,3-trifluoro-2-methoxy-2-phenylpropanamide derivatives (MTPA amides) deposited in the Cambridge Structural Database (CSD) were examined statistically as Racid-enantiomers. The majority of dihedral angles (48/58, ca. 83%) of the amide carbonyl groups and the trifluoromethyl groups ranged from -30° to 0° with an average angle θ1 of -13°. The other conformational properties were also clarified: (1) one of the fluorine atoms was antiperiplanar (ap) to the amide carbonyl group, forming a staggered conformation; (2) the MTPA amides prepared from primary amines showed a Z form in amide moieties; (3) in the case of the MTPA amide prepared from a primary amine possessing secondary alkyl groups (i.e., Mosher-type MTPA amide), the dihedral angles between the methine groups and the carbonyl groups were syn and indicative of a moderate conformational flexibility; (4) the phenyl plane was inclined from the O-Cchiral bond of the methoxy moiety with an average dihedral angle θ2 of +21°; (5) the methyl group of the methoxy moiety was ap to the ipso-carbon atom of the phenyl group.

  14. Crystal structures of four δ-keto esters and a Cambridge Structural Database analysis of cyano-halogen interactions.

    Science.gov (United States)

    Kamal, Kulsoom; Maurya, Hardesh K; Gupta, Atul; Vasudev, Prema G

    2015-10-01

    The revived interest in halogen bonding as a tool in pharmaceutical cocrystals and drug design has indicated that cyano-halogen interactions could play an important role. The crystal structures of four closely related δ-keto esters, which differ only in the substitution at a single C atom (by H, OMe, Cl and Br), are compared, namely ethyl 2-cyano-5-oxo-5-phenyl-3-(piperidin-1-yl)pent-2-enoate, C19H22N2O3, (1), ethyl 2-cyano-5-(4-methoxyphenyl)-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C20H24N2O4, (2), ethyl 5-(4-chlorophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21ClN2O3, (3), and the previously published ethyl 5-(4-bromophenyl)-2-cyano-5-oxo-3-(piperidin-1-yl)pent-2-enoate, C19H21BrN2O3, (4) [Maurya, Vasudev & Gupta (2013). RSC Adv. 3, 12955-12962]. The molecular conformations are very similar, while there are differences in the molecular assemblies. Intermolecular C-H...O hydrogen bonds are found to be the primary interactions in the crystal packing and are present in all four structures. The halogenated derivatives have additional aromatic-aromatic interactions and cyano-halogen interactions, further stabilizing the molecular packing. A database analysis of cyano-halogen interactions using the Cambridge Structural Database [CSD; Groom & Allen (2014). Angew. Chem. Int. Ed. 53, 662-671] revealed that about 13% of the organic molecular crystals containing both cyano and halogen groups have cyano-halogen interactions in their packing. Three geometric parameters for the C-X...N[triple-bond]C interaction (X = F, Cl, Br or I), viz. the N...X distance and the C-X...N and C-N...X angles, were analysed. The results indicate that all the short cyano-halogen contacts in the CSD can be classified as halogen bonds, which are directional noncovalent interactions.

  15. Using the Cambridge Structural Database to Teach Molecular Geometry Concepts in Organic Chemistry

    Science.gov (United States)

    Wackerly, Jay Wm.; Janowicz, Philip A.; Ritchey, Joshua A.; Caruso, Mary M.; Elliott, Erin L.; Moore, Jeffrey S.

    2009-01-01

    This article reports a set of two homework assignments that can be used in a second-year undergraduate organic chemistry class. These assignments were designed to help reinforce concepts of molecular geometry and to give students the opportunity to use a technological database and data mining to analyze experimentally determined chemical…

  16. Hydrogen-bond landscapes, geometry and energetics of squaric acid and its mono- and dianions: a Cambridge Structural Database, IsoStar and computational study.

    Science.gov (United States)

    Allen, Frank H; Cruz-Cabeza, Aurora J; Wood, Peter A; Bardwell, David A

    2013-10-01

    As part of a programme of work to extend central-group coverage in the Cambridge Crystallographic Data Centre's (CCDC) IsoStar knowledge base of intermolecular interactions, we have studied the hydrogen-bonding abilities of squaric acid (H2SQ) and its mono- and dianions (HSQ(-) and SQ(2-)) using the Cambridge Structural Database (CSD) along with dispersion-corrected density functional theory (DFT-D) calculations for a range of hydrogen-bonded dimers. The -OH and -C=O groups of H2SQ, HSQ(-) and SQ(2-) are potent donors and acceptors, as indicated by their hydrogen-bond geometries in available crystal structures in the CSD, and by the attractive energies calculated for their dimers with acetone and methanol, which were used as model acceptors and donors. The two anions have sufficient examples in the CSD for their addition as new central groups in IsoStar. It is also shown that charge- and resonance-assisted hydrogen bonds involving H2SQ and HSQ(-) are similar in strength to those made by carboxylate COO(-) acceptors, while hydrogen bonds made by the dianion SQ(2-) are somewhat stronger. The study reinforces the value of squaric acid and its anions as cocrystal formers and their actual and potential importance as isosteric replacements for carboxylic acid and carboxylate functions.

  17. Hydrogen-bond landscapes, geometry and energetics of squaric acid and its mono- and dianions: a Cambridge Structural Database, IsoStar and computational study.

    Science.gov (United States)

    Allen, Frank H; Cruz-Cabeza, Aurora J; Wood, Peter A; Bardwell, David A

    2013-10-01

    As part of a programme of work to extend central-group coverage in the Cambridge Crystallographic Data Centre's (CCDC) IsoStar knowledge base of intermolecular interactions, we have studied the hydrogen-bonding abilities of squaric acid (H2SQ) and its mono- and dianions (HSQ(-) and SQ(2-)) using the Cambridge Structural Database (CSD) along with dispersion-corrected density functional theory (DFT-D) calculations for a range of hydrogen-bonded dimers. The -OH and -C=O groups of H2SQ, HSQ(-) and SQ(2-) are potent donors and acceptors, as indicated by their hydrogen-bond geometries in available crystal structures in the CSD, and by the attractive energies calculated for their dimers with acetone and methanol, which were used as model acceptors and donors. The two anions have sufficient examples in the CSD for their addition as new central groups in IsoStar. It is also shown that charge- and resonance-assisted hydrogen bonds involving H2SQ and HSQ(-) are similar in strength to those made by carboxylate COO(-) acceptors, while hydrogen bonds made by the dianion SQ(2-) are somewhat stronger. The study reinforces the value of squaric acid and its anions as cocrystal formers and their actual and potential importance as isosteric replacements for carboxylic acid and carboxylate functions. PMID:24056361

  18. Hydrogen-bond landscapes, geometry and energetics of squaric acid and its mono- and dianions: a Cambridge Structural Database, IsoStar and computational study

    NARCIS (Netherlands)

    F.H. Allen; A.J. Cruz-Cabeza; P.A. Wood; D.A. Bardwell

    2013-01-01

    As part of a programme of work to extend central-group coverage in the Cambridge Crystallographic Data Centre's (CCDC) IsoStar knowledge base of intermolecular interactions, we have studied the hydrogen-bonding abilities of squaric acid (H(2)SQ) and its mono-and dianions (HSQ(-) and SQ(2-)) using th

  19. The Cambridge MRI database for animal models of Huntington disease.

    Science.gov (United States)

    Sawiak, Stephen J; Morton, A Jennifer

    2016-01-01

    We describe the Cambridge animal brain magnetic resonance imaging repository comprising 400 datasets to date from mouse models of Huntington disease. The data include raw images as well as segmented grey and white matter images with maps of cortical thickness. All images and phenotypic data for each subject are freely-available without restriction from (http://www.dspace.cam.ac.uk/handle/1810/243361/). Software and anatomical population templates optimised for animal brain analysis with MRI are also available from this site.

  20. A combined theoretical and Cambridge Structural Database study of π-hole pnicogen bonding complexes between electron rich molecules and both nitro compounds and inorganic bromides (YO2Br, Y = N, P, and As).

    Science.gov (United States)

    Bauzá, Antonio; Ramis, Rafael; Frontera, Antonio

    2014-04-17

    Quantum calculations at the DFT-D3/def2-TZVPD level of theory have been used to examine complexes between O2YBr (Y═N, P, and As) molecules and several Lewis bases, that is, NH3, H2O, and HF. The interactions of the lone pair of the ammonia, water, and hydrogen fluoride with the σ-hole and π-hole of O2YBr molecules have been considered. In general, the complexes where the Lewis base lone pair interacts with the π-hole are more favorable than those with σ-hole. The nature of the interactions has been characterized with the Bader theory of atoms in molecules (AIM). We have also studied the ability of trifluoronitromethane and nitromethane to interact with anions using their π-hole along with an analysis the Cambridge Structural Database. We have found a large number of hits that provide strong experimental support for ability of the nitryl (-NO2) group to interact with anions and Lewis bases. In some X-ray structures, the π-hole interaction is crucial in the crystal packing and has a strong influence in the solid state architecture of the complexes. Finally, due to the relevance in atmospheric chemistry, we have studied noncovalent σ/π-hole complexes of nitryl bromide with ozone. PMID:24679186

  1. Analysis of N-H···O hydrogen bonds in new C(O)-NH-P(O)-based phosphoric triamides and analogous structures deposited in the Cambridge Structural Database.

    Science.gov (United States)

    Pourayoubi, Mehrdad; Toghraee, Maryam; Divjakovic, Vladimir; van der Lee, Arie; Mancilla Percino, Teresa; Leyva Ramírez, Marco A; Saneei, Anahid

    2013-04-01

    Five new compounds belonging to the phosphoric triamide family have been synthesized: two of them with the formula XC(O)NHP(O)Y [X = CF3 (1) and CClF2 (2), Y = NHCH2C(CH3)2CH2NH] involving a 1,3-diazaphosphorinane ring part, and three 2,6-Cl2C6H3C(O)NHP(O)Z2 phosphoric triamides [Z = NHC(CH3)3 (3), N(CH3)(C6H11) (4) and N(CH3)(CH2C6H5) (5)]. The characterization was performed by (31)P{(1)H}, (1)H, (13)C NMR, IR spectroscopy besides (19)F NMR for fluorine containing compounds (1) and (2), and X-ray single-crystal structure analysis for (1), (3), (4) and (5). In each molecule the P atom has a distorted tetrahedral environment. The N atoms bonded to P atom have mainly sp(2) character with a very slight tendency to a pyramidal coordination for some amido groups. Different types of N-H···O hydrogen bonds have been analyzed for (1), (3), (4) and (5) and 118 other structures (including 194 hydrogen bonds) deposited in the Cambridge Structural Database, containing either C(O)-NH-P(O)[N(C)(C)]2 or C(O)-NH-P(O)[NH(C)]2. The participation of N(CP)-H···O=P [N(CP) = the nitrogen atom of the C(O)-NH-P(O) fragment], N-H···O=P, N-H···O=C and N(CP)-H···O=C hydrogen bonds in different hydrogen-bonded motifs are discussed. Moreover, the involvement of the O atoms of C=O or P=O in the [N(CP)-H][N-H]···O=P, [N-H]2···O=P, [N-H]2···O=C and [N-H]3···O=C groups are considered. A histogram of N···O distances, the distribution of N-H···O angles and the scatterplot of N-H···O angles versus N···O distances are studied.

  2. Structural Ceramics Database

    Science.gov (United States)

    SRD 30 NIST Structural Ceramics Database (Web, free access)   The NIST Structural Ceramics Database (WebSCD) provides evaluated materials property data for a wide range of advanced ceramics known variously as structural ceramics, engineering ceramics, and fine ceramics.

  3. Assessment of a Cambridge Structural Database-driven overlay program.

    Science.gov (United States)

    Giangreco, Ilenia; Olsson, Tjelvar S G; Cole, Jason C; Packer, Martin J

    2014-11-24

    We recently published an improved methodology for overlaying multiple flexible ligands and an extensive data set for validating pharmacophore programs. Here, we combine these two developments and present evidence of the effectiveness of the new overlay methodology at predicting correct superimpositions for systems with varying levels of complexity. The overlay program was able to generate correct predictions for 95%, 73%, and 39% of systems classified as easy, moderate, and hard, respectively.

  4. Learning about Intermolecular Interactions from the Cambridge Structural Database

    Science.gov (United States)

    Battle, Gary M.; Allen, Frank H.

    2012-01-01

    A clear understanding and appreciation of noncovalent interactions, especially hydrogen bonding, are vitally important to students of chemistry and the life sciences, including biochemistry, molecular biology, pharmacology, and medicine. The opportunities afforded by the IsoStar knowledge base of intermolecular interactions to enhance the…

  5. Interactive and Versatile Navigation of Structural Databases.

    Science.gov (United States)

    Korb, Oliver; Kuhn, Bernd; Hert, Jérôme; Taylor, Neil; Cole, Jason; Groom, Colin; Stahl, Martin

    2016-05-12

    We present CSD-CrossMiner, a novel tool for pharmacophore-based searches in crystal structure databases. Intuitive pharmacophore queries describing, among others, protein-ligand interaction patterns, ligand scaffolds, or protein environments can be built and modified interactively. Matching crystal structures are overlaid onto the query and visualized as soon as they are available, enabling the researcher to quickly modify a hypothesis on the fly. We exemplify the utility of the approach by showing applications relevant to real-world drug discovery projects, including the identification of novel fragments for a specific protein environment or scaffold hopping. The ability to concurrently search protein-ligand binding sites extracted from the Protein Data Bank (PDB) and small organic molecules from the Cambridge Structural Database (CSD) using the same pharmacophore query further emphasizes the flexibility of CSD-CrossMiner. We believe that CSD-CrossMiner closes an important gap in mining structural data and will allow users to extract more value from the growing number of available crystal structures. PMID:26745458

  6. Inorganic Crystal Structure Database (ICSD)

    Science.gov (United States)

    SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

  7. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    Science.gov (United States)

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  8. Healthy travel and the socio-economic structure of car commuting in Cambridge, UK: a mixed-methods analysis.

    Science.gov (United States)

    Goodman, Anna; Guell, Cornelia; Panter, Jenna; Jones, Natalia R; Ogilvie, David

    2012-06-01

    Car use is associated with substantial health and environmental costs but research in deprived populations indicates that car access may also promote psychosocial well-being within car-oriented environments. This mixed-method (quantitative and qualitative) study examined this issue in a more affluent setting, investigating the socio-economic structure of car commuting in Cambridge, UK. Our analyses involved integrating self-reported questionnaire data from 1142 participants in the Commuting and Health in Cambridge study (collected in 2009) and in-depth interviews with 50 participants (collected 2009-2010). Even in Britain's leading 'cycling city', cars were a key resource in bridging the gap between individuals' desires and their circumstances. This applied both to long-term life goals such as home ownership and to shorter-term challenges such as illness. Yet car commuting was also subject to constraints, with rush hour traffic pushing drivers to start work earlier and with restrictions on, or charges for, workplace parking pushing drivers towards multimodal journeys (e.g. driving to a 'park-and-ride' site then walking). These patterns of car commuting were socio-economically structured in several ways. First, the gradient of housing costs made living near Cambridge more expensive, affecting who could 'afford' to cycle and perhaps making cycling the more salient local marker of Bourdieu's class distinction. Nevertheless, cars were generally affordable in this relatively affluent, highly-educated population, reducing the barrier which distance posed to labour-force participation. Finally, having the option of starting work early required flexible hours, a form of job control which in Britain is more common among higher occupational classes. Following a social model of disability, we conclude that socio-economic advantage can make car-oriented environments less disabling via both greater affluence and greater job control, and in ways manifested across the full socio

  9. Distributed Structure-Searchable Toxicity Database Network

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Distributed Structure-Searchable Toxicity (DSSTox) Database Network provides a public forum for search and publishing downloadable, structure-searchable,...

  10. Philosophy at Cambridge

    OpenAIRE

    Lecky-Thompson, Jenni

    2012-01-01

    Newsletter of the Philosophy Faculty. Articles by: Simon Blackburn, 'From the Chair' ; Nick Treanor, 'Inaugural lecture: What is distinctive about human thought?' ; Clare Chambers, 'Political Philosophy at Cambridge' ; Alexis Papazoglou,'Aspects of philosophy at Cambridge' ; Peter Smith, 'Principia at 100' ; Nigel Crisp, 'Turning the World Upside Down' ; Cain Todd, 'Fiction, Emotion, Imagination'; Fraser MacBride, 'Philosophy, St John's, Cambridge, 1986.'

  11. Cambridge checkpoint English workbook 1

    CERN Document Server

    Reynolds, John

    2013-01-01

    This Workbook supports our bestselling Checkpoint English series, with exercises specifically matched to the Cambridge Progression tests and the Checkpoint English tests. - Offers plenty of additional questions for use in class or as homework. - Includes clearly identified questions on grammar and punctuation, comprehension, use of language and essay planning. - Follows the structure of the relevant textbook to ensure a thorough understanding of all aspects of the course. - Provides a space for Students to write their answers. This Workbook is matched to the Cambridge Secondary 1 Curriculum Fr

  12. SCOR: a structural classification of RNA database.

    Energy Technology Data Exchange (ETDEWEB)

    Klosterman, Peter S.; Tamura, Makio; Holbrook, Stephen R.; Brenner, Steven E.

    2001-10-10

    The Structural Classification of RNA (SCOR) database provides a survey of the three-dimensional motifs contained in 259 NMR and X-ray RNA structures. In one classification, the structures are grouped according to function. The RNA motifs, including internal and external loops, are also organized in a hierarchical classification. The 259 database entries contain 223 internal and 203 external loops; 52 entries consist of fully complementary duplexes. A classification of the well-characterized tertiary interactions found in the larger RNA structures is also included along with examples. The SCOR database is accessible at http://scor.lbl.gov.

  13. SCOR: a Structural Classification of RNA database.

    Science.gov (United States)

    Klosterman, Peter S; Tamura, Makio; Holbrook, Stephen R; Brenner, Steven E

    2002-01-01

    The Structural Classification of RNA (SCOR) database provides a survey of the three-dimensional motifs contained in 259 NMR and X-ray RNA structures. In one classification, the structures are grouped according to function. The RNA motifs, including internal and external loops, are also organized in a hierarchical classification. The 259 database entries contain 223 internal and 203 external loops; 52 entries consist of fully complementary duplexes. A classification of the well-characterized tertiary interactions found in the larger RNA structures is also included along with examples. The SCOR database is accessible at http://scor.lbl.gov.

  14. Cambridge Scientific Abstracts

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    正Meteorological and Environmental Research has been included by Cambridge Scientific Abstracts (CSA) since 2011. CSA is a retrieval system published by Cambridge Information Group. CSA was founded in the late 1950's,and became part of the CIG family in 1971. CSA's original mission was publishing secondary source materials relating to the physical sciences. Completely

  15. Cambridge Scientific Abstracts

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    Meteorological and Environmental Research has been included by Cambridge Scientific Abstracts (CSA) since 2011. CSA is a retrieval system published by Cambridge Information Group. CSA was founded in the late 1950’s,and became part of the CIG family in 1971. CSA’s original mission was publishing secondary source materials relating to the physical sciences. Completely

  16. The University of Cambridge

    Institute of Scientific and Technical Information of China (English)

    郭大任

    2007-01-01

    The University of Cambridge was founded in 1209,just a few decades after Oxford University,making it the second oldest university in the English-speaking world.Like“the other place”, the university is made up of 31 colleges and more than 100 departments,catering for around 15,500 students.Cambridge has a worldwide reputation for outstanding

  17. Cambridge checkpoint English workbook 2

    CERN Document Server

    Reynolds, John

    2014-01-01

    Build confidence and understanding throughout the year with hundreds of additional practice questions. This Workbook supports our bestselling Checkpoint series, with exercises specifically matched to the Cambridge Progression tests and the Checkpoint tests. - Develops understanding and builds confidence ahead of assessment with exercises matched to the tests - Ensures a thorough understanding of all aspects of the course by following the structure of the relevant textbook - Saves planning time with exercises that are suitable for use in class or as homework This Workbook is

  18. Cambridge checkpoint English workbook 3

    CERN Document Server

    Reynolds, John

    2014-01-01

    Build confidence and understanding throughout the year with hundreds of additional practice questions. This Workbook supports our bestselling Checkpoint series, with exercises specifically matched to the Cambridge Progression tests and the Checkpoint tests. - Develops understanding and builds confidence ahead of assessment with exercises matched to the tests - Ensures a thorough understanding of all aspects of the course by following the structure of the relevant textbook - Saves planning time with exercises that are suitable for use in class or as homework This Workbook is

  19. Fast Structural Search in Phylogenetic Databases

    Directory of Open Access Journals (Sweden)

    William H. Piel

    2005-01-01

    Full Text Available As the size of phylogenetic databases grows, the need for efficiently searching these databases arises. Thanks to previous and ongoing research, searching by attribute value and by text has become commonplace in these databases. However, searching by topological or physical structure, especially for large databases and especially for approximate matches, is still an art. We propose structural search techniques that, given a query or pattern tree P and a database of phylogenies D, find trees in D that are sufficiently close to P . The “closeness” is a measure of the topological relationships in P that are found to be the same or similar in a tree D in D. We develop a filtering technique that accelerates searches and present algorithms for rooted and unrooted trees where the trees can be weighted or unweighted. Experimental results on comparing the similarity measure with existing tree metrics and on evaluating the efficiency of the search techniques demonstrate that the proposed approach is promising

  20. Database on wind characteristics. Structure and philosophy

    DEFF Research Database (Denmark)

    Larsen, Gunner Chr.; Hansen, K.S.

    2001-01-01

    environments. The project partners are Sweden, Norway, U.S.A., The Netherlands, Japan and Denmark, with Denmark as the Operating Agent. The reporting of IEA R&D Annex XVII falls in three separate parts. Partone deals with the overall structure and philosophy behind the database, part two accounts in details......The main objective of IEA R&D Wind Annex XVII - Database on Wind Characteristics - is to provide wind energy planners and designers, as well as the international wind engineering community in general, with easy access to quality controlled measured windfield time series observed in a wide range of...

  1. Database on wind characteristics - Structure and philosophy

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, G.C.; Hansen, K.S.

    2001-11-01

    The main objective of IEA R and D Wind Annex XVII - Database on Wind Characteristics - is to provide wind energy planners and designers, as well as the international wind engineering community in general, with easy access to quality controlled measured wind field time series observed in a wide range of environments. The project partners are Sweden, Norway, U.S.A., The Netherlands, Japan and Denmark, with Denmark as the Operating Agent. The reporting of IEA R and D Annex XVII falls in three separate parts. Part one deals with the overall structure and philosophy behind the database, part two accounts in details for the available data in the established database bank and part three is the Users Manual describing the various ways to access and analyse the data. The present report constitutes the first part of the Annex XVII reporting, and it contains a detailed description of the database structure, the data quality control procedures, the selected indexing of the data and the hardware system. (au)

  2. Get Beyond Cambridge

    Institute of Scientific and Technical Information of China (English)

    毛竹晨

    2003-01-01

    In the past month I have been buried in my coursework- preparation of dis(学位论文) and studying for the exams. Spring is the most beautiful season at Cambridge. Yet it is also the quietest season for most of the undergraduate and master students. The imminent(即将到来的)exams and deadline for the submission (提交,呈递) of dissertation have dragged us back into the rooms and

  3. Cambridge IGCSE computer science

    CERN Document Server

    Watson, Dave; Konrad, Nina

    2015-01-01

    Endorsed by Cambridge International Examinations. Develop your students computational thinking and programming skills with complete coverage of the latest syllabus (0478) from experienced examiners and teachers. - Includes a Student CD-ROM with interactive tests, based on the short answer questions from both papers - Follows the order of the syllabus exactly, ensuring complete coverage - Introduces students to self-learning exercises, helping them learn how to use their knowledge in new scenarios This syllabus is for first examination from 2015.

  4. Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre.

    Science.gov (United States)

    Baldi, Pierre

    2011-12-27

    A response is presented to sentiments expressed in "Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre", recently published in the Journal of Chemical Information and Modeling, (1) which may give readers a misleading impression regarding significant impediments to scientific research posed by the CCDC.

  5. Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre.

    Science.gov (United States)

    Baldi, Pierre

    2011-12-27

    A response is presented to sentiments expressed in "Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre", recently published in the Journal of Chemical Information and Modeling, (1) which may give readers a misleading impression regarding significant impediments to scientific research posed by the CCDC. PMID:22107601

  6. PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.

    Science.gov (United States)

    Andrejasic, Miha; Praaenikar, Jure; Turk, Dusan

    2008-11-01

    The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/.

  7. PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.

    Science.gov (United States)

    Andrejasic, Miha; Praaenikar, Jure; Turk, Dusan

    2008-11-01

    The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/. PMID:19020347

  8. Visualization of database structures for information retrieval

    Directory of Open Access Journals (Sweden)

    Grete Lisbjerg Jensen

    1994-12-01

    Full Text Available This paper describes the Book House system, which is designed to support children's information retrieval in libraries as part of their education. It is a shareware program available on CD-ROM or floppy disks, and comprises functionality for database searching as well as for classifying and storing book information in the database. The system concept is based on an understanding of children's domain structures and their capabilities for categorization of information needs in connection with their activities in schools, in school libraries or in public libraries. These structures are visualized in the interface by using metaphors and multimedia technology. Through the use of text, images and animation, the Book House encourages children - even at a very early age - to learn by doing in an enjoyable way, which plays on their previous experiences with computer games. Both words and pictures can be used for searching; this makes the system suitable for all age groups. Even children who have not yet learned to read properly can, by selecting pictures, search for and find those books they would like to have read aloud. Thus, at the very beginning of their school life, they can learn to search for books on their own. For the library community, such a system will provide an extended service which will increase the number of children's own searches and also improve the relevance, quality and utilization of the book collections in the libraries. A market research report on the need for an annual indexing service for books in the Book House format is in preparation by the Danish Library Centre A/S.

  9. International Commercial Contracts, by Giuditta Cordero Moss. (Cambridge: Cambridge University Press, 2014)

    DEFF Research Database (Denmark)

    Lando, Ole

    2015-01-01

    Review of: Giuditta Cordero Moss, International Commercial Contracts. Cambridge: Cambridge University Press, 2014. XV + 329 pages. ISBN: 9781107684713......Review of: Giuditta Cordero Moss, International Commercial Contracts. Cambridge: Cambridge University Press, 2014. XV + 329 pages. ISBN: 9781107684713...

  10. An investigation into the impact of question structure on the performance of first year physics undergraduate students at the University of Cambridge

    Science.gov (United States)

    Gibson, Valerie; Jardine-Wright, Lisa; Bateman, Elizabeth

    2015-07-01

    We describe a study of the impact of exam question structure on the performance of first year Natural Sciences physics undergraduates from the University of Cambridge. The results show conclusively that a student’s performance improves when questions are scaffolded compared with university style questions. In a group of 77 female students we observe that the average exam mark increases by 13.4% for scaffolded questions, which corresponds to a 4.9 standard deviation effect. The equivalent observation for 236 male students is 9% (5.5 standard deviations). We also observe a correlation between exam performance and A2-level marks for UK students, and that students who receive their school education overseas, in a mixed gender environment, or at an independent school are more likely to receive a first class mark in the exam. These results suggest a mis-match between the problem-solving skills and assessment procedures between school and first year university and will provide key input into the future teaching and assessment of first year undergraduate physics students.

  11. BOOK REVIEW: Structures in the Universe by Exact Methods: Formation, Evolutions, Interactions (Cambridge Monographs on Mathematical Physics) Structures in the Universe by Exact Methods: Formation, Evolutions, Interactions (Cambridge Monographs on Mathematical Physics)

    Science.gov (United States)

    Coley, Alan

    2010-05-01

    In this book the use of inhomogeneous models in cosmology, both in modelling structure formation and interpreting cosmological observations, is discussed. The authors concentrate on exact solutions, and particularly the Lemaitre-Tolman (LT) and Szekeres models (the important topic of averaging is not discussed). The book serves to demonstrate that inhomogeneous metrics can generate realistic models of cosmic structure formation and nonlinear evolution and shows that general relativity has a lot more to offer to cosmology than just the standard spatially homogeneous FLRW model. I would recommend this book to people working in theoretical cosmology. In the introduction (and in the concluding chapter and throughout the book) a reasonable discussion of the potential problems with the standard FLRW cosmology is presented, and a list of examples illustrating the limitations of standard FLRW cosmology are discussed (including potential problems with perturbation methods). In particular, the authors argue that the assumptions of isotropy and spatial homogeneity (and consequently the Copernican principle) must be properly challenged and revisited. Indeed, it is possible for `good old general relativity' to be used to explain cosmological observations without introducing speculative elements. In part I of the book the necessary background is presented (readers need a background in general relativity theory at an advanced undergraduate or graduate level). There is a good (and easy to read) review of the exact spherically symmetric dust Lemaitre-Tolman model (LT) (often denoted the LTB model) and the Lemaitre and Szekeres models. Light propogation (i.e. null geodesics, for both central and off-center observers) in exact inhomogeneous (LT) models is reviewed. In part II a number of applications of exact inhomogeneous models are presented (taken mainly from the authors' own work). In chapter 4, the evolution of exact inhomogeneous models (primarily the LT model, but also the

  12. Food Composition Database Format and Structure: A User Focused Approach

    OpenAIRE

    Clancy, Annabel K.; Woods, Kaitlyn; McMahon, Anne; Probst, Yasmine

    2015-01-01

    This study aimed to investigate the needs of Australian food composition database user’s regarding database format and relate this to the format of databases available globally. Three semi structured synchronous online focus groups (M = 3, F = 11) and n = 6 female key informant interviews were recorded. Beliefs surrounding the use, training, understanding, benefits and limitations of food composition data and databases were explored. Verbatim transcriptions underwent preliminary coding follow...

  13. Food Composition Database Format and Structure: A User Focused Approach

    OpenAIRE

    Annabel K Clancy; Kaitlyn Woods; Anne McMahon; Yasmine Probst

    2015-01-01

    This study aimed to investigate the needs of Australian food composition database user's regarding database format and relate this to the format of databases available globally. Three semi structured synchronous online focus groups (M = 3, F = 11) and n = 6 female key informant interviews were recorded. Beliefs surrounding the use, training, understanding, benefits and limitations of food composition data and databases were explored. Verbatim transcriptions underwent preliminary coding follow...

  14. Reflections on Cambridge: Coffee shops and great ideas in Cambridge

    OpenAIRE

    Macfarlane, Alan.

    2012-01-01

    Alan Macfarlane reflects on the role of coffee shops in the development of scientific and computing theories in Cambridge - particularly string theory and probabalistic information retrieval systems. Filmed by Xu Bei in 2009.

  15. Database structure and file layout of Nuclear Power Plant Database. Database for design information on Light Water Reactors in Japan

    Energy Technology Data Exchange (ETDEWEB)

    Yamamoto, Nobuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment; Izumi, Fumio

    1995-12-01

    The Nuclear Power Plant Database (PPD) has been developed at the Japan Atomic Energy Research Institute (JAERI) to provide plant design information on domestic Light Water Reactors (LWRs) to be used for nuclear safety research and so forth. This database can run on the main frame computer in the JAERI Tokai Establishment. The PPD contains the information on the plant design concepts, the numbers, capacities, materials, structures and types of equipment and components, etc, based on the safety analysis reports of the domestic LWRs. This report describes the details of the PPD focusing on the database structure and layout of data files so that the users can utilize it efficiently. (author).

  16. The Cambridge Experimentation Review Board

    Science.gov (United States)

    Bulletin of the Atomic Scientists, 1977

    1977-01-01

    Reproduced is the report made by a citizens' group in Cambridge, Massachusetts and presented to the city council that outlines safety regulations for the conduct of recombinant DNA research at Harvard University and the Massachusetts Institute of Technology. (CS)

  17. A database/knowledge structure for a robotics vision system

    Science.gov (United States)

    Dearholt, D. W.; Gonzales, N. N.

    1987-01-01

    Desirable properties of robotics vision database systems are given, and structures which possess properties appropriate for some aspects of such database systems are examined. Included in the structures discussed is a family of networks in which link membership is determined by measures of proximity between pairs of the entities stored in the database. This type of network is shown to have properties which guarantee that the search for a matching feature vector is monotonic. That is, the database can be searched with no backtracking, if there is a feature vector in the database which matches the feature vector of the external entity which is to be identified. The construction of the database is discussed, and the search procedure is presented. A section on the support provided by the database for description of the decision-making processes and the search path is also included.

  18. The Developement of A Lattice Structured Database

    DEFF Research Database (Denmark)

    Bruun, Hans

    In this project we have investigated the possibilities to make a system based on the concept algebra described in [3], [4] and [5]. The concept algebra is used for ontology specification and knowledge representation. It is a distributive lattice extended with attribution operations. One of the main...... to a given set of inserted terms, that is the smallest lattice where the inserted terms preserve their value compared to the value in the initial algebra/lattice. The database is the dual representation of this most disjoint lattice. We develop algorithms to construct and make queries to the database....

  19. Data sharing at the University of Cambridge - open presentation for Cambridge academics, students and research staff

    OpenAIRE

    Teperek, Marta

    2016-01-01

    Presentation about research data sharing at the University of Cambridge given by Dr Marta Teperek on 20 January at central Cambridge, University of Cambridge. Presenation was open to all academics, research students and staff members.

  20. Learning Queries for Relational, Semi-structured, and Graph Databases

    OpenAIRE

    Ciucanu, Radu

    2013-01-01

    International audience Web applications store their data within various database models, such as relational, semi-structured, and graph data models to name a few. We study learning algorithms for queries for the above mentioned models. As a further goal, we aim to apply the results to learning cross-model database mappings, which can also be seen as queries across different schemas.

  1. A new relational database structure and online interface for the HITRAN database

    International Nuclear Information System (INIS)

    A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described. -- Highlights: • A new, interactive version of the HITRAN database is presented. • The data is stored in a structured fashion in a relational database. • The new HITRANonline interface offers increased functionality and easier error correction

  2. Cambridge IGCSE English first language

    CERN Document Server

    Reynolds, John

    2013-01-01

    Revised edition for the 2015 syllabus to help your students prepare for their examination and enhance their enjoyment of English. This title has been written for the revised Cambridge IGCSE First Language English (0500 and 0522) syllabuses, for first teaching from 2013. ? Develops the skills necessary to become a better reader and writer. ? Offers detailed advice and preparation for the examination. ? Teaches skills for successful writing of essays and coursework assignment. We are working with Cambridge International Examinations to gain endorsement for this title.

  3. How well are protein structures annotated in secondary databases?

    Science.gov (United States)

    Rother, Kristian; Michalsky, Elke; Leser, Ulf

    2005-09-01

    We investigated to what extent Protein Data Bank (PDB) entries are annotated with second-party information based on existing cross-references between PDB and 15 other databases. We report 2 interesting findings. First, there is a clear "annotation gap" for structures less than 7 years old for secondary databases that are manually curated. Second, the examined databases overlap with each other quite well, dividing the PDB into 2 well-annotated thirds and one poorly annotated third. Both observations should be taken into account in any study depending on the selection of protein structures by their annotation.

  4. Structural unsafety revealed by failure databases

    NARCIS (Netherlands)

    Terwel, K.; Boot, W.; Nelisse, M.

    2014-01-01

    After several major structural incidents in the Netherlands, such as the collapse of five balconies in Maastricht in 2001 resulting in two fatalities, various initiatives have been started to improve structural safety. Research studies were initiated on the characteristics, causes and consequences o

  5. A CADASTRAL SPATIAL DATA STORAGE STRUCTURE BASED ON RELATIONAL DATABASE

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper presents a cadastral spatial data storage structure based on relational database,the method and the procedure to realize it.The paper consists of three parts.In the first part,some existing problems in some de veloped cadastral management systems are discussed.These problems are the fo llowing four.1) The security of cadastral spatial data is difficult to be assure d.2) It is difficult to varify cadastral data and the integrality of cadastral d ata is diffi cult to be kept.3) To transmit and share cadastral data is difficult.4) The effi ciency of data access is low.In the second part,t he feasibility of using relational database to store spatial data is analyzed an d a new cadastral spatial data storage structure is presented.At the same time, the related table structures and field descriptions are given,and then the merits and demerits of this storage structure are analyzed in detail.In th e last part,through a real example,the detailed methods to make the new storag e structure a reality are given.Moreover,some involving key techniques of the ne w storage structure are discussed.These techniques are:1) the application of database transaction,2) the application of database trigger,3) and the appl ication of secure recovery of database.

  6. 33 CFR 117.549 - Cambridge Harbor.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Cambridge Harbor. 117.549 Section... DRAWBRIDGE OPERATION REGULATIONS Specific Requirements Maryland § 117.549 Cambridge Harbor. The draw of the S342 bridge, mile 0.1 at Cambridge, shall open on signal from 6 a.m. to 8 p.m.; except that, from...

  7. Databases

    Data.gov (United States)

    National Aeronautics and Space Administration — The databases of computational and experimental data from the first Aeroelastic Prediction Workshop are located here. The databases file names tell their contents...

  8. Databases

    Digital Repository Service at National Institute of Oceanography (India)

    Kunte, P.D.

    Information on bibliographic as well as numeric/textual databases relevant to coastal geomorphology has been included in a tabular form. Databases cover a broad spectrum of related subjects like coastal environment and population aspects, coastline...

  9. The Cambridge Infectious Diseases Consortium

    OpenAIRE

    Wood, James

    2010-01-01

    The Cambridge Infectious Diseases Consortium (CIDC) was established to provide a multi-institutional, world class quality environment for infectious disease research addressing important questions and for the recruitment and training of high quality veterinarians into careers in infectious disease research. The programme has been a demonstrable success in achieving these overall aims. The institutions that have played a key role in the consortium include the Department of Veterinary Medic...

  10. A new relational database structure and online interface for the HITRAN database

    Science.gov (United States)

    Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

    2013-11-01

    A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

  11. SKPDB: a structural database of shikimate pathway enzymes

    Directory of Open Access Journals (Sweden)

    de Azevedo Walter F

    2010-01-01

    Full Text Available Abstract Background The functional and structural characterisation of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design. The main interest in studying shikimate pathway enzymes involves the fact that they are essential for bacteria but do not occur in humans, making them selective targets for design of drugs that do not directly impact humans. Description The ShiKimate Pathway DataBase (SKPDB is a relational database applied to the study of shikimate pathway enzymes in microorganisms and plants. The current database is updated regularly with the addition of new data; there are currently 8902 enzymes of the shikimate pathway from different sources. The database contains extensive information on each enzyme, including detailed descriptions about sequence, references, and structural and functional studies. All files (primary sequence, atomic coordinates and quality scores are available for downloading. The modeled structures can be viewed using the Jmol program. Conclusions The SKPDB provides a large number of structural models to be used in docking simulations, virtual screening initiatives and drug design. It is freely accessible at http://lsbzix.rc.unesp.br/skpdb/.

  12. Databases

    Directory of Open Access Journals (Sweden)

    Nick Ryan

    2004-01-01

    Full Text Available Databases are deeply embedded in archaeology, underpinning and supporting many aspects of the subject. However, as well as providing a means for storing, retrieving and modifying data, databases themselves must be a result of a detailed analysis and design process. This article looks at this process, and shows how the characteristics of data models affect the process of database design and implementation. The impact of the Internet on the development of databases is examined, and the article concludes with a discussion of a range of issues associated with the recording and management of archaeological data.

  13. General Design Structure of Ontological Databases in Semantic Web

    Directory of Open Access Journals (Sweden)

    Aarti Singh,

    2010-05-01

    Full Text Available Ontologies are useful tool for data integration across heterogeneous data sets and the importance of ontologies is already widespread, yet ontology building is comparatively a less absorbed concept.Ontology specifies a set of vocabulary for a particular problem domain emphasizing on the meaning of terms. The motive of employing ontologies in semantic web directly relates to unabated change in thelanguages, which are being used to describe a problem. This switch among various languages directly changes the terms used in the definition of problem assuming that the meaning conveyed will be similar to former. However the semantics might change inevitably and the purpose of upgrading a language gets defeated. Therefore the ontological databases were introduced to overcome this issue. Although the general design structure of ontological database is still pending. The premise of this paper is to propose a designstructure for the development of ontological database in general. Also, a case study has been presented to analyze the proposed structure.

  14. Honorary Degree Congregation in Cambridge

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    One day in mid-June 2006 when I was on a visit to the Countryside Restoration Trust at Barton near Cambridge, Mr. Christopher Stevenson, the director of Program of Events for Newcomers & Academic Visitors, gave me a letter enclosing a notice and a ticket I booked nearly two months earlier. He told me that I was very lucky because a strictly limited number of tickets had been allocated to academic visitors. It was a ticket to admit me to the Honorary Degree Congregation and to the reception afterwards on Tuesday 27 June.

  15. Indexing and searching structure for multimedia database systems

    Science.gov (United States)

    Chen, ShuChing; Sista, Srinivas; Shyu, Mei-Ling; Kashyap, Rangasami L.

    1999-12-01

    Recently, multimedia database systems have emerged as a fruitful area for research due to the recent progress in high-speed communication networks, large capacity storage devices, digitized media,and data compression technologies over the last few years. Multimedia information has been used in a variety of applications including manufacturing, education, medicine, entertainment, etc. A multimedia database system integrates text, images, audio, graphics, database system is that all of the different media are brought together into one single unit, all controlled by a computer. As more information sources become available in multimedia systems, how to model and search the image processing techniques to model multimedia data. A Simultaneous Partition and Class Parameter Estimation algorithm that considers the problem of video frame segmentation as a joint estimation of the partition and class parameter variables has been developed and implemented to identify objects and their corresponding spatial relations. Based on the obtained object information, a web spatial model (WSM) is constructed. A WSM is a multimedia database searching structure to model the temporal and spatial relations of semantic objects so that multimedia database queries related to the objects' temporal and spatial relations on the images or video frames can be answered efficiently.

  16. The role of weak intermolecular C-H…F interactions in supramolecular assembly: Structural investigations on 3,5- dibenzylidene-piperidin-4-one and database analysis

    Indian Academy of Sciences (India)

    R S Rathore; N S Karthikeyan; Y Alekhya; K Sathiyanarayanan; P G Aravindan

    2011-07-01

    The fluorinated and non-fluorinated dibenzylidene-4-piperidones were synthesized and their structures examined using X-ray crystallography. Interestingly, the para-fluorosubstituted dibenzylidene compound, in contrast to other analogs, is characterized by C-H…F bonded one-dimensional packing motif. To evaluate the ability of hydrogen bond donors and acceptors for forming interactions, in general and competitive situation, we have defined statistical descriptors. Analysis of Cambridge Structural Database using these newly defined parameters reveals high propensity of C-H…F interactions in organic crystals. The present structural study suggests much larger role of fluorine driven intermolecular interactions that are even though weak, but possess significant ability to direct and alter the packing.

  17. Michael Byers, International Law and the Arctic (Cambridge: Cambridge Studies in International and Comparative law, Cambridge University Press, 2013

    Directory of Open Access Journals (Sweden)

    Rachael L. Johnstone

    2014-03-01

    Full Text Available A review of: Michael Byers, International Law and the Arctic, Cambridge Studies in International and Comparative law, Cambridge University Press, 2013. pp. 314 + xviii, 65.00 GBP (hardcover; 16.56GBP (kindle edition ISBN: 9781107042759 ISBN: 9781107042759

  18. A Novel Approach to Quantum Heuristics for Structured Database Search

    OpenAIRE

    Murphy, Brian

    2001-01-01

    An algorithm for structured database searching is presented and used to solve the set partition problem. O(n) oracle calls are required in order to obtain a solution, but the probability that this solution is optimal decreases exponentially with problem size. Each oracle call is followed by a measurement, implying that it is necessary to maintain quantum coherence for only one oracle call at a time.

  19. Trial access to Cambridge University Press ebooks

    CERN Multimedia

    CERN Library

    2011-01-01

    From 1 August till 31 October, CERN users are invited to enjoy a trial access to all Cambridge University Press electronic books: http://ebooks.cambridge.org/. Please don't hesitate to send feedback to library.desk@cern.ch.

  20. Mapping relational database into OWL Structure with data semantic preservation

    CERN Document Server

    Gherabi, Noreddine; Bahaj, Mohamed

    2012-01-01

    This paper proposes a solution for migrating an RDB into Web semantic. The solution takes an existing RDB as input, and extracts its metadata representation (MTRDB). Based on the MTRDB, a Canonical Data Model (CDM) is generated. Finally, the structure of the classification scheme in the CDM model is converted into OWL ontology and the recordsets of database are stored in owl document. A prototype has been implemented, which migrates a RDB into OWL structure, for demonstrate the practical applicability of our approach by showing how the results of reasoning of this technique can help improve the Web systems.

