WorldWideScience

Sample records for network database bind

  1. PL/SQL and Bind Variable: the two ways to increase the efficiency of Network Databases

    Directory of Open Access Journals (Sweden)

    Hitesh KUMAR SHARMA

    2011-12-01

    Full Text Available Modern data analysis applications are driven by the Network databases. They are pushing traditional database and data warehousing technologies beyond their limits due to their massively increasing data volumes and demands for low latency. There are three major challenges in working with network databases: interoperability due to heterogeneous data repositories, proactively due to autonomy of data sources and high efficiency to meet the application demand. This paper provides the two ways to meet the third challenge of network databases. This goal can be achieved by network database administrator with the usage of PL/SQL blocks and bind variable. The paper will explain the effect of PL/SQL block and bind variable on Network database efficiency to meet the modern data analysis application demand.

  2. Rett networked database

    DEFF Research Database (Denmark)

    Grillo, Elisa; Villard, Laurent; Clarke, Angus

    2012-01-01

    Rett syndrome (RTT) is a neurodevelopmental disorder with one principal phenotype and several distinct, atypical variants (Zappella, early seizure onset and congenital variants). Mutations in MECP2 are found in most cases of classic RTT but at least two additional genes, CDKL5 and FOXG1, can unde...... clinical features and mutations. We expect that the network will serve for the recruitment of patients into clinical trials and for developing quality measures to drive up standards of medical management....... underlie some (usually variant) cases. There is only limited correlation between genotype and phenotype. The Rett Networked Database (http://www.rettdatabasenetwork.org/) has been established to share clinical and genetic information. Through an "adaptor" process of data harmonization, a set of 293...... can expand indefinitely. Data are entered by a clinician in each center who supervises accuracy. This network was constructed to make available pooled international data for the study of RTT natural history and genotype-phenotype correlation and to indicate the proportion of patients with specific...

  3. Network-based Database Course

    DEFF Research Database (Denmark)

    Nielsen, J.N.; Knudsen, Morten; Nielsen, Jens Frederik Dalsgaard

    A course in database design and implementation has been de- signed, utilizing existing network facilities. The course is an elementary course for students of computer engineering. Its purpose is to give the students a theoretical database knowledge as well as practical experience with design...... and implementation. A tutorial relational database and the students self-designed databases are implemented on the UNIX system of Aalborg University, thus giving the teacher the possibility of live demonstrations in the lecture room, and the students the possibility of interactive learning in their working rooms...

  4. The NASA Fireball Network Database

    Science.gov (United States)

    Moser, Danielle E.

    2011-01-01

    The NASA Meteoroid Environment Office (MEO) has been operating an automated video fireball network since late-2008. Since that time, over 1,700 multi-station fireballs have been observed. A database containing orbital data and trajectory information on all these events has recently been compiled and is currently being mined for information. Preliminary results are presented here.

  5. The ESID Online Database network.

    Science.gov (United States)

    Guzman, D; Veit, D; Knerr, V; Kindle, G; Gathmann, B; Eades-Perner, A M; Grimbacher, B

    2007-03-01

    Primary immunodeficiencies (PIDs) belong to the group of rare diseases. The European Society for Immunodeficiencies (ESID), is establishing an innovative European patient and research database network for continuous long-term documentation of patients, in order to improve the diagnosis, classification, prognosis and therapy of PIDs. The ESID Online Database is a web-based system aimed at data storage, data entry, reporting and the import of pre-existing data sources in an enterprise business-to-business integration (B2B). The online database is based on Java 2 Enterprise System (J2EE) with high-standard security features, which comply with data protection laws and the demands of a modern research platform. The ESID Online Database is accessible via the official website (http://www.esid.org/). Supplementary data are available at Bioinformatics online.

  6. Nuclear technology databases and information network systems

    International Nuclear Information System (INIS)

    Iwata, Shuichi; Kikuchi, Yasuyuki; Minakuchi, Satoshi

    1993-01-01

    This paper describes the databases related to nuclear (science) technology, and information network. Following contents are collected in this paper: the database developed by JAERI, ENERGY NET, ATOM NET, NUCLEN nuclear information database, INIS, NUclear Code Information Service (NUCLIS), Social Application of Nuclear Technology Accumulation project (SANTA), Nuclear Information Database/Communication System (NICS), reactor materials database, radiation effects database, NucNet European nuclear information database, reactor dismantling database. (J.P.N.)

  7. Temporal Databases in Network Management

    National Research Council Canada - National Science Library

    Gupta, Ajay

    1998-01-01

    .... This thesis discusses issues involved with performing network management, specifically with means of reducing and storing the large quantity of data that networks management tools and systems generate...

  8. The Danish Collaborative Bacteraemia Network (DACOBAN) database

    DEFF Research Database (Denmark)

    Gradel, Kim Oren; Schønheyder, Henrik Carl; Arpi, Magnus

    2014-01-01

    % of the Danish population). The database also includes data on comorbidity from the Danish National Patient Registry, vital status from the Danish Civil Registration System, and clinical data on 31% of nonselected records in the database. Use of the unique civil registration number given to all Danish residents......The Danish Collaborative Bacteraemia Network (DACOBAN) research database includes microbiological data obtained from positive blood cultures from a geographically and demographically well-defined population serviced by three clinical microbiology departments (1.7 million residents, 32...... enables linkage to additional registries for specific research projects. The DACOBAN database is continuously updated, and it currently comprises 39,292 patients with 49,951 bacteremic episodes from 2000 through 2011. The database is part of an international network of population-based bacteremia...

  9. Network and Database Security: Regulatory Compliance, Network, and Database Security - A Unified Process and Goal

    Directory of Open Access Journals (Sweden)

    Errol A. Blake

    2007-12-01

    Full Text Available Database security has evolved; data security professionals have developed numerous techniques and approaches to assure data confidentiality, integrity, and availability. This paper will show that the Traditional Database Security, which has focused primarily on creating user accounts and managing user privileges to database objects are not enough to protect data confidentiality, integrity, and availability