  1. Serialization and persistent objects turning data structures into efficient databases

    CERN Document Server

    Soukup, Jiri

    2014-01-01

    Recently, the pressure for fast processing and efficient storage of large data with complex?relations increased beyond the capability of traditional databases. Typical examples include iPhone applications, computer aided design - both electrical and mechanical, biochemistry applications, and incremental compilers. Serialization, which is sometimes used in such situations is notoriously tedious and error prone.In this book, Jiri Soukup and Petr Macha?ek show in detail how to write programs which store their internal data automatically and transparently to disk. Together with special data structure libraries which treat relations among objects as first-class entities, and with a UML class-diagram generator, the core application code is much simplified. The benchmark chapter shows a typical example where persistent data is faster by the order of magnitude than with a traditional database, in both traversing and accessing the data.The authors explore and exploit advanced features of object-oriented languages in a...

  2. Dynamic Interval Index Structure in Constraint Database Systems

    Institute of Scientific and Technical Information of China (English)

    汪卫; 王宇君; 施伯乐

    2000-01-01

    Interval index structure plays an important role in constraint database systems. A dynamic interval index structure DM-tree is presented in this paper.The advantage of the DM-tree compared with other interval index structures is that the dynamic operations of insertion and deletion can be operated on the new structure. The storage complexity of the tree is O(n), and the query I/O complexity is O(logn+t/B). To improve the performance of the inserting and deleting operations,some methods such as neighbored-constraint and update-late are applied. The I/O complexity of inserting and deleting operations is the same as that in B-tree, i.e.,O(log n).

  3. Structural health monitoring system using internet and database technologies

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Chi Yeop; Choi, Man Yong; Kwon, Il Bum; Lee, Seung Seok [Nonstructive Measurment Lab., KRISS, Daejeon (Korea, Republic of)

    2003-07-01

    Structure health monitoring system should develope to be based on internet and database technology in order to manage efficiency large structures. This system is operated by internet connected with the side of structures. The monitoring system has some functions: self monitoring, self diagnosis, and self control etc. Self monitoring is the function of sensor fault detection. If some sensors are not normally worked, then this system can detect the fault sensors. Also Self diagnosis function repair the abnormal condition of sensors. And self control is the repair function of the monitoring system. Especially, the monitoring system can identify the replacement of sensors. For further study, the real application test will be performed to check some unconviniences.

  4. Structure health monitoring system using internet and database technologies

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, Il Bum; Kim, Chi Yeop; Choi, Man Yong; Lee, Seung Seok [Smart Measurment Group. Korea Resarch Institute of Standards and Science, Saejeon (Korea, Republic of)

    2003-05-15

    Structural health monitoring system should developed to be based on internet and database technology in order to manage efficiently large structures. This system is operated by internet connected with the side of structures. The monitoring system has some functions: self monitoring, self diagnosis, and self control etc. Self monitoring is the function of sensor fault detection. If some sensors are not normally worked, then this system can detect the fault sensors. Also Self diagnosis function repair the abnormal condition of sensors. And self control is the repair function of the monitoring system. Especially, the monitoring system can identify the replacement of sensors. For further study, the real application test will be performed to check some unconvince.

  5. Structural load inventory database for the Kansas City Plant

    Energy Technology Data Exchange (ETDEWEB)

    Hashimoto, P.S.; Johnson, M.W.; Nakaki, D.K. [EQE International, Inc., Irvine, CA (United States); Wilson, J.J.; Lynch, D.T.; Drury, M.A. [Allied-Signal Aerospace Co., Kansas City, MO (United States). Kansas City Div.

    1993-10-01

    This report discusses a structural load inventory database (LID) which has been developed to support configuration management at the DOE Kansas City Plant (KCP). The objective of the LID is to record loads supported by the plant structures and to provide rapid assessments of the impact of future facility modifications on structural adequacy. Development of the LID was initiated for the KCP`s Main Manufacturing Building. Field walkdowns were performed to determine all significant loads supported by the structure, including the weight of piping, service equipment, etc. These loads were compiled in the LID. Structural analyses for natural phenomena hazards were performed in accordance with UCRL-15910. Software to calculate demands on the structural members due to gravity loads, total demands including both gravity and seismic loads, and structural member demand-to-capacity ratios were also developed and integrated into the LID. Operation of the LID is menu-driven. The LID user has options to review and print existing loads and corresponding demand-to-capacity ratios, and to update the supported loads and demand-to-capacity ratios for any future facility modifications.

  6. Structural load inventory database for the Kansas City Plant

    International Nuclear Information System (INIS)

    A structural load inventory database (LID) has been developed to support configuration management at the DOE Kansas City Plant (KCP). The objective of the LID is to record loads supported by the plant structures and to provide rapid assessments of the impact of future facility modifications on structural adequacy. Development of the LID was initiated for the KCP's Main Manufacturing Building. Field walkdowns were performed to determine all significant loads supported by the structure, including the weight of piping, service equipment, etc. These loads were compiled in the LID. Structural analyses for natural phenomena hazards were performed in accordance with UCRL-15910. Software to calculate demands on the structural members due to gravity loads, total demands including both gravity and seismic loads, and structural member demand-to-capacity ratios were also developed and integrated into the LID. Operation of the LID is menu-driven. The LID user has options to review and print existing loads and corresponding demand-to-capacity ratios, and to update the supported loads and demand-to-capacity ratios for any future facility modifications

  7. Cambridge checkpoint English revision guide for the Cambridge secondary 1 test

    CERN Document Server

    Reynolds, John

    2013-01-01

    With Checkpoint English Revision Guide for the Cambridge Secondary 1 test you can aim for the best grade with the help of relevant and accessible notes, examiner advice plus questions and answers on each key topic. - Clear explanations of every topic covered in the Cambridge Secondary 1 Checkpoint English syllabus. - Builds revision skills you need for success in the test. - Exam tips wirtten by test setters and examiners giving you their expert advice. This text has not been through the Cambridge endorsement process.

  8. Cambridge checkpoint maths revision guide for the Cambridge secondary 1 test

    CERN Document Server

    Smith, Alan

    2013-01-01

    With Checkpoint Maths Revision Guide for the Cambridge Secondary 1 test you can aim for the best grade with the help of relevant and accessible notes, examiner advice plus questions and answers on each key topic. - Clear explanations of every topic covered in the Cambridge Secondary 1 Checkpoint Maths syllabus. - Builds revision skills you need for success in the test. - Exam tips wirtten by test setters and examiners giving you their expert advice. This text has not been through the Cambridge endorsement process.

  9. RScan: fast searching structural similarities for structured RNAs in large databases

    Directory of Open Access Journals (Sweden)

    Liu Guo-Ping

    2007-07-01

    Full Text Available Abstract Background Many RNAs have evolutionarily conserved secondary structures instead of primary sequences. Recently, there are an increasing number of methods being developed with focus on the structural alignments for finding conserved secondary structures as well as common structural motifs in pair-wise or multiple sequences. A challenging task is to search similar structures quickly for structured RNA sequences in large genomic databases since existing methods are too slow to be used in large databases. Results An implementation of a fast structural alignment algorithm, RScan, is proposed to fulfill the task. RScan is developed by levering the advantages of both hashing algorithms and local alignment algorithms. In our experiment, on the average, the times for searching a tRNA and an rRNA in the randomized A. pernix genome are only 256 seconds and 832 seconds respectively by using RScan, but need 3,178 seconds and 8,951 seconds respectively by using an existing method RSEARCH. Remarkably, RScan can handle large database queries, taking less than 4 minutes for searching similar structures for a microRNA precursor in human chromosome 21. Conclusion These results indicate that RScan is a preferable choice for real-life application of searching structural similarities for structured RNAs in large databases. RScan software is freely available at http://bioinfo.au.tsinghua.edu.cn/member/cxue/rscan/RScan.htm.

  10. Usage Of Dedicated Data Structures For Url Databases In A Large-Scale Crawling

    OpenAIRE

    Krzysztof Dorosz

    2009-01-01

    The article discuss usage of Berkeley DB data structures such as hash tables and b-trees forimplementation of a high performance URL database. The article presents a formal model fora data structures oriented URL database, which can be used as an alternative for a relationaloriented URL database.

  11. Storing an OWL 2 Ontology in a Relational Database Structure

    OpenAIRE

    Gorskis, Henrihs; Borisov, Arkady

    2015-01-01

    This paper examines the possibility of storing OWL 2 based ontology information in a classical relational database and reviews some existing methods for ontology databases. In most cases a database is a fitting solution for storing and sharing information among systems, clients or agents. Similarly, in order to make domain ontology information more accessible to systems, in a comparable way, it can be stored and provided in a database form. As of today, there is no consensus on a specific ont...

  12. 77 FR 3118 - Security Zone; Choptank River and Cambridge Channel, Cambridge, MD

    Science.gov (United States)

    2012-01-23

    ... 3118-3121] [FR Doc No: 2012-1172] DEPARTMENT OF HOMELAND SECURITY Coast Guard 33 CFR Part 165 [Docket No. USCG-2011-1164] RIN 1625-AA87 Security Zone; Choptank River and Cambridge Channel, Cambridge, MD..., U.S. Coast Guard, Captain of the Port Baltimore. [FR Doc. 2012-1172 Filed 1-20-12; 8:45 am]...

  13. OCR Cambridge nationals in ICT student book

    CERN Document Server

    Stuart, Sonia; Cushing, Steve

    2012-01-01

    Written by experts and in partnership with OCR, the brand-new OCR Cambridge Nationals in ICT Student's Book provides invaluable guidance for your teaching of the OCR Cambridge Nationals in ICT Level 1/2 . This textbook covers the mandatory Units 1 and 2 in detail, offering your students the knowledge and practice they require. Unit 1 - Understanding Computer Systems.; Coverage of use of applications and systems.; Case studies of how they are used for different purposes.; Exam style questions and guidance. Unit 2 - Using ICT to Create Business Solutions.; Coverage of the principles of use of re

  14. Cambridge IGCSE mathematics core and extended

    CERN Document Server

    Pimentel, Ric

    2013-01-01

    The most cost effective and straightforward way to teach the revised syllabus, with all the core and extended content covered by a single book and accompanying free digital resources.  . This title has been written for the revised Cambridge IGCSE Mathematics (0580) syllabus, for first teaching from 2013.  . ·         Gives students the practice they require to deepen their understanding through plenty of questions. ·         Consolidates learning with unique digital resources on the CD, included free with every Student's Book.  . We are working with Cambridge International Examinations to gain

  15. The Cambridge Jet Algorithm features and applications

    CERN Document Server

    Bentvelsen, Stanislaus Cornelius Maria

    1998-01-01

    Jet clustering algorithms are widely used to analyse hadronic events in high energy collisions. Recently a new clustering method, known as `Cambridge', has been introduced. In this article we present an algorithm to determine the transition values of ycut for this clustering scheme, which allows to resolve any event to a definite number of jets in the final state. We discuss some particularities of the Cambridge clustering method and compare its performance to the Durham clustering scheme for Monte Carlo generated e+e- annihilation events.

  16. Weizmann ties with Cambridge in physics contest

    CERN Multimedia

    Siegel, J

    2004-01-01

    "Scientists and students from the Weizmann Institute of Science in Rehovot and Cambridge University in England have tied for first place in a physics competition aimed at simulating the future functioning of the particle accelerator being built at the European center CERN and due to open in 2007" (1/2 page)

  17. AMO Database in KAERI and Atomic Structure Studies

    Science.gov (United States)

    Rhee, Yongjoo; Park, H. M.; Kwon, D. H.

    2005-05-01

    Atomic spectroscopy studies carried out at the Laboratory for Quantum Optics in Korea Atomic Energy Research Institute are introduced together with the AMO (Atomic, Molecular, and Optical) database established based upon those studies.

  18. GlycomeDB – integration of open-access carbohydrate structure databases

    Directory of Open Access Journals (Sweden)

    von der Lieth Claus-Wilhelm

    2008-09-01

    Full Text Available Abstract Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG, the Kyoto Encyclopedia of Genes and Genomes (KEGG and the Bacterial Carbohydrate Structure Database (BCSDB. We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource.

  19. University of Cambridge and MIT: Exploring Strategies for Digital Preservation for DSpace@Cambridge

    OpenAIRE

    Downing, Jim; Carpenter, Grace

    2005-01-01

    Cambridge University Library and MIT Libraries submit this proposal to share the outcomes of the digital preservation research work conducted through the DSpace@Cambridge project, concentrating on two main areas: Process Automation and Preservation Planning. Automation Digital preservation activity in its current form commonly involves a high level of human effort. In mediated archiving the archivist's efforts do not scale well. In self-archiving situations this effort can be a barri...

  20. 76 FR 12729 - Cambridge Environmental Inc; Transfer of Data

    Science.gov (United States)

    2011-03-08

    ... AGENCY Cambridge Environmental Inc; Transfer of Data AGENCY: Environmental Protection Agency (EPA... claimed as Confidential Business Information (CBI) by the submitter, will be transferred to Cambridge Environmental Inc. in accordance with 40 CFR 2.307(h)(3) and 2.308(i)(2). Cambridge Environmental Inc. has...

  1. Traffic Sign Recognition System based on Cambridge Correlator Image Comparator

    Directory of Open Access Journals (Sweden)

    J. Turan

    2012-06-01

    Full Text Available Paper presents basic information about application of Optical Correlator (OC, specifically Cambridge Correlator, in system to recognize of traffic sign. Traffic Sign Recognition System consists of three main blocks, Preprocessing, Optical Correlator and Traffic Sign Identification. The Region of Interest (ROI is defined and chosen in preprocessing block and then goes to Optical Correlator, where is compared with database of Traffic Sign. Output of Optical Correlation is correlation plane, which consist of highly localized intensities, know as correlation peaks. The intensity of spots provides a measure of similarity and position of spots, how images (traffic signs are relatively aligned in the input scene. Several experiments have been done with proposed system and results and conclusion are discussed.

  2. 40-Godišnjica institucije Cambridge Crystallographic Data Centre posvećene pohranjivanju podataka o molekularnim i kristalnim strukturama -

    Directory of Open Access Journals (Sweden)

    Molčanov, K.

    2006-06-01

    Full Text Available The article is dedicated to 40th anniversary of The Cambridge Crystallographic Data Centre (CCDC, the world-known centre (http://www.ccdc.cam.ac.uk responsible for deposition and control of crystallographic data, including atomic coordinates that define the three-dimensional structures of organic molecules and metal complexes containing organic ligands. Cambride Structural Database (CSD, one among the first established electronic databases, nowadays is the most significant crystallographic database in the world. CSD has about 400,000 deposited structures. The use of the extensive database, which is growing rapidly, needs support of efficient and sophisticated software for searching, analysing and visualising structural data. The seminal role of CSD in the research related to crystallography, chemistry, material sciences, solid state physics and chemistry, life sciences, pharmacology, and in particular in drug design, has been documented in more than 1300 scientific papers. The important issues of CCDC are the accuracy of deposited data and development of software that enables a wide variety of applications. Such demanding project requires higly competent team of experts; thus the article brings into focus the scientific approach of the team based on the long tradition in crystallography, modelling and informatics. The article is not dedicated to 40th anniversary of the centre only, but it also reveals how Cambridge Structural Database can be used in the research and teaching. The use of electronic media and computer graphics makes “data mining" very efficient and useful but also esthetically appealing due to the molecular architecture. At the Rudjer Bošković Institute, Zagreb, Croatia there is The National Affiliated Centre of Cambridge Crystallographic Data Centre responsible for communication and dissemination of CSD in Croatia, Slovenia and Macedonia. The use of CSD is illustrated by two examples performed and published by the presenting

  3. Crystallography Open Database – an open-access collection of crystal structures

    OpenAIRE

    Gražulis, Saulius; Chateigner, Daniel; Downs, Robert T.; Yokochi, A. F. T.; Quirós, Miguel; Lutterotti, Luca; Manakova, Elena; Butkus, Justas; Moeck, Peter; Le Bail, Armel

    2009-01-01

    The Crystallography Open Database (COD), which is a project that aims to gather all available inorganic, metal–organic and small organic molecule structural data in one database, is described. The database adopts an open-access model. The COD currently contains ∼80 000 entries in crystallographic information file format, with nearly full coverage of the International Union of Crystallography publications, and is growing in size and quality.

  4. INOH: ontology-based highly structured database of signal transduction pathways

    OpenAIRE

    Yamamoto, Satoko; Sakai, Noriko; Nakamura, Hiromi; Fukagawa, Hiroshi; Fukuda, Ken; Takagi, Toshihisa

    2011-01-01

    The Integrating Network Objects with Hierarchies (INOH) database is a highly structured, manually curated database of signal transduction pathways including Mammalia, Xenopus laevis, Drosophila melanogaster, Caenorhabditis elegans and canonical. Since most pathway knowledge resides in scientific articles, the database focuses on curating and encoding textual knowledge into a machine-processable form. We use a hierarchical pathway representation model with a compound graph, and every pathway c...

  5. GeneNet: a database on structure and functional organisation of gene networks

    OpenAIRE

    Ananko, E A; Podkolodny, N. L.; Stepanenko, I. L.; Ignatieva, E. V.; Podkolodnaya, O. A.; Kolchanov, N. A.

    2002-01-01

    The GeneNet database is designed for accumulation of information on gene networks. Original technology applied in GeneNet enables description of not only a gene network structure and functional relationships between components, but also metabolic and signal transduction pathways. Specialised software, GeneNet Viewer, automatically displays the graphical diagram of gene networks described in the database. Current release 3.0 of GeneNet database contains descriptions of 25 gene networks, 945 pr...

  6. URS DataBase: universe of RNA structures and their motifs.

    Science.gov (United States)

    Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

    2016-01-01

    The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/.

  7. Database Structure for the Indonesian Food Crop Monitoring System

    OpenAIRE

    Gary Stampley

    1992-01-01

    The development of the Indonesian Food Crop Monitoring System (FCMS) database required the compilation of general information on the principal food crops, as well as supportive data on climate, land use, prices, trade, and various macroeconomic conditions. The purpose for the collection and management of these data was twofold: (1) to support several specific food-crop policy analyses to be conducted by the FCMS project team, and (2) to provide a simple capability for monitoring and describin...

  8. Extending the Intermediate Data Structure (IDS) for longitudinal historical databases to include geographic data

    OpenAIRE

    Hedefalk, Finn; Harrie, Lars; Svensson, Patrick

    2014-01-01

    The Intermediate Data Structure (IDS) is a standardised database structure for longitudinal historical databases. Such a common structure facilitates data sharing and comparative research. In this study, we propose an extended version of IDS, named IDS-Geo, that also includes geographic data. The geographic data that will be stored in IDS-Geo are primarily buildings and/or property units, and the purpose of these geographic data is mainly to link individuals to places in space. When we want t...

  9. Increasing Database Performance through Optimizing Structure Query Language Join Statement

    Directory of Open Access Journals (Sweden)

    Ossama K. Muslih

    2010-01-01

    Full Text Available Problem statement: A join statement is a select statement with more than table in the FROM clause. A join predicate is a predicate in the WHERE clause that combines the columns of two of the tables in the join. Any database gives you the ability to join various tables together through different types of joins, resulting large number of rows to process. Query language can be used to join these tables and as it is well known query language should be declarative, so we can write alternative formulas to perform join statements. Different formulas provide variation in performance. Approach: This research presented a transparent middle layer between application interface front end and database back end. Results: The responsibilities of this layer were catching the SQL commands sent by application before reaching the database then examining these commands to see if they join more than one table, after that rewriting the SQL command taking into consideration the order of executing join predicates and none join predicates. This research focused on rewriting the SQL commands without application modification. Conclusion: Rewriting stage is the most complex stage because the system will restructure the SQL command with new syntax taking two things in its consideration, the first one was rewriting the command with better performance syntax after getting the help from recommendation dictionary, the second one was resulting the same data (output as previous old command.

  10. PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics

    Directory of Open Access Journals (Sweden)

    Rychlewski Leszek

    2006-02-01

    Full Text Available Abstract Background The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB. Many of these structures are functionally unannotated because they have no sequence similarity to proteins of known function. However, it is possible to successfully infer function using only structural similarity. Results Here we present the PDB-UF database, a web-accessible collection of predictions of enzymatic properties using structure-function relationship. The assignments were conducted for three-dimensional protein structures of unknown function that come from structural genomics initiatives. We show that 4 hypothetical proteins (with PDB accession codes: 1VH0, 1NS5, 1O6D, and 1TO0, for which standard BLAST tools such as PSI-BLAST or RPS-BLAST failed to assign any function, are probably methyltransferase enzymes. Conclusion We suggest that the structure-based prediction of an EC number should be conducted having the different similarity score cutoff for different protein folds. Moreover, performing the annotation using two different algorithms can reduce the rate of false positive assignments. We believe, that the presented web-based repository will help to decrease the number of protein structures that have functions marked as "unknown" in the PDB file. Availability http://paradox.harvard.edu/PDB-UF and http://bioinfo.pl/PDB-UF

  11. Alchemy in Cambridge. An Annotated Catalogue of Alchemical Texts and Illustrations in Cambridge Repositories.

    Science.gov (United States)

    Timmermann, Anke

    2015-01-01

    Alchemy in Cambridge captures the alchemical content of 56 manuscripts in Cambridge, in particular the libraries of Trinity College, Corpus Christi College and St John's College, the University Library and the Fitzwilliam Museum. As such, this catalogue makes visible a large number of previously unknown or obscured alchemica. While extant bibliographies, including those by M.R. James a century ago, were compiled by polymathic bibliographers for a wide audience of researchers, Alchemy in Cambridge benefits from the substantial developments in the history of alchemy, bibliography, and related scholarship in recent decades. Many texts are here identified for the first time. Another vital feature is the incorporation of information on alchemical illustrations in the manuscripts, intended to facilitate research on the visual culture of alchemy. The catalogue is aimed at historians of alchemy and science, and of high interest to manuscript scholars, historians of art and historians of college and university libraries. PMID:26245008

  12. Alchemy in Cambridge. An Annotated Catalogue of Alchemical Texts and Illustrations in Cambridge Repositories.

    Science.gov (United States)

    Timmermann, Anke

    2015-01-01

    Alchemy in Cambridge captures the alchemical content of 56 manuscripts in Cambridge, in particular the libraries of Trinity College, Corpus Christi College and St John's College, the University Library and the Fitzwilliam Museum. As such, this catalogue makes visible a large number of previously unknown or obscured alchemica. While extant bibliographies, including those by M.R. James a century ago, were compiled by polymathic bibliographers for a wide audience of researchers, Alchemy in Cambridge benefits from the substantial developments in the history of alchemy, bibliography, and related scholarship in recent decades. Many texts are here identified for the first time. Another vital feature is the incorporation of information on alchemical illustrations in the manuscripts, intended to facilitate research on the visual culture of alchemy. The catalogue is aimed at historians of alchemy and science, and of high interest to manuscript scholars, historians of art and historians of college and university libraries.

  13. Conceptual Level Design of Semi-structured Database System: Graph-semantic Based Approach

    OpenAIRE

    Anirban Sarkar

    2011-01-01

    This paper has proposed a Graph - semantic based conceptual model for semi-structured database system, called GOOSSDM, to conceptualize the different facets of such system in object oriented paradigm. The model defines a set of graph based formal constructs, variety of relationship types with participation constraints and rich set of graphical notations to specify the conceptual level design of semi-structured database system. The proposed design approach facilitates modeling of irregular, he...

  14. Semantic Label and Structure Model based Approach for Entity Recognition in Database Context

    OpenAIRE

    Kooli, Nihel; Belaïd, Abdel

    2015-01-01

    International audience —This paper proposes an entity recognition approach in scanned documents referring to their description in database records. First, using the database record values, the corresponding document fields are labeled. Second, entities are identified by their labels and ranked using a TF/IDF based score. For each entity, local labels are grouped into a graph. This graph is matched with a graph model (structure model) which represents geometric structures of local entity la...

  15. Cambridge IGCSE english as a second language

    CERN Document Server

    Reynolds, John

    2014-01-01

    Revised edition for the 2015 syllabus offering the easiest and most cost effective way to teach both the speaking and listening components with one set of books covering two years and free digital material. This title has been written for the revised Cambridge IGCSE English as a Second Language (0510 and 0511) syllabuses, for first teaching from 2013. ? Prepares students for their exams with a focus on assessed language features, such as inference, opinion and attitude. ? Develops language abilities at an appropriate pace with extra interactive tests on a free CD-ROM. We are working with Cambr

  16. The new Cambridge English course student 1

    CERN Document Server

    Swan, Michael

    1991-01-01

    The New Cambridge English Course is a course teachers and students can rely on to cover the complete range and depth of language and skills needed from beginner to upper-intermediate level. Each level is designed to provide at least 72 hours of class work using the Student's Book, with additional self-study material provided in the Practice Book. The course has a proven multi-syllabus approach which integrates work on all the vital aspects of language study: grammar, vocabulary, pronunciation, skills, notions and functions.

  17. Structured, unstructured, and semistructured search in semistructured databases

    OpenAIRE

    Balmin, Andrey

    2006-01-01

    A single framework for storing and querying XML data, using denormalized schema decompositions, can support both structured queries and unstructured searches, as well as serve as a foundation for combining the two forms of information access. XML data format becomes increasingly popular in applications that mix structured data and unstructured text. These applications require integration of structured query and text search mechanisms to access XML data. First, we introduce a framework for sto...

  18. Computer-aided visualization of database structural relationships

    International Nuclear Information System (INIS)

    Interactive computer graphic displays can be extremely useful in augmenting understandability of data structures. In complexly interrelated domains such as bibliographic thesauri and energy information systems, node and link displays represent one such tool. This paper presents examples of data structure representations found useful in these domains and discusses some of their generalizable components. 2 figures

  19. HD-RNAS: An automated hierarchical database of RNA structures

    Directory of Open Access Journals (Sweden)

    Shubhra Sankar eRay

    2012-04-01

    Full Text Available One of the important goals of most biological investigations is to classify and organize the experimental findings so that they are readily useful for deriving generalized rules. Although there is a huge amount of information on RNA structures in PDB, there are redundant files, ambiguous synthetic sequences etc. Moreover, a systematic hierarchical organization, reflecting RNA classification, is missing in PDB. In this investigation, we have classified all the available RNA crystal structures from PDB through a programmatic approach. Hence, it would be now a simple assignment to regularly update the classification as and when new structures are released. The classification can further determine (i a non-redundant set of RNA structures and (ii if available, a set of structures of identical sequence and function, which can highlight structural polymorphism, ligand-induced conformational alterations etc. Presently, we have classified the available structures (2095 PDB entries having RNA chain longer than 9 nucleotides solved by X-ray crystallography or NMR spectroscopy into nine functional classes. The structures of same function and same source are mostly seen to be similar with subtle differences depending on their functional complexation. The web-server is available online at http://www.saha.ac.in/biop/www/HD-RNAS.html and is updated regularly.

  20. An Extensible Schema-less Database Framework for Managing High-throughput Semi-Structured Documents

    Science.gov (United States)

    Maluf, David A.; Tran, Peter B.; La, Tracy; Clancy, Daniel (Technical Monitor)

    2002-01-01

    Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword searches of records for both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high throughput open database framework for managing, storing, and searching unstructured or semi structured arbitrary hierarchal models, XML and HTML.

  1. NETMARK: A Schema-less Extension for Relational Databases for Managing Semi-structured Data Dynamically

    Science.gov (United States)

    Maluf, David A.; Tran, Peter B.

    2003-01-01

    Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semi-structured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

  2. The method of design for seismic data database system based on tree structure

    Institute of Scientific and Technical Information of China (English)

    王喜珍; 滕云田; 高孟潭; 陈步云; 姜慧

    2005-01-01

    With the massive growth of the seismic data, it is required a new method to manage them. In this paper, the design method will be reported about relational database based on tree structure. Comparing with other designs, it is not only simpler and easier to organize data, but also can simplify the design process of the database. This method has been used to design database of the earthquake monitor center station of the earthquake monitoring system for the Yangtze River Three Gorges Project and has shown good results.

  3. PeptiSite: a structural database of peptide binding sites in 4D

    OpenAIRE

    Acharya, Chayan; Kufareva, Irina; Ilatovskiy, Andrey V.; Abagyan, Ruben

    2014-01-01

    We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with protein, peptide and small molecule partners. The unique features of the database include (1) the ensemble site representation that provides a fourth dimension to the otherwise three dimensional data, (2) comprehensive characterization of the binding site architecture that may consist of a mul...

  4. On the World Wide Web: Cost Effective Solutions to Database Searching

    OpenAIRE

    Decastro, Bart

    2012-01-01

    In a recent questionnaire survey of Cambridge Scientific subscribers, over 90% expressed preference for the delivery of abstracting/indexing services through the Internet. This fact has been the rationale for Cambridge Scientific's Internet initiative. Thirty-six of Cambridge Scientific's databases, previously available in print and CD-ROM, are now searchable through the World Wide Web. More recently, these databases have been clustered into eight sets, each with a unified index, covering cri...

  5. An Extensive Database of Electronic Structure Calculations between Transition Metals

    Science.gov (United States)

    Sayed, Shereef; Papaconstantopoulos, Dimitrios

    Density Functional Theory and its derived application methods, such as the Augmented Plane Wave (APW) method, have shown great success in predicting the fundamental properties of materials. In this work, we apply the APW method to explore the properties of diatomic pairs of transition metals in the CsCl structure, for all possible combinations. A total of 435 compounds have been studied. The predicted Density of States, and Band Structures are presented, along with predicted electron-phonon coupling and Stoner Criterion, in order to identify potential new superconducting or ferromagnetic materials. This work is performed to demonstrate the concept of ``high-throughput'' calculations at the crossing-point of ``Big Data'' and materials science. Us Dept of Energy.

  6. Web Entities Extraction Based on Semi-Structured Semantic Database

    Directory of Open Access Journals (Sweden)

    Fang Dong

    2013-07-01

    Full Text Available Web is the biggest source of information and contains many entities and relationships between them, extracting these data from Massive Web pages and Integrating to a Semi-Structured Data with rich semantics will be more conducive to the management and use of these web data. On this premise, a comprehensive method is proposed to perform extraction the entities and relationships from the webpages. The method consists of two steps: 1 The target Web pages which contains these entities will be found based on the combination of vision information and content of keyword, meanwhile recording the relationship between father and children target Web pages; 2 Extracting the entities with analysis of DOM tree structure of the obtained Web pages and definitions of some extraction rules. At last, the extracted data is organized into a Semi-Structured Data with special relationships. Experiments on a large number of HTML pages have showed that this method can get a high correct rate and coverage.

  7. The Whipple Museum and Cavendish Laboratory, Cambridge

    Science.gov (United States)

    Pippard, Brian

    The Whipple Museum is part of the History and Philosophy of Science Department in the University of Cambridge. It is on your right as soon as you enter Free School Lane from Pembroke Street, and is normally open between 1:30 and 4:30 P.M. on weekdays. The main room, a hall with hammer-beam roof, is a relic of Stephen Perse’s school (1624) now flourishing elsewhere in the city. It houses a large collection of mathematical, physical and astronomical instruments — abaci, Napier’s bones, slide rules; sextants and other surveying instruments; telescopes, compasses and pocket sundials (especially of ivory from Nuremberg 1500-1700); and a Grand Orrery by George Adams (1750). The gallery of a second room is used for special exhibitions, often of items from the well-stocked store. Some specialist catalogues have been compiled and are on sale.

  8. Teachers Learning: Professional Development and Education. Cambridge Education Research Series

    Science.gov (United States)

    McLaughlin, Colleen, Ed.

    2012-01-01

    "Teachers Learning: Professional Development and Education" is part of The Cambridge Education Research series, edited by senior colleagues at the University of Cambridge Faculty of Education, which has a longstanding tradition of involvement in high quality, innovative teacher education and continuing professional development.…

  9. Cambridge Illustrated History of Archaeology, edited by Paul G. Bahn, Cambridge University Press, New York, 1996

    OpenAIRE

    Douglas R. Givens

    1997-01-01

    The Cambridge Illustrated History of Archaeology is another in a series of volumes devoted to the history of archaeology that have appeared in recent time. Paul Bahn, the editor of the volume, has broken down his coverage of the history of worldwide archaeology into the following arrangement 'The Archaeology of Archaeology", "Old Worlds and New, 1500-1760", "Antiquarians and Explorers, 1760-1820", "Science and Romantic...

  10. MSV3d: database of human MisSense Variants mapped to 3D protein structure.

    Science.gov (United States)

    Luu, Tien-Dao; Rusu, Alin-Mihai; Walter, Vincent; Ripp, Raymond; Moulinier, Luc; Muller, Jean; Toursel, Thierry; Thompson, Julie D; Poch, Olivier; Nguyen, Hoan

    2012-01-01

    The elucidation of the complex relationships linking genotypic and phenotypic variations to protein structure is a major challenge in the post-genomic era. We present MSV3d (Database of human MisSense Variants mapped to 3D protein structure), a new database that contains detailed annotation of missense variants of all human proteins (20 199 proteins). The multi-level characterization includes details of the physico-chemical changes induced by amino acid modification, as well as information related to the conservation of the mutated residue and its position relative to functional features in the available or predicted 3D model. Major releases of the database are automatically generated and updated regularly in line with the dbSNP (database of Single Nucleotide Polymorphism) and SwissVar releases, by exploiting the extensive Décrypthon computational grid resources. The database (http://decrypthon.igbmc.fr/msv3d) is easily accessible through a simple web interface coupled to a powerful query engine and a standard web service. The content is completely or partially downloadable in XML or flat file formats. Database URL: http://decrypthon.igbmc.fr/msv3d.

  11. An Extensible "SCHEMA-LESS" Database Framework for Managing High-Throughput Semi-Structured Documents

    Science.gov (United States)

    Maluf, David A.; Tran, Peter B.

    2003-01-01

    Object-Relational database management system is an integrated hybrid cooperative approach to combine the best practices of both the relational model utilizing SQL queries and the object-oriented, semantic paradigm for supporting complex data creation. In this paper, a highly scalable, information on demand database framework, called NETMARK, is introduced. NETMARK takes advantages of the Oracle 8i object-relational database using physical addresses data types for very efficient keyword search of records spanning across both context and content. NETMARK was originally developed in early 2000 as a research and development prototype to solve the vast amounts of unstructured and semistructured documents existing within NASA enterprises. Today, NETMARK is a flexible, high-throughput open database framework for managing, storing, and searching unstructured or semi-structured arbitrary hierarchal models, such as XML and HTML.

  12. A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

    Science.gov (United States)

    Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

    2010-08-01

    The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.

  13. 76 FR 13665 - Cambridge Tool & Die, Including On-Site Leased Workers From Action Total Staffing, Cambridge, OH...

    Science.gov (United States)

    2011-03-14

    ... Register on January 26, 2011 (76 FR 4731). At the request of the State agency, the Department reviewed the... Employment and Training Administration Cambridge Tool & Die, Including On-Site Leased Workers From Action Total Staffing, Cambridge, OH; Amended Certification Regarding Eligibility To Apply for...

  14. Biofuel Database

    Science.gov (United States)

    Biofuel Database (Web, free access)   This database brings together structural, biological, and thermodynamic data for enzymes that are either in current use or are being considered for use in the production of biofuels.

  15. GALT protein database: querying structural and functional features of GALT enzyme.

    Science.gov (United States)

    d'Acierno, Antonio; Facchiano, Angelo; Marabotti, Anna

    2014-09-01

    Knowledge of the impact of variations on protein structure can enhance the comprehension of the mechanisms of genetic diseases related to that protein. Here, we present a new version of GALT Protein Database, a Web-accessible data repository for the storage and interrogation of structural effects of variations of the enzyme galactose-1-phosphate uridylyltransferase (GALT), the impairment of which leads to classic Galactosemia, a rare genetic disease. This new version of this database now contains the models of 201 missense variants of GALT enzyme, including heterozygous variants, and it allows users not only to retrieve information about the missense variations affecting this protein, but also to investigate their impact on substrate binding, intersubunit interactions, stability, and other structural features. In addition, it allows the interactive visualization of the models of variants collected into the database. We have developed additional tools to improve the use of the database by nonspecialized users. This Web-accessible database (http://bioinformatica.isa.cnr.it/GALT/GALT2.0) represents a model of tools potentially suitable for application to other proteins that are involved in human pathologies and that are subjected to genetic variations. PMID:24990533

  16. EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

    Science.gov (United States)

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-01

    Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co.

  17. Knowledge-driven multidimensional indexing structure for biomedical media database retrieval.

    Science.gov (United States)

    Scott, Grant; Shyu, Chi-Ren

    2007-05-01

    Today, biomedical media data are being generated at rates unimaginable only years ago. Content-based retrieval of biomedical media from large databases is becoming increasingly important to clinical, research, and educational communities. In this paper, we present the recently developed entropy balanced statistical (EBS) k-d tree and its applications to biomedical media, including a high-resolution computed tomography (HRCT) lung image database and the first real-time protein tertiary structure search engine. Our index utilizes statistical properties inherent in large-scale biomedical media databases for efficient and accurate searches. By applying concepts from pattern recognition and information theory, the EBS k-d tree is built through top-down decision tree induction. Experimentation shows similarity searches against a protein structure database of 53 363 structures consistently execute in less than 8.14 ms for the top 100 most similar structures. Additionally, we have shown improved retrieval precision over adaptive and statistical k-d trees. Retrieval precision of the EBS k-d tree is 81.6% for content-based retrieval of HRCT lung images and 94.9% at 10% recall for protein structure similarity search. The EBS k-d tree has enormous potential for use in biomedical applications embedded with ground-truth knowledge and multidimensional signatures.

  18. Structures in the communication between lexicographer and programmer: Database and interface

    DEFF Research Database (Denmark)

    Tarp, Sven

    2015-01-01

    This paper deals exclusively with e-lexicography. It intends to answer the question how much a lexicographer in charge of a new e-dictionary project should know about lexicographical structures, and how this knowledge could be communicated to the IT programmer designing the underlying database an...

  19. The CAMbridge Emission Line Surveyor (CAMELS)

    CERN Document Server

    Thomas, C N; Maiolino, R; Goldie, D J; Acedo, E de Lera; Wagg, J; Blundell, R; Paine, S; Zeng, L

    2014-01-01

    The CAMbridge Emission Line Surveyor (CAMELS) is a pathfinder program to demonstrate on-chip spectrometry at millimetre wavelengths. CAMELS will observe at frequencies from 103-114.7 GHz, providing 512 channels with a spectral resolution of R = 3000. In this paper we describe the science goals of CAMELS, the current system level design for the instrument and the work we are doing on the detailed designs of the individual components. In addition, we will discuss our efforts to understand the impact that the design and calibration of the filter bank on astronomical performance. The shape of the filter channels, the degree of overlap and the nature of the noise all effect how well the parameters of a spectral line can be recovered. We have developed a new and rigorous method for analysing performance, based on the concept of Fisher information. This can in be turn coupled to a detailed model of the science case, allowing design trade-offs to be properly investigated.

  20. Artificial Pancreas Project at Cambridge 2013.

    Science.gov (United States)

    Hovorka, R

    2015-08-01

    The development and clinical testing of closed-loop systems (the artificial pancreas) is underpinned by advances in continuous glucose monitoring and benefits from concerted academic and industry collaborative efforts. This review describes the progress of the Artificial Pancreas Project at the University of Cambridge from 2006 to 2014. Initial studies under controlled laboratory conditions, designed to collect representative safety and performance data, were followed by short to medium free-living unsupervised outpatient studies demonstrating the safety and efficacy of closed-loop insulin delivery using a model predictive control algorithm. Accompanying investigations included assessment of the psychosocial impact and key factors affecting glucose control such as insulin kinetics and glucose absorption. Translation to other disease conditions such as critical illness and Type 2 diabetes took place. It is concluded that innovation of iteratively enhanced closed-loop systems will provide tangible means to improve outcomes and quality of life in people with Type 1 diabetes and their families in the next decade.

  1. PASS2: an automated database of protein alignments organised as structural superfamilies

    Directory of Open Access Journals (Sweden)

    Sowdhamini Ramanathan

    2004-04-01

    Full Text Available Abstract Background The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2 database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. Description An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of

  2. pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

    Science.gov (United States)

    Varadi, Mihaly; Kosol, Simone; Lebrun, Pierre; Valentini, Erica; Blackledge, Martin; Dunker, A. Keith; Felli, Isabella C.; Forman-Kay, Julie D.; Kriwacki, Richard W.; Pierattelli, Roberta; Sussman, Joel; Svergun, Dmitri I.; Uversky, Vladimir N.; Vendruscolo, Michele; Wishart, David; Wright, Peter E.; Tompa, Peter

    2014-01-01

    The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. Owing to the inherent flexibility of IDPs, solution techniques are particularly appropriate for characterizing their biophysical properties, and structural ensembles in agreement with these data provide a convenient tool for describing the underlying conformational sampling. Database entries consist of (i) primary experimental data with descriptions of the acquisition methods and algorithms used for the ensemble calculations, and (ii) the structural ensembles consistent with these data, provided as a set of models in a Protein Data Bank format. PE-DB is open for submissions from the community, and is intended as a forum for disseminating the structural ensembles and the methodologies used to generate them. While the need to represent the IDP structures is clear, methods for determining and evaluating the structural ensembles are still evolving. The availability of the pE-DB database is expected to promote the development of new modeling methods and leads to a better understanding of how function arises from disordered states. PMID:24174539

  3. PeptiSite: a structural database of peptide binding sites in 4D.

    Science.gov (United States)

    Acharya, Chayan; Kufareva, Irina; Ilatovskiy, Andrey V; Abagyan, Ruben

    2014-03-21

    We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with protein, peptide and small molecule partners. The unique features of the database include: (1) the ensemble site representation that provides a fourth dimension to the otherwise three dimensional data, (2) comprehensive characterization of the binding site architecture that may consist of a multimeric protein assembly with cofactors and metal ions and (3) analysis of consensus interaction motifs within the ensembles and identification of conserved determinants of these interactions. Currently the database contains 585 proteins with 650 peptide-binding sites. http://peptisite.ucsd.edu/ link allows searching for the sites of interest and interactive visualization of the ensembles using the ActiveICM web-browser plugin. This structural database for protein-peptide interactions enables understanding of structural principles of these interactions and may assist the development of an efficient peptide docking benchmark. PMID:24406170

  4. Structure design and establishment of database application system for alien species in Shandong Province, China

    Institute of Scientific and Technical Information of China (English)

    GUO Wei-hua; LIU Heng; DU Ning; ZHANG Xin-shi; WANG Ren-qing

    2007-01-01

    This paper presents a case study on structure design and establishment of database application system for alien species in Shandong Province, integrating with Geographic Information System, computer network, and database technology to the research of alien species. The modules of alien species database, including classified data input, statistics and analysis, species pictures and distribution maps,and out date input, were approached by Visual Studio.net 2003 and Microsoft SQL server 2000. The alien species information contains the information of classification, species distinction characteristics, biological characteristics, original area, distribution area, the entering fashion and route, invasion time, invasion reason, interaction with the endemic species, growth state, danger state and spatial information, i.e.distribution map. Based on the above bases, several models including application, checking, modifying, printing, adding and returning models were developed. Furthermore, through the establishment of index tables and index maps, we can also spatially query the data like picture,text and GIS map data. This research established the technological platform of sharing information about scientific resource of alien species in Shandong Province, offering the basis for the dynamic inquiry of alien species, the warning technology of prevention and the fast reaction system. The database application system possessed the principles of good practicability, friendly user interface and convenient usage. It can supply full and accurate information inquiry services of alien species for the users and provide functions of dynamically managing the database for the administrator.

  5. Conceptual Level Design of Semi-structured Database System: Graph-semantic Based Approach

    Directory of Open Access Journals (Sweden)

    Anirban Sarkar

    2011-10-01

    Full Text Available This paper has proposed a Graph – semantic based conceptual model for semi-structured database system, called GOOSSDM, to conceptualize the different facets of such system in object oriented paradigm. The model defines a set of graph based formal constructs, variety of relationship types with participation constraints and rich set of graphical notations to specify the conceptual level design of semi-structured database system. The proposed design approach facilitates modeling of irregular, heterogeneous, hierarchical and non-hierarchical semi-structured data at the conceptual level. Moreover, the proposed GOOSSDM is capable to model XML document at conceptual level with the facility of document-centric design, ordering and disjunction characteristic. A rule based transformation mechanism of GOOSSDM schema into the equivalent XML Schema Definition (XSD also has been proposed in this paper. The concepts of the proposed conceptual model have been implemented using Generic Modeling Environment (GME.

  6. Ultra-Structure database design methodology for managing systems biology data and analyses

    Directory of Open Access Journals (Sweden)

    Hemminger Bradley M

    2009-08-01

    Full Text Available Abstract Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping. Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find

  7. Cohort profile: the Cambridge Baby Growth Study (CBGS)

    OpenAIRE

    Prentice, P.; Acerini, C. L.; Eleftheriou, A.; Hughes, I A; Ong, K K; Dunger, D B

    2015-01-01

    The Cambridge Baby Growth Study has been supported by the European Union Framework V, the World Cancer Research Foundation International, the Medical Research Council, the NIHR Cambridge Comprehensive Biomedical Research Centre, the Newlife Foundation for disabled children, the Mothercare Group Foundation, Mead Johnson Nutrition, the Evelyn Trust, the Wellbeing of Women, Diabetes UK and a collaborative research grant from the European Society for Paediatric Endocrinology.

  8. 3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale

    Science.gov (United States)

    Mazzocco, Giovanni; Lazniewski, Michal; Migdał, Piotr; Szczepińska, Teresa; Radomski, Jan P.; Plewczynski, Dariusz

    2016-01-01

    The influenza virus type A (IVA) is an important pathogen which is able to cause annual epidemics and even pandemics. This fact is the consequence of the antigenic shifts and drifts capabilities of IVA, caused by the high mutation rate and the reassortment capabilities of the virus. The hemagglutinin (HA) protein constitutes the main IVA antigen and has a crucial role in the infection mechanism, being responsible for the recognition of host-specific sialic acid derivatives. Despite the relative abundance of HA sequence and serological studies, comparative structure-based analysis of HA are less investigated. The 3DFlu database contains well annotated HA representatives: 1192 models and 263 crystallographic structures. The relations between these proteins are defined using different metrics and are visualized as a network in the provided web interface. Moreover structural and sequence comparison of the proteins can be explored. Metadata information (e.g. protein identifier, IVA strain, year and location of infection) can enhance the exploration of the presented data. With our database researchers gain a useful tool for the exploration of high quality HA models, viewing and comparing changes in the HA viral subtypes at several information levels (sequence, structure, ESP). The complete and integrated view of those relations might be useful to determine the efficiency of transmission, pathogenicity and for the investigation of evolutionary tendencies of the influenza virus. Database URL: http://nucleus3d.cent.uw.edu.pl/influenza PMID:27694207

  9. Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins

    Directory of Open Access Journals (Sweden)

    Bradley Michael E

    2006-02-01

    Full Text Available Abstract Background When accurate models for the divergent evolution of protein sequences are integrated with complementary biological information, such as folded protein structures, analyses of the combined data often lead to new hypotheses about molecular physiology. This represents an excellent example of how bioinformatics can be used to guide experimental research. However, progress in this direction has been slowed by the lack of a publicly available resource suitable for general use. Results The precomputed Magnum database offers a solution to this problem for ca. 1,800 full-length protein families with at least one crystal structure. The Magnum deliverables include 1 multiple sequence alignments, 2 mapping of alignment sites to crystal structure sites, 3 phylogenetic trees, 4 inferred ancestral sequences at internal tree nodes, and 5 amino acid replacements along tree branches. Comprehensive evaluations revealed that the automated procedures used to construct Magnum produced accurate models of how proteins divergently evolve, or genealogies, and correctly integrated these with the structural data. To demonstrate Magnum's capabilities, we asked for amino acid replacements requiring three nucleotide substitutions, located at internal protein structure sites, and occurring on short phylogenetic tree branches. In the cellular retinoid binding protein family a site that potentially modulates ligand binding affinity was discovered. Recruitment of cellular retinol binding protein to function as a lens crystallin in the diurnal gecko afforded another opportunity to showcase the predictive value of a browsable database containing branch replacement patterns integrated with protein structures. Conclusion We integrated two areas of protein science, evolution and structure, on a large scale and created a precomputed database, known as Magnum, which is the first freely available resource of its kind. Magnum provides evolutionary and structural

  10. Transformation of Wiktionary entry structure into tables and relations in a relational database schema

    CERN Document Server

    Krizhanovsky, A A

    2010-01-01

    This paper addresses the question of automatic data extraction from the Wiktionary, which is a multilingual and multifunctional dictionary. Wiktionary is a collaborative project working on the same principles as the Wikipedia. The Wiktionary entry is a plain text from the text processing point of view. Wiktionary guidelines prescribe the entry layout and rules, which should be followed by editors of the dictionary. The presence of the structure of a Wiktionary article and formatting rules allows transforming the Wiktionary entry structure into tables and relations in a relational database schema, which is a part of a machine-readable dictionary (MRD). The paper describes how the flat text of the Wiktionary entry was extracted, converted, and stored in the specially designed relational database. The MRD contains the definitions, semantic relations, and translations extracted from the English and Russian Wiktionaries. The parser software is released under the open source license agreement (GPL), to facilitate i...

  11. A Reference Database for Circular Dichroism Spectroscopy Covering Fold and Secondary Structure Space

    International Nuclear Information System (INIS)

    Circular Dichroism (CD) spectroscopy is a long-established technique for studying protein secondary structures in solution. Empirical analyses of CD data rely on the availability of reference datasets comprised of far-UV CD spectra of proteins whose crystal structures have been determined. This article reports on the creation of a new reference dataset which effectively covers both secondary structure and fold space, and uses the higher information content available in synchrotron radiation circular dichroism (SRCD) spectra to more accurately predict secondary structure than has been possible with existing reference datasets. It also examines the effects of wavelength range, structural redundancy and different means of categorizing secondary structures on the accuracy of the analyses. In addition, it describes a novel use of hierarchical cluster analyses to identify protein relatedness based on spectral properties alone. The databases are shown to be applicable in both conventional CD and SRCD spectroscopic analyses of proteins. Hence, by combining new bioinformatics and biophysical methods, a database has been produced that should have wide applicability as a tool for structural molecular biology

  12. Data in support of UbSRD: The Ubiquitin Structural Relational Database.

    Science.gov (United States)

    Harrison, Joseph S; Jacobs, Tim M; Houlihan, Kevin; Van Doorslaer, Koenraad; Kuhlman, Brian

    2015-12-01

    This article provides information to support the database article titled "UbSRD: The Ubiquitin Structural Relational Database" (Harrison et al., 2015) [1] . The ubiquitin-like homology fold (UBL) represents a large family that encompasses both post-translational modifications, like ubiquitin (UBQ) and SUMO, and functional domains on many biologically important proteins like Parkin, UHRF1 (ubiquitin-like with PDB and RING finger domains-1), and Usp7 (ubiquitin-specific protease-7) (Zhang et al., 2015; Rothbart et al., 2013; Burroughs et al., 2012; Wauer et al., 2015) [2], [3], [4], [5]. The UBL domain can participate in several unique protein-protein interactions (PPI) since protein adducts can be attached to and removed from amino groups of lysine side chains and the N-terminus of proteins. Given the biological significance of UBL domains, many have been characterized with high-resolution techniques, and for UBQ and SUMO, many protein complexes have been characterized. We identified all the UBL domains in the PDB and created a relational database called UbSRD (Ubiquitin Structural Relational Database) by using structural analysis tools in the Rosetta (Leaver et al., 2013; O'Meara et al., 2015; Leaver-fay et al., 2011) [1], [6], [7], [8]. Querying UbSRD permitted us to report many quantitative properties of UBQ and SUMO recognition at different types interfaces (noncovalent: NC, conjugated: CJ, and deubiquitanse: DB). In this data article, we report the average number of non-UBL neighbors, secondary structure of interacting motifs, and the type of inter-molecular hydrogen bonds for each residue of UBQ and SUMO. Additionally, we used PROMALS3D to generate a multiple sequence alignment used to construct a phylogram for the entire set of UBLs (Pei and Grishin, 2014) [9]. The data described here will be generally useful to scientists studying the molecular basis for recognition of UBQ or SUMO. PMID:26958617

  13. Data in support of UbSRD: The Ubiquitin Structural Relational Database.

    Science.gov (United States)

    Harrison, Joseph S; Jacobs, Tim M; Houlihan, Kevin; Van Doorslaer, Koenraad; Kuhlman, Brian

    2015-12-01

    This article provides information to support the database article titled "UbSRD: The Ubiquitin Structural Relational Database" (Harrison et al., 2015) [1] . The ubiquitin-like homology fold (UBL) represents a large family that encompasses both post-translational modifications, like ubiquitin (UBQ) and SUMO, and functional domains on many biologically important proteins like Parkin, UHRF1 (ubiquitin-like with PDB and RING finger domains-1), and Usp7 (ubiquitin-specific protease-7) (Zhang et al., 2015; Rothbart et al., 2013; Burroughs et al., 2012; Wauer et al., 2015) [2], [3], [4], [5]. The UBL domain can participate in several unique protein-protein interactions (PPI) since protein adducts can be attached to and removed from amino groups of lysine side chains and the N-terminus of proteins. Given the biological significance of UBL domains, many have been characterized with high-resolution techniques, and for UBQ and SUMO, many protein complexes have been characterized. We identified all the UBL domains in the PDB and created a relational database called UbSRD (Ubiquitin Structural Relational Database) by using structural analysis tools in the Rosetta (Leaver et al., 2013; O'Meara et al., 2015; Leaver-fay et al., 2011) [1], [6], [7], [8]. Querying UbSRD permitted us to report many quantitative properties of UBQ and SUMO recognition at different types interfaces (noncovalent: NC, conjugated: CJ, and deubiquitanse: DB). In this data article, we report the average number of non-UBL neighbors, secondary structure of interacting motifs, and the type of inter-molecular hydrogen bonds for each residue of UBQ and SUMO. Additionally, we used PROMALS3D to generate a multiple sequence alignment used to construct a phylogram for the entire set of UBLs (Pei and Grishin, 2014) [9]. The data described here will be generally useful to scientists studying the molecular basis for recognition of UBQ or SUMO.

  14. Information structure design for databases a practical guide to data modelling

    CERN Document Server

    Mortimer, Andrew J

    2014-01-01

    Computer Weekly Professional Series: Information Structure Design for Databases: A Practical Guide to Data modeling focuses on practical data modeling covering business and information systems. The publication first offers information on data and information, business analysis, and entity relationship model basics. Discussions cover degree of relationship symbols, relationship rules, membership markers, types of information systems, data driven systems, cost and value of information, importance of data modeling, and quality of information. The book then takes a look at entity relationship mode

  15. DOE Order 5480.28 natural phenomena hazards mitigation system, structure, component database

    International Nuclear Information System (INIS)

    This document describes the Prioritization Phase Database that was prepared for the Project Hanford Management Contractors to support the implementation of DOE Order 5480.28. Included within this document are three appendices which contain the prioritized list of applicable Project Hanford Management Contractors Systems, Structures, and Components. These appendices include those assets that comply with the requirements of DOE Order 5480.28, assets for which a waiver will be recommended, and assets requiring additional information before compliance can be ascertained

  16. Michele Renee Salzman, Marvina A. Sweeney & William Adler (eds., The Cambridge History of Religions in the Ancient World (2 vols. (New York: Cambridge University Press, 2013

    Directory of Open Access Journals (Sweden)

    Giorgio Baruchello

    2014-03-01

    Full Text Available Review of: Michele Renee Salzman, Marvina A. Sweeney & William Adler (eds., The Cambridge History of Religions in the Ancient World (2 vols. (New York: Cambridge University Press, 2013

  17. 数据库技术发展的新方向——非结构化数据库%New Orientation of the Database Technology Development——Non-Structure Database

    Institute of Scientific and Technical Information of China (English)

    李慧; 颜显森

    2001-01-01

    With the development of Internet, many disadvantages of the traditional relational database have been discovered. Under such circumstances, the non-structure database comes into being. This paper mainly discusses the definition, background, characteristics and advantages of the non-structure database.

  18. Knowledge-Based Optimization of Molecular Geometries Using Crystal Structures.

    Science.gov (United States)

    Cole, Jason C; Groom, Colin R; Korb, Oliver; McCabe, Patrick; Shields, Gregory P

    2016-04-25

    This paper describes a novel way to use the structural information contained in the Cambridge Structural Database (CSD) to drive geometry optimization of organic molecules. We describe how CSD structural information is transformed into objective functions for gradient-based optimization to provide good quality geometries for a large variety of organic molecules. Performance is assessed by minimizing different sets of organic molecules reporting RMSD movements for bond lengths, valence angles, torsion angles, and heavy atom positions. PMID:26977906

  19. Worries of Pregnant Women: Testing the Farsi Cambridge Worry Scale.

    Science.gov (United States)

    Mortazavi, Forough; Akaberi, Arash

    2016-01-01

    Pregnancy adds many sources of concerns to women's daily life worries. Excessive worry can affect maternal physiological and psychological state that influences the pregnancy outcomes. The aim of this study was to validate the Cambridge Worry Scale (CWS) in a sample of Iranian pregnant women. After translation of the CWS, ten experts evaluated the items and added six items to the 17-item scale. In a descriptive cross-sectional study, 405 of pregnant women booked for prenatal care completed the Farsi CWS. We split the sample randomly. Exploratory factor analysis (EFA) was conducted on the first half of the sample to disclose the factorial structure of the 23-item scale. The results of the EFA on the Farsi CWS indicated four factors altogether explained 51.5% of variances. Confirmatory factor analysis (CFA) was done on the second half of the sample. The results of the CFA showed that the model fit our data (chi-square/df = 2.02, RMSEA = 0.071, SRMR = 0.071, CFI = 0.95, and NNFI = 0.94). Cronbach's alpha coefficient for the Farsi CWS was 0.883. The Farsi CWS is a reliable and valid instrument for understanding common pregnancy worries in the third trimester of pregnancy in Iranian women. PMID:27293974

  20. Worries of Pregnant Women: Testing the Farsi Cambridge Worry Scale.

    Science.gov (United States)

    Mortazavi, Forough; Akaberi, Arash

    2016-01-01

    Pregnancy adds many sources of concerns to women's daily life worries. Excessive worry can affect maternal physiological and psychological state that influences the pregnancy outcomes. The aim of this study was to validate the Cambridge Worry Scale (CWS) in a sample of Iranian pregnant women. After translation of the CWS, ten experts evaluated the items and added six items to the 17-item scale. In a descriptive cross-sectional study, 405 of pregnant women booked for prenatal care completed the Farsi CWS. We split the sample randomly. Exploratory factor analysis (EFA) was conducted on the first half of the sample to disclose the factorial structure of the 23-item scale. The results of the EFA on the Farsi CWS indicated four factors altogether explained 51.5% of variances. Confirmatory factor analysis (CFA) was done on the second half of the sample. The results of the CFA showed that the model fit our data (chi-square/df = 2.02, RMSEA = 0.071, SRMR = 0.071, CFI = 0.95, and NNFI = 0.94). Cronbach's alpha coefficient for the Farsi CWS was 0.883. The Farsi CWS is a reliable and valid instrument for understanding common pregnancy worries in the third trimester of pregnancy in Iranian women.

  1. The Reticular Chemistry Structure Resource (RCSR) database of, and symbols for, crystal nets.

    Science.gov (United States)

    O'Keeffe, Michael; Peskov, Maxim A; Ramsden, Stuart J; Yaghi, Omar M

    2008-12-01

    During the past decade, interest has grown tremendously in the design and synthesis of crystalline materials constructed from molecular clusters linked by extended groups of atoms. Most notable are metal-organic frameworks (MOFs), in which polyatomic inorganic metal-containing clusters are joined by polytopic linkers. (Although these materials are sometimes referred to as coordination polymers, we prefer to differentiate them, because MOFs are based on strong linkages that yield robust frameworks.) The realization that MOFs could be designed and synthesized in a rational way from molecular building blocks led to the emergence of a discipline that we call reticular chemistry. MOFs can be represented as a special kind of graph called a periodic net. Such descriptions date back to the earliest crystallographic studies but have become much more common recently because thousands of new structures and hundreds of underlying nets have been reported. In the simplest cases (e.g., the structure of diamond), the atoms in the crystal become the vertices of the net, and bonds are the links (edges) that connect them. In the case of MOFs, polyatomic groups act as the vertices and edges of the net. Because of the explosive growth in this area, a need has arisen for a universal system of nomenclature, classification, identification, and retrieval of these topological structures. We have developed a system of symbols for the identification of three periodic nets of interest, and this system is now in wide use. In this Account, we explain the underlying methodology of assigning symbols and describe the Reticular Chemistry Structure Resource (RCSR), in which about 1600 such nets are collected and illustrated in a database that can be searched by symbol, name, keywords, and attributes. The resource also contains searchable data for polyhedra and layers. The database entries come from systematic enumerations or from known chemical compounds or both. In the latter case, references to

  2. Sequence and structural analyses of nuclear export signals in the NESdb database.

    Science.gov (United States)

    Xu, Darui; Farmer, Alicia; Collett, Garen; Grishin, Nick V; Chook, Yuh Min

    2012-09-01

    We compiled >200 nuclear export signal (NES)-containing CRM1 cargoes in a database named NESdb. We analyzed the sequences and three-dimensional structures of natural, experimentally identified NESs and of false-positive NESs that were generated from the database in order to identify properties that might distinguish the two groups of sequences. Analyses of amino acid frequencies, sequence logos, and agreement with existing NES consensus sequences revealed strong preferences for the Φ1-X(3)-Φ2-X(2)-Φ3-X-Φ4 pattern and for negatively charged amino acids in the nonhydrophobic positions of experimentally identified NESs but not of false positives. Strong preferences against certain hydrophobic amino acids in the hydrophobic positions were also revealed. These findings led to a new and more precise NES consensus. More important, three-dimensional structures are now available for 68 NESs within 56 different cargo proteins. Analyses of these structures showed that experimentally identified NESs are more likely than the false positives to adopt α-helical conformations that transition to loops at their C-termini and more likely to be surface accessible within their protein domains or be present in disordered or unobserved parts of the structures. Such distinguishing features for real NESs might be useful in future NES prediction efforts. Finally, we also tested CRM1-binding of 40 NESs that were found in the 56 structures. We found that 16 of the NES peptides did not bind CRM1, hence illustrating how NESs are easily misidentified.

  3. Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database

    Directory of Open Access Journals (Sweden)

    Bickerton George R

    2011-07-01

    Full Text Available Abstract Background Structural studies are increasingly providing huge amounts of information on multi-protein assemblies. Although a complete understanding of cellular processes will be dependent on an explicit characterization of the intermolecular interactions that underlie these assemblies and mediate molecular recognition, these are not well described by standard representations. Results Here we present PICCOLO, a comprehensive relational database capturing the details of structurally characterized protein-protein interactions. Interactions are described at the level of interacting pairs of atoms, residues and polypeptide chains, with the physico-chemical nature of the interactions being characterized. Distance and angle terms are used to distinguish 12 different interaction types, including van der Waals contacts, hydrogen bonds and hydrophobic contacts. The explicit aim of PICCOLO is to underpin large-scale analyses of the properties of protein-protein interfaces. This is exemplified by an analysis of residue propensity and interface contact preferences derived from a much larger data set than previously reported. However, PICCOLO also supports detailed inspection of particular systems of interest. Conclusions The current PICCOLO database comprises more than 260 million interacting atom pairs from 38,202 protein complexes. A web interface for the database is available at http://www-cryst.bioc.cam.ac.uk/piccolo.

  4. DATABASE STRUCTURE FOR THE INTEGRATION OF RS WITH GIS BASED ON SEMANTIC NETWORK

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The integration of remote sensing (RS) with geographical information sy stem (GIS) is a hotspot in geographical information science.A good da tabase structure is important to the integration of RS with GIS,which should be b eneficial to the complete integration of RS with GIS,able to deal with the disag reement between the resolution of remote sensing images and the precision of GIS data,and also helpful to the knowledge discovery and exploitation.In this pap er,the database structure storing the spatial data based on semantic network is presented.This database structure has several advantages.Firstly,the spatial data is stored as raster data with space index,so the image processing can be done directly on the GIS data that is stored hierarchically according to the di stinguishing precision.Secondly,the simple objects are aggregated into compl ex ones.Thirdly,because we use the indexing tree to depict the relationship of aggregation and the indexing pictures expressed by 2_D strings to describe the topolo gy structure of the objects,the concepts of surrounding and region are expressed clearly and the semantic content of the landscape can be illustrated well.All the factors that affect the recognition of the objects are depicted in the facto r space,which provides a uniform mathematical frame for the fusion of the seman tic and non_semantic information.Lastly,the object node,knowledge node and th e indexing node are integrated into one node.This feature enhances the ability of system in knowledge expressing,intelligent inference and association.The ap plication shows that this database structure can benefit the interpretation of r emote sensing image with the information of GIS.

  5. VnD: a structure-centric database of disease-related SNPs and drugs.

    Science.gov (United States)

    Yang, Jin Ok; Oh, Sangho; Ko, Gunhwan; Park, Seong-Jin; Kim, Woo-Yeon; Lee, Byungwook; Lee, Sanghyuk

    2011-01-01

    Numerous genetic variations have been found to be related to human diseases. Significant portion of those affect the drug response as well by changing the protein structure and function. Therefore, it is crucial to understand the trilateral relationship among genomic variations, diseases and drugs. We present the variations and drugs (VnD), a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. VnD was built in three steps. First, we integrated various resources systematically to deduce catalogs of disease-related genes, single nucleotide polymorphisms (SNPs), protein mutations and relevant drugs. VnD contains 137,195 disease-related gene records (13,940 distinct genes) and 16,586 genetic variation records (1790 distinct variations). Next, we carried out structure modeling and docking simulation for wild-type and mutant proteins to examine the structural and functional consequences of non-synonymous SNPs in the drug-related genes. Conformational changes in 590 wild-type and 4437 mutant proteins from drug-related genes were included in our database. Finally, we investigated the structural and biochemical properties relevant to drug binding such as the distribution of SNPs in proximal protein pockets, thermo-chemical stability, interactions with drugs and physico-chemical properties. The VnD database, available at http://vnd.kobic.re.kr:8080/VnD/ or vandd.org, would be a useful platform for researchers studying the underlying mechanism for association among genetic variations, diseases and drugs.

  6. Mime, Music and Drama on the Eighteenth-Century Stage. The Ballet d'Action. Edward Nye, Cambridge-New York, Cambridge University Press, 2011

    Directory of Open Access Journals (Sweden)

    Stefania Onesti

    2012-11-01

    Full Text Available Mime, Music and Drama on the Eighteenth-Century Stage by Edward Nye (Cambridge University Press, 2011 has the merit of inspiring a strong reflection on ballet d'action, connected with cultural, literaturary and philosophic environment of Eighteenth century. The author, with brilliant insight and careful historical research, explores the most debated issues of the new genre, providing an unusual interpretation. The review traces the focal points and the structure of the book, developing further consideration of some of the most challenging aspects offered by the text.

  7. SuperLigands – a database of ligand structures derived from the Protein Data Bank

    Directory of Open Access Journals (Sweden)

    Preissner Robert

    2005-05-01

    Full Text Available Abstract Background Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function. Description Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients. Conclusion SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research.

  8. SuperLigands – a database of ligand structures derived from the Protein Data Bank

    Science.gov (United States)

    Michalsky, Elke; Dunkel, Mathias; Goede, Andrean; Preissner, Robert

    2005-01-01

    Background Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function. Description Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed via Tanimoto coefficients. Conclusion SuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research. PMID:15943884

  9. NRLiSt BDB, the manually curated nuclear receptors ligands and structures benchmarking database.

    Science.gov (United States)

    Lagarde, Nathalie; Ben Nasr, Nesrine; Jérémie, Aurore; Guillemain, Hélène; Laville, Vincent; Labib, Taoufik; Zagury, Jean-François; Montes, Matthieu

    2014-04-10

    Nuclear receptors (NRs) constitute an important class of drug targets. We created the most exhaustive NR-focused benchmarking database to date, the NRLiSt BDB (NRs ligands and structures benchmarking database). The 9905 compounds and 339 structures of the NRLiSt BDB are ready for structure-based and ligand-based virtual screening. In the present study, we detail the protocol used to generate the NRLiSt BDB and its features. We also give some examples of the errors that we found in ChEMBL that convinced us to manually review all original papers. Since extensive and manually curated experimental data about NR ligands and structures are provided in the NRLiSt BDB, it should become a powerful tool to assess the performance of virtual screening methods on NRs, to assist the understanding of NR's function and modulation, and to support the discovery of new drugs targeting NRs. NRLiSt BDB is freely available online at http://nrlist.drugdesign.fr .

  10. Searching the protein structure database for ligand-binding site similarities using CPASS v.2

    Directory of Open Access Journals (Sweden)

    Caprez Adam

    2011-01-01

    Full Text Available Abstract Background A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as "hypothetical" or "uncharacterized" protein. Our Comparison of Protein Active-Site Structures (CPASS v.2 database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR protocol and has been successfully applied to aid the annotation of a number of proteins of unknown function. Findings We report a major upgrade to our CPASS software and database that significantly improves its broad utility. CPASS v.2 is designed with a layered architecture to increase flexibility and portability that also enables job distribution over the Open Science Grid (OSG to increase speed. Similarly, the CPASS interface was enhanced to provide more user flexibility in submitting a CPASS query. CPASS v.2 now allows for both automatic and manual definition of ligand-binding sites and permits pair-wise, one versus all, one versus list, or list versus list comparisons. Solvent accessible surface area, ligand root-mean square difference, and Cβ distances have been incorporated into the CPASS similarity function to improve the quality of the results. The CPASS database has also been updated. Conclusions CPASS v.2 is more than an order of magnitude faster than the original implementation, and allows for multiple simultaneous job submissions. Similarly, the CPASS database of ligand-defined binding sites has increased in size by ~ 38%, dramatically increasing the likelihood of a positive search result. The modification to the CPASS similarity function is effective in reducing CPASS similarity scores

  11. Sir Joseph Barcroft, Cambridge placental and fetal research (1933-1966) and inter-generational Science.

    Science.gov (United States)

    Boyd, Robert; Boyd, C A Richard

    2010-01-01

    The nature of Cambridge (UK) placental and fetal research in the middle third of the twentieth century is reviewed on the basis of published literature and personal recollection. Joseph Barcroft is a central figure who came to fetal research late in an extremely productive career which is briefly sketched. Contemporaneous Cambridge academics in the field included J.D. Boyd (the authors father), J. Hammond, F.H.A. Marshall, R.A. McCance, J. Needham, A.S. Parkes and Elsie Widdowson. The then current Cambridge academic geography is explained and features of its scientific life such as funding, institutional structure and ethos, teaching and clinical duties, domestic and gender roles, and political context, including war and empire, are briefly considered. The testing of research findings against general principles and use of quantitative thinking are identified as important features. Intergenerational connections, often within individual families, are identified as a striking feature. The long-term impact of Cambridge work of this period; locally, in current trophoblast and feto-placental genetic research, in Oxford in probably influencing G.S. Dawes research leadership, and internationally, especially through D.H. Barron, and through him to the Denver School, is considered. That human placental and embryological specimens collected by J.D. Boyd have received a new lease of life as the "Boyd Collection", including use by Allen Enders is noted. Mechanisms for the maintenance of scientific quality and productivity during the period, mainly through the scientist himself relying on an internalised sense of "obligation", are contrasted with those current in the UK and more widely; formal peer-review at frequent intervals, with subsequent allocation of short-term funding. The strengths and weaknesses of each are considered.

  12. 8th Cambridge Workshop on Universal Access and Assistive Technology

    CERN Document Server

    Lazar, Jonathan; Heylighen, Ann; Dong, Hua

    2016-01-01

    This book presents the proceedings of the 8th Cambridge Workshop on Universal Access and Assistive Technology (CWUAAT '14), incorporating the 11th Cambridge Workshop on Rehabilitation Robotics, held in Cambridge, England in March 2016. It presents novel and state-of-the-art research from an international group of leaders in the fields of universal access and assistive technology. It explores various issues including the reconciliation of usability, accessibility and inclusive design, the design of inclusive assistive and rehabilitation systems, measuring product demand and human capabilities, data mining and visualizing inclusion, legislation in inclusive design, and situational inclusive interfaces (automotive and aerospace). This book provides an invaluable resource to researchers, postgraduates, design practitioners, therapists and clinical practitioners, as well as design teachers.

  13. Cambridge international AS and A level mathematics statistics

    CERN Document Server

    Porkess, Roger; Konrad, Nina

    2012-01-01

    This brand new series has been written for the University of Cambridge International Examinations course for AS and A Level Mathematics (9709). This title covers the requirements of S1 and S2. The authors are experienced examiners and teachers who have written extensively at this level, so have ensured all mathematical concepts are explained using language and terminology that is appropriate for students across the world. Students are provded with clear and detailed worked examples and questions from Cambridge International past papers, so they have the opportunity for plenty of essenti

  14. Cambridge international AS and A level mathematics mechanics

    CERN Document Server

    Porkess, Roger

    2012-01-01

    This brand new series has been written for the University of Cambridge International Examinations course for AS and A Level Mathematics (9709). This title covers the requirements of M1 and M2. The authors are experienced examiners and teachers who have written extensively at this level, so have ensured all mathematical concepts are explained using language and terminology that is appropriate for students across the world. Students are provded with clear and detailed worked examples and questions from Cambridge International past papers, so they have the opportunity for plenty of essential exam

  15. Automated clustering of ensembles of alternative models in protein structure databases.

    Science.gov (United States)

    Domingues, Francisco S; Rahnenführer, Jörg; Lengauer, Thomas

    2004-06-01

    Experimentally determined protein structures have been classified in different public databases according to their structural and evolutionary relationships. Frequently, alternative structural models, determined using X-ray crystallography or NMR spectroscopy, are available for a protein. These models can present significant structural dissimilarity. Currently there is no classification available for these alternative structures. In order to classify them, we developed STRuster, an automated method for clustering ensembles of structural models according to their backbone structure. The method is based on the calculation of carbon alpha (Calpha) distance matrices. Two filters are applied in the calculation of the dissimilarity measure in order to identify both large and small (but significant) backbone conformational changes. The resulting dissimilarity value is used for hierarchical clustering and partitioning around medoids (PAM). Hierarchical clustering reflects the hierarchy of similarities between all pairs of models, while PAM groups the models into the 'optimal' number of clusters. The method has been applied to cluster the structures in each SCOP species level and can be easily applied to any other sets of conformers. The results are available at: http://bioinf.mpi-sb.mpg.de/projects/struster/. PMID:15319469

  16. KLIFS: a knowledge-based structural database to navigate kinase-ligand interaction space.

    Science.gov (United States)

    van Linden, Oscar P J; Kooistra, Albert J; Leurs, Rob; de Esch, Iwan J P; de Graaf, Chris

    2014-01-23

    Protein kinases regulate the majority of signal transduction pathways in cells and have become important targets for the development of designer drugs. We present a systematic analysis of kinase-ligand interactions in all regions of the catalytic cleft of all 1252 human kinase-ligand cocrystal structures present in the Protein Data Bank (PDB). The kinase-ligand interaction fingerprints and structure database (KLIFS) contains a consistent alignment of 85 kinase ligand binding site residues that enables the identification of family specific interaction features and classification of ligands according to their binding modes. We illustrate how systematic mining of kinase-ligand interaction space gives new insights into how conserved and selective kinase interaction hot spots can accommodate the large diversity of chemical scaffolds in kinase ligands. These analyses lead to an improved understanding of the structural requirements of kinase binding that will be useful in ligand discovery and design studies.

  17. Developing STR databases on structured populations: the native South Siberian population versus the Russian population.

    Science.gov (United States)

    Zhivotovsky, Lev A; Malyarchuk, Boris A; Derenko, Miroslava V; Wozniak, Marcin; Grzybowski, Tomasz

    2009-09-01

    Developing a forensic DNA database on a population that consists of local ethnic groups separated by physical and cultural barriers is questionable as it can be genetically subdivided. On the other side, small sizes of ethnic groups, especially in alpine regions where they are sub-structured further into small villages, prevent collecting a large sample from each ethnic group. For such situations, we suggest to obtain both a total population database on allele frequencies across ethnic groups and a list of theta-values between the groups and the total data. We have genotyped 558 individuals from the native population of South Siberia, consisting of nine ethnic groups, at 17 autosomal STR loci of the kit packages AmpFlSTR SGM Plus i, Cyrillic AmpFlSTR Profiler Plus. The groups differentiate from each other with average theta-values of around 1.1%, and some reach up to three to four percent at certain loci. There exists between-village differentiation as well. Therefore, a database for the population of South Siberia is composed of data on allele frequencies in the pool of ethnic groups and data on theta-values that indicate variation in allele frequencies across the groups. Comparison to additional data on northeastern Asia (the Chukchi and Koryak) shows that differentiation in allele frequencies among small groups that are separated by large geographic distance can be even greater. In contrast, populations of Russians that live in large cities of the European part of Russia are homogeneous in allele frequencies, despite large geographic distance between them, and thus can be described by a database on allele frequencies alone, without any specific information on theta-values.

  18. EK3D: an E. coli K antigen 3-dimensional structure database.

    Science.gov (United States)

    Kunduru, Bharathi Reddy; Nair, Sanjana Anilkumar; Rathinavelan, Thenmalarchelvi

    2016-01-01

    A very high rate of multidrug resistance (MDR) seen among Gram-negative bacteria such as Escherichia, Klebsiella, Salmonella, Shigella, etc. is a major threat to public health and safety. One of the major virulent determinants of Gram-negative bacteria is capsular polysaccharide or K antigen located on the bacterial outer membrane surface, which is a potential drug & vaccine target. It plays a key role in host-pathogen interactions as well as host immune evasion and thus, mandates detailed structural information. Nonetheless, acquiring structural information of K antigens is not straightforward due to their innate enormous conformational flexibility. Here, we have developed a manually curated database of K antigens corresponding to various E. coli serotypes, which differ from each other in their monosaccharide composition, linkage between the monosaccharides and their stereoisomeric forms. Subsequently, we have modeled their 3D structures and developed an organized repository, namely EK3D that can be accessed through www.iith.ac.in/EK3D/. Such a database would facilitate the development of antibacterial drugs to combat E. coli infections as it has evolved resistance against 2 major drugs namely, third-generation cephalosporins and fluoroquinolones. EK3D also enables the generation of polymeric K antigens of varying lengths and thus, provides comprehensive information about E. coli K antigens. PMID:26615200

  19. Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration.

    Science.gov (United States)

    Gražulis, Saulius; Daškevič, Adriana; Merkys, Andrius; Chateigner, Daniel; Lutterotti, Luca; Quirós, Miguel; Serebryanaya, Nadezhda R; Moeck, Peter; Downs, Robert T; Le Bail, Armel

    2012-01-01

    Using an open-access distribution model, the Crystallography Open Database (COD, http://www.crystallography.net) collects all known 'small molecule / small to medium sized unit cell' crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated ~150,000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.

  20. SGCEdb: a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans

    OpenAIRE

    David H Johnson; Tsao, Jun; Luo, Ming; Carson, Mike

    2005-01-01

    The SGCEdb () database/interface serves the primary purpose of reporting progress of the Structural Genomics of Caenorhabditis elegans project at the University of Alabama at Birmingham. It stores and analyzes results of experiments ranging from solubility screening arrays to individual protein purification and structure solution. External databases and algorithms are referenced and evaluated for target selection in the human, C.elegans and Pneumocystis carinii genomes. The flexible and reusa...

  1. The Cambridge Face Tracker: Accurate, Low Cost Measurement of Head Posture Using Computer Vision and Face Recognition Software

    Science.gov (United States)

    Thomas, Peter B. M.; Baltrušaitis, Tadas; Robinson, Peter; Vivian, Anthony J.

    2016-01-01

    Purpose We validate a video-based method of head posture measurement. Methods The Cambridge Face Tracker uses neural networks (constrained local neural fields) to recognize facial features in video. The relative position of these facial features is used to calculate head posture. First, we assess the accuracy of this approach against videos in three research databases where each frame is tagged with a precisely measured head posture. Second, we compare our method to a commercially available mechanical device, the Cervical Range of Motion device: four subjects each adopted 43 distinct head postures that were measured using both methods. Results The Cambridge Face Tracker achieved confident facial recognition in 92% of the approximately 38,000 frames of video from the three databases. The respective mean error in absolute head posture was 3.34°, 3.86°, and 2.81°, with a median error of 1.97°, 2.16°, and 1.96°. The accuracy decreased with more extreme head posture. Comparing The Cambridge Face Tracker to the Cervical Range of Motion Device gave correlation coefficients of 0.99 (P < 0.0001), 0.96 (P < 0.0001), and 0.99 (P < 0.0001) for yaw, pitch, and roll, respectively. Conclusions The Cambridge Face Tracker performs well under real-world conditions and within the range of normally-encountered head posture. It allows useful quantification of head posture in real time or from precaptured video. Its performance is similar to that of a clinically validated mechanical device. It has significant advantages over other approaches in that subjects do not need to wear any apparatus, and it requires only low cost, easy-to-setup consumer electronics. Translational Relevance Noncontact assessment of head posture allows more complete clinical assessment of patients, and could benefit surgical planning in future. PMID:27730008

  2. Cambridge Illustrated History of Archaeology, edited by Paul G. Bahn, Cambridge University Press, New York, 1996

    Directory of Open Access Journals (Sweden)

    Douglas R. Givens

    1997-11-01

    Full Text Available The Cambridge Illustrated History of Archaeology is another in a series of volumes devoted to the history of archaeology that have appeared in recent time. Paul Bahn, the editor of the volume, has broken down his coverage of the history of worldwide archaeology into the following arrangement 'The Archaeology of Archaeology", "Old Worlds and New, 1500-1760", "Antiquarians and Explorers, 1760-1820", "Science and Romanticism, 1820-1860", "The Search for Human Origins, 1860-1920", "Archaeology Comes of Age, 1920-1960", "New Techniques and Competing Philosophies, 1960-1990",and "Current Controversies and Future Trends". Bahn's volume explores many of the major developments in archaeological practice from both in the classical world and was as from the practice of archaeology in the Americas. The volume even gives the reader a glimpse into the origins and growth of archaeology in New Zealand. Of particular interest is coverage of the history of early archaeological efforts having to do with early studies of human origins.

  3. Performance modelling of the Cambridge Fast Ring protocol

    NARCIS (Netherlands)

    Zafirovic-Vukotic, M.; Niemegeers, I.G.

    1988-01-01

    The Cambridge Fast Ring is high-speed slotted ring. The features that make it suitable for use at very large transmission rates are the synchronous transmission, the simplicity of the medium-access-control protocol, and the possibility of immediate retransmission of erroneous packets. A novel analyt

  4. The Cambridge Primary Review: A Reply to R. J. Campbell

    Science.gov (United States)

    Armstrong, Michael

    2010-01-01

    The author was disappointed by R. J. Campbell's sour critique of the Cambridge Primary Review in "FORUM" Volume 52 Number 1 2010. His description of the Review's proposals on curriculum and pedagogy as "backward-looking, cumbersome and partial" is such a bizarre misjudgement that it calls for some response. The author comments in turn on R. J.…

  5. A structure to support queries in object-oriented database using fuzzy XML tags

    OpenAIRE

    Bahareh Fahimian; Ali Harounabadi

    2014-01-01

    Every day, we deal with the information, which are under uncertainty and managing this type of information with classical database systems brings a disadvantageous loss of data semantics along. Therefore, advanced database modeling techniques are necessary. Entrance of object orienting concept in databases helps relational database gradually use object oriented database in various fields. With the advances in this field, simple objects alone are not able to include complex data types and comp...

  6. Collecting Taxes Database

    Data.gov (United States)

    US Agency for International Development — The Collecting Taxes Database contains performance and structural indicators about national tax systems. The database contains quantitative revenue performance...

  7. Frameworks for Generalization Constraints and Operations Based o n Object_oriented Data Structure in Database Generalization

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The constraints and the operations play an important role in database generaliza tion.They guide and govern database generalization.The constraints are translation of the required conditions that should take into account not only the objects and relationships among objects but also spatial d a ta schema (classification and aggregation hierarchy) associated with the final e xi sting database.The operations perform the actions of generalization in support o f data reduction in the database. The constraints in database generalization are still lack of research.There is still the lack of frameworks to express the con straints and the operations on the basis of object_oriented data structure in da tabase generalization.This paper focuses on the frameworks for generalization op erations and constraints on the basis of object_oriented data structure in datab ase gen eralization.The constraints as the attributes of the object and the operations a s the methods of the object can be encapsulated in classes. They have the in heritance and polymorphism property. So the framework of the constraints and the operations which are based on object_oriented data structure can be eas ily understood and implemented. The constraint and the operations based on obje ct_oriented database are proposed based on object_oriented database.The framewor ks for generalization operations,constraints and relations among objects based o n object_oriented data structure in database generalization are designed.The cat egorical database generalization is concentrated on in this paper.

  8. Structural kinematics based damage zone prediction in gradient structures using vibration database

    Science.gov (United States)

    Talha, Mohammad; Ashokkumar, Chimpalthradi R.

    2014-05-01

    To explore the applications of functionally graded materials (FGMs) in dynamic structures, structural kinematics based health monitoring technique becomes an important problem. Depending upon the displacements in three dimensions, the health of the material to withstand dynamic loads is inferred in this paper, which is based on the net compressive and tensile displacements that each structural degree of freedom takes. These net displacements at each finite element node predicts damage zones of the FGM where the material is likely to fail due to a vibration response which is categorized according to loading condition. The damage zone prediction of a dynamically active FGMs plate have been accomplished using Reddy's higher-order theory. The constituent material properties are assumed to vary in the thickness direction according to the power-law behavior. The proposed C0 finite element model (FEM) is applied to get net tensile and compressive displacement distributions across the structures. A plate made of Aluminum/Ziconia is considered to illustrate the concept of structural kinematics-based health monitoring aspects of FGMs.

  9. 78 FR 52802 - Manufacturer of Controlled Substances; Notice of Application; Cambridge Isotope Lab

    Science.gov (United States)

    2013-08-26

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Drug Enforcement Administration Manufacturer of Controlled Substances; Notice of Application; Cambridge Isotope Lab... 01, 2013, Cambridge Isotope Lab, 50 Frontage Road, Andover, Massachusetts 01810, made application...

  10. 77 FR 38086 - Manufacturer of Controlled Substances, Notice of Application, Cambridge Isotope Lab

    Science.gov (United States)

    2012-06-26

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF JUSTICE Drug Enforcement Administration Manufacturer of Controlled Substances, Notice of Application, Cambridge Isotope Lab... 7, 2012, Cambridge Isotope Lab, 50 Frontage Road, Andover, Massachusetts 01810, made application...

  11. Database development and management

    CERN Document Server

    Chao, Lee

    2006-01-01

    Introduction to Database Systems Functions of a DatabaseDatabase Management SystemDatabase ComponentsDatabase Development ProcessConceptual Design and Data Modeling Introduction to Database Design Process Understanding Business ProcessEntity-Relationship Data Model Representing Business Process with Entity-RelationshipModelTable Structure and NormalizationIntroduction to TablesTable NormalizationTransforming Data Models to Relational Databases .DBMS Selection Transforming Data Models to Relational DatabasesEnforcing ConstraintsCreating Database for Business ProcessPhysical Design and Database

  12. And Now What about Reforming Cambridge Governance?

    Science.gov (United States)

    Evans, G. R.

    2009-01-01

    After its recent Assurance visit from HEFCE, Oxford went through a high profile public debate at the end of which its academic community voted against moving to a governance structure which would have given Oxford a majority of external members on its Council. The Higher Education Funding Council asked Oxford to answer eight questions justifying…

  13. Format and structure of a database on health and environmental impacts of different energy systems for electricity generation

    International Nuclear Information System (INIS)

    There is considerable interest in the application of techniques of comparative risk assessment in the planning of energy mixes for electricity generation, and particularly in the integration of health and environmental impacts in the decision-making process. To assist this it is planned to establish an internationally coordinated database on the health and environmental effects of different energy sources. This document introduces the structure and format of the database, and contains in addition eighteen papers prepared for Technical Committee Meetings to discuss the proposed database. These papers have all been indexed separately. Refs, figs, tabs and graphs

  14. A database paradigm for the management of DICOM-RT structure sets using a geographic information system

    International Nuclear Information System (INIS)

    We devise a paradigm for representing the DICOM-RT structure sets in a database management system, in such way that secondary calculations of geometric information can be performed quickly from the existing contour definitions. The implementation of this paradigm is achieved using the PostgreSQL database system and the PostGIS extension, a geographic information system commonly used for encoding geographical map data. The proposed paradigm eliminates the overhead of retrieving large data records from the database, as well as the need to implement various numerical and data parsing routines, when additional information related to the geometry of the anatomy is desired.

  15. A database paradigm for the management of DICOM-RT structure sets using a geographic information system

    Science.gov (United States)

    Shao, Weber; Kupelian, Patrick A.; Wang, Jason; Low, Daniel A.; Ruan, Dan

    2014-03-01

    We devise a paradigm for representing the DICOM-RT structure sets in a database management system, in such way that secondary calculations of geometric information can be performed quickly from the existing contour definitions. The implementation of this paradigm is achieved using the PostgreSQL database system and the PostGIS extension, a geographic information system commonly used for encoding geographical map data. The proposed paradigm eliminates the overhead of retrieving large data records from the database, as well as the need to implement various numerical and data parsing routines, when additional information related to the geometry of the anatomy is desired.

  16. 40 CFR 81.205 - Zanesville-Cambridge Intrastate Air Quality Control Region.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Zanesville-Cambridge Intrastate Air... Air Quality Control Regions § 81.205 Zanesville-Cambridge Intrastate Air Quality Control Region. The Zanesville-Cambridge Intrastate Air Quality Control Region (Ohio) consists of the territorial...

  17. 75 FR 38128 - Sensata Technologies MA, Inc., Power Controls Division, Formerly Known As Airpax Corp., Cambridge...

    Science.gov (United States)

    2010-07-01

    ... As Airpax Corp., Cambridge, Maryland, Including Employees of Sensata Technologies MA, Inc., Power Controls Division Formerly Known As Airpax Corp., Cambridge, Maryland Working Off-Site in Falmouth... known as Airpax Corporation, Cambridge, Maryland. The notice will soon be published in the...

  18. A structured vocabulary for indexing dietary supplements in databases in the United States

    Science.gov (United States)

    Food composition databases are critical to assess and plan dietary intakes. Dietary supplement databases are also needed because dietary supplements make significant contributions to total nutrient intakes. However, no uniform system exists for classifying dietary supplement products and indexing ...

  19. A grammar based methodology for structural motif finding in ncRNA database search.

    Science.gov (United States)

    Quest, Daniel; Tapprich, William; Ali, Hesham

    2007-01-01

    In recent years, sequence database searching has been conducted through local alignment heuristics, pattern-matching, and comparison of short statistically significant patterns. While these approaches have unlocked many clues as to sequence relationships, they are limited in that they do not provide context-sensitive searching capabilities (e.g. considering pseudoknots, protein binding positions, and complementary base pairs). Stochastic grammars (hidden Markov models HMMs and stochastic context-free grammars SCFG) do allow for flexibility in terms of local context, but the context comes at the cost of increased computational complexity. In this paper we introduce a new grammar based method for searching for RNA motifs that exist within a conserved RNA structure. Our method constrains computational complexity by using a chain of topology elements. Through the use of a case study we present the algorithmic approach and benchmark our approach against traditional methods.

  20. Metaphor Analysis of Chinese Premier Wen’s Cambridge Speech

    Institute of Scientific and Technical Information of China (English)

    LUO Luo

    2014-01-01

    Metaphor is more than an ostensible decoration of language. It is an integral part of human thought of ideologized world. This article analyzes the metaphor use of Chinese Premier Wen Jiabao’s speech at Cambridge in February 2009, in an at-tempt to display how the preferred metaphors serve the purpose of this speech and reflect Premier Wen ’s construction of Chi-na’s situation.

  1. University of Cambridge deploys Procket Networks' PRO/8801

    CERN Multimedia

    2003-01-01

    Procket Networks, a provider of high performance Internet Protocol (IP) technology and products has announced that the University of Cambridge has deployed the PRO/8801(TM) router into its research network to develop industry-leading deep packet inspection applications. The major application for this deployment is to identify and understand new traffic patterns created by large scale scientific computations and downloads such as the GRID (1 page).

  2. The competition for the Woodwardian Chair of Geology, Cambridge 1873.

    OpenAIRE

    O'Connor, A

    2005-01-01

    In 1873 the chair of geology at the University of Cambridge fell vacant following the death of Adam Sedgwick. Nine candidates stepped forward, hoping to fill the post. The correspondence generated in the ensuing battle illuminates two areas of particular interest. First, the strategies hidden behind bland lists of successive professors: candidates, peers and patrons manoeuvred to influence the outcome of the competition and competitors tried to reinforce their geological respectability by col...

  3. Philosophy at Cambridge, Newsletter of the Faculty of Philosophy

    OpenAIRE

    2008-01-01

    Philosophy Newsletter. Articles by: Edward Craig - From the Chairman. Onora O'Neill - "It's the newspapers I can't stand. Serena Olsaretti - The 2004 Annual Royal Institute of Philosophy Conference. Mary Leng - Mathematical Knowledge Conference. Postgraduate Conference. Jane Heal - Facts, Fables and Funds. Hugh Mellor - Uses and Abuses of Probability. Amanda Boyle - Nobody Knows Anything: Philosophy, Film and Me. Jaime Whyte - Seven Years at Cambridge Alex Oliver...

  4. Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation.

    Science.gov (United States)

    Poos, Kathrin; Smida, Jan; Nathrath, Michaela; Maugg, Doris; Baumhoer, Daniel; Neumann, Anna; Korsching, Eberhard

    2014-01-01

    Osteosarcoma (OS) is the most common primary bone cancer exhibiting high genomic instability. This genomic instability affects multiple genes and microRNAs to a varying extent depending on patient and tumor subtype. Massive research is ongoing to identify genes including their gene products and microRNAs that correlate with disease progression and might be used as biomarkers for OS. However, the genomic complexity hampers the identification of reliable biomarkers. Up to now, clinico-pathological factors are the key determinants to guide prognosis and therapeutic treatments. Each day, new studies about OS are published and complicate the acquisition of information to support biomarker discovery and therapeutic improvements. Thus, it is necessary to provide a structured and annotated view on the current OS knowledge that is quick and easily accessible to researchers of the field. Therefore, we developed a publicly available database and Web interface that serves as resource for OS-associated genes and microRNAs. Genes and microRNAs were collected using an automated dictionary-based gene recognition procedure followed by manual review and annotation by experts of the field. In total, 911 genes and 81 microRNAs related to 1331 PubMed abstracts were collected (last update: 29 October 2013). Users can evaluate genes and microRNAs according to their potential prognostic and therapeutic impact, the experimental procedures, the sample types, the biological contexts and microRNA target gene interactions. Additionally, a pathway enrichment analysis of the collected genes highlights different aspects of OS progression. OS requires pathways commonly deregulated in cancer but also features OS-specific alterations like deregulated osteoclast differentiation. To our knowledge, this is the first effort of an OS database containing manual reviewed and annotated up-to-date OS knowledge. It might be a useful resource especially for the bone tumor research community, as specific

  5. Characterizing the genetic structure of a forensic DNA database using a latent variable approach.

    Science.gov (United States)

    Kruijver, Maarten

    2016-07-01

    Several problems in forensic genetics require a representative model of a forensic DNA database. Obtaining an accurate representation of the offender database can be difficult, since databases typically contain groups of persons with unregistered ethnic origins in unknown proportions. We propose to estimate the allele frequencies of the subpopulations comprising the offender database and their proportions from the database itself using a latent variable approach. We present a model for which parameters can be estimated using the expectation maximization (EM) algorithm. This approach does not rely on relatively small and possibly unrepresentative population surveys, but is driven by the actual genetic composition of the database only. We fit the model to a snapshot of the Dutch offender database (2014), which contains close to 180,000 profiles, and find that three subpopulations suffice to describe a large fraction of the heterogeneity in the database. We demonstrate the utility and reliability of the approach with three applications. First, we use the model to predict the number of false leads obtained in database searches. We assess how well the model predicts the number of false leads obtained in mock searches in the Dutch offender database, both for the case of familial searching for first degree relatives of a donor and searching for contributors to three-person mixtures. Second, we study the degree of partial matching between all pairs of profiles in the Dutch database and compare this to what is predicted using the latent variable approach. Third, we use the model to provide evidence to support that the Dutch practice of estimating match probabilities using the Balding-Nichols formula with a native Dutch reference database and θ=0.03 is conservative. PMID:27128695

  6. Prefetching J+-Tree: A Cache-Optimized Main Memory Database Index Structure

    Institute of Scientific and Technical Information of China (English)

    Hua Luan; Xiao-Yong Du; Sha Wang

    2009-01-01

    As the speed gap between main memory and modern processors continues to widen, the cache behavior becomes more important for main memory database systems (MMDBs). Indexing technique is a key component of MMDBs. Unfortunately, the predominant indexes -- B+-trees and T-trees -- have been shown to utilize cache poorly, which triggers the development of many cache-conscious indexes, such as CSB+-trees and pB+-trees. Most of these cache-conscious indexes are variants of conventional B+-trees, and have better cache performance than B+-trees. In this paper, we develop a novel J+-tree index, inspired by the Judy structure which is an associative array data structure, and propose a more cacheoptimized index -- Prefetching J+-tree (pJ+-tree), which applies prefetching to J+-tree to accelerate range scan operations. The J+-tree stores all the keys in its leaf nodes and keeps the reference values of leaf nodes in a Judy structure, which makes J+-tree not only hold the advantages of Judy (such as fast single value search) but also outperform it in other aspects. For example, J+-trees can achieve better performance on range queries than Judy. The pJ+-tree index exploits prefetching techniques to further improve the cache behavior of J+-trees and yields a speedup of 2.0 on range scans. Compared with B+-trees, CSB+-trees, pB+-trees and T-trees, our extensive experimental study shows that pJ+-trees can provide better performance on both time (search, scan, update) and space aspects.

  7. CarbBank: A structural and bibliographic database for complex carbohydrates

    Energy Technology Data Exchange (ETDEWEB)

    Albersheim, P.

    1992-06-01

    The CarbBank project has several key facets: building a computer database that presents carbohydrate sequence information derived from the published literature, programming to create computer applications that use the information in the database, creating software for multiple computer platforms, and distributing software to end users.

  8. PROCARB: A Database of Known and Modelled Carbohydrate-Binding Protein Structures with Sequence-Based Prediction Tools

    Directory of Open Access Journals (Sweden)

    Adeel Malik

    2010-01-01

    Full Text Available Understanding of the three-dimensional structures of proteins that interact with carbohydrates covalently (glycoproteins as well as noncovalently (protein-carbohydrate complexes is essential to many biological processes and plays a significant role in normal and disease-associated functions. It is important to have a central repository of knowledge available about these protein-carbohydrate complexes as well as preprocessed data of predicted structures. This can be significantly enhanced by tools de novo which can predict carbohydrate-binding sites for proteins in the absence of structure of experimentally known binding site. PROCARB is an open-access database comprising three independently working components, namely, (i Core PROCARB module, consisting of three-dimensional structures of protein-carbohydrate complexes taken from Protein Data Bank (PDB, (ii Homology Models module, consisting of manually developed three-dimensional models of N-linked and O-linked glycoproteins of unknown three-dimensional structure, and (iii CBS-Pred prediction module, consisting of web servers to predict carbohydrate-binding sites using single sequence or server-generated PSSM. Several precomputed structural and functional properties of complexes are also included in the database for quick analysis. In particular, information about function, secondary structure, solvent accessibility, hydrogen bonds and literature reference, and so forth, is included. In addition, each protein in the database is mapped to Uniprot, Pfam, PDB, and so forth.

  9. WORKING WITH ARCHIVES: CAMBRIDGE ECONOMICS THROUGH THE MAGNIFYING GLASS

    Directory of Open Access Journals (Sweden)

    Maria Cristina Marcuzzo

    2012-12-01

    Full Text Available Research in economics using documentary archives provides clearer interpretations about the ideas and their development throughout time, in the context of the writing process in relation to the interlocutors and antagonists, and the nature of the problems addressed. This document presents examples of works with tough drafts, correspondence, tables of contents, notes, and related material of four economists of the "Cambridge Group": Piero Sraffa, Richard Kahn, Joan Robinson, and John Maynard Keynes. In each case the findings and importance of the research done in the files are described.

  10. Cambridge IGCSE and international certificate French foreign language

    CERN Document Server

    Grime, Yvette; Thacker, Mike

    2013-01-01

    This brand-new Student Book provides a grammar-led approach with extensive exam preparation that will help you develop independent, culturally aware students of French ready for the exam. The book is written to the latest Cambridge International Examinations syllabus by experienced teachers. Extensive use of French reflects the style of the exams and, with specific advice and practice, it helps students use the acquired skills to their best ability. Topics on Francophone cultures are integrated throughout to ensure students gain the cultural awareness that is at the heart of this qualification

  11. Skin Regeneration Symposium Cambridge, 12-13 April 2016.

    Science.gov (United States)

    Hill, Rosalind

    2016-07-01

    The Annual Skin Regeneration Symposium, held in Cambridge, UK, 12-13 April 2016, explored the latest advancements in skin repair, regeneration and restoration, and the impact this has on patients. With over 140 delegates from the disciplines of burn and trauma care, chronic wounds and esthetic medicine, the symposium sparked lively debate and the sharing of results from interesting case studies, clinical trials and basic research to support the use of a Regenerative Epithelial Suspension produced using the ReCell(®) technology. Furthermore, it enabled delegates and speakers alike to share ideas and discuss how to improve the quality of care for patients. PMID:27357476

  12. Skin Regeneration Symposium Cambridge, 12-13 April 2016.

    Science.gov (United States)

    Hill, Rosalind

    2016-07-01

    The Annual Skin Regeneration Symposium, held in Cambridge, UK, 12-13 April 2016, explored the latest advancements in skin repair, regeneration and restoration, and the impact this has on patients. With over 140 delegates from the disciplines of burn and trauma care, chronic wounds and esthetic medicine, the symposium sparked lively debate and the sharing of results from interesting case studies, clinical trials and basic research to support the use of a Regenerative Epithelial Suspension produced using the ReCell(®) technology. Furthermore, it enabled delegates and speakers alike to share ideas and discuss how to improve the quality of care for patients.

  13. EMBANKS: Towards Disk Based Algorithms For Keyword-Search In Structured Databases

    OpenAIRE

    Gupta, Nitin

    2011-01-01

    In recent years, there has been a lot of interest in the field of keyword querying relational databases. A variety of systems such as DBXplorer [ACD02], Discover [HP02] and ObjectRank [BHP04] have been proposed. Another such system is BANKS, which enables data and schema browsing together with keyword-based search for relational databases. It models tuples as nodes in a graph, connected by links induced by foreign key and other relationships. The size of the database graph that BANKS uses is ...

  14. Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.

    Science.gov (United States)

    Akune, Yukie; Lin, Chi-Hung; Abrahams, Jodie L; Zhang, Jingyu; Packer, Nicolle H; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P

    2016-08-01

    Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database. PMID:27318307

  15. A Preliminary Study on the Multiple Mapping Structure of Classification Systems for Heterogeneous Databases

    OpenAIRE

    Seok-Hyoung Lee; Hwan-Min Kim; Ho-Seop Choe

    2012-01-01

    While science and technology information service portals and heterogeneous databases produced in Korea and other countries are integrated, methods of connecting the unique classification systems applied to each database have been studied. Results of technologists' research, such as, journal articles, patent specifications, and research reports, are organically related to each other. In this case, if the most basic and meaningful classification systems are not connected, it is difficult to ach...

  16. Data on publications, structural analyses, and queries used to build and utilize the AlloRep database.

    Science.gov (United States)

    Sousa, Filipa L; Parente, Daniel J; Hessman, Jacob A; Chazelle, Allen; Teichmann, Sarah A; Swint-Kruse, Liskin

    2016-09-01

    The AlloRep database (www.AlloRep.org) (Sousa et al., 2016) [1] compiles extensive sequence, mutagenesis, and structural information for the LacI/GalR family of transcription regulators. Sequence alignments are presented for >3000 proteins in 45 paralog subfamilies and as a subsampled alignment of the whole family. Phenotypic and biochemical data on almost 6000 mutants have been compiled from an exhaustive search of the literature; citations for these data are included herein. These data include information about oligomerization state, stability, DNA binding and allosteric regulation. Protein structural data for 65 proteins are presented as easily-accessible, residue-contact networks. Finally, this article includes example queries to enable the use of the AlloRep database. See the related article, "AlloRep: a repository of sequence, structural and mutagenesis data for the LacI/GalR transcription regulators" (Sousa et al., 2016) [1]. PMID:27508249

  17. MetalS(3), a database-mining tool for the identification of structurally similar metal sites.

    Science.gov (United States)

    Valasatava, Yana; Rosato, Antonio; Cavallaro, Gabriele; Andreini, Claudia

    2014-08-01

    We have developed a database search tool to identify metal sites having structural similarity to a query metal site structure within the MetalPDB database of minimal functional sites (MFSs) contained in metal-binding biological macromolecules. MFSs describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such a local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. The database search tool, which we called MetalS(3) (Metal Sites Similarity Search), can be accessed through a Web interface at http://metalweb.cerm.unifi.it/tools/metals3/ . MetalS(3) uses a suitably adapted version of an algorithm that we previously developed to systematically compare the structure of the query metal site with each MFS in MetalPDB. For each MFS, the best superposition is kept. All these superpositions are then ranked according to the MetalS(3) scoring function and are presented to the user in tabular form. The user can interact with the output Web page to visualize the structural alignment or the sequence alignment derived from it. Options to filter the results are available. Test calculations show that the MetalS(3) output correlates well with expectations from protein homology considerations. Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS(3) to obtain mechanistic and functional hints regardless of homology.

  18. Sediment remediation of the Hespeler Mill Pond, Cambridge, Ontario

    Energy Technology Data Exchange (ETDEWEB)

    Angeloni, D.; Eby, M.; Jarvis, S.; Martin, P. [Univ. of Guelph, School of Engineering, Guelph, Ontario (Canada)]. E-mail: danielle.angeloni@earthtech.ca

    2002-06-15

    'Full text:' Low dissolved oxygen levels and large accumulated sediment remediation alternatives were examined to assemble the Hespeler Mill Pond, Cambridge (HMP) into a healthier and more desirable recreational area in the City of Cambridge. The theory that a large amount of sediment has been deposited into the HMP from the Speed River upstream over a number of years predicts the depressed oxygen levels, high nutrient-loading rates and the odour problems in the summer months. The initial phase in the remediation plan for this project involved extensive background research and investigation. The focus was on determining the characteristics of the sediment and the history of the pond, to ultimately decide if the sediment was the source of the issues. Dissolved oxygen field tests and sediment sampling were conducted to get information on the magnitude of the problem and the environmental hazards potentially present in the pond. The pond was modelled utilising the Streeter-Phelps oxygen-sag model to predict the oxygen deficit. Biochemical Oxygen Demand (BOD{sub 5}) testing was completed to determine the oxygen demand in the pond. These tests were conducted by using water samples obtained from various sample points at the pond. The proposed solution is a combined dredging and aeration approach. Mechanical dredging using a clamshell bucket and the installation of aerators is expected to solve the dissolved oxygen and water quality issues. (author)

  19. An integrated photogrammetric and spatial database management system for producing fully structured data using aerial and remote sensing images.

    Science.gov (United States)

    Ahmadi, Farshid Farnood; Ebadi, Hamid

    2009-01-01

    3D spatial data acquired from aerial and remote sensing images by photogrammetric techniques is one of the most accurate and economic data sources for GIS, map production, and spatial data updating. However, there are still many problems concerning storage, structuring and appropriate management of spatial data obtained using these techniques. According to the capabilities of spatial database management systems (SDBMSs); direct integration of photogrammetric and spatial database management systems can save time and cost of producing and updating digital maps. This integration is accomplished by replacing digital maps with a single spatial database. Applying spatial databases overcomes the problem of managing spatial and attributes data in a coupled approach. This management approach is one of the main problems in GISs for using map products of photogrammetric workstations. Also by the means of these integrated systems, providing structured spatial data, based on OGC (Open GIS Consortium) standards and topological relations between different feature classes, is possible at the time of feature digitizing process. In this paper, the integration of photogrammetric systems and SDBMSs is evaluated. Then, different levels of integration are described. Finally design, implementation and test of a software package called Integrated Photogrammetric and Oracle Spatial Systems (IPOSS) is presented. PMID:22574014

  20. An Integrated Photogrammetric and Spatial Database Management System for Producing Fully Structured Data Using Aerial and Remote Sensing Images

    Directory of Open Access Journals (Sweden)

    Farshid Farnood Ahmadi

    2009-03-01

    Full Text Available 3D spatial data acquired from aerial and remote sensing images by photogrammetric techniques is one of the most accurate and economic data sources for GIS, map production, and spatial data updating. However, there are still many problems concerning storage, structuring and appropriate management of spatial data obtained using these techniques. According to the capabilities of spatial database management systems (SDBMSs; direct integration of photogrammetric and spatial database management systems can save time and cost of producing and updating digital maps. This integration is accomplished by replacing digital maps with a single spatial database. Applying spatial databases overcomes the problem of managing spatial and attributes data in a coupled approach. This management approach is one of the main problems in GISs for using map products of photogrammetric workstations. Also by the means of these integrated systems, providing structured spatial data, based on OGC (Open GIS Consortium standards and topological relations between different feature classes, is possible at the time of feature digitizing process. In this paper, the integration of photogrammetric systems and SDBMSs is evaluated. Then, different levels of integration are described. Finally design, implementation and test of a software package called Integrated Photogrammetric and Oracle Spatial Systems (IPOSS is presented.

  1. Logical database design principles

    CERN Document Server

    Garmany, John; Clark, Terry

    2005-01-01

    INTRODUCTION TO LOGICAL DATABASE DESIGNUnderstanding a Database Database Architectures Relational Databases Creating the Database System Development Life Cycle (SDLC)Systems Planning: Assessment and Feasibility System Analysis: RequirementsSystem Analysis: Requirements Checklist Models Tracking and Schedules Design Modeling Functional Decomposition DiagramData Flow Diagrams Data Dictionary Logical Structures and Decision Trees System Design: LogicalSYSTEM DESIGN AND IMPLEMENTATION The ER ApproachEntities and Entity Types Attribute Domains AttributesSet-Valued AttributesWeak Entities Constraint

  2. The Cambridge Equation with government activity revisited A Equação de Cambridge com atividade governamental revisitada

    Directory of Open Access Journals (Sweden)

    Ricardo Silva Azevedo Araujo

    2010-12-01

    Full Text Available This paper offers an analysis of the steady-state distributional features found in a Kaldor-Pasinetti process, in which the government sector is allowed to run persistent deficits that may be financed through different instruments. Productive capital and bonds generate single rates of return, while workers' saving propensity remains uniform. This paper seeks to establish a generalization of Cambridge Eauqtion, considering the specific contributions of Steedman (1972, Pasinetti (1989, Dalziel (1991, and Faria (2000.Neste artigo faz-se uma análise das características distributivas do processo Kaldor-Pasinetti, assumindo-se que o setor governamental incorre em persistentes déficits que podem ser financiados através de diferentes instrumentos, como a emissão de títulos e de moeda. Através dessa abordagem é possível estudar como a atividade governamental afeta a distribuição de renda entre capitalistas e trabalhadores e assim obter generalizações do Teorema de Cambridge em que versões anteriores como as de Steedman (1972, Pasinetti (1989, Dalziel (1991 e Faria (2000 surgem como casos particulares.

  3. Pengaruh Kualitas Pelayanan terhadap Kepuasan Konsumen pada Cosa Nostra Bistro Cambridge Medan ( Study Pada Cosa Nostra Bistro Cambridge City Square, Medan)

    OpenAIRE

    Sihombing, Boy Martua

    2015-01-01

    This study entitled "The Effect of Service Quality on Customer Satisfaction in the Cosa Nostra Bistro Cambridge Field". This study aims to determine the effect of service quality indicators consisting of physical evidence, reliability, responsiveness, assurance, and empathy towards customer satisfaction on Cosa Nostra Bistro Cambridge Field. The theory used in this study is the theory related to service quality and customer satisfaction. The sample in this study as many as 90 people were t...

  4. 7th Cambridge Workshops on Universal Access and Assistive Technology

    CERN Document Server

    Lazar, J; Heylighen, A; Dong, H; Inclusive Designing : Joining Usability, Accessibility, and Inclusion

    2014-01-01

    ‘Inclusive Designing’ presents the proceedings of the seventh Cambridge Workshop on Universal Access and Assistive Technology (CWUAAT '14). It represents a unique multi-disciplinary workshop for the Inclusive Design Research community where designers, computer scientists, engineers, architects, ergonomists, policymakers and user communities can exchange ideas. The research presented at CWUAAT '14 develops methods, technologies, tools and guidance that support product designers and architects to design for the widest possible population for a given range of capabilities, within a contemporary social and economic context. In the context of developing demographic changes leading to greater numbers of older people and people with disabilities, the general field of Inclusive Design Research strives to relate the capabilities of the population to the design of products. Inclusive populations of older people contain a greater variation in sensory, cognitive and physical user capabilities. These variations may be...

  5. Anneli Randla kaitses doktorikraadi Cambridge'is / Anneli Randla ; interv. Reet Varblane

    Index Scriptorium Estoniae

    Randla, Anneli

    1999-01-01

    5. mail kaitses Cambridge'is esimese eesti kunstiteadlasena doktorikraadi Anneli Randla. Töö teema: kerjusmungaordukloostrite arhitektuur Põhja-Euroopas. Juhendaja dr. Deborah Howard. Doktorikraadile esitatavatest nõudmistest, doktoritöö kaitsmisest, magistrikraadi kaitsnu õppimisvõimalustest Cambridge's.

  6. A snuff, Sir? Et ego in Arcadia - op sabbatical in Cambridge

    NARCIS (Netherlands)

    Hondius, E.H.

    2005-01-01

    Een maand lang heb ik in Cambridge onderzoek mogen doen. In deze column wil ik daar verslag van uitbrengen. Niet van mijn onderzoek — ik heb vooral rondgekeken in de bibliotheek en gesproken met collega's om te zien wat momenteel in de common law te koop is - maar van Cambridge zelf.

  7. Reflections on Cambridge: University examinations - how did they begin and how do they work?

    OpenAIRE

    Macfarlane, Alan

    2012-01-01

    Standing in one of the old examination halls in Cambridge, Alan Macfarlane talks about the invention of competitive university examinations (in mathematics in the earlier C19) and the central role of Cambridge as one of the biggest exam setting boards in the world. Also what Camrbdige examinations are thought to be testing.

  8. Success in the US: Are Cambridge International Assessments Good Preparation for University Study?

    Science.gov (United States)

    Shaw, Stuart; Bailey, Clare

    2011-01-01

    This article focuses on the research being conducted by University of Cambridge International Examinations (Cambridge) to ensure that its international assessments prepare students as well as Advanced Placement and International Baccalaureate for continued studies in colleges and universities. The primary purpose of the research is to highlight…

  9. Investigating the Impact of Cambridge International Assessments on U.S. Stakeholders: Student and Teacher Perceptions

    Science.gov (United States)

    Shaw, Stuart

    2011-01-01

    As part of the continuing program to study the impact of its international assessments, the University of Cambridge International Examinations ("Cambridge") has undertaken a series of studies investigating the impact on a range of US stakeholders. This paper reports on research designed to respond to a series of washback and impact questions…

  10. 77 FR 64143 - Manufacturer of Controlled Substances; Notice of Registration; Cambridge Isotope Lab

    Science.gov (United States)

    2012-10-18

    ... Enforcement Administration Manufacturer of Controlled Substances; Notice of Registration; Cambridge Isotope Lab By Notice dated June 18, 2012, and published in the Federal Register on June 26, 2012, 77 FR 38086, Cambridge Isotope Lab, 50 Frontage Road, Andover, Massachusetts 01810, made application by renewal to...

  11. Assessing the Impact of Arts and Humanities Research at the University of Cambridge. Technical Report

    Science.gov (United States)

    Levitt, Ruth; Celia, Claire; Diepeveen, Stephanie; Chonaill, Siobhan Ni; Rabinovich, Lila; Tiessen, Jan

    2010-01-01

    This project for the University of Cambridge and the Arts and Humanities Research Council (AHRC) assesses the impacts of arts and humanities research at the University of Cambridge. Evidence from interviews, a survey of research staff and detailed case studies indicates that these disciplines already have a broad range of impacts. Many of these…

  12. KALIMER database development

    International Nuclear Information System (INIS)

    KALIMER database is an advanced database to utilize the integration management for liquid metal reactor design technology development using Web applications. KALIMER design database is composed of results database, Inter-Office Communication (IOC), 3D CAD database, and reserved documents database. Results database is a research results database during all phase for liquid metal reactor design technology development of mid-term and long-term nuclear R and D. IOC is a linkage control system inter sub project to share and integrate the research results for KALIMER. 3D CAD database is a schematic overview for KALIMER design structure. And reserved documents database is developed to manage several documents and reports since project accomplishment

  13. KALIMER database development

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Kwan Seong; Lee, Yong Bum; Jeong, Hae Yong; Ha, Kwi Seok

    2003-03-01

    KALIMER database is an advanced database to utilize the integration management for liquid metal reactor design technology development using Web applications. KALIMER design database is composed of results database, Inter-Office Communication (IOC), 3D CAD database, and reserved documents database. Results database is a research results database during all phase for liquid metal reactor design technology development of mid-term and long-term nuclear R and D. IOC is a linkage control system inter sub project to share and integrate the research results for KALIMER. 3D CAD database is a schematic overview for KALIMER design structure. And reserved documents database is developed to manage several documents and reports since project accomplishment.

  14. Database and data structure for the novel TOF-PET detector developed for J-PET project

    CERN Document Server

    Czerwiński, E; Bednarski, T; Białas, P; Kapłon, Ł; Kochanowski, A; Korcyl, G; Kowal, J; Kowalski, P; Kozik, T; Krzemień, W; Kubicz, E; Molenda, M; Moskal, P; Niedźwiecki, Sz; Pałka, M; Pawlik, M; Raczyński, L; Rudy, Z; Salabura, P; Sharma, N G; Silarski, M; Słomski, A; Smyrski, J; Strzelecki, A; Wieczorek, A; Wiślicki, W; Zoń, N

    2014-01-01

    The complexity of the hardware and the amount of data collected during the PET imaging process require application of modern methods of efficient data organization and processing. In this article we will discuss the data structures and the flow of collected data from the novel TOF-PET medical scanner which is being developed at the Jagiellonian University. The developed data format reflects: registration process of the gamma quanta emitted from positron-electron annihilation, Front-End Electronic (FEE) structure and required input information for the image reconstruction. In addition, the system database fulfills possible demands of the evolving J-PET project.

  15. Intensive cisplatin/oral etoposide for epithelial ovarian cancer: the Cambridge Gynae-Oncology Centre experience: too toxic for relapse?

    Science.gov (United States)

    Gounaris, Ioannis; Iddawela, Mahesh; Parkinson, Christine; Pratt, Jennie; Hatcher, Helen; Basu, Bristi; Tan, Li Tee; Brenton, James D; Earl, Helena M

    2016-03-01

    Intensive cisplatin and oral etoposide for relapsed epithelial ovarian cancer (EOC), commonly known as the van der Burg (VDB) protocol, has been reported to improve response rates and progression-free survival. We report on all patients with relapsed EOC treated on the VDB protocol at the Cambridge Gynae-Oncology Centre. From the institutional databases, we identified all patients treated since 2001. We extracted demographic, clinical, treatment, and toxicity data and outcomes. We used Cox regression to identify predictors of survival. A total of 35 patients were treated on the VDB protocol. Toxicity was significant, with grade 3/4 fatigue, nausea and vomiting affecting 46, 46 and 29% of patients, respectively. Six patients had grade 3/4 infection and four (11%) deaths occurred on treatment. Efficacy was encouraging, with a radiological response rate of 43%, a median progression-free survival of 5.8 months and a median overall survival of 14.1 months. No significant difference in efficacy was seen between platinum-resistant and sensitive patients. We report significant activity of the VDB protocol in a routine clinical setting. However, the high rates of serious toxicity and treatment-related deaths among patients treated with palliative intent proved unacceptable. The Cambridge Gynae-Oncology Centre no longer uses this regimen in women with relapsed EOC.

  16. TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites.

    Science.gov (United States)

    Wallace, A C; Borkakoti, N; Thornton, J M

    1997-11-01

    It is well established that sequence templates such as those in the PROSITE and PRINTS databases are powerful tools for predicting the biological function and tertiary structure for newly derived protein sequences. The number of X-ray and NMR protein structures is increasing rapidly and it is apparent that a 3D equivalent of the sequence templates is needed. Here, we describe an algorithm called TESS that automatically derives 3D templates from structures deposited in the Brookhaven Protein Data Bank. While a new sequence can be searched for sequence patterns, a new structure can be scanned against these 3D templates to identify functional sites. As examples, 3D templates are derived for enzymes with an O-His-O "catalytic triad" and for the ribonucleases and lysozymes. When these 3D templates are applied to a large data set of nonidentical proteins, several interesting hits are located. This suggests that the development of a 3D template database may help to identify the function of new protein structures, if unknown, as well as to design proteins with specific functions.

  17. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.

    Science.gov (United States)

    Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll

    2016-01-01

    Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. PMID:26612862

  18. EMBANKS: Towards Disk Based Algorithms For Keyword-Search In Structured Databases

    CERN Document Server

    Gupta, Nitin

    2011-01-01

    In recent years, there has been a lot of interest in the field of keyword querying relational databases. A variety of systems such as DBXplorer [ACD02], Discover [HP02] and ObjectRank [BHP04] have been proposed. Another such system is BANKS, which enables data and schema browsing together with keyword-based search for relational databases. It models tuples as nodes in a graph, connected by links induced by foreign key and other relationships. The size of the database graph that BANKS uses is proportional to the sum of the number of nodes and edges in the graph. Systems such as SPIN, which search on Personal Information Networks and use BANKS as the backend, maintain a lot of information about the users' data. Since these systems run on the user workstation which have other demands of memory, such a heavy use of memory is unreasonable and if possible, should be avoided. In order to alleviate this problem, we introduce EMBANKS (acronym for External Memory BANKS), a framework for an optimized disk-based BANKS sy...

  19. DMPD: Structural and functional analyses of bacterial lipopolysaccharides. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 12106784 Structural and functional analyses of bacterial lipopolysaccharides. Carof...html) (.csml) Show Structural and functional analyses of bacterial lipopolysaccharides. PubmedID 12106784 Title Structural and functi...onal analyses of bacterial lipopolysaccharides. Authors

  20. The investigation of coherent structures in the wall region of a supersonic turbulent boundary layer based on DNS database

    Institute of Scientific and Technical Information of China (English)

    HUANG ZhangFeng; ZHOU Heng; LUO JiSheng

    2007-01-01

    Through temporal mode direct numerical simulation, flow field database of a fully developed turbulent boundary layer on a flat plate with Mach number 4.5 and Reynolds number Reθ=1094 has been obtained. Commonly used detection methods in experiments are applied to detecting coherent structures in the flow field,and it is found that coherent structures do exist in the wall region of a supersonic turbulent boundary layer. The detected results show that a low-speed streak is detected by using the Mu-level method, the rising parts of this streak are detected by using the second quadrant method, and the crossing regions from a low-speed streak to the high-speed one are detected by using the VITA method respectively.Notwithstanding that different regions are detected by different methods, they are all accompanied by quasi-stream-wise vortex structures.

  1. The investigation of coherent structures in the wall region of a supersonic turbulent boundary layer based on DNS database

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Through temporal mode direct numerical simulation, flow field database of a fully developed turbulent boundary layer on a flat plate with Mach number 4.5 and Reynolds number Reθ =1094 has been obtained. Commonly used detection meth- ods in experiments are applied to detecting coherent structures in the flow field, and it is found that coherent structures do exist in the wall region of a supersonic turbulent boundary layer. The detected results show that a low-speed streak is de- tected by using the Mu-level method, the rising parts of this streak are detected by using the second quadrant method, and the crossing regions from a low-speed streak to the high-speed one are detected by using the VITA method respectively. Notwithstanding that different regions are detected by different methods, they are all accompanied by quasi-stream-wise vortex structures.

  2. Structure and contents of a new geomorphological GIS database linked to a geomorphological map — With an example from Liden, central Sweden

    NARCIS (Netherlands)

    M. Gustavsson; A.C. Seijmonsbergen; E. Kolstrup

    2008-01-01

    This paper presents the structure and contents of a standardised geomorphological GIS database that stores comprehensive scientific geomorphological data and constitutes the basis for processing and extracting spatial thematic data. The geodatabase contains spatial information on morphography/morpho

  3. DMPD: Intracellular TLR signaling: a structural perspective on human disease. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 16785490 Intracellular TLR signaling: a structural perspective on human disease. La...gnaling: a structural perspective on human disease. PubmedID 16785490 Title Intracellular TLR signaling: a s...tructural perspective on human disease. Authors Lasker MV, Nair SK. Publication J

  4. 1919: psychology and psychoanalysis, Cambridge and London - Myers, Jones and MacCurdy.

    Science.gov (United States)

    Forrester, John

    2008-01-01

    Viewing the reception of psychoanalysis in Britain from Cambridge, the paper examines the intertwining histories of the post-War British Psychological Society and the founding of the British Psycho-Analytical Society, following the initiatives of the two principal psychological entrepreneurs of the era, Charles Myers and Ernest Jones, Reforms in Cambridge in which psychoanalysis played a significant part are analysed, including the foundation of a Clinic for Nervous Diseases and the establishment of a separate Department of Experimental Psychology. The career of J. T. MacCurdy, Jones's student and Lecturer in Psychopathology at Cambridge, is discussed.

  5. RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures

    OpenAIRE

    Popenda, Mariusz; Błażewicz, Marek; Szachniuk, Marta; Adamiak, Ryszard W.

    2007-01-01

    The RNA FRABASE is a web-accessible engine with a relational database, which allows for the automatic search of user-defined, 3D RNA fragments within a set of RNA structures. This is a new tool to search and analyse RNA structures, directed at the 3D structure modelling. The user needs to input either RNA sequence(s) and/or secondary structure(s) given in a ‘dot-bracket’ notation. The algorithm searching for the requested 3D RNA fragments is very efficient. As of August 2007, the database con...

  6. The hermeneutics of mental symptoms in the Cambridge School

    Directory of Open Access Journals (Sweden)

    Massimiliano Aragona

    2015-12-01

    Full Text Available Current Psychiatry is in crisis. Decades of neuroscientific research have not yet delivered adequate explanations or treatments. One reason for this failure may be the wrongness of its central assumption, namely that mental symptoms and disorders are natural kinds. The Cambridge School has proposed that a new Epistemology must be constructed for Psychiatry, and that this should start with the development of a new model of mental symptom-formation. ‘Mental symptoms’ should be considered as hermeneutic co-constructions occurring in a intersubjective space created by the dialogue between sufferer and healer. Subjective experiences (caused either by neurobiological or psychosocial upheaval penetrate the awareness of sufferers causing perplexity and/or distress. To understand, handle and communicate these experiences, sufferers proceed to configure them by means of templates borrowed from their own culture. Importantly, however, the same neurobiological information can be configured into different symptoms; and different neurobiological information into the same symptom. Therefore, ‘mental symptoms’ are dissimilar hybrid combinations of neurobiological and cultural information. To be ethical, therapeutic interventions must take into account such dissimilarities. Blind manipulation of the brain in all cases should be considered as counterproductive.

  7. Who Needs a Revision? 20 Years of Cambridge Shunt Lab.

    Science.gov (United States)

    Czosnyka, Zofia; Czosnyka, Marek; Pickard, John D; Chari, Aswin

    2016-01-01

    Shunt testing independent of manufacturers provides knowledge that can significantly improve the management of patients with hydrocephalus. The Cambridge Shunt Evaluation Laboratory was created 20 years ago. Thanks to financial support from the Department of Health (1993-1998), all shunts in use in the UK were systematically evaluated, with "blue reports" being published. Later new devices were tested as they appeared in public domain.Twenty-six models have been evaluated. The majority of the valves had a non-physiologically low hydrodynamic resistance that may result in over-drainage, both related to posture and during nocturnal cerebral vasogenic waves. A long distal catheter increases the resistance of these valves by 100-200 %. Drainage through valves without a siphon-preventing mechanism is very sensitive to body posture. Shunts with siphon-preventing accessories offer a reasonable resistance to negative outlet pressure. Bench parameters were used to test shunt performance in vivo using infusion tests. A criterion for correctly performing a shunt procedure was established. Pressure measured in the shunt prechamber during the plateau phase of infusion should not remain more than 5 mmHg above the le shunt's operating pressure plus hydrodynamic resistance of the valve multiplied by the infusion rate. "Critical levels" for every shunt and every performance level have been used in the shunt testing wizard of ICM+ software.

  8. Development and current status of the "Cambridge" loudness models.

    Science.gov (United States)

    Moore, Brian C J

    2014-10-13

    This article reviews the evolution of a series of models of loudness developed in Cambridge, UK. The first model, applicable to stationary sounds, was based on modifications of the model developed by Zwicker, including the introduction of a filter to allow for the effects of transfer of sound through the outer and middle ear prior to the calculation of an excitation pattern, and changes in the way that the excitation pattern was calculated. Later, modifications were introduced to the assumed middle-ear transfer function and to the way that specific loudness was calculated from excitation level. These modifications led to a finite calculated loudness at absolute threshold, which made it possible to predict accurately the absolute thresholds of broadband and narrowband sounds, based on the assumption that the absolute threshold corresponds to a fixed small loudness. The model was also modified to give predictions of partial loudness-the loudness of one sound in the presence of another. This allowed predictions of masked thresholds based on the assumption that the masked threshold corresponds to a fixed small partial loudness. Versions of the model for time-varying sounds were developed, which allowed prediction of the masked threshold of any sound in a background of any other sound. More recent extensions incorporate binaural processing to account for the summation of loudness across ears. In parallel, versions of the model for predicting loudness for hearing-impaired ears have been developed and have been applied to the development of methods for fitting multichannel compression hearing aids.

  9. Life Cycle Assessment of concrete structures using public databases : Comparison of a fictitious bridge and tunnel

    OpenAIRE

    Boulenger, Maxime

    2011-01-01

    Concrete structures represent a huge investment in terms of materials and energy and they lead to significant environmental impacts. Thus, there is a need to choose the most sustainable and eco-friendly alternative. From this perspective, this report aims to evaluate the environmental impacts associated with the construction of two fictitious structures: a bridge and a tunnel. To fully assess and fairly compare the environmental burdens of those two structures, the life cycle assessment (LCA)...

  10. Database Description - RPSD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us RPSD Datab...ase Description General information of database Database name RPSD Alternative name Summary inform...n National Institute of Agrobiological Sciences Toshimasa Yamazaki E-mail : Database classification Structure Datab...idopsis thaliana Taxonomy ID: 3702 Taxonomy Name: Glycine max Taxonomy ID: 3847 Database description We have...nts such as rice, and have put together the result and related informations. This database contains the basi

  11. Digital bedrock mapping at the Geological Survey of Norway: BGS SIGMA tool and in-house database structure

    Science.gov (United States)

    Gasser, Deta; Viola, Giulio; Bingen, Bernard

    2016-04-01

    Since 2010, the Geological Survey of Norway has been implementing and continuously developing a digital workflow for geological bedrock mapping in Norway, from fieldwork to final product. Our workflow is based on the ESRI ArcGIS platform, and we use rugged Windows computers in the field. Three different hardware solutions have been tested over the past 5 years (2010-2015). (1) Panasonic Toughbook CE-19 (2.3 kg), (2) Panasonic Toughbook CF H2 Field (1.6 kg) and (3) Motion MC F5t tablet (1.5 kg). For collection of point observations in the field we mainly use the SIGMA Mobile application in ESRI ArcGIS developed by the British Geological Survey, which allows the mappers to store georeferenced comments, structural measurements, sample information, photographs, sketches, log information etc. in a Microsoft Access database. The application is freely downloadable from the BGS websites. For line- and polygon work we use our in-house database, which is currently under revision. Our line database consists of three feature classes: (1) bedrock boundaries, (2) bedrock lineaments, and (3) bedrock lines, with each feature class having up to 24 different attribute fields. Our polygon database consists of one feature class with 38 attribute fields enabling to store various information concerning lithology, stratigraphic order, age, metamorphic grade and tectonic subdivision. The polygon and line databases are coupled via topology in ESRI ArcGIS, which allows us to edit them simultaneously. This approach has been applied in two large-scale 1:50 000 bedrock mapping projects, one in the Kongsberg domain of the Sveconorwegian orogen, and the other in the greater Trondheim area (Orkanger) in the Caledonian belt. The mapping projects combined collection of high-resolution geophysical data, digital acquisition of field data, and collection of geochronological, geochemical and petrological data. During the Kongsberg project, some 25000 field observation points were collected by eight

  12. RNA 3D Structural Motifs: Definition, Identification, Annotation, and Database Searching

    Science.gov (United States)

    Nasalean, Lorena; Stombaugh, Jesse; Zirbel, Craig L.; Leontis, Neocles B.

    Structured RNA molecules resemble proteins in the hierarchical organization of their global structures, folding and broad range of functions. Structured RNAs are composed of recurrent modular motifs that play specific functional roles. Some motifs direct the folding of the RNA or stabilize the folded structure through tertiary interactions. Others bind ligands or proteins or catalyze chemical reactions. Therefore, it is desirable, starting from the RNA sequence, to be able to predict the locations of recurrent motifs in RNA molecules. Conversely, the potential occurrence of one or more known 3D RNA motifs may indicate that a genomic sequence codes for a structured RNA molecule. To identify known RNA structural motifs in new RNA sequences, precise structure-based definitions are needed that specify the core nucleotides of each motif and their conserved interactions. By comparing instances of each recurrent motif and applying base pair isosteriCity relations, one can identify neutral mutations that preserve its structure and function in the contexts in which it occurs.

  13. DCC Briefing Paper: Database archiving

    OpenAIRE

    Müller, Heiko

    2009-01-01

    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 focuses on archiving data that are maintained under the control of a database management system and structured under a database schema, e.g., a relational database. The primary goal of database archiving is to maintain access to data in case it is late...

  14. Plastination in Anatomy Learning: An Experience at Cambridge University.

    Science.gov (United States)

    Latorre, Rafael; Bainbridge, David; Tavernor, Angie; López Albors, Octavio

    2016-01-01

    Due to lack of objective data, the benefits of using plastination in combination with wet dissection in teaching gross anatomy are unknown. The aim of this study was to obtain objective evidence from students regarding the effectiveness of combining plastinated specimens (PS) with an established gross anatomy education program at Cambridge University that uses wet cadaver dissection and small-group tutorials. For a complete academic year, a total of 135 PS were used alongside wet cadaver dissections. The PS were also available for small-group tutorials. An anonymous closed questionnaire, using a 5-point numerical-estimation Likert scale, was used to gather information relating to the effectiveness of the PS. The level of student satisfaction with the combined use of wet dissections and PS was high, although higher (p<.05) for second-year students (98.4%) than for first-year students (95.5%). Students felt the specimens allowed them to see details that were often more difficult to identify in their dissections, for instance nerves. Voluntary use of PS was higher (p<.01) for second-year students (96.9%), who had previously experienced anatomy teaching with cadaver dissection alone, than for first-year students (77.7%). Overall, 97.7% of all students thought that the PS helped them understand and learn anatomy. All students surveyed (100%) recommended the use of PS in the future. Students considered the use of PS in the dissection room combined with wet cadaver dissection to be beneficial when learning anatomy, particularly when combined with their use during small-group tutorials.

  15. Nano Si preparation by constant cell voltage electrolysis of FFC-Cambridge Process in molten CaCl2

    Institute of Scientific and Technical Information of China (English)

    Ji; Zhao; Shengmei; Lu; Linyan; Hu; Can; Li

    2013-01-01

    Using FFC-Cambridge Process to prepare Si from SiO2 is a promising method to prepare nanostructured and highly pure silicon for solar cells.However,the method still has many problems unsolved and the controlling effect of the cell voltage on silicon product is not clear.Here we report in this article that nano cluster-like silicon product with purity of 99.95%has been prepared by complete conversion of raw material SiO2,quartz glass plate,using constant cell voltage electrolysis FFC-Cambridge Process.By analysis of XRD,EDS,TEM,HRTEM and ICP-AES as well as the discussion from the thermodynamics calculation,the morphology and components of the product based on the change of cell voltage are clarified.It is clear that pure silicon could be prepared at the cell voltage of 1.7 2.1 V in this reaction system.The silicon material have cluster-like structure which are made of silicon nanoparticles in 20 100 nm size.Interestingly,the cluster-like nano structure of the silicon can be tuned by the used cell voltage.The purity,yield and the energy cost of silicon product prepared at the optimized cell voltage are discussed.The purity of the silicon product could be further improved,hence this method is promising for the preparation of solar grade silicon in future.

  16. STUDY ON THE CONCEPT DESIGN PROCESS FOR THE CRASHWORTHINESS IMPROVEMENT OF AN AUTOMOTIVE BODY STRUCTURE USING A KNOWLEDGEBASED DATABASE

    Directory of Open Access Journals (Sweden)

    W. Y. Ki

    2016-04-01

    Full Text Available The purpose of this study is to propose a concept design process for crashworthiness improvement of automotive body structure using technical information on the major joints and members of vehicles. First, in order to collect the technical information on major joints and members, 43 vehicles were selected using benchmark data. The collected technical information for the selected vehicles was the cross sectional shapes of each joint and member which were used for the analysis of joint stiffness, crashworthiness and static stiffness of the member to make a database along with cross section properties. This study applied a statistical technique to perform a concept design of an automotive body using the analyzed information and selected cross section meeting the design objectives. The criteria for the selection of the cross section were defined by subdividing the defined design objectives of an automotive body structure and constraints into members and joints. In order to configure an analysis model of an automotive body structure using the selected cross section, a shape parametric model was used and crashworthiness was assessed to evaluate the configured automotive body structure. The evaluation result showed that the crashworthiness was improved by 15% and 12% respectively compared to an existing body structure. In addition, the weight of the body structure was reduced by 4.2%. Through this study, the process that can rapidly and effectively derive and evaluate the concept design of an automotive body structure was defined. It is expected that, henceforth, this process will be helpful for the study of automotive body structures.

  17. GRAD: On Graph Database Modeling

    OpenAIRE

    Ghrab, Amine; Romero, Oscar; Skhiri, Sabri; Vaisman, Alejandro; Zimányi, Esteban

    2016-01-01

    Graph databases have emerged as the fundamental technology underpinning trendy application domains where traditional databases are not well-equipped to handle complex graph data. However, current graph databases support basic graph structures and integrity constraints with no standard algebra. In this paper, we introduce GRAD, a native and generic graph database model. GRAD goes beyond traditional graph database models, which support simple graph structures and constraints. Instead, GRAD pres...

  18. Hydrogen bonding in oxalic acid and its complexes: A database study of neutron structures

    Indian Academy of Sciences (India)

    R Chitra; Amit Das; R R Choudhury; M Ramanadham; R Chidambaram

    2004-08-01

    The basic result of carboxylic group that the oxygen atom of the –OH never seems to be a hydrogen bond acceptor is violated in the cases, namely urea oxalic acid and bis urea oxalic acid complexes, where the hydroxyl oxygen atom is an acceptor of a weak N–H... O hydrogen bond. The parameters of this hydrogen bond, respectively in these structures are: hydrogen acceptor distance 2.110 Å and 2.127 Å and the bending angle at hydrogen, 165.6° and 165.8°. The bond strength around the hydroxyl oxygen is close to 1.91 valence units, indicating that it has hardly any strength left to form hydrogen bonds. These two structures being highly planar, force the formation of this hydrogen bond. As oxalic acid is the common moiety, the structures of the two polymorphs, -oxalic acid and -oxalic acid, also were looked into in terms of hydrogen bonding and packing.

  19. Artificial Intelligence in Prediction of Secondary Protein Structure Using CB513 Database

    Science.gov (United States)

    Avdagic, Zikrija; Purisevic, Elvir; Omanovic, Samir; Coralic, Zlatan

    2009-01-01

    In this paper we describe CB513 a non-redundant dataset, suitable for development of algorithms for prediction of secondary protein structure. A program was made in Borland Delphi for transforming data from our dataset to make it suitable for learning of neural network for prediction of secondary protein structure implemented in MATLAB Neural-Network Toolbox. Learning (training and testing) of neural network is researched with different sizes of windows, different number of neurons in the hidden layer and different number of training epochs, while using dataset CB513. PMID:21347158

  20. Database storage structure analysis of MS Structured Query Language Server%SQL Server数据库存储结构分析

    Institute of Scientific and Technical Information of China (English)

    张锦文

    2014-01-01

    针对结构化查询语言(SQL)Server 2000数据库的主数据文件的存储结构进行了解剖。通过对大量的数据库主数据文件的解读统计分析,阐述了数据库主数据文件的存储结构,推导出主数据文件中数据页、页面标题、记录标题、记录偏移量数组的逻辑结构,推导出记录存放顺序和数据类型代码。通过编程做了一些实例,得出解读数据库主数据文件的基本方法,为手工恢复数据库提供了技术途径。%The-primary-data-file-storage-structure-of-Microsoft(MS)-Structured-Query-Language(SQL)-Server-is-analyzed.-By-reading-and-calculating-large-amount-of-primary-data-files-in-databases,the-storage-structure-of-primary-data-file-is-stated,the-logic-structure-of-data-page,data-title,record-title-and-data-offset-array-in-the-primary-data-file-are-derived,and-the-storing-order-and-the-data-type-code-are-revealed.-The-essential-method-of-reading-primary-data-file-of-databases-is-summarized-and-validated-by-some-experimental-programs,-which-provides-an-approach-for-recovering-database-manually.

  1. Development of novel repellents using structure-activity modeling of compounds in the USDA archival database

    Science.gov (United States)

    The United States Department of Agriculture (USDA) has developed repellents and insecticides for the U.S. military since 1942. Repellency and toxicity data for over 30,000 compounds are contained within the USDA archive. Repellency data from subsets of similarly structured compounds were used to dev...

  2. SU-E-QI-16: Reproducibility of Computed Tomography Quantitative Structural Features Using the FDA Thoracic Phantom Image Database

    Energy Technology Data Exchange (ETDEWEB)

    Budzevich, M; Grove, O; Balagurunathan, Y; Gu, Y; Wang, H; Oliver, J; Latifi, K; Zhang, G; Dilling, T; Gillies, R; Moros, E; Lee, H. [Moffitt Cancer Center and Research Institute, Tampa, FL (United States)

    2014-06-15

    Purpose: To assess the reproducibility of quantitative structural features using images from the computed tomography thoracic FDA phantom database under different scanning conditions. Methods: Development of quantitative image features to describe lesion shape and size, beyond conventional RECIST measures, is an evolving area of research in need of benchmarking standards. Gavrielides et al. (2010) scanned a FDA-developed thoracic phantom with nodules of various Hounsfield units (HU) values, shapes and sizes close to vascular structures using several scanners and varying scanning conditions/parameters; these images are in the public domain. We tested six structural features, namely, Convexity, Perimeter, Major Axis, Minor Axis, Extent Mean and Eccentricity, to characterize lung nodules. Convexity measures lesion irregularity referenced to a convex surface. Previously, we showed it to have prognostic value in lung adenocarcinoma. The above metrics and RECIST measures were evaluated on three spiculated (8mm/-300HU, 12mm/+30HU and 15mm/+30HU) and two non-spiculated (8mm/+100HU and 10mm/+100HU) nodules (from layout 2) imaged at three different mAs values: 25, 100 and 200 mAs; on a Phillips scanner (16-slice Mx8000-IDT; 3mm slice thickness). The nodules were segmented semi-automatically using a commercial software tool; the same HU range was used for all nodules. Results: Analysis showed convexity having the lowest maximum coefficient of variation (MCV): 1.1% and 0.6% for spiculated and non-spiculated nodules, respectively, much lower compared to RECIST Major and Minor axes whose MCV were 10.1% and 13.4% for spiculated, and 1.9% and 2.3% for non-spiculated nodules, respectively, across the various mAs. MCVs were consistently larger for speculated nodules. In general, the dependence of structural features on mAs (noise) was low. Conclusion: The FDA phantom CT database may be used for benchmarking of structural features for various scanners and scanning conditions; we used

  3. SU-E-QI-16: Reproducibility of Computed Tomography Quantitative Structural Features Using the FDA Thoracic Phantom Image Database

    International Nuclear Information System (INIS)

    Purpose: To assess the reproducibility of quantitative structural features using images from the computed tomography thoracic FDA phantom database under different scanning conditions. Methods: Development of quantitative image features to describe lesion shape and size, beyond conventional RECIST measures, is an evolving area of research in need of benchmarking standards. Gavrielides et al. (2010) scanned a FDA-developed thoracic phantom with nodules of various Hounsfield units (HU) values, shapes and sizes close to vascular structures using several scanners and varying scanning conditions/parameters; these images are in the public domain. We tested six structural features, namely, Convexity, Perimeter, Major Axis, Minor Axis, Extent Mean and Eccentricity, to characterize lung nodules. Convexity measures lesion irregularity referenced to a convex surface. Previously, we showed it to have prognostic value in lung adenocarcinoma. The above metrics and RECIST measures were evaluated on three spiculated (8mm/-300HU, 12mm/+30HU and 15mm/+30HU) and two non-spiculated (8mm/+100HU and 10mm/+100HU) nodules (from layout 2) imaged at three different mAs values: 25, 100 and 200 mAs; on a Phillips scanner (16-slice Mx8000-IDT; 3mm slice thickness). The nodules were segmented semi-automatically using a commercial software tool; the same HU range was used for all nodules. Results: Analysis showed convexity having the lowest maximum coefficient of variation (MCV): 1.1% and 0.6% for spiculated and non-spiculated nodules, respectively, much lower compared to RECIST Major and Minor axes whose MCV were 10.1% and 13.4% for spiculated, and 1.9% and 2.3% for non-spiculated nodules, respectively, across the various mAs. MCVs were consistently larger for speculated nodules. In general, the dependence of structural features on mAs (noise) was low. Conclusion: The FDA phantom CT database may be used for benchmarking of structural features for various scanners and scanning conditions; we used

  4. Dual Half Edge Data Structure in Database for Big Data in GIS

    Science.gov (United States)

    Goudarzi, M.; Asghari, M.; Boguslawski, P.; Rahman, A. A.

    2015-10-01

    In GIS, different types of data structures have been proposed in order to represent 3D models and examining the relationship between spatial objects. The Dual Half-Edge (DHE) is a data structure that permits the simultaneous representation of the geometry and topology of models with a special focus on building interiors. In this paper, from the storage cost point of view, the G-Maps model is analyzed and compared with the DHE model, since they have some features in common and also G-Maps is used widely in GIS. The primary result shows that the DHE is more efficient than the G-Maps with regard to the storage cost.

  5. MetalPDB: a database of metal sites in biological macromolecular structures

    OpenAIRE

    C. Andreini; Cavallaro, G.; Lorenzini, S.; Rosato, A.

    2013-01-01

    We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the ...

  6. Medicinal Plants Database and Three Dimensional Structure of the Chemical Compounds from Medicinal Plants in Indonesia

    OpenAIRE

    Arry Yanuar; Abdul Mun'im; Akma Bertha Aprima Lagho; Rezi Riadhi Syahdi; Marjuqi Rahmat; Heru Suhartanto

    2011-01-01

    During this era of new drug designing, medicinal plants had become a very interesting object of further research. Pharmacology screening of active compound of medicinal plants would be time consuming and costly. Molecular docking is one of the in silico method which is more efficient compare to in vitro or in vivo method for its capability of finding the active compound in medicinal plants. In this method, three-dimensional structure becomes very important in the molecular docking methods, so...

  7. Neuromorphic hardware databases for exploring structure-function relationships in the brain.

    OpenAIRE

    Breslin, C; O'Lenskie, A

    2001-01-01

    Neuromorphic hardware is the term used to describe full custom-designed integrated circuits, or silicon 'chips', that are the product of neuromorphic engineering--a methodology for the synthesis of biologically inspired elements and systems, such as individual neurons, retinae, cochleas, oculomotor systems and central pattern generators. We focus on the implementation of neurons and networks of neurons, designed to illuminate structure-function relationships. Neuromorphic hardware can be cons...

  8. Identification of promiscuous ene-reductase activity by mining structural databases using active site constellations.

    Science.gov (United States)

    Steinkellner, Georg; Gruber, Christian C; Pavkov-Keller, Tea; Binter, Alexandra; Steiner, Kerstin; Winkler, Christoph; Lyskowski, Andrzej; Schwamberger, Orsolya; Oberer, Monika; Schwab, Helmut; Faber, Kurt; Macheroux, Peter; Gruber, Karl

    2014-01-01

    The exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. Here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites ('catalophores'). As a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated C-C double bonds) and compare them with known ene-reductases, that is, members of the Old Yellow Enzyme family. Despite completely different amino acid sequences, overall structures and protein folds, high-resolution crystal structures reveal equivalent binding modes of typical Old Yellow Enzyme substrates and ligands. Biochemical and biocatalytic data show that the two enzymes indeed possess ene-reductase activity and reveal an inverted stereopreference compared with Old Yellow Enzymes for some substrates. This method could thus be a tool for the identification of viable starting points for the development and engineering of novel biocatalysts. PMID:24954722

  9. Solid State Structures of Alkali Metal Ion Complexes Formed by Low-Molecular-Weight Ligands of Biological Relevance.

    Science.gov (United States)

    Aoki, Katsuyuki; Murayama, Kazutaka; Hu, Ning-Hai

    2016-01-01

    This chapter provides structural data, mainly metal binding sites/modes, observed in crystal structures of alkali metal ion complexes containing low-molecular-weight ligands of biological relevance, mostly obtained from the Cambridge Structural Database (the CSD version 5.35 updated to February 2014). These ligands include (i) amino acids and small peptides, (ii) nucleic acid constituents (excluding quadruplexes and other oligonucleotides), (iii) simple carbohydrates, and (iv) naturally occurring antibiotic ionophores. For some representative complexes of these ligands, some details on the environment of the metal coordination and structural characteristics are described. PMID:26860299

  10. Relational databases

    CERN Document Server

    Bell, D A

    1986-01-01

    Relational Databases explores the major advances in relational databases and provides a balanced analysis of the state of the art in relational databases. Topics covered include capture and analysis of data placement requirements; distributed relational database systems; data dependency manipulation in database schemata; and relational database support for computer graphics and computer aided design. This book is divided into three sections and begins with an overview of the theory and practice of distributed systems, using the example of INGRES from Relational Technology as illustration. The

  11. Insights from the DNA databases: approaches to the phylogenetic structure of Acanthamoeba.

    Science.gov (United States)

    Fuerst, Paul A

    2014-11-01

    Species of Acanthamoeba have been traditionally described using morphology (primarily cyst structure), or cytology of nuclear division (used by Pussard and Pons, 1977). Twenty-plus putative species were proposed based on such criteria. Morphology, however, is often plastic, dependent upon culture conditions. DNA sequences of the nuclear small subunit (18S) rRNA that can be used for the study of the phylogeny of Acanthamoeba have increased from a single sequence in 1986 to more than 1800 in 2013. Some of the patterns of the sequence data for Acanthamoeba are reviewed, and some of the insights that this data illuminates are illustrated. In particular, the data suggest the existence of 20 or more genotypic types, a number not dissimilar to the number of named species of Acanthamoeba. However, molecular studies make clear that the relationship between phylogenetic relatedness and species names as we know them for Acanthamoeba is tenuous at best.

  12. A database study of intermolecular NH...O hydrogen bonds for carboxylates, sulfonates and monohydrogen phosphonates

    International Nuclear Information System (INIS)

    A search of the Cambridge Structural Database (CSD, version 5.05, 1993) was performed in order to compare the geometrical features of the hydrogen bonds involving on the one hand amino groups and on the other hand carboxylates, sulfonates or monohydrogen phosponates. Phosphonates were not considered because only four entries containing amino and phosphonate moieities were located in the CSD. The hydroxylic group of monohydrogen phosphonates primarily acts as a hydrogen-bond donor. The three moieties under study show NH..O hydrogen bonds with similar geometrical features. This statistical analysis has focused on the hydrogen-bond distances and angles and on the distributions of the H atoms around the acceptor O atoms of carboxylates, sulfonates or monohydrogen phosphonates. (orig.)

  13. Database Application Schema Forensics

    OpenAIRE

    Hector Quintus Beyers; Olivier, Martin S; Hancke, Gerhard P.

    2014-01-01

    The application schema layer of a Database Management System (DBMS) can be modified to deliver results that may warrant a forensic investigation. Table structures can be corrupted by changing the metadata of a database or operators of the database can be altered to deliver incorrect results when used in queries. This paper will discuss categories of possibilities that exist to alter the application schema with some practical examples. Two forensic environments are introduced where a forensic ...

  14. Categorical Database Generalization

    Institute of Scientific and Technical Information of China (English)

    LIU Yaolin; Martin Molenaar; AI Tinghua; LIU Yanfang

    2003-01-01

    This paper focuses on the issues of categorical database gen-eralization and emphasizes the roles ofsupporting data model, integrated datamodel, spatial analysis and semanticanalysis in database generalization.The framework contents of categoricaldatabase generalization transformationare defined. This paper presents an in-tegrated spatial supporting data struc-ture, a semantic supporting model andsimilarity model for the categorical da-tabase generalization. The concept oftransformation unit is proposed in generalization.

  15. Secondary structural analysis of proteins based on 13C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database

    International Nuclear Information System (INIS)

    Magic-angle-spinning solid-state 13C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-13C,15N labeled samples. To overcome this problem, we present a method for assigning 13C chemical shifts and secondary structures from unresolved two-dimensional 13C–13C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to 13Cα, 13Cβ, and 13C′ chemical shifts and cross-peak intensities. The experimental 13C–13C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific Cα, Cβ, and C′ chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50–200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved 13C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.

  16. Assessment and Requirements of Nuclear Reaction Databases for GCR Transport in the Atmosphere and Structures

    Science.gov (United States)

    Cucinotta, F. A.; Wilson, J. W.; Shinn, J. L.; Tripathi, R. K.

    1998-01-01

    The transport properties of galactic cosmic rays (GCR) in the atmosphere, material structures, and human body (self-shielding) am of interest in risk assessment for supersonic and subsonic aircraft and for space travel in low-Earth orbit and on interplanetary missions. Nuclear reactions, such as knockout and fragmentation, present large modifications of particle type and energies of the galactic cosmic rays in penetrating materials. We make an assessment of the current nuclear reaction models and improvements in these model for developing required transport code data bases. A new fragmentation data base (QMSFRG) based on microscopic models is compared to the NUCFRG2 model and implications for shield assessment made using the HZETRN radiation transport code. For deep penetration problems, the build-up of light particles, such as nucleons, light clusters and mesons from nuclear reactions in conjunction with the absorption of the heavy ions, leads to the dominance of the charge Z = 0, 1, and 2 hadrons in the exposures at large penetration depths. Light particles are produced through nuclear or cluster knockout and in evaporation events with characteristically distinct spectra which play unique roles in the build-up of secondary radiation's in shielding. We describe models of light particle production in nucleon and heavy ion induced reactions and make an assessment of the importance of light particle multiplicity and spectral parameters in these exposures.

  17. Community Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This excel spreadsheet is the result of merging at the port level of several of the in-house fisheries databases in combination with other demographic databases...

  18. BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures

    International Nuclear Information System (INIS)

    We present two new databases of NMR-derived distance and dihedral angle restraints: the Database Of Converted Restraints (DOCR) and the Filtered Restraints Database (FRED). These databases currently correspond to 545 proteins with NMR structures deposited in the Protein Databank (PDB). The criteria for inclusion were that these should be unique, monomeric proteins with author-provided experimental NMR data and coordinates available from the PDB capable of being parsed and prepared in a consistent manner. The Wattos program was used to parse the files, and the CcpNmr FormatConverter program was used to prepare them semi-automatically. New modules, including a new implementation of Aqua in the BioMagResBank (BMRB) software Wattos were used to analyze the sets of distance restraints (DRs) for inconsistencies, redundancies, NOE completeness, classification and violations with respect to the original coordinates. Restraints that could not be associated with a known nomenclature were flagged. The coordinates of hydrogen atoms were recalculated from the positions of heavy atoms to allow for a full restraint analysis. The DOCR database contains restraint and coordinate data that is made consistent with each other and with IUPAC conventions. The FRED database is based on the DOCR data but is filtered for use by test calculation protocols and longitudinal analyses and validations. These two databases are available from websites of the BMRB and the Macromolecular Structure Database (MSD) in various formats: NMR-STAR, CCPN XML, and in formats suitable for direct use in the software packages CNS and CYANA

  19. The Thiamine diphosphate dependent Enzyme Engineering Database: A tool for the systematic analysis of sequence and structure relations

    Directory of Open Access Journals (Sweden)

    Radloff Robert

    2010-02-01

    Full Text Available Abstract Background Thiamine diphosphate (ThDP-dependent enzymes form a vast and diverse class of proteins, catalyzing a wide variety of enzymatic reactions including the formation or cleavage of carbon-sulfur, carbon-oxygen, carbon-nitrogen, and especially carbon-carbon bonds. Although very diverse in sequence and domain organisation, they share two common protein domains, the pyrophosphate (PP and the pyrimidine (PYR domain. For the comprehensive and systematic comparison of protein sequences and structures the Thiamine diphosphate (ThDP-dependent Enzyme Engineering Database (TEED was established. Description The TEED http://www.teed.uni-stuttgart.de contains 12048 sequence entries which were assigned to 9443 different proteins and 379 structure entries. Proteins were assigned to 8 different superfamilies and 63 homologous protein families. For each family, the TEED offers multisequence alignments, phylogenetic trees, and family-specific HMM profiles. The conserved pyrophosphate (PP and pyrimidine (PYR domains have been annotated, which allows the analysis of sequence similarities for a broad variety of proteins. Human ThDP-dependent enzymes are known to be involved in many diseases. 20 different proteins and over 40 single nucleotide polymorphisms (SNPs of human ThDP-dependent enzymes were identified in the TEED. Conclusions The online accessible version of the TEED has been designed to serve as a navigation and analysis tool for the large and diverse family of ThDP-dependent enzymes.

  20. Database Administrator

    Science.gov (United States)

    Moore, Pam

    2010-01-01

    The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

  1. Accessing and using chemical databases

    DEFF Research Database (Denmark)

    Nikolov, Nikolai Georgiev; Pavlov, Todor; Niemelä, Jay Russell;

    2013-01-01

    Computer-based representation of chemicals makes it possible to organize data in chemical databases-collections of chemical structures and associated properties. Databases are widely used wherever efficient processing of chemical information is needed, including search, storage, retrieval, and di...... are included about the OASIS database and platform and the Danish (Q)SAR Database online. Various types of chemical database resources are discussed, together with a list of examples....

  2. Biological Macromolecule Crystallization Database

    Science.gov (United States)

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  3. Physical database design for an object-oriented database system

    OpenAIRE

    Scholl, Marc H.

    1994-01-01

    Object-oriented database systems typically offer a variety of structuring capabilities to model complex objects. This flexibility, together with type (or class) hierarchies and computed "attributes"§ (methods), poses a high demand on the physical design of object-oriented databases. Similar to traditional databases, it is hardly ever true that the conceptual structure of the database is also a good, that is, effcient, internal one. Rather, data representing the conceptual objects may be stru...

  4. Taxonomic review of the New World spider genus Elaver O. Pickard-Cambridge, 1898 (Araneae, Clubionidae).

    Science.gov (United States)

    Saturnino, Regiane; Bonaldo, Alexandre Bragio

    2015-11-23

    Elaver O. Pickard-Cambridge, 1898 is characterized and redescribed, including 49 species occurring from the United States to Argentina. Thirty seven previously known species are redescribed: Elaver achuca (Roddy, 1966) revalidated, E. balboae (Chickering, 1937), E. barroana (Chickering, 1937), E. calcarata (Kraus, 1955), E. carlota (Bryant, 1940), E. chisosa (Roddy, 1966), E. crinophora (Franganillo, 1934), E. crocota (O. Pickard-Cambridge, 1896), E. albicans (Franganillo, 1930) name restored, E. depuncta O. Pickard-Cambridge, 1898, E. elaver (Bryant, 1940), E. excepta (L. Koch, 1866), E. grandivulva (Mello-Leitão, 1930), E. hortoni (Chickering, 1937), E. implicata (Gertsch, 1941), E. juana (Bryant, 1940), E. kohlsi (Gertsch & Jellison, 1939), E. linguata (F.O. Pickard-Cambridge, 1900), E. madera (Roddy, 1966), E. mirabilis (O. Pickard-Cambridge, 1896) new. comb., E. mulaiki (Gertsch, 1935), E. multinotata (Chickering, 1937), E. orvillei (Chickering, 1937), E. placida O. Pickard-Cambridge, 1898, E. portoricensis (Petrunkevitch, 1930), E. quadrata (Kraus, 1955), E. richardi (Gertsch, 1941), E. sericea O. Pickard-Cambridge, 1898, E. sigillata (Petrunkevitch, 1925), E. simplex (O. Pickard-Cambridge, 1896), E. texana (Gertsch, 1933), E. tigrina O. Pickard-Cambridge, 1898 name restored, E. tricuspis (F.O. Pickard-Cambridge, 1900), E. tristani (Banks, 1909), E. tumivulva (Banks, 1909), E. valvula (F.O. Pickard-Cambridge, 1900) and E. wheeleri (Roewer, 1933). Ten new species are described: E. candelaria n. sp. and E. helenae n. sp. from Mexico; E. arawakan n. sp. from Haiti; E. lizae n. sp. from Costa Rica; E. darwichi n. sp. from Ecuador; E. juruti n. sp., E. tourinhoae n. sp. and E. vieirae n. sp. from Brazil; E. shinguito n. sp. from Peru and E. beni n. sp. from Bolivia. The female of E. hortoni is described for the first time. Lectotypes are designated for E. sigillata and its actual female is described for the first time. Four new synonyms are proposed: E. languida

  5. Categorical database generalization in GIS

    NARCIS (Netherlands)

    Liu, Y.

    2002-01-01

    Key words: Categorical database, categorical database generalization, Formal data structure, constraints, transformation unit, classification hierarchy, aggregation hierarchy, semantic similarity, data model, Delaunay triangulation

  6. Hazard Analysis Database Report

    CERN Document Server

    Grams, W H

    2000-01-01

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

  7. Nutrition in medical education: reflections from an initiative at the University of Cambridge

    Directory of Open Access Journals (Sweden)

    Ball L

    2014-05-01

    Full Text Available Lauren Ball,1 Jennifer Crowley,2 Celia Laur,3 Minha Rajput-Ray,3 Stephen Gillam,4 Sumantra Ray3 1Nutrition and Dietetics, School of Allied Health Sciences, Centre for Health Practice Innovation, Griffith University, Queensland, Brisbane, Australia; 2Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; 3Need for Nutrition Education/Innovation Programme, Medical Research Council Human Nutrition Research, Cambridge, UK; 4Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge, Cambridge, UK Abstract: Landmark reports have confirmed that it is within the core responsibilities of doctors to address nutrition in patient care. There are ongoing concerns that doctors receive insufficient nutrition education during medical training. This paper provides an overview of a medical nutrition education initiative at the University of Cambridge, School of Clinical Medicine, including 1 the approach to medical nutrition education, 2 evaluation of the medical nutrition education initiative, and 3 areas identified for future improvement. The initiative utilizes a vertical, spiral approach during the clinically focused years of the Cambridge undergraduate and graduate medical degrees. It is facilitated by the Nutrition Education Review Group, a group associated with the UK Need for Nutrition Education/Innovation Programme, and informed by the experiences of their previous nutrition education interventions. Three factors were identified as contributing to the success of the nutrition education initiative including the leadership and advocacy skills of the nutrition academic team, the variety of teaching modes, and the multidisciplinary approach to teaching. Opportunities for continuing improvement to the medical nutrition education initiative included a review of evaluation tools, inclusion of nutrition in assessment items, and further alignment of the Cambridge curriculum with the

  8. Analysis and Assessment of Cambridge English Skills Real Reading 2 within the Scope of Communicative Approach

    Institute of Scientific and Technical Information of China (English)

    张润霞

    2015-01-01

    this essay analyzes and assesses Cambridge English Skills Real Reading 2 from the perspective of communicative approach.The first part analyzes the theoretical basis of the textbook,including the organizational,pragmatic competence.The second part analyzes the syllabus contents.The last part analyzes the material and tasks of it.In summary,Cambridge English Skills Real Reading 2 is mainly communicative textbook from several aspects based on the detailed assessment and explanation.It can be helpful to the designing of reading textbooks.

  9. Water quality in the Cambridge, Massachusetts, drinking-water source area, 2005-8

    Science.gov (United States)

    Smith, Kirk P.; Waldron, Marcus C.

    2015-01-01

    During 2005-8, the U.S. Geological Survey, in cooperation with the Cambridge, Massachusetts, Water Department, measured concentrations of sodium and chloride, plant nutrients, commonly used pesticides, and caffeine in base-flow and stormwater samples collected from 11 tributaries in the Cambridge drinking-water source area. These data were used to characterize current water-quality conditions, to establish a baseline for future comparisons, and to describe trends in surface-water quality. The data also were used to assess the effects of watershed characteristics on surface-water quality and to inform future watershed management.

  10. CarbBank: A structural and bibliographic database for complex carbohydrates. Progress report, September 15, 1991--September 14, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Albersheim, P.

    1992-06-01

    The CarbBank project has several key facets: building a computer database that presents carbohydrate sequence information derived from the published literature, programming to create computer applications that use the information in the database, creating software for multiple computer platforms, and distributing software to end users.

  11. GALT Protein Database, a Bioinformatics Resource for the Manage-ment and Analysis of Structural Features of a Galactosemia-related Protein and Its Mutants

    Institute of Scientific and Technical Information of China (English)

    Antonio d'Acierno; Angelo Facchiano; Anna Marabotti

    2009-01-01

    We describe the GALT-Prot database and its related web-based application that have been developed to collect information about the structural and functional effects of mutations on the human enzyme galactose-1-phosphate uridyltransferase (GALT) involved in the genetic disease named galactosemia type Ⅰ. Besides a list of missense mutations at gene and protein sequence levels, GALT-Prot reports the analysis results of mutant GALT structures. In addition to the structural information about the wild-type enzyme, the database also includes structures of over 100 single point mutants simulated by means of a computational procedure, and the analysis to each mutant was made with several bioinformatics programs in order to investigate the effect of the mutations. The web-based interface allows querying of the database, and several links are also provided in order to guarantee a high integration with other resources already present on the web. Moreover, the architecture of the database and the web application is flexible and can be easily adapted to store data related to other proteins with point mutations. GALT-Prot is freely available at http://bioinformatica.isa.cnr.it/GALT/.

  12. 网络数据库用户界面的使用便利性研究%Study on User-friendly Interfaces of Web-based Databases

    Institute of Scientific and Technical Information of China (English)

    桂君; 郭依群

    2001-01-01

    Based on a comparative study of Cambridge Scientific Abstracts' Internet Database Service and OCLC's FirstSearch, this paper discusses the user-friendly interfaces of Web-based databases according to their characteristics such as database selection, search strategy formulation and reformulation, online help and result output.

  13. ALICE Geometry Database

    CERN Document Server

    Santo, J

    1999-01-01

    The ALICE Geometry Database project consists of the development of a set of data structures to store the geometrical information of the ALICE Detector. This Database will be used in Simulation, Reconstruction and Visualisation and will interface with existing CAD systems and Geometrical Modellers.At the present time, we are able to read a complete GEANT3 geometry, to store it in our database and to visualise it. On disk, we store different geometry files in hierarchical fashion, and all the nodes, materials, shapes, configurations and transformations distributed in this tree structure. The present status of the prototype and its future evolution will be presented.

  14. Psychiatry in the Harvard Medical School-Cambridge Integrated Clerkship: An Innovative, Year-Long Program

    Science.gov (United States)

    Griswold, Todd; Bullock, Christopher; Gaufberg, Elizabeth; Albanese, Mark; Bonilla, Pedro; Dvorak, Ramona; Epelbaum, Claudia; Givon, Lior; Kueppenbender, Karsten; Joseph, Robert; Boyd, J. Wesley; Shtasel, Derri

    2012-01-01

    Objective: The authors present what is to their knowledge the first description of a model for longitudinal third-year medical student psychiatry education. Method: A longitudinal, integrated psychiatric curriculum was developed, implemented, and sustained within the Harvard Medical School-Cambridge Integrated Clerkship. Curriculum elements…

  15. Final Report of Cambridge Conference on School Mathematics, January 1962 - August 1970.

    Science.gov (United States)

    Cambridge Conference on School Mathematics, Newton, MA.

    The Cambridge Conference on School Mathematics (CCSM) was an association of prominent mathematicians who had a concern for mathematics education at school level, from kindergarten through grade twelve. These mathematicians organized three main conferences in three areas of mathematics education, and have carried on activities related to the…

  16. Measuring impairments in memory and executive function in older people using the Revised Cambridge Cognitive Examination.

    NARCIS (Netherlands)

    Kessels, R.P.C.; Mimpen, G.; Melis, R.J.F.; Olde Rikkert, M.G.M.

    2009-01-01

    OBJECTIVES: The Revised Cambridge Cognitive Examination (CAMCOG-R) is a cognitive screen that has been used to discriminate individuals with dementia from cognitively intact older people. It consists of items assessing various cognitive domains, but the construct validity of the cognitive subscores

  17. Measuring Impairments in Memory and Executive Function in Older People Using the Revised Cambridge Cognitive Examination

    NARCIS (Netherlands)

    Kessels, R.P.C.; Mimpen, G.; Melis, R.J.F.; Olde Rikkert, M.G.M.

    2009-01-01

    Objectives: The Revised Cambridge Cognitive Examination (CAMCOG-R) is a cognitive screen that has been used to discriminate individuals with dementia from cognitively intact older people. It consists of items assessing various cognitive domains, but the construct validity of the cognitive subscores

  18. Ideology, Class and Rationality: A Critique of Cambridge International Examinations' "Thinking Skills" Curriculum

    Science.gov (United States)

    Lim, Leonel

    2012-01-01

    This article undertakes a critique of the aims and objectives of "Thinking Skills", one of the most widely and internationally used curricula in the teaching of thinking, offered by the University of Cambridge International Examinations. By engaging in a critical discourse analysis of how political and class biases are (re-)produced in the forms…

  19. Legacies, Policies and Prospects: One Year on from the Cambridge Primary Review

    Science.gov (United States)

    Alexander, Robin

    2011-01-01

    This article features the "Cambridge Primary Review." The "Review" has been supported from the beginning by Esmee Fairbairn Foundation, and this has given it the independence which is essential to its credibility. Its remit was to investigate, report and make recommendations on the condition and future of primary education in England. Its scope…

  20. The Singapore-Cambridge General Certificate of Education Advanced-Level General Paper Examination

    Science.gov (United States)

    Hassan, Nurul Huda; Shih, Chih-Min

    2013-01-01

    This article describes and reviews the Singapore-Cambridge General Certificate of Education Advanced Level General Paper (GP) examination. As a written test that is administered to preuniversity students, the GP examination is internationally recognised and accepted by universities and employers as proof of English competence. In this article, the…

  1. Linguistic Turn and Gendering Language in the Cambridge Advanced Learner's Dictionary

    Science.gov (United States)

    Arimbi, Diah A.; Kwary, Deny A.

    2016-01-01

    Language constructs how humans perceive things. Since language is a human construction, it tends to be biased as it is mainly men's construction. Using gender perspectives, this paper attempts to discuss the imbalance in gender representations found in the examples given in an English learner's dictionary, that is, the "Cambridge Advanced…

  2. Up the Garden Path: A Chemical Trail through the Cambridge University Botanic Garden

    Science.gov (United States)

    Battle, Gary M.; Kyd, Gwenda O.; Groom, Colin R.; Allen, Frank H.; Day, Juliet; Upson, Timothy

    2012-01-01

    The living world is a rich source of chemicals with many medicines, dyes, flavorings, and foodstuffs having their origins in compounds produced by plants. We describe a chemical trail through the plant holdings of the Cambridge University Botanic Gardens. Visitors to the gardens are provided with a laminated trail guide with 22 stopping points…

  3. The Target of the Question: A Taxonomy of Textual Features for Cambridge University "O" Levels English

    Science.gov (United States)

    Benjamin, Shanti Isabelle

    2015-01-01

    This study investigates the typical textual features that are most frequently targeted in short-answer reading comprehension questions of the Cambridge University "O" Level English Paper 2. Test writers' awareness of how textual features impact on understanding of meanings in text decisions will determine to great extent their decisions…

  4. Curriculum, Pedagogy, and the Cambridge Primary Review: A Response to R. J. Campbell

    Science.gov (United States)

    Armstrong, Michael

    2011-01-01

    This article presents the author's response to R.J. Campbell's critique of the "Cambridge Primary Review," which was published in the autumn of 2009. The author argues that Campbell's description of the "Review's" central proposals on curriculum and pedagogy as "backward-looking and inadequately theorised" is so misjudged as to call for a…

  5. What To Look for in ESL Admission Tests: Cambridge Certificate Exams, IELTS, and TOEFL.

    Science.gov (United States)

    Chalhoub-Deville, Micheline; Turner, Carolyn E.

    2000-01-01

    Familiarizes test users with issues to consider when employing assessments for screening and admission purposes. Examines the purpose, content, and scoring methods of three English-as-a-Second-Language admissions tests--the Cambridge certificate exams, International English Language Teaching System, and Test of English as a Foreign…

  6. Structural investigation of the β-cyclodextrin complexes with linalool and isopinocampheol - Influence of monoterpenes cyclicity on the host-guest stoichiometry

    Science.gov (United States)

    Ceborska, Magdalena

    2016-05-01

    The crystal structures of the complexes of β-cyclodextrin with two chiral terpene alcohols are presented. (-)-Linalool forms the complex of a 2:2 host-guest stoichiometry, while the complex with (-)-isopinocampheol exhibits a 2:3 stoichiometry. The comparison of the crystal structures with the data for other complexes of β-cyclodextrin with chiral monoterpene alcohols obtained from Cambridge Structural Database (CSD) highlights the tendency of linear and monocyclic alcohols to form complexes of 2:2 stoichiometry whereas bicyclic alcohols prefer to form 2:3 host-guest inclusion complexes.

  7. 多维空间索引结构SHG-Tree%SHG-Tree: An Efficient Index Structure of Spatial Database

    Institute of Scientific and Technical Information of China (English)

    刘胤田; 刘应明; 徐开阔; 曾涛; 唐常杰

    2009-01-01

    To improve query efiqeieney of multidimensional spatial database, a new index structure named spatial hypercube grid tree (SHG-Tree) is proposed. By decreasing the occurrence of node split and recombination during insert/delete operations, and avoiding range comparison between query range and candidate entities during query operations, SHG-Tree based index method can efficiently support the common operations over spatial database containing objects with dynamic region. The main contributions include: (1) Proposes two type of SHG-Tree for n-dimensional space. The hierarchical structure of SHG-Tree reflects the region overlapping relationship of hypereube grid units with different granularity. (2) Proposes three linearization strategies to present the bounding rectangle of spatial object as a union of variant granularity hypereube grids. (3) Gives the realization of different spatial query operations based on SHG-Tree. (4) Demonstrates the efficiency of SHG-Tree by extensive experiments. Experiments result shows query operation can be limited into ten milliseconds to ensure the real-time of query.%R-Tree及其变种的多维索引结构在数据的操作过程中通过对空间的分隔和不断调整将整个空间划分为大小不等的子空间以容纳足够的空间对象,这种方法能有效地实现多维空间对象的索引,但不能避免频繁的节点分裂与重组操作所造成的计算开销,也不能避免对叶子节点中的候选对象进行空间匹配所带来的计算开销.提出了一种能有效解决上述问题的索引结构:SHG-Tree.基于SHG-Tree的索引方法将多维空间划分为不同粒度的格子单元并将这些格子单元通过SHG-Tree按空间包含关系组织为层次树结构,同一层的格子互不相交且空间范围固定.空间对象通过文中提出的线性化方法转换为一系列不同粒度的互不相交的空间格子,进而将对象在其覆盖的格子中注册以实现空间对象至SHG-Tree的映

  8. Database Manager

    Science.gov (United States)

    Martin, Andrew

    2010-01-01

    It is normal practice today for organizations to store large quantities of records of related information as computer-based files or databases. Purposeful information is retrieved by performing queries on the data sets. The purpose of DATABASE MANAGER is to communicate to students the method by which the computer performs these queries. This…

  9. An XCT image database system

    International Nuclear Information System (INIS)

    In this paper, an expansion of X-ray CT (XCT) examination history database to XCT image database is discussed. The XCT examination history database has been constructed and used for daily examination and investigation in our hospital. This database consists of alpha-numeric information (locations, diagnosis and so on) of more than 15,000 cases, and for some of them, we add tree structured image data which has a flexibility for various types of image data. This database system is written by MUMPS database manipulation language. (author)

  10. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

    Directory of Open Access Journals (Sweden)

    Wasik Szymon

    2010-05-01

    Full Text Available Abstract Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA

  11. Requirements for a new nuclear data structure. Part 2: Implementation Plan Prepared by WPEC Subgroup No.38 (subgroup title: 'A modern nuclear database structure beyond the ENDF format')

    International Nuclear Information System (INIS)

    This document summarizes the implementation plan developed during the second meeting of the WPEC Subgroup 38 (SG38), which was organized to develop a new evaluated nuclear data structure 1 and then oversee the transition from the current standard (ENDF-6) to the new structure. Part 1 of this document, adopted by WPEC in May 2013, lays out the vision and goals for the new structure. In this second step, SG38 develops a community plan to address these needs and requirements. The plan laid out here represents a consensus on how to execute the project, what work will be done, and to some degree how it will be done and the people involved. During the development of the vision and goals for the new format it was recognized that the application of modern programming and database practices will have significant benefits for nuclear reaction databases, both for those of us engaged in producing this data and those who utilize the data for applications. It was also appreciated that additional benefits would be realized if the low-level data containers used for storing reaction data were general enough to be shared with other nuclear data products, such as EXFOR, RIPL, and ENSDF, so that codes interfacing with these different databases could share the same set of routines for reading and writing data structures. However, it was also acknowledged that adoption of these new tools and capabilities will be difficult without some supporting infrastructure in place to use the new data structure, specifically open source codes to manipulate, search, plot, and process the data, as well as tools to translate data to other formats in current use and to check the data for quality. In order to address this broad set of goals, the SG38 project decided to organize the work around seven different products: 1. Low-level data structures; 2. Top-level reaction hierarchy; 3. Particle properties hierarchy; 4. Visualization, manipulation, and processing tools; 5. API for reading and writing data

  12. Assessment of the structural and functional impact of in-frame mutations of the DMD gene, using the tools included in the eDystrophin online database

    Directory of Open Access Journals (Sweden)

    Nicolas Aurélie

    2012-07-01

    Full Text Available Abstract Background Dystrophin is a large essential protein of skeletal and heart muscle. It is a filamentous scaffolding protein with numerous binding domains. Mutations in the DMD gene, which encodes dystrophin, mostly result in the deletion of one or several exons and cause Duchenne (DMD and Becker (BMD muscular dystrophies. The most common DMD mutations are frameshift mutations resulting in an absence of dystrophin from tissues. In-frame DMD mutations are less frequent and result in a protein with partial wild-type dystrophin function. The aim of this study was to highlight structural and functional modifications of dystrophin caused by in-frame mutations. Methods and results We developed a dedicated database for dystrophin, the eDystrophin database. It contains 209 different non frame-shifting mutations found in 945 patients from a French cohort and previous studies. Bioinformatics tools provide models of the three-dimensional structure of the protein at deletion sites, making it possible to determine whether the mutated protein retains the typical filamentous structure of dystrophin. An analysis of the structure of mutated dystrophin molecules showed that hybrid repeats were reconstituted at the deletion site in some cases. These hybrid repeats harbored the typical triple coiled-coil structure of native repeats, which may be correlated with better function in muscle cells. Conclusion This new database focuses on the dystrophin protein and its modification due to in-frame deletions in BMD patients. The observation of hybrid repeat reconstitution in some cases provides insight into phenotype-genotype correlations in dystrophin diseases and possible strategies for gene therapy. The eDystrophin database is freely available: http://edystrophin.genouest.org/.

  13. A New On-Land Seismogenic Structure Source Database from the Taiwan Earthquake Model (TEM Project for Seismic Hazard Analysis of Taiwan

    Directory of Open Access Journals (Sweden)

    J. Bruce H. Shyu

    2016-09-01

    Full Text Available Taiwan is located at an active plate boundary and prone to earthquake hazards. To evaluate the island’s seismic risk, the Taiwan Earthquake Model (TEM project, supported by the Ministry of Sciences and Technology, evaluates earthquake hazard, risk, and related social and economic impact models for Taiwan through multidisciplinary collaboration. One of the major tasks of TEM is to construct a complete and updated seismogenic structure database for Taiwan to assess future seismic hazards. Toward this end, we have combined information from pre-existing databases and data obtained from new analyses to build an updated and digitized three-dimensional seismogenic structure map for Taiwan. Thirty-eight on-land active seismogenic structures are identified. For detailed information of individual structures such as their long-term slip rates and potential recurrence intervals, we collected data from existing publications, as well as calculated from results of our own field surveys and investigations. We hope this updated database would become a significant constraint for seismic hazard assessment calculations in Taiwan, and would provide important information for engineers and hazard mitigation agencies.

  14. Database Replication

    CERN Document Server

    Kemme, Bettina

    2010-01-01

    Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

  15. Probabilistic Databases

    CERN Document Server

    Suciu, Dan; Koch, Christop

    2011-01-01

    Probabilistic databases are databases where the value of some attributes or the presence of some records are uncertain and known only with some probability. Applications in many areas such as information extraction, RFID and scientific data management, data cleaning, data integration, and financial risk assessment produce large volumes of uncertain data, which are best modeled and processed by a probabilistic database. This book presents the state of the art in representation formalisms and query processing techniques for probabilistic data. It starts by discussing the basic principles for rep

  16. Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.

    Science.gov (United States)

    Klosterman, Peter S; Hendrix, Donna K; Tamura, Makio; Holbrook, Stephen R; Brenner, Steven E

    2004-01-01

    Release 2.0.1 of the Structural Classification of RNA (SCOR) database, http://scor.lbl.gov, contains a classification of the internal and hairpin loops in a comprehensive collection of 497 NMR and X-ray RNA structures. This report discusses findings of the classification that have not been reported previously. The SCOR database contains multiple examples of a newly described RNA motif, the extruded helical single strand. Internal loop base triples are classified in SCOR according to their three-dimensional context. These internal loop triples contain several examples of a frequently found motif, the minor groove AGC triple. SCOR also presents the predominant and alternate conformations of hairpin loops, as shown in the most well represented tetraloops, with consensus sequences GNRA, UNCG and ANYA. The ubiquity of the GNRA hairpin turn motif is illustrated by its presence in complex internal loops.

  17. Dealer Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The dealer reporting databases contain the primary data reported by federally permitted seafood dealers in the northeast. Electronic reporting was implemented May...

  18. RDD Databases

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database was established to oversee documents issued in support of fishery research activities including experimental fishing permits (EFP), letters of...

  19. Fashion Information Database

    Institute of Scientific and Technical Information of China (English)

    LI Jun; WU Hai-yan; WANG Yun-yi

    2002-01-01

    In the field of fashion industry, it is a bottleneck of how to control and apply the information in the procedure of fashion merchandising. By the aid of digital technology,a perfect and practical fashion information database could be established so that high- quality and efficient,low-cost and characteristic fashion merchandising system could be realized. The basic structure of fashion information database is discussed.

  20. National database

    DEFF Research Database (Denmark)

    Kristensen, Helen Grundtvig; Stjernø, Henrik

    1995-01-01

    Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen.......Artikel om national database for sygeplejeforskning oprettet på Dansk Institut for Sundheds- og Sygeplejeforskning. Det er målet med databasen at samle viden om forsknings- og udviklingsaktiviteter inden for sygeplejen....

  1. Masters of Theory Cambridge and the Rise of Mathematical Physics

    CERN Document Server

    Warwick, Andrew

    2011-01-01

    Winner of the the Susan Elizabeth Abrams Prize in History of Science.When Isaac Newton published the Principia three centuries ago, only a few scholars were capable of understanding his conceptually demanding work. Yet this esoteric knowledge quickly became accessible in the nineteenth and early twentieth centuries when Britain produced many leading mathematical physicists. In this book, Andrew Warwick shows how the education of these "masters of theory" led them to transform our understanding of everything from the flight of a boomerang to the structure of the universe. Warwick focuses on Cam

  2. The Plant Ontology Database: A Community Resource for Plant Structure and Developmental Stages Controlled Vocabulary and Annotations

    Science.gov (United States)

    The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a controlled vocabulary(ontology) for plants. The ontology allows users to ascribe attributes o...

  3. The Cambridge Car Memory Test: a task matched in format to the Cambridge Face Memory Test, with norms, reliability, sex differences, dissociations from face memory, and expertise effects.

    Science.gov (United States)

    Dennett, Hugh W; McKone, Elinor; Tavashmi, Raka; Hall, Ashleigh; Pidcock, Madeleine; Edwards, Mark; Duchaine, Bradley

    2012-06-01

    Many research questions require a within-class object recognition task matched for general cognitive requirements with a face recognition task. If the object task also has high internal reliability, it can improve accuracy and power in group analyses (e.g., mean inversion effects for faces vs. objects), individual-difference studies (e.g., correlations between certain perceptual abilities and face/object recognition), and case studies in neuropsychology (e.g., whether a prosopagnosic shows a face-specific or object-general deficit). Here, we present such a task. Our Cambridge Car Memory Test (CCMT) was matched in format to the established Cambridge Face Memory Test, requiring recognition of exemplars across view and lighting change. We tested 153 young adults (93 female). Results showed high reliability (Cronbach's alpha = .84) and a range of scores suitable both for normal-range individual-difference studies and, potentially, for diagnosis of impairment. The mean for males was much higher than the mean for females. We demonstrate independence between face memory and car memory (dissociation based on sex, plus a modest correlation between the two), including where participants have high relative expertise with cars. We also show that expertise with real car makes and models of the era used in the test significantly predicts CCMT performance. Surprisingly, however, regression analyses imply that there is an effect of sex per se on the CCMT that is not attributable to a stereotypical male advantage in car expertise.

  4. VizieR Online Data Catalog: Fourth Cambridge Survey (4C) (Pilkington+ 1965; Gower+ 1967)

    Science.gov (United States)

    Pilkington, J. D. H.; Scott, P. F.

    1996-04-01

    The Fourth Cambridge Radio Survey (4C) Catalogue contains all survey data from the papers of Pilkington and Scott (1965MmRAS..69..183P) and Gower, Scott and Wills (1967MmRAS..71...49G). These data result from a survey of radio sources between declinations -07 and +80 degrees using the large Cambridge interferometer at 178 MHz. The computerized catalog contains for each source the 4C number, 1950 position, measured flux density, accuracy class, galactic coordinates, and remarks. For some sources miscellaneous brief comments such as cross identifications to the 3C catalog or remarks on contamination from nearby sources are given at the ends of the data records. A flag (*) is included if there are additional remarks in the published catalog. (1 data file).

  5. Hazard Analysis Database Report

    Energy Technology Data Exchange (ETDEWEB)

    GRAMS, W.H.

    2000-12-28

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

  6. Nutrition in medical education: reflections from an initiative at the University of Cambridge

    OpenAIRE

    Ball L; Crowley J; Laur C; Rajput-Ray M; Gillam S; Ray S

    2014-01-01

    Lauren Ball,1 Jennifer Crowley,2 Celia Laur,3 Minha Rajput-Ray,3 Stephen Gillam,4 Sumantra Ray3 1Nutrition and Dietetics, School of Allied Health Sciences, Centre for Health Practice Innovation, Griffith University, Queensland, Brisbane, Australia; 2Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand; 3Need for Nutrition Education/Innovation Programme, Medical Research Council Human Nutrition Research, Cambridge, UK; 4Department of Public Health and Primary C...

  7. Item Response Theory Analyses of the Cambridge Face Memory Test (CFMT)

    OpenAIRE

    Cho, Sun-Joo; Wilmer, Jeremy; Herzmann, Grit; McGugin, Rankin; Fiset, Daniel; Van Gulick, Ana E.; Ryan, Katie; Gauthier, Isabel

    2015-01-01

    We evaluated the psychometric properties of the Cambridge face memory test (CFMT; Duchaine & Nakayama, 2006). First, we assessed the dimensionality of the test with a bi-factor exploratory factor analysis (EFA). This EFA analysis revealed a general factor and three specific factors clustered by targets of CFMT. However, the three specific factors appeared to be minor factors that can be ignored. Second, we fit a unidimensional item response model. This item response model showed that the CFMT...

  8. Hindi translation and validation of Cambridge-Hopkins Diagnostic Questionnaire for RLS (CHRLSq)

    OpenAIRE

    Ravi Gupta; Richard P Allan; Ashwini Pundeer; Sourav Das; Mohan Dhyani; Deepak Goel

    2015-01-01

    Background: Restless legs syndrome also known as Willis-Ekbom′s Disease (RLS/WED) is a common illness. Cambridge-Hopkins diagnostic questionnaire for RLS (CHRLSq) is a good diagnostic tool and can be used in the epidemiological studies. However, its Hindi version is not available. Thus, this study was conducted to translate and validate it in the Hindi speaking population. Materials and Methods: After obtaining the permission from the author of the CHRLSq, it was translated into Hindi languag...

  9. PET/MRI in the infarcted mouse heart with the Cambridge split magnet

    Energy Technology Data Exchange (ETDEWEB)

    Buonincontri, Guido, E-mail: gb396@cam.ac.uk [Wolfson Brain Imaging Centre, University of Cambridge, Box 65, Addenbrooke' s Hospital, Hills Road, Cambridge, CB2 0QQ (United Kingdom); Sawiak, Stephen J. [Wolfson Brain Imaging Centre, University of Cambridge, Box 65, Addenbrooke' s Hospital, Hills Road, Cambridge, CB2 0QQ (United Kingdom); Behavioural and Clinical Neuroscience Institute, University of Cambridge, Cambridge (United Kingdom); Methner, Carmen; Krieg, Thomas [Department of Medicine, University of Cambridge, Cambridge (United Kingdom); Hawkes, Robert C.; Adrian Carpenter, T. [Wolfson Brain Imaging Centre, University of Cambridge, Box 65, Addenbrooke' s Hospital, Hills Road, Cambridge, CB2 0QQ (United Kingdom)

    2013-02-21

    Chronic heart failure, as a result of acute myocardial infarction, is a leading cause of death worldwide. Combining diagnostic imaging modalities may aid the direct assessment of experimental treatments targeting heart failure in vivo. Here we present preliminary data using the Cambridge combined PET/MRI imaging system in a mouse model of acute myocardial infarction. The split-magnet design can deliver uncompromised MRI and PET performance, for better assessment of disease and treatment in a preclinical environment.

  10. The art and science of consultations in bovine medicine: Use of modified Calgary - Cambridge guides

    OpenAIRE

    Petrovski, Kiro R.; Michelle Mc Arthur

    2015-01-01

    This article describes few steps of the application of the modified Calgary-Cambridge Guides (CCG) to consultations in bovine medicine. A review of pertinent clinical communication skills literature in human medicine was integrated with the burgeoning research within veterinary medicine. In particular, there are more recent studies examining companion animal veterinarian’s communication skills and outcomes which can be extrapolated to practitioners. This was integrated into a teaching example...

  11. Nutrition in medical education: reflections from an initiative at the University of Cambridge.

    Science.gov (United States)

    Ball, Lauren; Crowley, Jennifer; Laur, Celia; Rajput-Ray, Minha; Gillam, Stephen; Ray, Sumantra

    2014-01-01

    Landmark reports have confirmed that it is within the core responsibilities of doctors to address nutrition in patient care. There are ongoing concerns that doctors receive insufficient nutrition education during medical training. This paper provides an overview of a medical nutrition education initiative at the University of Cambridge, School of Clinical Medicine, including 1) the approach to medical nutrition education, 2) evaluation of the medical nutrition education initiative, and 3) areas identified for future improvement. The initiative utilizes a vertical, spiral approach during the clinically focused years of the Cambridge undergraduate and graduate medical degrees. It is facilitated by the Nutrition Education Review Group, a group associated with the UK Need for Nutrition Education/Innovation Programme, and informed by the experiences of their previous nutrition education interventions. Three factors were identified as contributing to the success of the nutrition education initiative including the leadership and advocacy skills of the nutrition academic team, the variety of teaching modes, and the multidisciplinary approach to teaching. Opportunities for continuing improvement to the medical nutrition education initiative included a review of evaluation tools, inclusion of nutrition in assessment items, and further alignment of the Cambridge curriculum with the recommended UK medical nutrition education curriculum. This paper is intended to inform other institutions in ongoing efforts in medical nutrition education.

  12. Databases as an information service

    Science.gov (United States)

    Vincent, D. A.

    1983-01-01

    The relationship of databases to information services, and the range of information services users and their needs for information is explored and discussed. It is argued that for database information to be valuable to a broad range of users, it is essential that access methods be provided that are relatively unstructured and natural to information services users who are interested in the information contained in databases, but who are not willing to learn and use traditional structured query languages. Unless this ease of use of databases is considered in the design and application process, the potential benefits from using database systems may not be realized.

  13. Adaptation of the Cambridge Pulmonary Hypertension Outcome Review (CAMPHOR into French-Canadian and English-Canadian

    Directory of Open Access Journals (Sweden)

    Donna Coffin

    2008-01-01

    Full Text Available BACKGROUND: The Cambridge Pulmonary Hypertension Outcome Review (CAMPHOR is the first disease-specific instrument for assessing patient-reported symptoms, functioning and quality of life (QoL in pulmonary arterial hypertension (PAH.

  14. Biological Databases

    Directory of Open Access Journals (Sweden)

    Kaviena Baskaran

    2013-12-01

    Full Text Available Biology has entered a new era in distributing information based on database and this collection of database become primary in publishing information. This data publishing is done through Internet Gopher where information resources easy and affordable offered by powerful research tools. The more important thing now is the development of high quality and professionally operated electronic data publishing sites. To enhance the service and appropriate editorial and policies for electronic data publishing has been established and editors of article shoulder the responsibility.

  15. Test pit excavation within currently occupied rural settlements: results of the University of Cambridge CORS project in 2011

    OpenAIRE

    Lewis, Carenza

    2012-01-01

    2011 saw the seventh year of test pit excavation within currently occupied rural settlements (CORS) in East Anglia carried out under the supervision of Access Cambridge Archaeology (ACA) directed by Dr Carenza Lewis at the University of Cambridge. As in previous years, this archaeological activity combines education and university outreach (particularly within the secondary school sector) with the archaeological investigation of currently occupied rural settlements (CO...

  16. IAEA Coordinated Research Project on the Establishment of a Material Properties Database for Irradiated Core Structural Components for Continued Safe Operation and Lifetime Extension of Ageing Research Reactors

    International Nuclear Information System (INIS)

    Today more than 50% of operating Research Reactors (RRs) are over 45 years old. Thus, ageing management is one of the most important issues to face in order to ensure availability (including life extension), reliability and safe operation of these facilities for the future. Management of the ageing process requires, amongst others, the predictions for the behavior of structural materials of primary components subjected to irradiation such as reactor vessel and core support structures, many of which are extremely difficult or impossible to replace. In fact, age-related material degradation mechanisms resulted in high profile, unplanned and lengthy shutdowns and unique regulatory processes of relicensing the facilities in recent years. These could likely have been prevented by utilizing available data for the implementation of appropriate maintenance and surveillance programmes. This IAEA Coordinated Research Project (CRP) will provide an international forum to establish a material properties Database for irradiated core structural materials and components. It is expected that this Database will be used by research reactor operators and regulators to help predict ageing related degradation. This would be useful to minimize unpredicted outages due to ageing processes of primary components and to mitigate lengthy and costly shutdowns. The Database will be a compilation of data from RRs operators' inputs, comprehensive literature reviews and experimental data from RRs. Moreover, the CRP will specify further activities needed to be addressed in order to bridge the gaps in the new created Database, for potential follow-on activities. As per today, 13 Member States (MS) confirmed their agreement to contribute to the development of the Database, covering a wide number of materials and properties. The present publication incorporates two parts: the first part includes details on the pre-CRP Questionnaire, including the conclusions drawn from the answers received from the MS

  17. IPD: the Immuno Polymorphism Database.

    Science.gov (United States)

    Robinson, James; Marsh, Steven G E

    2007-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer cell immunoglobulin-like receptors (KIRs); IPD-MHC, a database of sequences of the major histocompatibility complex (MHC) of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC, share the same database structure. PMID:18449992

  18. 结构化查询语言在实时数据库中的应用%Application of Structured Query Language in Real-time Database

    Institute of Scientific and Technical Information of China (English)

    佟志飞

    2013-01-01

    Structured Query Language is a database query and programming language. It can be descriptive and its flexibility and strong function have made it to be the current database for batching processing of common language and inquires. Today, the data capacity of industrial control industry is increasing and thus the demand of data query quality. owards the structured query language development becomes an inexorable trend for configuration software data inquiring. This paper takesof Daqing Zijin Bridge Software Technology CO., LTD as an example, discusses the applications of structured query language in real-time database and technical methods to adapt to the time series data query.%结构化查询语言是一种数据库查询和程序设计语言,它的可描述性、灵活性及强大的功能已使它成为当前数据批量查询及处理的通用语言。现今,在数据处理量日益增长的工控行业,对数据查询质量的要求也在不断的提高,向着结构化查询语言方向发展成了实时数据库数据查询的一种必然趋势。本文以紫金桥软件技术有限公司的《紫金桥实时数据库》软件为例,论述结构化查询语言在实时数据库中的应用以及为适应时间序列数据查询而提供的技术手段。

  19. DMPD: Structure, function and regulation of the Toll/IL-1 receptor adaptor proteins. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17667936 Structure, function and regulation of the Toll/IL-1 receptor adaptor prote... (.svg) (.html) (.csml) Show Structure, function and regulation of the Toll/IL-1 receptor adaptor proteins. ...PubmedID 17667936 Title Structure, function and regulation of the Toll/IL-1 recep

  20. Biological Databases for Behavioral Neurobiology

    OpenAIRE

    Baker, Erich J

    2012-01-01

    Databases are, at their core, abstractions of data and their intentionally derived relationships. They serve as a central organizing metaphor and repository, supporting or augmenting nearly all bioinformatics. Behavioral domains provide a unique stage for contemporary databases, as research in this area spans diverse data types, locations, and data relationships. This chapter provides foundational information on the diversity and prevalence of databases, how data structures support the variou...

  1. MammoGrid: a mammography database

    CERN Multimedia

    2002-01-01

    What would be the advantages if physicians around the world could gain access to a unique mammography database? The answer may come from MammoGrid, a three-year project under the Fifth Framework Programme of the EC. Led by CERN, MammoGrid involves the UK (the Universities of Oxford, Cambridge and the West of England, Bristol, plus the company Mirada Solutions of Oxford), and Italy (the Universities of Pisa and Sassari and the Hospitals in Udine and Torino). The aim of the project is, in light of emerging GRID technology, to develop a Europe-wide database of mammograms. The database will be used to investigate a set of important healthcare applications as well as the potential of the GRID to enable healthcare professionals throughout the EU to work together effectively. The contributions of the partners include building the GRID-database infrastructure, developing image processing and Computer Aided Detection techniques, and making the clinical evaluation. The first project meeting took place at CERN in Sept...

  2. The CATH database

    Directory of Open Access Journals (Sweden)

    Knudsen Michael

    2010-02-01

    Full Text Available Abstract The CATH database provides hierarchical classification of protein domains based on their folding patterns. Domains are obtained from protein structures deposited in the Protein Data Bank and both domain identification and subsequent classification use manual as well as automated procedures. The accompanying website http://www.cathdb.info provides an easy-to-use entry to the classification, allowing for both browsing and downloading of data. Here, we give a brief review of the database, its corresponding website and some related tools.

  3. Applicability of the Calgary-Cambridge Guide to Dog and Cat Owners for Teaching Veterinary Clinical Communications.

    Science.gov (United States)

    Englar, Ryane E; Williams, Melanie; Weingand, Kurt

    2016-01-01

    Effective communication in health care benefits patients. Medical and veterinary schools not only have a responsibility to teach communication skills, the American Veterinary Medical Association (AVMA) Council on Education (COE) requires that communication be taught in all accredited colleges of veterinary medicine. However, the best strategy for designing a communications curriculum is unclear. The Calgary-Cambridge Guide (CCG) is one of many models developed in human medicine as an evidence-based approach to structuring the clinical consultation through 71 communication skills. The model has been revised by Radford et al. (2006) for use in veterinary curricula; however, the best approach for veterinary educators to teach communication remains to be determined. This qualitative study investigated if one adaptation of the CCG currently taught at Midwestern University College of Veterinary Medicine (MWU CVM) fulfills client expectations of what constitutes clinically effective communication. Two focus groups (cat owners and dog owners) were conducted with a total of 13 participants to identify common themes in veterinary communication. Participants compared communication skills they valued to those taught by MWU CVM. The results indicated that while the CCG skills that MWU CVM adopted are applicable to cat and dog owners, they are not comprehensive. Participants expressed the need to expand the skillset to include compassionate transparency and unconditional positive regard. Participants also expressed different communication needs that were attributed to the species of companion animal owned.

  4. Brief history of the Cambridge STEM aberration correction project and its progeny.

    Science.gov (United States)

    Brown, L Michael; Batson, Philip E; Dellby, Niklas; Krivanek, Ondrej L

    2015-10-01

    We provide a brief history of the project to correct the spherical aberration of the scanning transmission electron microscope (STEM) that started in Cambridge (UK) and continued in Kirkland (WA, USA), Yorktown Heights (NY, USA), and other places. We describe the project in the full context of other aberration correction research and related work, partly in response to the incomplete context presented in the paper "In quest of perfection in electron optics: A biographical sketch of Harald Rose on the occasion of his 80th birthday", recently published in Ultramicroscopy.

  5. Database Application Schema Forensics

    Directory of Open Access Journals (Sweden)

    Hector Quintus Beyers

    2014-12-01

    Full Text Available The application schema layer of a Database Management System (DBMS can be modified to deliver results that may warrant a forensic investigation. Table structures can be corrupted by changing the metadata of a database or operators of the database can be altered to deliver incorrect results when used in queries. This paper will discuss categories of possibilities that exist to alter the application schema with some practical examples. Two forensic environments are introduced where a forensic investigation can take place in. Arguments are provided why these environments are important. Methods are presented how these environments can be achieved for the application schema layer of a DBMS. A process is proposed on how forensic evidence should be extracted from the application schema layer of a DBMS. The application schema forensic evidence identification process can be applied to a wide range of forensic settings.

  6. Database Vs Data Warehouse

    Directory of Open Access Journals (Sweden)

    2007-01-01

    Full Text Available Data warehouse technology includes a set of concepts and methods that offer the users useful information for decision making. The necessity to build a data warehouse arises from the necessity to improve the quality of information in the organization. The date proceeding from different sources, having a variety of forms - both structured and unstructured, are filtered according to business rules and are integrated in a single large data collection. Using informatics solutions, managers have understood that data stored in operational systems - including databases, are an informational gold mine that must be exploited. Data warehouses have been developed to answer the increasing demands for complex analysis, which could not be properly achieved with operational databases. The present paper emphasizes some of the criteria that information application developers can use in order to choose between a database solution or a data warehouse one.

  7. A Study of Security Association Database Structure Oriented to IP Security%面向 IPSec 的关联数据库结构的研究

    Institute of Scientific and Technical Information of China (English)

    肖道举; 李馨; 陈晓苏

    2001-01-01

    在分析IP安全机制、网络密钥交换和安全关联的基础上,确定了基于IP安全机制的关联数据库所应包含的基本数据结构,并给出了在Linux环境下的结构说明及其中每个参数的具体含义和作用.%To implement internet key exchange(IKE) cooperating with IP security(IPSec), the date-structures is proposed which should be included in the security association database(SADB) using by IKE oriented to IPSec after analyzing the specific features of the IPSec. IKE & security association (SA), realization of the date-structures in LINUX is given. The functions of all parameters are illustrated. This is the base of the internet key exchange implementation.

  8. Technology Solutions Case Study: Boiler Control Replacement for Hydronically Heated Multifamily Buildings, Cambridge, Massachusetts

    Energy Technology Data Exchange (ETDEWEB)

    None

    2014-11-01

    The ARIES Collaborative, a U.S. Department of Energy Building America research team, partnered with NeighborWorks America affiliate Homeowners' Rehab Inc. (HRI) of Cambridge, Massachusetts, to study improvements to the central hydronic heating system in one of the nonprofit's housing developments. The heating controls in the three-building, 42-unit Columbia Cambridge Alliance for Spanish Tenants housing development were upgraded. Fuel use in the development was excessive compared to similar properties. A poorly insulated thermal envelope contributed to high energy bills, but adding wall insulation was not cost-effective or practical. The more cost-effective option was improving heating system efficiency, which faced several obstacles, including inflexible boiler controls and failed thermostatic radiator valves. Boiler controls were replaced with systems that offer temperature setbacks and one that controls heat based on apartment temperature in addition to outdoor temperature. Utility bill analysis shows that post-retrofit weather-normalized heating energy use was reduced by 10%-31% (average of 19%). Indoor temperature cutoff reduced boiler runtime (and therefore heating fuel consumption) by 28% in the one building in which it was implemented. Nearly all savings were obtained during night which had a lower indoor temperature cut off (68°F) than day (73° F). This implies that the outdoor reset curve was appropriately adjusted for this building for daytime operation. Nighttime setback of heating system supply water temperature had no discernable impact on boiler runtime or gas bills.

  9. Heliospheric tomography using interplanetary scintillation observations 1. Combined Nagoya and Cambridge data

    Science.gov (United States)

    Jackson, B. V.; Hick, P. L.; Kojima, M.; Yokobe, A.

    1998-06-01

    We have produced a computer assisted tomography program that optimizes a three-dimensional model to fit observational data. We have used this program with interplanetary scintillation data from Nagoya, Japan, and Cambridge, England. The program iterates to a least squares solution fit of observed data using solar rotation and solar wind motion to provide perspective views of each point in space accessible to the observations. We plot the optimized model as Carrington maps in velocity V and density Ne for the two data sets with resolutions of 10° in heliographic longitude and latitude. We map the model to 1 AU and compare this to in situ observations from the IMP spacecraft. From this comparison we find ΔNe~Ne0.3. We plot Carrington maps extrapolated to the solar surface to compare with Yohkoh Soft X ray Telescope (SXT), Sacramento Peak green line, and Mark III K-coronameter observations. High velocities modeled at the solar surface for individual rotations trace coronal holes (including polar ones) observed in SXT data. Regions of high density modeled from the Cambridge scintillation level data generally show a high correlation with regions of high solar activity observed as bright in Yohkoh SXT and green line observations. There is also a general correspondence of the regions of high density and the areas which are bright in K-coronameter observations.

  10. The factors influencing car use in a cycle-friendly city: the case of Cambridge.

    Science.gov (United States)

    Carse, Andrew; Goodman, Anna; Mackett, Roger L; Panter, Jenna; Ogilvie, David

    2013-04-01

    Encouraging people out of their cars and into other modes of transport, which has major advantages for health, the environment and urban development, has proved difficult. Greater understanding of the influences that lead people to use the car, particularly for shorter journeys, may help to achieve this. This paper examines the predictors of car use compared with the bicycle to explore how it may be possible to persuade more people to use the bicycle instead of the car. Multivariable logistic regression was used to examine the socio-demographic, transport and health-related correlates of mode choice for work, shopping and leisure trips in Cambridge, a city with high levels of cycling by UK standards. The key findings are that commuting distance and free workplace parking were strongly associated with use of the car for work trips, and car availability and lower levels of education were associated with car use for leisure, shopping and short-distanced commuting trips. The case of Cambridge shows that more policies could be adopted, particularly a reduction in free car parking, to increase cycling and reduce the use of the car, especially over short distances.

  11. PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features.

    Science.gov (United States)

    Gandhimathi, Arumugam; Ghosh, Pritha; Hariharaputran, Sridhar; Mathew, Oommen K; Sowdhamini, R

    2016-01-01

    Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at http://caps.ncbs.res.in/pass2/. PMID:26553811

  12. Segmentation of anatomical structures in chest radiographs using supervised methods: a comparative study on a public database.

    Science.gov (United States)

    van Ginneken, Bram; Stegmann, Mikkel B; Loog, Marco

    2006-02-01

    The task of segmenting the lung fields, the heart, and the clavicles in standard posterior-anterior chest radiographs is considered. Three supervised segmentation methods are compared: active shape models, active appearance models and a multi-resolution pixel classification method that employs a multi-scale filter bank of Gaussian derivatives and a k-nearest-neighbors classifier. The methods have been tested on a publicly available database of 247 chest radiographs, in which all objects have been manually segmented by two human observers. A parameter optimization for active shape models is presented, and it is shown that this optimization improves performance significantly. It is demonstrated that the standard active appearance model scheme performs poorly, but large improvements can be obtained by including areas outside the objects into the model. For lung field segmentation, all methods perform well, with pixel classification giving the best results: a paired t-test showed no significant performance difference between pixel classification and an independent human observer. For heart segmentation, all methods perform comparably, but significantly worse than a human observer. Clavicle segmentation is a hard problem for all methods; best results are obtained with active shape models, but human performance is substantially better. In addition, several hybrid systems are investigated. For heart segmentation, where the separate systems perform comparably, significantly better performance can be obtained by combining the results with majority voting. As an application, the cardio-thoracic ratio is computed automatically from the segmentation results. Bland and Altman plots indicate that all methods perform well when compared to the gold standard, with confidence intervals from pixel classification and active appearance modeling very close to those of a human observer. All results, including the manual segmentations, have been made publicly available to facilitate

  13. Stackfile Database

    Science.gov (United States)

    deVarvalho, Robert; Desai, Shailen D.; Haines, Bruce J.; Kruizinga, Gerhard L.; Gilmer, Christopher

    2013-01-01

    This software provides storage retrieval and analysis functionality for managing satellite altimetry data. It improves the efficiency and analysis capabilities of existing database software with improved flexibility and documentation. It offers flexibility in the type of data that can be stored. There is efficient retrieval either across the spatial domain or the time domain. Built-in analysis tools are provided for frequently performed altimetry tasks. This software package is used for storing and manipulating satellite measurement data. It was developed with a focus on handling the requirements of repeat-track altimetry missions such as Topex and Jason. It was, however, designed to work with a wide variety of satellite measurement data [e.g., Gravity Recovery And Climate Experiment -- GRACE). The software consists of several command-line tools for importing, retrieving, and analyzing satellite measurement data.

  14. Moving Observer Support for Databases

    DEFF Research Database (Denmark)

    Bukauskas, Linas

    architecture to exchange data between database and visualization. Thus, the interaction of the visualizer and the database is kept to the minimum, which most often leads to superfluous data being passed from database to visualizer. This Ph.D. thesis presents a novel tight coupling of database and visualizer....... The thesis discusses the VR-tree, an extension of the R-tree that enables observer relative data extraction. To support incremental observer position relative data extraction the thesis proposes the Volatile Access Structure (VAST). VAST is a main memory structure that caches nodes of the VR-tree. VAST...... and visualization systems. The thesis describes other techniques that extend the functionality of an observer aware database to support the extraction of the N most visible objects. This functionality is particularly useful if the number of newly visible objects is still too large. The thesis investigates how...

  15. Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis.

    Science.gov (United States)

    Blohm, Philipp; Frishman, Goar; Smialowski, Pawel; Goebels, Florian; Wachinger, Benedikt; Ruepp, Andreas; Frishman, Dmitrij

    2014-01-01

    Knowledge about non-interacting proteins (NIPs) is important for training the algorithms to predict protein-protein interactions (PPIs) and for assessing the false positive rates of PPI detection efforts. We present the second version of Negatome, a database of proteins and protein domains that are unlikely to engage in physical interactions (available online at http://mips.helmholtz-muenchen.de/proj/ppi/negatome). Negatome is derived by manual curation of literature and by analyzing three-dimensional structures of protein complexes. The main methodological innovation in Negatome 2.0 is the utilization of an advanced text mining procedure to guide the manual annotation process. Potential non-interactions were identified by a modified version of Excerbt, a text mining tool based on semantic sentence analysis. Manual verification shows that nearly a half of the text mining results with the highest confidence values correspond to NIP pairs. Compared to the first version the contents of the database have grown by over 300%.

  16. Relationship Between Structural Alerts in NSAIDs and Idiosyncratic Hepatotoxicity : An Analysis of Spontaneous Report Data from the WHO Database

    NARCIS (Netherlands)

    Jessurun, Naomi; van Puijenbroek, Eugene

    2015-01-01

    BACKGROUND: Idiosyncratic drug reactions such as hepatotoxicity and blood dyscrasias represent one of the major causes of drug withdrawal from the market. According to the reactive metabolite (RM) concept, this may be due to the metabolic activation of structural alerts (SAs), functionalities in the

  17. Identification of Five Structurally Unrelated Quorum-Sensing Inhibitors of Pseudomonas aeruginosa from a Natural-Derivative Database

    DEFF Research Database (Denmark)

    Tan, Sean Yang-Yi; Chua, Song-Lin; Chen, Yicai;

    2013-01-01

    (QSIs), have been shown to effectively block QS and subsequently attenuate the virulence of Pseudomonas aeruginosa, as well as increasing its susceptibility to both antibiotics and the immune system. In this study, a structure-based virtual screening (SB-VS) approach was used for the discovery of novel...

  18. Analysis of Wave Reflection from Structures with Berms Through an Extensive Database and 2DV Numerical Modelling

    DEFF Research Database (Denmark)

    Zanuttigh, Barbara; van der Meer, Jentsje W.; Andersen, Thomas Lykke;

    2009-01-01

    This paper analyses wave reflection from permeable structures with a berm, including reshaping cases. Data are obtained from recent wave flume experiments and from 2DV numerical simulations performed with the COBRAS-UC code. The objectives of this research were to identify the proper representati...

  19. Index Structure Supporting Cache Optimization in Main Memory Database%支持MMDB缓存优化的索引结构研究

    Institute of Scientific and Technical Information of China (English)

    张少娴

    2012-01-01

    Aiming at the cache mismatch problem of index in main memory database, a MCTH-tree index structure is proposes based on cache optimization. It gives attention to the effects of cache misses and TLB misses. According to index structure analysis, it is concluded that MCTH-tree supports cache optimization. Detailed description on data structure and operation algorithm are given. A series of experiments show that MCTH-tree is verified to have better effectiveness and superiority compared with the relevant index structure.%针对目前内存数据库中索引缓存失配的问题,提出一种基于缓存优化的MCTH树索引结构.它不仅考虑到缓存失配对系统性能的影响,同时也考虑到TLB失配的因素,对MCTH树索引结构的分析和实验测试表明:MCTH树索引结构与相关索引结构相比具有更好的有效性和优越性.

  20. Dealing with an information overload of health science data: structured utilisation of libraries, distributed knowledge in databases and Web content.

    Science.gov (United States)

    Hoelzer, Simon; Schweiger, Ralf K; Rieger, Joerg; Meyer, Michael

    2006-01-01

    The organizational structures of web contents and electronic information resources must adapt to the demands of a growing volume of information and user requirements. Otherwise the information society will be threatened by disinformation. The biomedical sciences are especially vulnerable in this regard, since they are strongly oriented toward text-based knowledge sources. Here sustainable improvement can only be achieved by using a comprehensive, integrated approach that not only includes data management but also specifically incorporates the editorial processes, including structuring information sources and publication. The technical resources needed to effectively master these tasks are already available in the form of the data standards and tools of the Semantic Web. They include Rich Site Summaries (RSS), which have become an established means of distributing and syndicating conventional news messages and blogs. They can also provide access to the contents of the previously mentioned information sources, which are conventionally classified as 'deep web' content.

  1. Dealing with an information overload of health science data: structured utilisation of libraries, distributed knowledge in databases and Web content.

    Science.gov (United States)

    Hoelzer, Simon; Schweiger, Ralf K; Rieger, Joerg; Meyer, Michael

    2006-01-01

    The organizational structures of web contents and electronic information resources must adapt to the demands of a growing volume of information and user requirements. Otherwise the information society will be threatened by disinformation. The biomedical sciences are especially vulnerable in this regard, since they are strongly oriented toward text-based knowledge sources. Here sustainable improvement can only be achieved by using a comprehensive, integrated approach that not only includes data management but also specifically incorporates the editorial processes, including structuring information sources and publication. The technical resources needed to effectively master these tasks are already available in the form of the data standards and tools of the Semantic Web. They include Rich Site Summaries (RSS), which have become an established means of distributing and syndicating conventional news messages and blogs. They can also provide access to the contents of the previously mentioned information sources, which are conventionally classified as 'deep web' content. PMID:17108575

  2. Improving decoy databases for protein folding algorithms

    KAUST Repository

    Lindsey, Aaron

    2014-01-01

    Copyright © 2014 ACM. Predicting protein structures and simulating protein folding are two of the most important problems in computational biology today. Simulation methods rely on a scoring function to distinguish the native structure (the most energetically stable) from non-native structures. Decoy databases are collections of non-native structures used to test and verify these functions. We present a method to evaluate and improve the quality of decoy databases by adding novel structures and removing redundant structures. We test our approach on 17 different decoy databases of varying size and type and show significant improvement across a variety of metrics. We also test our improved databases on a popular modern scoring function and show that they contain a greater number of native-like structures than the original databases, thereby producing a more rigorous database for testing scoring functions.

  3. Principal Component Analysis Coupled with Artificial Neural Networks—A Combined Technique Classifying Small Molecular Structures Using a Concatenated Spectral Database

    Directory of Open Access Journals (Sweden)

    Mihail Lucian Birsa

    2011-10-01

    Full Text Available In this paper we present several expert systems that predict the class identity of the modeled compounds, based on a preprocessed spectral database. The expert systems were built using Artificial Neural Networks (ANN and are designed to predict if an unknown compound has the toxicological activity of amphetamines (stimulant and hallucinogen, or whether it is a nonamphetamine. In attempts to circumvent the laws controlling drugs of abuse, new chemical structures are very frequently introduced on the black market. They are obtained by slightly modifying the controlled molecular structures by adding or changing substituents at various positions on the banned molecules. As a result, no substance similar to those forming a prohibited class may be used nowadays, even if it has not been specifically listed. Therefore, reliable, fast and accessible systems capable of modeling and then identifying similarities at molecular level, are highly needed for epidemiological, clinical, and forensic purposes. In order to obtain the expert systems, we have preprocessed a concatenated spectral database, representing the GC-FTIR (gas chromatography-Fourier transform infrared spectrometry and GC-MS (gas chromatography-mass spectrometry spectra of 103 forensic compounds. The database was used as input for a Principal Component Analysis (PCA. The scores of the forensic compounds on the main principal components (PCs were then used as inputs for the ANN systems. We have built eight PC-ANN systems (principal component analysis coupled with artificial neural network with a different number of input variables: 15 PCs, 16 PCs, 17 PCs, 18 PCs, 19 PCs, 20 PCs, 21 PCs and 22 PCs. The best expert system was found to be the ANN network built with 18 PCs, which accounts for an explained variance of 77%. This expert system has the best sensitivity (a rate of classification C = 100% and a rate of true positives TP = 100%, as well as a good selectivity (a rate of true negatives TN

  4. Bericht uber den 2. Internationalen Kongress fur Angewandte Linguistik. Cambridge 8.-12. IX. 1969. [Report on the Second International Congress for Applied Linguistics, Cambridge, Dec. 8-12, 1969.

    Science.gov (United States)

    Mohr, Peter

    This paper is a summary report on the Second International Congress of Applied Linguistics held in Cambridge, England in September 1969. Because of the large number of papers delivered, only a selection of the papers delivered in any one section of the Congress are considered, and the author attempts to identify current interests and trends in…

  5. Aromatic rings in chemical and biological recognition: energetics and structures.

    Science.gov (United States)

    Salonen, Laura M; Ellermann, Manuel; Diederich, François

    2011-05-16

    This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations. PMID:21538733

  6. Space-Filling Curves as a Novel Crystal Structure Representation for Machine Learning Models

    CERN Document Server

    Jasrasaria, Dipti; Rappoport, Dmitrij; Aspuru-Guzik, Alan

    2016-01-01

    A fundamental problem in applying machine learning techniques for chemical problems is to find suitable representations for molecular and crystal structures. While the structure representations based on atom connectivities are prevalent for molecules, two-dimensional descriptors are not suitable for describing molecular crystals. In this work, we introduce the SFC-M family of feature representations, which are based on Morton space-filling curves, as an alternative means of representing crystal structures. Latent Semantic Indexing (LSI) was employed in a novel setting to reduce sparsity of feature representations. The quality of the SFC-M representations were assessed by using them in combination with artificial neural networks to predict Density Functional Theory (DFT) single point, Ewald summed, lattice, and many-body dispersion energies of 839 organic molecular crystal unit cells from the Cambridge Structural Database that consist of the elements C, H, N, and O. Promising initial results suggest that the S...

  7. Debate on Bruce Bimber´s Book Information and American Democracy. Cambridge University Press, 2003

    Directory of Open Access Journals (Sweden)

    Karpf, David

    2011-12-01

    Full Text Available Not availablePresentation José Manuel Robles Abstract of Information and American Democracy. Cambridge University Press, 2003 Bruce Bimber From Regimes to Ecologies: Globalizing Bruce Bimber’s Model of Information and Politics Steven Livingston Internet, new forms of power and democracy José Luís Garcia Internet: A Technological Tool and Changes in Political Power Liu Gang Information and American Democracy in the era of web 2.0 Lorenzo Mosca What Comes Next?: Bimber’s Information Revolutions and Institutional Disruptions David Karpf Online Political Information and Online Political Participation José Manuel Robles Digital Media and Political Change: A Response to Garcia, Karpf, Livingston, Liu, Mosca, and Robles Bruce Bimber

  8. Does the Cambridge Automated Neuropsychological Test Battery (CANTAB) Distinguish Between Cognitive Domains in Healthy Older Adults?

    Science.gov (United States)

    Lenehan, Megan E; Summers, Mathew J; Saunders, Nichole L; Summers, Jeffery J; Vickers, James C

    2016-04-01

    The Cambridge Neuropsychological Test Automated Battery (CANTAB) is a semiautomated computer interface for assessing cognitive function. We examined whether CANTAB tests measured specific cognitive functions, using established neuropsychological tests as a reference point. A sample of 500 healthy older (M = 60.28 years, SD = 6.75) participants in the Tasmanian Healthy Brain Project completed battery of CANTAB subtests and standard paper-based neuropsychological tests. Confirmatory factor analysis identified four factors: processing speed, verbal ability, episodic memory, and working memory. However, CANTAB tests did not consistently load onto the cognitive domain factors derived from traditional measures of the same function. These results indicate that five of the six CANTAB subtests examined did not load onto single cognitive functions. These CANTAB tests may lack the sensitivity to measure discrete cognitive functions in healthy populations or may measure other cognitive domains not included in the traditional neuropsychological battery.

  9. Experience from two decades of the Cambridge Rapid Access Neurology Clinic.

    Science.gov (United States)

    Axinte, Laura T; Fiddes, Barnaby D; Donaghy, Alastair; Whyte, Adam; Allen, Chris; Sawcer, Stephen J; Adam, Robert J; Stacpoole, Sybil R L

    2015-10-01

    We report on the evolution of the rapid access neurology clinic (established in 1995) at Addenbrooke's Hospital, Cambridge. Annualised attendance data demonstrate an ever increasing demand, with primary headache disorders now accounting for more than 40% of referrals. Secondary causes of headache (including intracranial tumours, idiopathic intracranial hypertension, carotid or vertebral artery dissection and subdural haematomas) remain infrequent. In all such cases, there were additional diagnostic clues. The number of patients referred with problems related to chronic neurological diseases has fallen considerably, reflecting the roles of specialist nurses and clinics. Imaging investigation of choice shifted from computerised tomography scan (45 to 16%) towards magnetic resonance imaging (17 to 47%). Management is increasingly on an outpatient basis, often without the need for a follow-up appointment. The experience presented here should inform further development of rapid access neurology clinics across the UK and suggests the need for acute headache services, in line with those for transient ischaemic attack and first seizure.

  10. Database Description - AT Atlas | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us AT Atlas... Database Description General information of database Database name AT Atlas Alternative name Advanced Technologies Atlas...sing protein biosynthesis. Database description AT Atlas will make you familiar with the accomplishments by ...research groups of Protein Production, Structural Analysis and Chemical Regulation in the Targeted Proteins Research Program. AT Atla...base Site Policy | Contact Us Database Description - AT Atlas | LSDB Archive ...

  11. The long-term impact of urbanisation on aquatic plants: Cambridge and the River Cam.

    Science.gov (United States)

    Preston, C D; Sheail, J; Armitage, P; Davy-Bowker, J

    2003-10-01

    Historical and contemporary records have been used to assess the impact of urbanisation on the aquatic plants of the River Cam and its narrow floodplain in Cambridge. Of the 62 native aquatic plant species which have been recorded in the study area since 1660, 40 (65%) were still present in the period 1985-1999 whereas 22 (35%) are apparently extinct. There is a striking relationship between the fate of species and their trophic requirements, with species of less eutrophic habitats having suffered disproportionately. Historical records demonstrate that the River Cam became grossly polluted by sewage from Cambridge in the 19th century, but the chemical and biological quality of the river improved from 1897 onwards. However, the majority of the species recorded from the river and nearby ditches persisted until after maximum incidence of sewage pollution, which may even have stimulated the growth of 'weed' in the river. Losses of aquatic plant species from two riparian commons, Coe Fen (35%) and Sheep's Green (50%), have been particularly great. The level of these and other areas of low-lying common land by the river has been systematically raised by the controlled tipping of waste in hollows, followed by levelling and resowing. The main effects of urbanisation on the flora therefore arose from the transformation of riparian pastures into suburban open spaces. Commons which are used purely for amenity purposes have lost almost all their aquatic plant species. Those which are still grazed retain more, and continuance of grazing is probably essential if a varied aquatic flora is to be maintained. The interpretation of botanical records in terms of recorded management history is likely to throw further light on the processes of urbanisation, although the number of sites with a sufficiently detailed botanical record may be limited. PMID:14499527

  12. Assessing the Impact of the Cambridge International Acceleration Program on U.S. University Determinants of Success: A Multi-Level Modeling Approach

    Science.gov (United States)

    Shaw, Stuart; Warren, Jayne; Gill, Tim

    2014-01-01

    This article focuses on the research being conducted by Cambridge International Examinations (Cambridge) to ensure that its international assessments prepare students as well as other acceleration programs for continued study in U.S. colleges and universities. The study, which builds on previous freshman GPA data modeling work using data supplied…

  13. Mammalian Mitochondrial ncRNA Database

    OpenAIRE

    Anandakumar, Shanmugam; Vijayakumar, Saravanan; Arumugam, Nagarajan; Gromiha, M. Michael

    2015-01-01

    Mammalian Mitochondrial ncRNA is a web-based database, which provides specific information on non-coding RNA in mammals. This database includes easy searching, comparing with BLAST and retrieving information on predicted structure and its function about mammalian ncRNAs. Availability The database is available for free at http://www.iitm.ac.in/bioinfo/mmndb/

  14. Conceptual Design of a Prototype LSST Database

    Energy Technology Data Exchange (ETDEWEB)

    Nikolaev, S; Huber, M E; Cook, K H; Abdulla, G; Brase, J

    2004-10-07

    This document describes a preliminary design for Prototype LSST Database (LSST DB). They identify key components and data structures and provide an expandable conceptual schema for the database. The authors discuss the potential user applications and post-processing algorithm to interact with the database, and give a set of example queries.

  15. The magnet components database system

    Energy Technology Data Exchange (ETDEWEB)

    Baggett, M.J. (Brookhaven National Lab., Upton, NY (USA)); Leedy, R.; Saltmarsh, C.; Tompkins, J.C. (Superconducting Supercollider Lab., Dallas, TX (USA))

    1990-01-01

    The philosophy, structure, and usage MagCom, the SSC magnet components database, are described. The database has been implemented in Sybase (a powerful relational database management system) on a UNIX-based workstation at the Superconducting Super Collider Laboratory (SSCL); magnet project collaborators can access the database via network connections. The database was designed to contain the specifications and measured values of important properties for major materials, plus configuration information (specifying which individual items were used in each cable, coil, and magnet) and the test results on completed magnets. These data will facilitate the tracking and control of the production process as well as the correlation of magnet performance with the properties of its constituents. 3 refs., 10 figs.

  16. Database systems for knowledge-based discovery.

    Science.gov (United States)

    Jagarlapudi, Sarma A R P; Kishan, K V Radha

    2009-01-01

    Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery.

  17. Database systems for knowledge-based discovery.

    Science.gov (United States)

    Jagarlapudi, Sarma A R P; Kishan, K V Radha

    2009-01-01

    Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery. PMID:19727614

  18. Tartu Ülikooli teadur kaitses Cambridgeì Ülikoolis doktorikraadi / Krõõt Nõges

    Index Scriptorium Estoniae

    Nõges, Krõõt

    2006-01-01

    Tartu Ülikooli filosoofia osakonna teadur ja eetikakeskuse stipendiaat Eva Piirimäe kaitses Cambridgeì Ülikoolis doktorikraadi ideede ajaloo erialal doktoritööga "Thomas Abbt (1738-1766) and the Philosophical Genesis of German Nationalism"

  19. Two new spider species of the genus Chrysso O. P.-Cambridge, 1882 (Araneae, Theridiidae) in Hainan Island, China

    OpenAIRE

    Bao-Shi Zhang; Feng Zhang

    2012-01-01

    Abstract Two new spider species of the genus Chrysso O. P.-Cambridge, 1882 are reported from Hainan Island, China, Chrysso bifurca sp. n. (male, female) and Chrysso bicuspidata sp. n. (male, female). Chrysso bimaculata Yoshida, 1998is recorded from China for the first time.

  20. M-DCPS Student Performance in International Baccalaureate and Cambridge Advanced International Certificate of Education Programs. Research Brief. Volume 1102

    Science.gov (United States)

    Blazer, Christie

    2011-01-01

    This Research Brief summarizes the performance of M-DCPS students participating in the International Baccalaureate (IB) and Cambridge Advanced International Certificate of Education (AICE) programs. Outcome data are provided for the eight M-DCPS schools offering the two programs and corresponding examinations. Participation in international…

  1. Degrees of Influence: The Politics of Honorary Degrees in the Universities of Oxford and Cambridge, 1900-2000

    Science.gov (United States)

    Heffernan, Michael; Jons, Heike

    2007-01-01

    The universities of Oxford and Cambridge had developed different attitudes towards the award of honorary degrees through the early and middle decades of the twentieth century. Recently, both have adopted a similar cautious and apolitical stance. This essay describes the role of honorary degrees in the production and reproduction of their cultural…

  2. Jonathan Schlefer, The Assumptions Economists Make (Cambridge, Mass., and London: Belknap Press of Harvard University Press, 2012

    Directory of Open Access Journals (Sweden)

    Stuart Winchester

    2013-03-01

    Full Text Available A review of the book by Jonathan Schlefer: The Assumptions Economists Make (Cambridge, Mass., and London: Belknap Press of Harvard University Press, 2012, €26,10 / £21.95 / US$28.95, 356pp HBK (English, ISBN: 9780674052260.

  3. A Language for Fuzzy Statistical Database

    OpenAIRE

    Katti, C. P; S.Guglani

    2013-01-01

    Fuzzy statistical database is a database used for fuzzy statistical analysis purpose. A fuzzy statistical tableis a tabular representation of fuzzy statistics and is a useful data structure for fuzzy statistical database.Primitive fuzzy statistical tables are a building block of fuzzy statistical table. In this paper we defined thefuzzy statistical join operator in the framework of fuzzy statistical database. The fuzzy statisticaldependency preservation property will be discussed for the fuzz...

  4. Database theory and SQL practice using Access

    International Nuclear Information System (INIS)

    This book introduces database theory and SQL practice using Access. It is comprised of seven chapters, which give description of understanding database with basic conception and DMBS, understanding relational database with examples of it, building database table and inputting data using access 2000, structured Query Language with introduction, management and making complex query using SQL, command for advanced SQL with understanding conception of join and virtual table, design on database for online bookstore with six steps and building of application with function, structure, component, understanding of the principle, operation and checking programming source for application menu.

  5. Databases and their application

    NARCIS (Netherlands)

    E.C. Grimm; R.H.W Bradshaw; S. Brewer; S. Flantua; T. Giesecke; A.M. Lézine; H. Takahara; J.W.,Jr Williams

    2013-01-01

    During the past 20 years, several pollen database cooperatives have been established. These databases are now constituent databases of the Neotoma Paleoecology Database, a public domain, multiproxy, relational database designed for Quaternary-Pliocene fossil data and modern surface samples. The poll

  6. Unit 66 - Database Creation

    OpenAIRE

    Unit 61, CC in GIS; National Center for Geographic Information and Analysis (UC Santa Barbara, SUNY at Buffalo, University of Maine)

    1990-01-01

    This unit examines the planning and management issues involved in the physical creation of the database. It describes some issues in database creation, key hardware parameters of the system, partitioning the database for tiles and layers and converting data for the database. It illustrates these through an example from the Flathead National Forest in northwestern Montana, where a resource management database was required.

  7. MINT: the Molecular INTeraction database

    OpenAIRE

    Chatr-aryamontri, Andrew; Ceol, Arnaud; Palazzi, Luisa Montecchi; Nardelli, Giuliano; Schneider, Maria Victoria; Castagnoli, Luisa; Cesareni, Gianni

    2006-01-01

    The Molecular INTeraction database (MINT, ) aims at storing, in a structured format, information about molecular interactions (MIs) by extracting experimental details from work published in peer-reviewed journals. At present the MINT team focuses the curation work on physical interactions between proteins. Genetic or computationally inferred interactions are not included in the database. Over the past four years MINT has undergone extensive revision. The new version of MINT is based on a comp...

  8. BioMagResBank database with sets of experimental NMR constraints corresponding to the structures of over 1400 biomolecules deposited in the Protein Data Bank

    International Nuclear Information System (INIS)

    Experimental constraints associated with NMR structures are available from the Protein Data Bank (PDB) in the form of 'Magnetic Resonance' (MR) files. These files contain multiple types of data concatenated without boundary markers and are difficult to use for further research. Reported here are the results of a project initiated to annotate, archive, and disseminate these data to the research community from a searchable resource in a uniform format. The MR files from a set of 1410 NMR structures were analyzed and their original constituent data blocks annotated as to data type using a semi-automated protocol. A new software program called Wattos was then used to parse and archive the data in a relational database. From the total number of MR file blocks annotated as constraints, it proved possible to parse 84% (3337/3975). The constraint lists that were parsed correspond to three data types (2511 distance, 788 dihedral angle, and 38 residual dipolar couplings lists) from the three most popular software packages used in NMR structure determination: XPLOR/CNS (2520 lists), DISCOVER (412 lists), and DYANA/DIANA (405 lists). These constraints were then mapped to a developmental version of the BioMagResBank (BMRB) data model. A total of 31 data types originating from 16 programs have been classified, with the NOE distance constraint being the most commonly observed. The results serve as a model for the development of standards for NMR constraint deposition in computer-readable form. The constraints are updated regularly and are available from the BMRB web site (http://www.bmrb.wisc.edu)

  9. World Religion Database

    OpenAIRE

    Dekker, Jennifer

    2009-01-01

    This article reviews the new database released by Brill entitled World Religion Database (WRD). It compares WRD to other religious demography tools available and rates the database on a 5 point scale.

  10. Open geochemical database

    Science.gov (United States)

    Zhilin, Denis; Ilyin, Vladimir; Bashev, Anton

    2010-05-01

    available yet. We hope that open database will help exchanging geochemical information and call everybody for sharing the geochemical data. We also call for feedback on the structure, interface and operation of the database.

  11. Human cancer databases (review).

    Science.gov (United States)

    Pavlopoulou, Athanasia; Spandidos, Demetrios A; Michalopoulos, Ioannis

    2015-01-01

    Cancer is one of the four major non‑communicable diseases (NCD), responsible for ~14.6% of all human deaths. Currently, there are >100 different known types of cancer and >500 genes involved in cancer. Ongoing research efforts have been focused on cancer etiology and therapy. As a result, there is an exponential growth of cancer‑associated data from diverse resources, such as scientific publications, genome‑wide association studies, gene expression experiments, gene‑gene or protein‑protein interaction data, enzymatic assays, epigenomics, immunomics and cytogenetics, stored in relevant repositories. These data are complex and heterogeneous, ranging from unprocessed, unstructured data in the form of raw sequences and polymorphisms to well‑annotated, structured data. Consequently, the storage, mining, retrieval and analysis of these data in an efficient and meaningful manner pose a major challenge to biomedical investigators. In the current review, we present the central, publicly accessible databases that contain data pertinent to cancer, the resources available for delivering and analyzing information from these databases, as well as databases dedicated to specific types of cancer. Examples for this wealth of cancer‑related information and bioinformatic tools have also been provided. PMID:25369839

  12. USAID Anticorruption Projects Database

    Data.gov (United States)

    US Agency for International Development — The Anticorruption Projects Database (Database) includes information about USAID projects with anticorruption interventions implemented worldwide between 2007 and...

  13. Caching in Multidimensional Databases

    OpenAIRE

    Szépkúti, István

    2011-01-01

    One utilisation of multidimensional databases is the field of On-line Analytical Processing (OLAP). The applications in this area are designed to make the analysis of shared multidimensional information fast [9]. On one hand, speed can be achieved by specially devised data structures and algorithms. On the other hand, the analytical process is cyclic. In other words, the user of the OLAP application runs his or her queries one after the other. The output of the last query may be there (at lea...

  14. Database Systems - Present and Future

    Directory of Open Access Journals (Sweden)

    2009-01-01

    Full Text Available The database systems have nowadays an increasingly important role in the knowledge-based society, in which computers have penetrated all fields of activity and the Internet tends to develop worldwide. In the current informatics context, the development of the applications with databases is the work of the specialists. Using databases, reach a database from various applications, and also some of related concepts, have become accessible to all categories of IT users. This paper aims to summarize the curricular area regarding the fundamental database systems issues, which are necessary in order to train specialists in economic informatics higher education. The database systems integrate and interfere with several informatics technologies and therefore are more difficult to understand and use. Thus, students should know already a set of minimum, mandatory concepts and their practical implementation: computer systems, programming techniques, programming languages, data structures. The article also presents the actual trends in the evolution of the database systems, in the context of economic informatics.

  15. Item response theory analyses of the Cambridge Face Memory Test (CFMT).

    Science.gov (United States)

    Cho, Sun-Joo; Wilmer, Jeremy; Herzmann, Grit; McGugin, Rankin Williams; Fiset, Daniel; Van Gulick, Ana E; Ryan, Kaitlin F; Gauthier, Isabel

    2015-06-01

    We evaluated the psychometric properties of the Cambridge Face Memory Test (CFMT; Duchaine & Nakayama, 2006). First, we assessed the dimensionality of the test with a bifactor exploratory factor analysis (EFA). This EFA analysis revealed a general factor and 3 specific factors clustered by targets of CFMT. However, the 3 specific factors appeared to be minor factors that can be ignored. Second, we fit a unidimensional item response model. This item response model showed that the CFMT items could discriminate individuals at different ability levels and covered a wide range of the ability continuum. We found the CFMT to be particularly precise for a wide range of ability levels. Third, we implemented item response theory (IRT) differential item functioning (DIF) analyses for each gender group and 2 age groups (age ≤ 20 vs. age > 21). This DIF analysis suggested little evidence of consequential differential functioning on the CFMT for these groups, supporting the use of the test to compare older to younger, or male to female, individuals. Fourth, we tested for a gender difference on the latent facial recognition ability with an explanatory item response model. We found a significant but small gender difference on the latent ability for face recognition, which was higher for women than men by 0.184, at age mean 23.2, controlling for linear and quadratic age effects. Finally, we discuss the practical considerations of the use of total scores versus IRT scale scores in applications of the CFMT.

  16. Minimal exposure technique in the Cambridge University 600kV high resolution electron microscope

    International Nuclear Information System (INIS)

    Radiation damage due to the incident electron beam imposes a fundamental limitation on the information obtainable by electron microscopy about organic materials; it is desirable therefore that exposure of the specimen to the electron beam should be restricted to the actual period during which the image is being recorded. A description is given of methods employed in the observation of the organic aromatic hydrocarbons quaterrylene, ovalene and coronene with the Cambridge University 600kV high resolution electron microscope (HREM). In particular, the condenser-objective mode of operation of this microscope lends itself to the use of an area-defining aperture below the second condenser lens conjugate with the specimen. Furthermore, operation at the higher accelerating voltage of this instrument could be anticipated to reduce the rate of damage, depending on the dominant beam-specimen interaction, whilst the increased width of the first broad band of the contrast transfer function of this microscope at the optimum defocus may overcome the reported resolution limitation of current 100kV microscopes for the observation of related materials. (author)

  17. Swift observations of unidentified radio sources in the revised Third Cambridge Catalogue

    Science.gov (United States)

    Maselli, A.; Massaro, F.; Cusumano, G.; La Parola, V.; Harris, D. E.; Paggi, A.; Liuzzo, E.; Tremblay, G. R.; Baum, S. A.; O'Dea, C. P.

    2016-08-01

    We have investigated a group of unassociated radio sources included in the Third Cambridge Catalogue (3CR) to increase the multifrequency information on them and possibly obtain an identification. We have carried out an observational campaign with the Swift satellite to observe with the Ultraviolet/Optical Telescope (UVOT) and the X-Ray Telescope (XRT) the field of view of 21 bright NRAO VLA Sky Survey (NVSS) sources within the positional uncertainty region of the 3CR sources. Furthermore, we have searched in the recent AllWISE Source Catalogue for infrared sources matching the position of these NVSS sources. We have detected significant emission in the soft X-ray band for nine of the investigated NVSS sources. To all of them, and in four cases with no soft X-ray association, we have associated a Wide-field Infrared Survey Explorer infrared counterpart. Eight of these infrared candidates have not been proposed earlier in the literature. In the five remaining cases our candidate matches one among a few optical candidates suggested for the same 3CR source in previous studies. No source has been detected in the UVOT filters at the position of the NVSS objects, confirming the scenario that all of them are heavily obscured. With this in mind, a spectroscopic campaign, preferably in the infrared band, will be necessary to establish the nature of the sources that we have finally identified.

  18. Graph Database for Collaborative Communities

    OpenAIRE

    Soussi, Rania; Aufaure, Marie-Aude; Baazaoui, Hajer

    2011-01-01

    Data manipulated in an enterprise context are structured data as well as unstructured data such as emails, documents, and social networks. Graphs are a natural way of representing and modeling such data (structured, semistructured, and unstructured ones) in a unified manner. The main advantage of such a structure relies on the dynamic aspect and the capability to represent relations, even multiple ones, between objects. Recent database research work shows a growing interest in the definition ...

  19. Predictive toxicology of chemicals and database mining

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The toxic chemicals from the database Registry of Toxic Effects of Chemical Substances (RTECS) were analyzed by structural similarity comparison, which shows that the structure patterns or characteristics of toxic chemicals exist in a sufficiently large database. Then, a two-step strategy was proposed to explore noncongeneric toxic chemicals in the database: the screening of structure patterns by similarity comparison and the derivation of detailed relationship between structure and activity by using comparative molecular field analysis (CoMFA) of Quantitative Structure-Activity Relationship (QSAR) technologies. From the performance of the procedure, such a stepwise scheme is demonstrated to be feasible and effective to mine a database of toxic chemicals. It can be anticipated that database mining of toxic chemicals will be a new area for predictive toxicology of chemicals.

  20. Cloud Databases: A Paradigm Shift in Databases

    Directory of Open Access Journals (Sweden)

    Indu Arora

    2012-07-01

    Full Text Available Relational databases ruled the Information Technology (IT industry for almost 40 years. But last few years have seen sea changes in the way IT is being used and viewed. Stand alone applications have been replaced with web-based applications, dedicated servers with multiple distributed servers and dedicated storage with network storage. Cloud computing has become a reality due to its lesser cost, scalability and pay-as-you-go model. It is one of the biggest changes in IT after the rise of World Wide Web. Cloud databases such as Big Table, Sherpa and SimpleDB are becoming popular. They address the limitations of existing relational databases related to scalability, ease of use and dynamic provisioning. Cloud databases are mainly used for data-intensive applications such as data warehousing, data mining and business intelligence. These applications are read-intensive, scalable and elastic in nature. Transactional data management applications such as banking, airline reservation, online e-commerce and supply chain management applications are write-intensive. Databases supporting such applications require ACID (Atomicity, Consistency, Isolation and Durability properties, but these databases are difficult to deploy in the cloud. The goal of this paper is to review the state of the art in the cloud databases and various architectures. It further assesses the challenges to develop cloud databases that meet the user requirements and discusses popularly used Cloud databases.

  1. General database for ground water site information.

    Science.gov (United States)

    de Dreuzy, Jean-Raynald; Bodin, Jacques; Le Grand, Hervé; Davy, Philippe; Boulanger, Damien; Battais, Annick; Bour, Olivier; Gouze, Philippe; Porel, Gilles

    2006-01-01

    In most cases, analysis and modeling of flow and transport dynamics in ground water systems require long-term, high-quality, and multisource data sets. This paper discusses the structure of a multisite database (the H+ database) developed within the scope of the ERO program (French Environmental Research Observatory, http://www.ore.fr). The database provides an interface between field experimentalists and modelers, which can be used on a daily basis. The database structure enables the storage of a large number of data and data types collected from a given site or multiple-site network. The database is well suited to the integration, backup, and retrieval of data for flow and transport modeling in heterogeneous aquifers. It relies on the definition of standards and uses a templated structure, such that any type of geolocalized data obtained from wells, hydrological stations, and meteorological stations can be handled. New types of platforms other than wells, hydrological stations, and meteorological stations, and new types of experiments and/or parameters could easily be added without modifying the database structure. Thus, we propose that the database structure could be used as a template for designing databases for complex sites. An example application is the H+ database, which gathers data collected from a network of hydrogeological sites associated with the French Environmental Research Observatory.

  2. A robust method of measuring other-race and other-ethnicity effects: the Cambridge Face Memory Test format.

    Science.gov (United States)

    McKone, Elinor; Stokes, Sacha; Liu, Jia; Cohan, Sarah; Fiorentini, Chiara; Pidcock, Madeleine; Yovel, Galit; Broughton, Mary; Pelleg, Michel

    2012-01-01

    Other-race and other-ethnicity effects on face memory have remained a topic of consistent research interest over several decades, across fields including face perception, social psychology, and forensic psychology (eyewitness testimony). Here we demonstrate that the Cambridge Face Memory Test format provides a robust method for measuring these effects. Testing the Cambridge Face Memory Test original version (CFMT-original; European-ancestry faces from Boston USA) and a new Cambridge Face Memory Test Chinese (CFMT-Chinese), with European and Asian observers, we report a race-of-face by race-of-observer interaction that was highly significant despite modest sample size and despite observers who had quite high exposure to the other race. We attribute this to high statistical power arising from the very high internal reliability of the tasks. This power also allows us to demonstrate a much smaller within-race other ethnicity effect, based on differences in European physiognomy between Boston faces/observers and Australian faces/observers (using the CFMT-Australian).

  3. Quantitative Study and Structure Visualization of Scientific Publications in the Field of Information Management in Web of Science Database during 1988-2009

    Directory of Open Access Journals (Sweden)

    Afshin Hamdipour

    2012-12-01

    Full Text Available The present study endeavored to analysis the scientific publications that were indexed in the Web of Science database as the information management records and the visualization of science structure in this field during 1988-2009. The research method was scientometrics. During the study period, 1120 records in the field of information management have been published. These records were extracted in the form of plain text files and stored in a PC. Then they were analyzed by ISI.exe and HistCite softwares. Author's coefficient collaboration (CC was grown from zero in 1988 to 0.33 in 2009. Average coefficient collaboration between the authors was 0.22 which confirmed low authors collaboration in this area. The records have been published in 63 languages. Among these records the English language with 93.8 % possessed the highest proportion. City University London and the University of Sheffield in England had the most common publications in information management field. Based on the number of published records, T.D. Wilson with 13 records and 13 citations ranked as the first. The average number of global citations to 112 documents has been equal to 8.78. Despite the participation of different countries in the production of documents, more than 28.9% of records have been produced in the United States. According to results, 10 countries have published more than 72.4 percent of the records. City University London and the University of Sheffield have had highest frequency in this area. 15 journals have published 564 records (50.4% of the total productions. Finally, by implementation of scientific software HistCite map drawing clustered and authors, articles and four effective specific subjects were introduced..

  4. Arvustus. Katri Lõhmus. Caring Autonomy. European Human Rights Law and the Challenge of Individualism. Cambridge University Press 2015, 246 lk / Lauri Mälksoo

    Index Scriptorium Estoniae

    Mälksoo, Lauri, 1975-

    2016-01-01

    Arvustus: Katri Lõhmus. Caring Autonomy. European Human Rights Law and the Challenge of Individualism. Cambridge University Press 2015, 246 lk. Euroopa inimõiguste ja põhivabaduste kaitse konventsiooni artikli 8 sisustamisest

  5. Potential reductions of street solids and phosphorus in urban watersheds from street cleaning, Cambridge, Massachusetts, 2009-11

    Science.gov (United States)

    Sorenson, Jason R.

    2013-01-01

    Material accumulating and washing off urban street surfaces and ultimately into stormwater drainage systems represents a substantial nonpoint source of solids, phosphorus, and other constituent loading to waterways in urban areas. Cost and lack of usable space limit the type and number of structural stormwater source controls available to municipalities and other public managers. Non-structural source controls such as street cleaning are commonly used by cities and towns for construction, maintenance and aesthetics, and may reduce contaminant loading to waterways. Effectiveness of street cleaning is highly variable and potential improvements to water quality are not fully understood. In 2009, the U.S. Geological Survey, in cooperation with the Massachusetts Department of Environmental Protection, the U.S. Environmental Protection Agency, and the city of Cambridge, Massachusetts, and initiated a study to better understand the physical and chemical nature of the organic and inorganic solid material on street surfaces, evaluate the performance of a street cleaner at removing street solids, and make use of the Source Loading and Management Model (SLAMM) to estimate potential reductions in solid and phosphorus loading to the lower Charles River from various street-cleaning technologies and frequencies. Average yield of material on streets collected between May and December 2010, was determined to be about 740 pounds per curb-mile on streets in multifamily land use and about 522 pounds per curb-mile on commercial land-use streets. At the end-of-winter in March 2011, about 2,609 and 4,788 pounds per curb-mile on average were collected from streets in multifamily and commercial land-use types, respectively. About 86 percent of the total street-solid yield from multifamily and commercial land-use streets was greater than or equal to 0.125 millimeters in diameter (or very fine sand). Observations of street-solid distribution across the entire street width indicated that as

  6. Space-time structure

    CERN Document Server

    Schrödinger, Erwin

    1985-01-01

    In response to repeated requests this classic book on space-time structure by Professor Erwin Schrödinger is now available in the Cambridge Science Classics series. First published in 1950, and reprinted in 1954 and 1960, this lucid and profound exposition of Einstein's 1915 theory of gravitation still provides valuable reading for students and research workers in the field.

  7. Cambridge-Cranfield High Performance Computing Facility (HPCF) purchases ten Sun Fire(TM) 15K servers to dramatically increase power of eScience research

    CERN Multimedia

    2002-01-01

    "The Cambridge-Cranfield High Performance Computing Facility (HPCF), a collaborative environment for data and numerical intensive computing privately run by the University of Cambridge and Cranfield University, has purchased 10 Sun Fire(TM) 15K servers from Sun Microsystems, Inc.. The total investment, which includes more than $40 million in Sun technology, will dramatically increase the computing power, reliability, availability and scalability of the HPCF" (1 page).

  8. Correlates of time spent walking and cycling to and from work: baseline results from the commuting and health in Cambridge study

    OpenAIRE

    Panter Jenna; Griffin Simon; Jones Andrew; Mackett Roger; Ogilvie David

    2011-01-01

    Abstract Purpose Environmental perceptions and psychological measures appear to be associated with walking and cycling behaviour; however, their influence is still unclear. We assessed these associations using baseline data from a quasi-experimental cohort study of the effects of major transport infrastructural developments in Cambridge, UK. Methods Postal surveys were sent to adults who travel to work in Cambridge (n = 1582). Questions asked about travel modes and time spent travelling to an...

  9. Databases for INDUS-1 and INDUS-2

    International Nuclear Information System (INIS)

    The databases for Indus are relational databases designed to store various categories of data related to the accelerator. The data archiving and retrieving system in Indus is based on a client/sever model. A general purpose commercial database is used to store parameters and equipment data for the whole machine. The database manages configuration, on-line and historical databases. On line and off line applications distributed in several systems can store and retrieve the data from the database over the network. This paper describes the structure of databases for Indus-1 and Indus-2 and their integration within the software architecture. The data analysis, design, resulting data-schema and implementation issues are discussed. (author)

  10. The art and science of consultations in bovine medicine: Use of modified Calgary - Cambridge guides

    Directory of Open Access Journals (Sweden)

    Kiro R. Petrovski

    2015-10-01

    Full Text Available This article describes few steps of the application of the modified Calgary-Cambridge Guides (CCG to consultations in bovine medicine. A review of pertinent clinical communication skills literature in human medicine was integrated with the burgeoning research within veterinary medicine. In particular, there are more recent studies examining companion animal veterinarian’s communication skills and outcomes which can be extrapolated to practitioners. This was integrated into a teaching example of a reproductive case consultation. The first article deals with the 1 Preparation, 2 Initiating the Session and 3 Gathering Information sections. The aim of the modified CCG is to provide a set of skills to facilitate a relationship-centred approach to consultations in bovine medicine, both at the individual animal and population level. They were initially developed for human medicine and expanded recently for use in veterinary medicine. The CCG enable the practitioner to facilitate interacting with that particular client at the time of the consultation. It is likely that the majority of practitioners do use many of the skills recommended by the modified CCG. These skills are often gained through experience. However, they may not use the skills intentionally and with purpose for a specific communication goal or outcome. Practitioners can improve their communication skills using the set of skills as recommended by the modified CCG. They allow the practitioner to gain insight into the client’s understanding of the problem, including underlying aetiology, epidemiology and pathophysiology. The guides also provide opportunity to understand client’s expectations regarding the outcome, motivation and willingness to change and adherence.

  11. Hindi translation and validation of Cambridge-Hopkins Diagnostic Questionnaire for RLS (CHRLSq

    Directory of Open Access Journals (Sweden)

    Ravi Gupta

    2015-01-01

    Full Text Available Background: Restless legs syndrome also known as Willis-Ekbom′s Disease (RLS/WED is a common illness. Cambridge-Hopkins diagnostic questionnaire for RLS (CHRLSq is a good diagnostic tool and can be used in the epidemiological studies. However, its Hindi version is not available. Thus, this study was conducted to translate and validate it in the Hindi speaking population. Materials and Methods: After obtaining the permission from the author of the CHRLSq, it was translated into Hindi language by two independent translators. After a series of forward and back translations, the finalized Hindi version was administered to two groups by one of the authors, who were blinded to the clinical diagnosis. First group consisted of RLS/WED patients, where diagnosis was made upon face to face interview and the other group - the control group included subjects with somatic symptoms disorders or exertional myalgia or chronic insomnia. Each group had 30 subjects. Diagnosis made on CHRLSq was compared with the clinical diagnosis. Statistical Analysis: Analysis was done using Statistical Package for Social Sciences (SPSS v 21.0. Descriptive statistics was calculated. Proportions were compared using chi-square test; whereas, categorical variables were compared using independent sample t-test. Sensitivity, specificity, and positive predictive value of the translated version of questionnaire were calculated. Results: Average age was comparable between the cases and control group (RLS/WED = 39.1 ± 10.1 years vs 36.2 ± 11.4 years in controls; P = 0.29. Women outnumbered men in the RLS/WED group (87% in RLS/WED group vs 57% among controls; χ2 = 6.64; P = 0.01. Both the sensitivity and specificity of the translated version was 83.3%. It had the positive predictive value of 86.6%. Conclusion: Hindi version of CHRLSq has positive predictive value of 87% and it can be used to diagnose RLS in Hindi speaking population.

  12. Evaluation of a brief anti-stigma campaign in Cambridge: do short-term campaigns work?

    Directory of Open Access Journals (Sweden)

    Henderson Claire

    2010-06-01

    Full Text Available Abstract Background In view of the high costs of mass-media campaigns, it is important to understand whether it is possible for a media campaign to have significant population effects over a short period of time. This paper explores this question specifically in reference to stigma and discrimination against people with mental health problems using the Time to Change Cambridge anti-stigma campaign as an example. Methods 410 face-to-face interviews were performed pre, during and post campaign activity to assess campaign awareness and mental health-related knowledge, attitudes and behaviours. Results Although campaign awareness was not sustained following campaign activity, significant and sustained shifts occurred for mental health-related knowledge items. Specifically, there was a 24% (p If a friend had a mental health problem, I know what advice to give them to get professional help, following the campaign. Additionally, for the statement: Medication can be an effective treatment for people with mental health problems, there was a 10% rise (p = 0.05 in the proportion of interviewees responding 'agree' or 'strongly agree' following the campaign. These changes, however, were not evident for attitudinal or behaviour related questions. Conclusions Although these results only reflect the impact of one small scale campaign, these preliminary findings suggest several considerations for mass-media campaign development and evaluation strategies such as: (1 Aiming to influence outcomes pertaining to knowledge in the short term; (2 Planning realistic and targeted outcomes over the short, medium and long term during sustained campaigns; and (3 Monitoring indirect campaign effects such as social discourse or other social networking/contact in the evaluation.

  13. Validation of the Cambridge Prospective Memory Test (Hong Kong Chinese version) for people with stroke.

    Science.gov (United States)

    Man, David W K; Chan, M K L; Yip, C C K

    2015-01-01

    This study aimed to develop and evaluate a Hong Kong Chinese version of the Cambridge Prospective Memory Test (CAMPROMPT-HKCV). Thirty-three subjects at least one year post-stroke participated in the study. They were simultaneously rated on version A of the CAMPROMPT-HKCV by two testers to establish its internal consistency and inter-rater reliability. Raters used the parallel versions of the test (A and B), in rating 10 patients within 2 weeks to establish the parallel form reliability. Another 10 were also assessed on the same day using both version A of the CAMPROMPT-HKCV and the Rivermead Behavioural Memory Test-Chinese version (RBMT-CV) to establish concurrent validity. A new group of 40 stroke patients and 44 healthy controls was recruited to establish its sensitivity and specificity. Results indicated that test-retest reliability on time-based, event-based and total scores, and inter-rater reliability for versions A and B of the test were high. Cronbach's alpha of the event-based score was higher than that of the time-based score. The reliability and concurrent validity of the parallel forms were established. There was a significant difference in performance on CAMPROMPT-HKCV (version A) between the stroke group and the healthy control group. ROC analysis showed that the ability of the cut-off CAMPROMPT-HKCV (total score) to differentiate PM problems was 20.5 (out of 36) with sensitivity at 95.5% and specificity at 55.9%. Further study in developing stratified norms across different age groups in Chinese-speaking stroke patients is recommended.

  14. Caching in Multidimensional Databases

    CERN Document Server

    Szépkúti, István

    2011-01-01

    One utilisation of multidimensional databases is the field of On-line Analytical Processing (OLAP). The applications in this area are designed to make the analysis of shared multidimensional information fast [9]. On one hand, speed can be achieved by specially devised data structures and algorithms. On the other hand, the analytical process is cyclic. In other words, the user of the OLAP application runs his or her queries one after the other. The output of the last query may be there (at least partly) in one of the previous results. Therefore caching also plays an important role in the operation of these systems. However, caching itself may not be enough to ensure acceptable performance. Size does matter: The more memory is available, the more we gain by loading and keeping information in there. Oftentimes, the cache size is fixed. This limits the performance of the multidimensional database, as well, unless we compress the data in order to move a greater proportion of them into the memory. Caching combined ...

  15. Metadata queries for complex database systems

    OpenAIRE

    O'Connor, Gerald

    2004-01-01

    Federated Database Management Systems (FDBS) are very complex. Component databases can be heterogeneous, autonomous and distributed, accounting for these different characteristics in building a FDBS is a difficult engineering problem. The Common Data Model (CDM) is what is used to represent the data in the FDBS. It must be semantically rich to correctly represent the data from diverse component databases which differ in structure, datamodel, semantics and content. In this research project we ...

  16. MULTI-RESOLUTION SEAMLESS IMAGE DATABASE

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    This paper presents the basic concepts and principles,data structure and high efficient spatial index for multi-resolution image database.The database is characterized by arrangement of multi-resource image data and seamless mosaic,distribution-based storage and management,integration with other spatial database software such as GeoStar and GeoGrid developed by Wuhan Technical University of Surveying and Mapping.

  17. Aero/fluids database system

    Science.gov (United States)

    Reardon, John E.; Violett, Duane L., Jr.

    1991-01-01

    The AFAS Database System was developed to provide the basic structure of a comprehensive database system for the Marshall Space Flight Center (MSFC) Structures and Dynamics Laboratory Aerophysics Division. The system is intended to handle all of the Aerophysics Division Test Facilities as well as data from other sources. The system was written for the DEC VAX family of computers in FORTRAN-77 and utilizes the VMS indexed file system and screen management routines. Various aspects of the system are covered, including a description of the user interface, lists of all code structure elements, descriptions of the file structures, a description of the security system operation, a detailed description of the data retrieval tasks, a description of the session log, and a description of the archival system.

  18. Cell Centred Database (CCDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Cell Centered Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated...

  19. Native Health Research Database

    Science.gov (United States)

    ... APP WITH JAVASCRIPT TURNED OFF. THE NATIVE HEALTH DATABASE REQUIRES JAVASCRIPT IN ORDER TO FUNCTION. PLEASE ENTER ... To learn more about searching the Native Health Database, click here. Keywords Title Author Source of Publication ...

  20. AIDSinfo Drug Database

    Science.gov (United States)

    ... Widgets Order Publications Skip Nav AIDS info Drug Database Home > Drugs Español small medium large Text Size ... health care providers and patients. Search the Drug Database Help × Search by drug name Performs a search ...

  1. Database Urban Europe

    NARCIS (Netherlands)

    Sleutjes, B.; de Valk, H.A.G.

    2016-01-01

    Database Urban Europe: ResSegr database on segregation in The Netherlands. Collaborative research on residential segregation in Europe 2014–2016 funded by JPI Urban Europe (Joint Programming Initiative Urban Europe).

  2. Scopus database: a review.

    Science.gov (United States)

    Burnham, Judy F

    2006-03-08

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

  3. Web database development

    OpenAIRE

    Tsardas, Nikolaos A.

    2001-01-01

    This thesis explores the concept of Web Database Development using Active Server Pages (ASP) and Java Server Pages (JSP). These are among the leading technologies in the web database development. The focus of this thesis was to analyze and compare the ASP and JSP technologies, exposing their capabilities, limitations, and differences between them. Specifically, issues related to back-end connectivity using Open Database Connectivity (ODBC) and Java Database Connectivity (JDBC), application ar...

  4. IP Geolocation Databases: Unreliable?

    OpenAIRE

    Poese, Ingmar; Uhlig, Steve; Kaafar, Mohamed Ali; Donnet, Benoît; Gueye, Bamba

    2011-01-01

    The most widely used technique for IP geolocation con- sists in building a database to keep the mapping between IP blocks and a geographic location. Several databases are available and are frequently used by many services and web sites in the Internet. Contrary to widespread belief, geolo- cation databases are far from being as reliable as they claim. In this paper, we conduct a comparison of several current geolocation databases -both commercial and free- to have an insight of the limitation...

  5. Refactoring of a Database

    OpenAIRE

    Dsousa, Ayeesha; Bhatia, Shalini

    2009-01-01

    The technique of database refactoring is all about applying disciplined and controlled techniques to change an existing database schema. The problem is to successfully create a Database Refactoring Framework for databases. This paper concentrates on the feasibility of adapting this concept to work as a generic template. To retain the constraints regardless of the modifications to the metadata, the paper proposes a MetaData Manipulation Tool to facilitate change. The tool adopts a Template Des...

  6. Scopus database: a review

    OpenAIRE

    Burnham, Judy F.

    2006-01-01

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

  7. Ageing Management Program Database

    International Nuclear Information System (INIS)

    The aspects of plant ageing management (AM) gained increasing attention over the last ten years. Numerous technical studies have been performed to study the impact of ageing mechanisms on the safe and reliable operation of nuclear power plants. National research activities have been initiated or are in progress to provide the technical basis for decision making processes. The long-term operation of nuclear power plants is influenced by economic considerations, the socio-economic environment including public acceptance, developments in research and the regulatory framework, the availability of technical infrastructure to maintain and service the systems, structures and components as well as qualified personnel. Besides national activities there are a number of international activities in particular under the umbrella of the IAEA, the OECD and the EU. The paper discusses the process, procedure and database developed for Slovenian Nuclear Safety Administration (SNSA) surveillance of ageing process of Nuclear power Plant Krsko.(author)

  8. Automated Oracle database testing

    CERN Document Server

    CERN. Geneva

    2014-01-01

    Ensuring database stability and steady performance in the modern world of agile computing is a major challenge. Various changes happening at any level of the computing infrastructure: OS parameters & packages, kernel versions, database parameters & patches, or even schema changes, all can potentially harm production services. This presentation shows how an automatic and regular testing of Oracle databases can be achieved in such agile environment.

  9. CTD_DATABASE - Cascadia tsunami deposit database

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have...

  10. A perspective on databases and data mining

    NARCIS (Netherlands)

    Holsheimer, M.; Kersten, M.L.; Mannila, H.; Toivonen, H.

    1995-01-01

    We discuss the use of database methods for data mining. Recently impressive results have been achieved for some data mining problems using highly specialized and clever data structures. We study how well one can manage by using general purpose database management systems. We illustrate our ideas by

  11. Hydrologic, Water-Quality, and Meteorological Data for the Cambridge, Massachusetts, Drinking-Water Source Area, Water Year 2006

    Science.gov (United States)

    Smith, Kirk P.

    2008-01-01

    Records of water quantity, water quality, and meteorological parameters were continuously collected from three reservoirs, two primary streams, and four subbasin tributaries in the Cambridge, Massachusetts, drinking-water source area during water year 2006 (October 2005 through September 2006). Water samples were collected during base-flow conditions and storms in the subbasins of the Cambridge Reservoir and Stony Brook Reservoir drainage areas and analyzed for dissolved calcium, sodium, chloride, and sulfate; total nitrogen and phosphorus; and polar pesticides and metabolites. These data were collected to assist watershed administrators in managing the drinking-water source area and to identify potential sources of contaminants and trends in contaminant loading to the water supply. Monthly reservoir contents for the Cambridge Reservoir varied from about 59 to 98 percent of capacity during water year 2006, while monthly reservoir contents for the Stony Brook Reservoir and the Fresh Pond Reservoir was maintained at greater than 83 and 94 percent of capacity, respectively. If water demand is assumed to be 15 million gallons per day by the city of Cambridge, the volume of water released from the Stony Brook Reservoir to the Charles River during the 2006 water year is equivalent to an annual water surplus of about 127 percent. Recorded precipitation in the source area was about 16 percent greater for the 2006 water year than for the previous water year and was between 12 and 73 percent greater than for any recorded amount since water year 2002. The monthly mean specific-conductance values for all continuously monitored stations within the drinking-water source area were generally within the range of historical data collected since water year 1997, and in many cases were less than the historical medians. The annual mean specific conductance of 738 uS/cm (microsiemens per centimeter) for water discharged from the Cambridge Reservoir was nearly identical to the annual

  12. Natural language Interface for Database-A Brief review

    Directory of Open Access Journals (Sweden)

    Neelu Nihalani

    2011-03-01

    Full Text Available Information is playing an important role in our lives. One of the major sources of information is databases. Databases and database technology are having major impact on the growing use of computers. Almost all IT applications are storing and retrieving information from databases. Retrieving information database requires knowledge of database languages like SQL. The Structured Query Language (SQL norms are been pursued in almost all languages for relational database systems. However, not everybody is able to write SQL queries as they may not be aware of the structure of the database. So this has led to the development of Intelligent Database System ( IDBS . There is an overwhelming need for non-expert users to query relational databases in their natural language instead of working with the values of the attributes. As a result many intelligent natural language interfaces to databases have been developed, which provides flexible options for manipulating queries. The idea of using Natural Language instead of SQL has prompted the development of new type of processing called Natural language Interface to Database. NLIDB is a step towards the development of intelligent database systems (IDBS to enhance the users in performing flexible querying in databases. This paper is an introduction to Intelligent Database System and Natural Language Interface to Databases. Then a brief overview of NLIDB subcomponents is given and then discussion then moves on to NLIDB architectures and various approaches for the development of NLIDB systems.

  13. Nuclear power economic database

    International Nuclear Information System (INIS)

    Nuclear power economic database (NPEDB), based on ORACLE V6.0, consists of three parts, i.e., economic data base of nuclear power station, economic data base of nuclear fuel cycle and economic database of nuclear power planning and nuclear environment. Economic database of nuclear power station includes data of general economics, technique, capital cost and benefit, etc. Economic database of nuclear fuel cycle includes data of technique and nuclear fuel price. Economic database of nuclear power planning and nuclear environment includes data of energy history, forecast, energy balance, electric power and energy facilities

  14. An Interoperable Cartographic Database

    Directory of Open Access Journals (Sweden)

    Slobodanka Ključanin

    2007-05-01

    Full Text Available The concept of producing a prototype of interoperable cartographic database is explored in this paper, including the possibilities of integration of different geospatial data into the database management system and their visualization on the Internet. The implementation includes vectorization of the concept of a single map page, creation of the cartographic database in an object-relation database, spatial analysis, definition and visualization of the database content in the form of a map on the Internet. 

  15. HCSD: the human cancer secretome database

    DEFF Research Database (Denmark)

    Feizi, Amir; Banaei-Esfahani, Amir; Nielsen, Jens

    2015-01-01

    database is limiting the ability to query the increasing community knowledge. We therefore developed the Human Cancer Secretome Database (HCSD) to fulfil this gap. HCSD contains >80 000 measurements for about 7000 nonredundant human proteins collected from up to 35 high-throughput studies on 17 cancer......The human cancer secretome database (HCSD) is a comprehensive database for human cancer secretome data. The cancer secretome describes proteins secreted by cancer cells and structuring information about the cancer secretome will enable further analysis of how this is related with tumor biology...

  16. Electronic database of arterial aneurysms

    Directory of Open Access Journals (Sweden)

    Fabiano Luiz Erzinger

    2014-12-01

    Full Text Available Background:The creation of an electronic database facilitates the storage of information, as well as streamlines the exchange of data, making easier the exchange of knowledge for future research.Objective:To construct an electronic database containing comprehensive and up-to-date clinical and surgical data on the most common arterial aneurysms, to help advance scientific research.Methods:The most important specialist textbooks and articles found in journals and on internet databases were reviewed in order to define the basic structure of the protocol. Data were computerized using the SINPE© system for integrated electronic protocols and tested in a pilot study.Results:The data entered onto the system was first used to create a Master protocol, organized into a structure of top-level directories covering a large proportion of the content on vascular diseases as follows: patient history; physical examination; supplementary tests and examinations; diagnosis; treatment; and clinical course. By selecting items from the Master protocol, Specific protocols were then created for the 22 arterial sites most often involved by aneurysms. The program provides a method for collection of data on patients including clinical characteristics (patient history and physical examination, supplementary tests and examinations, treatments received and follow-up care after treatment. Any information of interest on these patients that is contained in the protocol can then be used to query the database and select data for studies.Conclusions:It proved possible to construct a database of clinical and surgical data on the arterial aneurysms of greatest interest and, by adapting the data to specific software, the database was integrated into the SINPE© system, thereby providing a standardized method for collection of data on these patients and tools for retrieving this information in an organized manner for use in scientific studies.

  17. The Calgary-Cambridge Referenced Observation Guides: an aid to defining the curriculum and organizing the teaching in communication training programmes.

    Science.gov (United States)

    Kurtz, S M; Silverman, J D

    1996-03-01

    Effective communication between doctor and patient is a core clinical skill. It is increasingly recognized that it should and can be taught with the same rigour as other basic medical sciences. To validate this teaching, it is important to define the content of communication training programmes by stating clearly what is to be learnt. We therefore describe a practical teaching tool, the Calgary-Cambridge Referenced Observation Guides, that delineates and structures the skills which aid doctor-patient communication. We provide detailed references to substantiate the research and theoretical basis of these individual skills. The guides form the foundation of a sound communication curriculum and are offered as a starting point for programme directors, facilitators and learners at all levels. We describe how these guides can also be used on an everyday basis to help facilitators teach and students learn within the experiential methodology that has been shown to be central to communication training. The learner-centred and opportunistic approach used in communication teaching makes it difficult for learners to piece together their evolving understanding of communication. The guides give practical help in countering this problem by providing: an easily accessible aide-mémoire; a recording instrument that makes feedback more systematic; and an overall conceptual framework within which to organize the numerous skills that are discovered one by one as the communication curriculum unfolds. PMID:8736242

  18. Cyrtarachne keralensis Jose, 2011 is a junior synonym of Anepsion maritatum (O. Pickard-Cambridge, 1877) (Araneae, Araneidae).

    Science.gov (United States)

    Malamel, Jobi J; Sankaran, Pradeep M; Joseph, Mathew M; Sebastian, Pothalil A

    2015-11-05

    The Indo-pacific araneid genus Anepsion, with A. rhomboides (L. Koch, 1867) as the type species, was erected by Strand in 1929. He proposed the name Anepsion as a replacement name for Anepsia L. Koch, 1871, preoccupied by Anepsia Gistl, 1848, a dipteran genus (OBIS Australia, 2015). The genus was revised by Chrysanthus (1961, 1969) and currently has 16 described species and 1 subspecies (World Spider Catalog 2015). In the present paper, we are reporting the genus from India for the first time and synonymising Cyrtarachne keralensis Jose, 2011 with Anepsion maritatum O. Pickard-Cambridge, 1877. A redescription and illustrations of both male and female of A. maritatum are provided.

  19. The crystal structure of Z-Gly-Aib-Gly-Aib-OtBu.

    Science.gov (United States)

    Gessmann, Renate; Brückner, Hans; Aivaliotis, Michalis; Petratos, Kyriacos

    2015-06-01

    The synthetic peptide Z-Gly-Aib-Gly-Aib-OtBu was dissolved in methanol and crystallized in a mixture of ethyl acetate and petroleum ether. The crystals belong to the centrosymmetric space group P4/n that is observed less than 0.3% in the Cambridge Structural Database. The first Gly residue assumes a semi-extended conformation (φ ±62°, ψ ∓131°). The right-handed peptide folds in two consecutive β-turns of type II' and type I or an incipient 310 -helix, and the left-handed counterpart folds accordingly in the opposite configuration. In the crystal lattice, one molecule is linked to four neighbors in the ab-plane via hydrogen bonds. These bonds form a continuous network of left- and right-handed molecules. The successive ab-planes stack via apolar contacts in the c-direction. An ethyl acetate molecule is situated on and close to the fourfold axis.

  20. Nuclear Concrete Materials Database Phase I Development

    Energy Technology Data Exchange (ETDEWEB)

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

    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.

  1. XML databases and the semantic web

    CERN Document Server

    Thuraisingham, Bhavani

    2002-01-01

    Efficient access to data, sharing data, extracting information from data, and making use of the information have become urgent needs for today''s corporations. With so much data on the Web, managing it with conventional tools is becoming almost impossible. New tools and techniques are necessary to provide interoperability as well as warehousing between multiple data sources and systems, and to extract information from the databases. XML Databases and the Semantic Web focuses on critical and new Web technologies needed for organizations to carry out transactions on the Web, to understand how to use the Web effectively, and to exchange complex documents on the Web.This reference for database administrators, database designers, and Web designers working in tandem with database technologists covers three emerging technologies of significant impact for electronic business: Extensible Markup Language (XML), semi-structured databases, and the semantic Web. The first two parts of the book explore these emerging techn...

  2. Evolution of a Structure-Searchable Database into a Prototype for a High-Fidelity SmartPhone App for 62 Common Pesticides Used in Delaware

    OpenAIRE

    D'Souza, Malcolm J.; Barile, Benjamin; Aaron F. Givens

    2015-01-01

    Synthetic pesticides are widely used in the modern world for human benefit. They are usually classified according to their intended pest target. In Delaware (DE), approximately 42 percent of the arable land is used for agriculture. In order to manage insectivorous and herbaceous pests (such as insects, weeds, nematodes, and rodents), pesticides are used profusely to biologically control the normal pest's life stage. In this undergraduate project, we first created a usable relational database ...

  3. Tracing thyroid hormone-disrupting compounds: database compilation and structure-activity evaluation for an effect-directed analysis of sediment.

    Science.gov (United States)

    Weiss, Jana M; Andersson, Patrik L; Zhang, Jin; Simon, Eszter; Leonards, Pim E G; Hamers, Timo; Lamoree, Marja H

    2015-07-01

    A variety of anthropogenic compounds has been found to be capable of disrupting the endocrine systems of organisms, in laboratory studies as well as in wildlife. The most widely described endpoint is estrogenicity, but other hormonal disturbances, e.g., thyroid hormone disruption, are gaining more and more attention. Here, we present a review and chemical characterization, using principal component analysis, of organic compounds that have been tested for their capacity to bind competitively to the thyroid hormone transport protein transthyretin (TTR). The database contains 250 individual compounds and technical mixtures, of which 144 compounds are defined as TTR binders. Almost one third of these compounds (n = 52) were even more potent than the natural hormone thyroxine (T4). The database was used as a tool to assist in the identification of thyroid hormone-disrupting compounds (THDCs) in an effect-directed analysis (EDA) study of a sediment sample. Two compounds could be confirmed to contribute to the detected TTR-binding potency in the sediment sample, i.e., triclosan and nonylphenol technical mixture. They constituted less than 1% of the TTR-binding potency of the unfractionated extract. The low rate of explained activity may be attributed to the challenges related to identification of unknown contaminants in combination with the limited knowledge about THDCs in general. This study demonstrates the need for databases containing compound-specific toxicological properties. In the framework of EDA, such a database could be used to assist in the identification and confirmation of causative compounds focusing on thyroid hormone disruption. PMID:25986900

  4. Workshop to establish databases of carbohydrate spectra

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The workshop was organized to formulate guidelines for establishing spectral databases of complex carbohydrates. The databases will enable the scientific community to avoid the great waste of research effort and funds that frequently occurs when carbohydrate chemists are forced to duplicate the structural characterization of previously characterized complex carbohydrates. Chemists waste their effort on repetitive characterizations because in the absence of spectral databases they are unaware they are analyzing a known molecule until they have completely determined its structure. Chemists will be able to avoid much of this wasted effort when the collections of mass and of nuclear magnetic resonance (NMR) spectra initiated at the workshop are subsequently developed into searchable databases. Then scientists only need query the databases with the spectrum or with information defining the spectrum of an unidentified carbohydrate to find out if it has been previously characterized.

  5. A Deductive Database Approach for Complex Objects

    Institute of Scientific and Technical Information of China (English)

    陈其明

    1990-01-01

    A deductive database approach for complex objects reasoning is proposed,which is characterized by handling predicates nesting in terms of mapping hierarchically structured rules and facts to a flattened Horn-clause implementation scheme.

  6. Database design and database administration for a kindergarten

    OpenAIRE

    Vítek, Daniel

    2009-01-01

    The bachelor thesis deals with creation of database design for a standard kindergarten, installation of the designed database into the database system Oracle Database 10g Express Edition and demonstration of the administration tasks in this database system. The verification of the database was proved by a developed access application.

  7. Genome Statute and Legislation Database

    Science.gov (United States)

    ... Database Welcome to the Genome Statute and Legislation Database The Genome Statute and Legislation Database is comprised ... the National Society of Genetic Counselors . Search the Database Search Tips You may select one or more ...

  8. Diagnosis of mild chronic pancreatitis (Cambridge classification): Comparative study using secretin injection-magnetic resonance cholangiopancreatography and endoscopic retrograde pancreatography

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    AIM: To investigate the usefulness of secretin injection MRCP for the diagnosis of mild chronic pancreatitis. METHODS: Sixteen patients having mild chronic pancreatitis according to the Cambridge classification and 12 control subjects with no abnormal findings on the pancreatogram were examined for the diagnostic accuracy of secretin injection-MRCP regarding abnormal branch pancreatic ducts associated with mild chronic pancreatitis (Cambridge Classification), using endoscopic retrograde cholangiopancreatography (ERCP) for comparison. RESULTS: The sensitivity and specificity for abnormal branch pancreatic ducts determined by two reviewers were respectively 55%-63% and 75%-83% in the head, 57%-64% and 82%-83% in the body, and 44%-44%and 72%-76% in the tail of the pancreas. The sensitivity and specificity for mild chronic pancreatitis were 56%-63% and 92%-92%, respectively. Interobserver abnormal branch pancreatic duct and of mild chronic pancreatitis was good to excellent. CONCLUSION: Secretin injection-MRCP might be useful for the diagnosis of mild chronic pancreatitis.

  9. The Cambridge Face Memory Test for Children (CFMT-C): a new tool for measuring face recognition skills in childhood.

    Science.gov (United States)

    Croydon, Abigail; Pimperton, Hannah; Ewing, Louise; Duchaine, Brad C; Pellicano, Elizabeth

    2014-09-01

    Face recognition ability follows a lengthy developmental course, not reaching maturity until well into adulthood. Valid and reliable assessments of face recognition memory ability are necessary to examine patterns of ability and disability in face processing, yet there is a dearth of such assessments for children. We modified a well-known test of face memory in adults, the Cambridge Face Memory Test (Duchaine & Nakayama, 2006, Neuropsychologia, 44, 576-585), to make it developmentally appropriate for children. To establish its utility, we administered either the upright or inverted versions of the computerised Cambridge Face Memory Test - Children (CFMT-C) to 401 children aged between 5 and 12 years. Our results show that the CFMT-C is sufficiently sensitive to demonstrate age-related gains in the recognition of unfamiliar upright and inverted faces, does not suffer from ceiling or floor effects, generates robust inversion effects, and is capable of detecting difficulties in face memory in children diagnosed with autism. Together, these findings indicate that the CFMT-C constitutes a new valid assessment tool for children's face recognition skills.

  10. Conditioning Probabilistic Databases

    CERN Document Server

    Koch, Christoph

    2008-01-01

    Past research on probabilistic databases has studied the problem of answering queries on a static database. Application scenarios of probabilistic databases however often involve the conditioning of a database using additional information in the form of new evidence. The conditioning problem is thus to transform a probabilistic database of priors into a posterior probabilistic database which is materialized for subsequent query processing or further refinement. It turns out that the conditioning problem is closely related to the problem of computing exact tuple confidence values. It is known that exact confidence computation is an NP-hard problem. This has lead researchers to consider approximation techniques for confidence computation. However, neither conditioning nor exact confidence computation can be solved using such techniques. In this paper we present efficient techniques for both problems. We study several problem decomposition methods and heuristics that are based on the most successful search techn...

  11. Database Optimizing Services

    Directory of Open Access Journals (Sweden)

    Adrian GHENCEA

    2010-12-01

    Full Text Available Almost every organization has at its centre a database. The database provides support for conducting different activities, whether it is production, sales and marketing or internal operations. Every day, a database is accessed for help in strategic decisions. The satisfaction therefore of such needs is entailed with a high quality security and availability. Those needs can be realised using a DBMS (Database Management System which is, in fact, software for a database. Technically speaking, it is software which uses a standard method of cataloguing, recovery, and running different data queries. DBMS manages the input data, organizes it, and provides ways of modifying or extracting the data by its users or other programs. Managing the database is an operation that requires periodical updates, optimizing and monitoring.

  12. Glycine Betaine Recognition through Cation−π Interactions in Crystal Structures of Glycine Betaine Complexes with C-Ethyl-pyrogallol[4]arene and C-Ethyl-resorcin[4]arene as Receptors

    Directory of Open Access Journals (Sweden)

    Ikuhide Fujisawa

    2013-04-01

    Full Text Available The glycine betaine (betaine, interacts with several types of proteins with diverse structures in vivo, and in the contact regions, the aromatic rings of protein residues are frequently found beside the trimethylammonium group of betaine, implying the importance of the cation−π interactions in recognition of this molecule. The crystal structures determined by X-ray crystallography of the complexes of betaine and C-ethyl-pyrogallol[4]arene (pyrogallol cyclic tetramer: PCT and betaine and C-ethyl-resorcin[4]arene (resorcinol cyclic tetramer: RCT mimic the conformations of betaine and protein complexes and show that the clathrate conformations are retained by the cation−π interactions. The difference of the conformation feature of betaine in the Protein Data Bank and in the Cambridge Structural Database was found by chance during the research and analyzed with the torsion angles.

  13. Hydrologic, Water-Quality, and Meteorological Data for the Cambridge, Massachusetts, Drinking-Water Source Area, Water Year 2005

    Science.gov (United States)

    Smith, Kirk P.

    2007-01-01

    Records of water quantity, water quality, and meteorological parameters were continuously collected from three reservoirs, two primary streams, and four subbasin tributaries in the Cambridge, Massachusetts, drinking-water source area during water year 2005 (October 2004 through September 2005). Water samples were collected during base-flow conditions and storms in the subbasins of the Cambridge Reservoir and Stony Brook Reservoir drainage areas and analyzed for selected elements, organic constituents, suspended sediment, and Escherichia coli bacteria. These data were collected to assist watershed administrators in managing the drinking-water source area and to identify potential sources of contaminants and trends in contaminant loading to the water supply. Monthly reservoir capacities for the Cambridge Reservoir varied from about 59 to 98 percent during water year 2005, while monthly reservoir capacities for the Stony Brook Reservoir and the Fresh Pond Reservoir were maintained at capacities greater than 84 and 96 percent, respectively. Assuming a water demand of 15 million gallons per day by the city of Cambridge, the volume of water released from the Stony Brook Reservoir to the Charles River during the 2005 water year is equivalent to an annual water surplus of about 119 percent. Recorded precipitation in the source area for the 2005 water year was within 2 inches of the total annual precipitation for the previous 2 water years. The monthly mean specific conductances for the outflow of the Cambridge Reservoir were similar to historical monthly mean values. However, monthly mean specific conductances for Stony Brook near Route 20, in Waltham (U.S. Geological Survey station 01104460), which is the principal tributary feeding the Stony Brook Reservoir, were generally higher than the medians of the monthly mean specific conductances for the period of record. Similarly, monthly mean specific conductances for a small tributary to Stony Brook (U.S. Geological Survey

  14. Supply Chain Initiatives Database

    Energy Technology Data Exchange (ETDEWEB)

    None

    2012-11-01

    The Supply Chain Initiatives Database (SCID) presents innovative approaches to engaging industrial suppliers in efforts to save energy, increase productivity and improve environmental performance. This comprehensive and freely-accessible database was developed by the Institute for Industrial Productivity (IIP). IIP acknowledges Ecofys for their valuable contributions. The database contains case studies searchable according to the types of activities buyers are undertaking to motivate suppliers, target sector, organization leading the initiative, and program or partnership linkages.

  15. Database management systems

    CERN Document Server

    Pallaw, Vijay Krishna

    2010-01-01

    The text covers the fundamental concept and a complete guide to the prac- tical implementation of Database Management Systems. Concepts includes SQL, PL/SQL. These concepts include aspects of Database design, Data- base Languages, and Database System implementation. The entire book is divided into five units to ensure the smooth flow of the subject. The extra methodology makes it very useful for students as well as teachers.

  16. Web Technologies And Databases

    OpenAIRE

    Irina-Nicoleta Odoraba

    2011-01-01

    The database means a collection of many types of occurrences of logical records containing relationships between records and data elementary aggregates. Management System database (DBMS) - a set of programs for creating and operation of a database. Theoretically, any relational DBMS can be used to store data needed by a Web server. Basically, it was observed that the simple DBMS such as Fox Pro or Access is not suitable for Web sites that are used intensively. For large-scale Web applications...

  17. An organic database system

    OpenAIRE

    Kersten, Martin; Siebes, Arno

    1999-01-01

    The pervasive penetration of database technology may suggest that we have reached the end of the database research era. The contrary is true. Emerging technology, in hardware, software, and connectivity, brings a wealth of opportunities to push technology to a new level of maturity. Furthermore, ground breaking results are obtained in Quantum- and DNA-computing using nature as inspiration for its computational models. This paper provides a vision on a new brand of database architectures, i.e....

  18. Nuclear Science References Database

    OpenAIRE

    PRITYCHENKO B.; Běták, E.; B. Singh; Totans, J.

    2013-01-01

    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...

  19. Fingerprint databases for theorems

    OpenAIRE

    Billey, Sara C.; Tenner, Bridget E.

    2013-01-01

    We discuss the advantages of searchable, collaborative, language-independent databases of mathematical results, indexed by "fingerprints" of small and canonical data. Our motivating example is Neil Sloane's massively influential On-Line Encyclopedia of Integer Sequences. We hope to encourage the greater mathematical community to search for the appropriate fingerprints within each discipline, and to compile fingerprint databases of results wherever possible. The benefits of these databases are...

  20. Searching Databases with Keywords

    Institute of Scientific and Technical Information of China (English)

    Shan Wang; Kun-Long Zhang

    2005-01-01

    Traditionally, SQL query language is used to search the data in databases. However, it is inappropriate for end-users, since it is complex and hard to learn. It is the need of end-user, searching in databases with keywords, like in web search engines. This paper presents a survey of work on keyword search in databases. It also includes a brief introduction to the SEEKER system which has been developed.

  1. DOE Order 5480.28 Hanford facilities database

    Energy Technology Data Exchange (ETDEWEB)

    Hayenga, J.L., Westinghouse Hanford

    1996-09-01

    This document describes the development of a database of DOE and/or leased Hanford Site Facilities. The completed database will consist of structure/facility parameters essential to the prioritization of these structures for natural phenomena hazard vulnerability in compliance with DOE Order 5480.28, `Natural Phenomena Hazards Mitigation`. The prioritization process will be based upon the structure/facility vulnerability to natural phenomena hazards. The ACCESS based database, `Hanford Facilities Site Database`, is generated from current Hanford Site information and databases.

  2. Smart Location Database - Download

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Smart Location Database (SLD) summarizes over 80 demographic, built environment, transit service, and destination accessibility attributes for every census...

  3. Database principles programming performance

    CERN Document Server

    O'Neil, Patrick

    2014-01-01

    Database: Principles Programming Performance provides an introduction to the fundamental principles of database systems. This book focuses on database programming and the relationships between principles, programming, and performance.Organized into 10 chapters, this book begins with an overview of database design principles and presents a comprehensive introduction to the concepts used by a DBA. This text then provides grounding in many abstract concepts of the relational model. Other chapters introduce SQL, describing its capabilities and covering the statements and functions of the programmi

  4. Smart Location Database - Service

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Smart Location Database (SLD) summarizes over 80 demographic, built environment, transit service, and destination accessibility attributes for every census...

  5. IVR EFP Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database contains trip-level reports submitted by vessels participating in Exempted Fishery projects with IVR reporting requirements.

  6. Residency Allocation Database

    Data.gov (United States)

    Department of Veterans Affairs — The Residency Allocation Database is used to determine allocation of funds for residency programs offered by Veterans Affairs Medical Centers (VAMCs). Information...

  7. Veterans Administration Databases

    Science.gov (United States)

    The Veterans Administration Information Resource Center provides database and informatics experts, customer service, expert advice, information products, and web technology to VA researchers and others.

  8. Database Publication Practices

    DEFF Research Database (Denmark)

    Bernstein, P.A.; DeWitt, D.; Heuer, A.;

    2005-01-01

    There has been a growing interest in improving the publication processes for database research papers. This panel reports on recent changes in those processes and presents an initial cut at historical data for the VLDB Journal and ACM Transactions on Database Systems.......There has been a growing interest in improving the publication processes for database research papers. This panel reports on recent changes in those processes and presents an initial cut at historical data for the VLDB Journal and ACM Transactions on Database Systems....

  9. Transporter Classification Database (TCDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Transporter Classification Database details a comprehensive classification system for membrane transport proteins known as the Transporter Classification (TC)...

  10. License - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available Trypanosomes Database License License to Use This Database Last updated : 2014/02/04 You may use this database...ense terms regarding the use of this database and the requirements you must follow in using this database.... The license for this database is specified in the Creative Commons Attribution-Sha...re Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: ...e . With regard to this database, you are licensed to: freely access part or whole of this database, and acq

  11. Extracting Schema from an OEM Database

    Institute of Scientific and Technical Information of China (English)

    沈一栋

    1998-01-01

    While the schema-less feature of the OEM(Object Exchange Modl)gives flexibility in representing semi-structured data,it brings difficulty in formulating database queries. Extracting schema from an OEM database then becomes an important research topic.This paper presents a new approach to this topic with th following reatures.(1)In addition to representing th nested label structure of an OEM database,the proposed OEM schema keeps up-tp-date information about instance objects of the database,The object-level information is useful in speeding up query evaluation.(2)The OEM schema is explicitly represented as a label-set,which is easy to construct and update.(3)The OEM schema of a database is statically built and dynamically updated.The time complexity of building the OEM schems is linear in the size of the OEM database.(4)The approach is applicable to a wide range of areas where the underlying schema is much smaller than the database itself(e.g.data warehouses that are made from a set of heterogeneous databases).

  12. 关系数据库理论的与或图等价性分析%Equivalent Analysis of Hypergraph for Relational Database Structure

    Institute of Scientific and Technical Information of China (English)

    李天庆; 张毅; 许俊华; 胡东成

    2001-01-01

    The relational database can be applied based on the rigorous mathematical foundation. But its mathematical theory is too abstract so that its application is kept far beyond the development of theory. The graph theory is then introduced in the paper and the hypergraph is adopted to represent the relational database. Based on the equivalent analysis of hypergraph compared with the traditional ways for relational database,a straight and profound describing tool is designed to achieve the better and easier design,maintenance and amendence via computer programs.%关系数据库有着严密的数学基础,但同时也过于抽象,使理论与应用存在较大差距。文章将图论引入关系数据库,利用与或图的形式来表达关系数据库,同时对基于与或图的关系数据库和传统的关系数据库做关系模式、函数依赖理论、规范理论的等价性分析,并由此提出了一种新的更加直观、深刻的关系数据库描述工具,用以实现关系数据库的计算机设计、维护和修改的程序化。

  13. Structural studies and antimicrobial properties of norcembrane diterpenoid from an Indian soft coral Sinularia inelegans Tixier-Durivault

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, K.S.; Kaminsky, W.H.; Rodrigues, C.; Naik, C.G.

    Research (CSIR), India. We thank the reviewers for helpful suggestions. Supplementary material Crystallographic data for the structural analysis have been deposited at the Cambridge Crystallographic Data Centre (CCDC), with CCDC No. 673651 for 1...

  14. BISC: binary subcomplexes in proteins database.

    Science.gov (United States)

    Juettemann, Thomas; Gerloff, Dietlind L

    2011-01-01

    Binary subcomplexes in proteins database (BISC) is a new protein-protein interaction (PPI) database linking up the two communities most active in their characterization: structural biology and functional genomics researchers. The BISC resource offers users (i) a structural perspective and related information about binary subcomplexes (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD; (ii) selected web services to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces. Among other uses we envision that this resource can help identify possible false positive PPI in current database records. BISC is freely available at http://bisc.cse.ucsc.edu. PMID:21081561

  15. GRAPH DATABASES AND GRAPH VIZUALIZATION

    OpenAIRE

    Klančar, Jure

    2013-01-01

    The thesis presents graph databases. Graph databases are a part of NoSQL databases, which is why this thesis presents basics of NoSQL databases as well. We have focused on advantages of graph databases compared to rela- tional databases. We have used one of native graph databases (Neo4j), to present more detailed processing of graph databases. To get more acquainted with graph databases and its principles, we developed a simple application that uses a Neo4j graph database to...

  16. CDS - Database Administrator's Guide

    Science.gov (United States)

    Day, J. P.

    This guide aims to instruct the CDS database administrator in: o The CDS file system. o The CDS index files. o The procedure for assimilating a new CDS tape into the database. It is assumed that the administrator has read SUN/79.

  17. An organic database system

    NARCIS (Netherlands)

    Kersten, M.L.; Siebes, A.P.J.M.

    1999-01-01

    The pervasive penetration of database technology may suggest that we have reached the end of the database research era. The contrary is true. Emerging technology, in hardware, software, and connectivity, brings a wealth of opportunities to push technology to a new level of maturity. Furthermore, gro

  18. Children's Culture Database (CCD)

    DEFF Research Database (Denmark)

    Wanting, Birgit

    a Dialogue inspired database with documentation, network (individual and institutional profiles) and current news , paper presented at the research seminar: Electronic access to fiction, Copenhagen, November 11-13, 1996......a Dialogue inspired database with documentation, network (individual and institutional profiles) and current news , paper presented at the research seminar: Electronic access to fiction, Copenhagen, November 11-13, 1996...

  19. Atomic Spectra Database (ASD)

    Science.gov (United States)

    SRD 78 NIST Atomic Spectra Database (ASD) (Web, free access)   This database provides access and search capability for NIST critically evaluated data on atomic energy levels, wavelengths, and transition probabilities that are reasonably up-to-date. The NIST Atomic Spectroscopy Data Center has carried out these critical compilations.

  20. Neutrosophic Relational Database Decomposition

    OpenAIRE

    Meena Arora; Ranjit Biswas; Dr. U.S.Pandey

    2011-01-01

    In this paper we present a method of decomposing a neutrosophic database relation with Neutrosophic attributes into basic relational form. Our objective is capable of manipulating incomplete as well as inconsistent information. Fuzzy relation or vague relation can only handle incomplete information. Authors are taking the Neutrosophic Relational database [8],[2] to show how imprecise data can be handled in relational schema.

  1. A Quality System Database

    Science.gov (United States)

    Snell, William H.; Turner, Anne M.; Gifford, Luther; Stites, William

    2010-01-01

    A quality system database (QSD), and software to administer the database, were developed to support recording of administrative nonconformance activities that involve requirements for documentation of corrective and/or preventive actions, which can include ISO 9000 internal quality audits and customer complaints.

  2. Internet Based Open Access Crystallographic Databases

    Science.gov (United States)

    Upreti, Girish; Seipel, Bjoern; Harvey, Morgan; Garrick, Will; Moeck, Peter

    2006-05-01

    Two freely accessible crystallographic databases are discussed: the Crystallographic Open Database (COD, http://crystallography.net) which contains over 37,000 crystal structures, and the Nano-Crystallography Database (NCD, http://nanocrystallography.research.pdx.edu) which we recently started to support image-based nanocrystallography and (nano) materials science education. Both databases collect crystallographic relevant information in a standardized format; the Crystallographic Information File (CIF). CIF is the standard file format adopted by the International Union of Crystallography (http://iucr.org) for the archiving and distribution of crystallographic information. A subset of the COD, the Predicted Crystallographic Online Database, allows for 3D structural displays of structural polyhedra and wireframes of approximately 2,600 entries. Since electron microscopist are interested in simple, yet technologically important materials, the crystallographic information for those materials will be included in our database. At our NCD site, entries in the COD and the NCD can be visualized in three dimensions (3D) along with (2D) lattice fringe fingerprints plots. The latter supports the identification of unknown nanocrystal phases from high-resolution transmission electron microscopy (HRTEM) images. Morphological crystal information from the database ``Bestimmungstabellen f"ur Kristalle/ ???????????? ??????????,'' (A.K. Boldyrew and W.W. Doliwo-Dobrowolsky, Zentrales Wissenschaftlichers Institute der Geologie und Sch"urfung, Leningrad/ Moscow, 1937/1939) will also be included in the NCD to support image-based nanocrystallography in 3D.

  3. The LHCb configuration database

    CERN Document Server

    Abadie, L; Van Herwijnen, Eric; Jacobsson, R; Jost, B; Neufeld, N

    2005-01-01

    The aim of the LHCb configuration database is to store information about all the controllable devices of the detector. The experiment's control system (that uses PVSS ) will configure, start up and monitor the detector from the information in the configuration database. The database will contain devices with their properties, connectivity and hierarchy. The ability to store and rapidly retrieve huge amounts of data, and the navigability between devices are important requirements. We have collected use cases to ensure the completeness of the design. Using the entity relationship modelling technique we describe the use cases as classes with attributes and links. We designed the schema for the tables using relational diagrams. This methodology has been applied to the TFC (switches) and DAQ system. Other parts of the detector will follow later. The database has been implemented using Oracle to benefit from central CERN database support. The project also foresees the creation of tools to populate, maintain, and co...

  4. A Fast Algorithm for Mining Sequential Patterns from Large Databases

    Institute of Scientific and Technical Information of China (English)

    CHEN Ning; CHEN An; ZHOU Longxiang; LIU Lu

    2001-01-01

    Mining sequential patterns from large databases has been recognized by many researchers as an attractive task of data mining and knowledge discovery. Previous algorithms scan the databases for many times, which is often unendurable due to the very large amount of databases. In this paper, the authors introduce an effective algorithm for mining sequential patterns from large databases.In the algorithm, the original database is not used at all for counting the support of sequences after the first pass. Rather, a tidlist structure generated in the previous pass is employed for the purpose based on set intersection operations, avoiding the multiple scans of the databases.

  5. The Filistatidae in the Caribbean region, with a description of the new genus Antilloides, revision of the genus Filistatoides F. O. P.-Cambridge and notes on Kukulcania Lehtinen (Arachnida, Araneae).

    Science.gov (United States)

    Brescovit, Antonio D; Ruiz, Alexander Sánchez; Garcia, Giraldo Alayón

    2016-07-07

    A synopsis of Caribbean filistatid diversity is recorded herein. A new genus, Antilloides, is proposed for five new species exclusively found in the Antilles: A. abeli n. sp., A. cubitas n. sp., and A. mesoliticus n. sp. from Cuba; A. haitises n. sp. from the Dominican Republic; and A. zozo n. sp. from the U. S. Virgin Islands and Puerto Rico. The genus Filistatoides is revised and includes four species: the type species F. insignis F.O.P. Cambridge, which occurs only in Guatemala; the female is described here for the first time; F. polita Franganillo sp. reval., comb. nov., which occurs only in Cuba; F. xichu n. sp. described from Mexico; and F. milloti (Zapfe) which does not appear to belong to the genus based on morphological structures. Additionally, Kukulcania isolinae Alayón is synonymized with Kukulcania hibernalis (Hentz), and new records of its distribution are included for the Greater and Lesser Antilles.

  6. Tsunami early warning in the Mediterranean: role, structure and tricks of pre-computed tsunami simulation databases and matching/forecasting algorithms

    Science.gov (United States)

    Armigliato, Alberto; Pagnoni, Gianluca; Tinti, Stefano

    2014-05-01

    The general idea that pre-computed simulated scenario databases can play a key role in conceiving tsunami early warning systems is commonly accepted by now. But it was only in the last decade that it started to be applied to the Mediterranean region, taking special impulse from initiatives like the GDACS and from recently concluded EU-funded projects such as TRIDEC and NearToWarn. With reference to these two projects and with the possibility of further developing this research line in the frame of the FP7 ASTARTE project, we discuss some results we obtained regarding two major topics, namely the strategies applicable to the tsunami scenario database building and the design and performance assessment of a timely and "reliable" elementary-scenario combination algorithm to be run in real-time. As for the first theme, we take advantage of the experience gained in the test areas of Western Iberia, Rhodes (Greece) and Cyprus to illustrate the criteria with which a "Matching Scenario Database" (MSDB) can be built. These involve 1) the choice of the main tectonic tsunamigenic sources (or areas), 2) their tessellation with matrices of elementary faults whose dimension heavily depend on the particular studied area and must be a compromise between the needs to represent the tsunamigenic area in sufficient detail and of limiting the number of scenarios to be simulated, 3) the computation of the scenarios themselves, 4) the choice of the relevant simulation outputs and the standardisation of their formats. Regarding the matching/forecast algorithm, we want it to select and combine the MSDB elements based on the initial earthquake magnitude and location estimate, and to produce a forecast of (at least) the tsunami arrival time, amplitude and period at the closest tide-level sensors and in all needed forecast points. We discuss the performance of the algorithm in terms of the time needed to produce the forecast after the earthquake is detected. In particular, we analyse the

  7. A Case Study for a Digital Seabed Database:Bohai Sea Engineering Geology Database

    Institute of Scientific and Technical Information of China (English)

    SU Tianyun; ZHAI Shikui; LIU Baohua; LIANG Ruicai; ZHENG Yanpeng; WANG Yong

    2006-01-01

    This paper discusses the designing plan of ORACLE-based Bohai Sea engineering geology database structure from requisition analysis, conceptual structure analysis, logical structure analysis, physical structure analysis and security designing.In the study, we used the object-oriented Unified Modeling Language (UML) to model the conceptual structure of the database and used the powerful function of data management which the object-oriented and relational database ORACLE provides to organize and manage the storage space and improve its security performance.By this means, the database can provide rapid and highly effective performance in data storage, maintenance and query to satisfy the application requisition of the Bohai Sea Oilfield Paradigm Area Information System.

  8. Building, Testing and Evaluating Database Clusters : OSA project

    OpenAIRE

    Kushanova, Olga

    2014-01-01

    The purpose of this study was to research idea and functionality of clustered database systems. Since relational databases started to lose their functionality in modern data size and manipulation a new solution had to be found to overcome the limitations. On one side the relational databases started to support clustered implementations, which made the database more reliable and helped to achieve better performance. On the other side, a totally new data store structure came with NoSQL movement...

  9. Working with graphs in relational and non-relational databases

    OpenAIRE

    Malej, Blaž

    2016-01-01

    The thema of this diploma thesis are graph databases and the comparison between graph databases and relational databases. Graph databases are used to store and process all kinds of graph data. Graphs, as a data structure in computer science, are a set of vertices which are connected with things called edges. Using this principle, we can effectively model various real life examples, e.g. social network of Facebook, for which we could store in graph entities of friends as nodes, and friendships...

  10. A framework to model real-time databases

    CERN Document Server

    Idoudi, Nizar; Duvallet, Claude; Sadeg, Bruno; Bouaziz, Rafik; Gargouri, Faiez

    2010-01-01

    Real-time databases deal with time-constrained data and time-constrained transactions. The design of this kind of databases requires the introduction of new concepts to support both data structures and the dynamic behaviour of the database. In this paper, we give an overview about different aspects of real-time databases and we clarify requirements of their modelling. Then, we present a framework for real-time database design and describe its fundamental operations. A case study demonstrates the validity of the structural model and illustrates SQL queries and Java code generated from the classes of the model

  11. TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico.

    Science.gov (United States)

    Chen, Calvin Yu-Chian

    2011-01-06

    Rapid advancing computational technologies have greatly speeded up the development of computer-aided drug design (CADD). Recently, pharmaceutical companies have increasingly shifted their attentions toward traditional Chinese medicine (TCM) for novel lead compounds. Despite the growing number of studies on TCM, there is no free 3D small molecular structure database of TCM available for virtual screening or molecular simulation. To address this shortcoming, we have constructed TCM Database@Taiwan (http://tcm.cmu.edu.tw/) based on information collected from Chinese medical texts and scientific publications. TCM Database@Taiwan is currently the world's largest non-commercial TCM database. This web-based database contains more than 20,000 pure compounds isolated from 453 TCM ingredients. Both cdx (2D) and Tripos mol2 (3D) formats of each pure compound in the database are available for download and virtual screening. The TCM database includes both simple and advanced web-based query options that can specify search clauses, such as molecular properties, substructures, TCM ingredients, and TCM classification, based on intended drug actions. The TCM database can be easily accessed by all researchers conducting CADD. Over the last eight years, numerous volunteers have devoted their time to analyze TCM ingredients from Chinese medical texts as well as to construct structure files for each isolated compound. We believe that TCM Database@Taiwan will be a milestone on the path towards modernizing traditional Chinese medicine.

  12. A Study of Geolocation Databases

    CERN Document Server

    Shavitt, Yuval

    2010-01-01

    The geographical location of Internet IP addresses has an importance both for academic research and commercial applications. Thus, both commercial and academic databases and tools are available for mapping IP addresses to geographic locations. Evaluating the accuracy of these mapping services is complex since obtaining diverse large scale ground truth is very hard. In this work we evaluate mapping services using an algorithm that groups IP addresses to PoPs, based on structure and delay. This way we are able to group close to 100,000 IP addresses world wide into groups that are known to share a geo-location with high confidence. We provide insight into the strength and weaknesses of IP geolocation databases, and discuss their accuracy and encountered anomalies.

  13. Hellenic Woodland Database

    OpenAIRE

    Fotiadis, Georgios; Tsiripidis, Ioannis; Bergmeier, Erwin; Dimopolous, Panayotis

    2012-01-01

    The Hellenic Woodland Database (GIVD ID EU-GR-006) includes relevés from 59 sources, approximately, as well as unpublished relevés. In total 4,571 relevés have already been entered in the database, but the database is going to continue growing in the near future. Species abundances are recorded according the 7-grade Braun-Blanquet scale. The oldest relevés date back to 1963. For the majority of relevés (more than 90%) environmental data (e.g. altitude, slope aspect, inclination) exis...

  14. LandIT Database

    DEFF Research Database (Denmark)

    Iftikhar, Nadeem; Pedersen, Torben Bach

    2010-01-01

    and reporting purposes. This paper presents the LandIT database; which is result of the LandIT project, which refers to an industrial collaboration project that developed technologies for communication and data integration between farming devices and systems. The LandIT database in principal is based...... on the ISOBUS standard; however the standard is extended with additional requirements, such as gradual data aggregation and flexible exchange of farming data. This paper describes the conceptual and logical schemas of the proposed database based on a real-life farming case study....

  15. Product Licenses Database Application

    CERN Document Server

    Tonkovikj, Petar

    2016-01-01

    The goal of this project is to organize and centralize the data about software tools available to CERN employees, as well as provide a system that would simplify the license management process by providing information about the available licenses and their expiry dates. The project development process is consisted of two steps: modeling the products (software tools), product licenses, legal agreements and other data related to these entities in a relational database and developing the front-end user interface so that the user can interact with the database. The result is an ASP.NET MVC web application with interactive views for displaying and managing the data in the underlying database.

  16. Update History of This Database - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...Trypanosomes Database Update History of This Database Date Update contents 2014/05/07 The contact informatio...p://www.tanpaku.org/tdb/ ) is opened. Joomla SEF URLs by Artio About This Database Database Description Download License Update... History of This Database Site Policy | Contact Us Update History of This Database - Trypanosomes Database | LSDB Archive ...

  17. Unit 43 - Database Concepts I

    OpenAIRE

    Unit 61, CC in GIS; White, Gerald (ACER)

    1990-01-01

    This unit outlines fundamental concepts in database systems and their integration with GIS, including advantages of a database approach, views of a database, database management systems (DBMS), and alternative database models. Three models—hierarchical, network and relational—are discussed in greater detail.

  18. The Jungle Database Search Engine

    DEFF Research Database (Denmark)

    Bøhlen, Michael Hanspeter; Bukauskas, Linas; Dyreson, Curtis

    1999-01-01

    Information spread in in databases cannot be found by current search engines. A database search engine is capable to access and advertise database on the WWW. Jungle is a database search engine prototype developed at Aalborg University. Operating through JDBC connections to remote databases, Jung...

  19. Some operations on database universes

    OpenAIRE

    Brock, E.O. de

    1997-01-01

    Operations such as integration or modularization of databases can be considered as operations on database universes. This paper describes some operations on database universes. Formally, a database universe is a special kind of table. It turns out that various operations on tables constitute interesting operations on database universes as well.

  20. Trajectories of Offending and Their Relation to Life Failure in Late Middle Age: Findings from the Cambridge Study in Delinquent Development

    Science.gov (United States)

    Piquero, Alex R.; Farrington, David P.; Nagin, Daniel S.; Moffitt, Terrie E.

    2010-01-01

    Researchers have hypothesized that over the life course, criminal offending varies with problems in other domains, including life failure and physical and mental health. To examine this issue, the authors use data from the Cambridge Study in Delinquent Development, a prospective longitudinal survey of 411 South London males first studied at age 8…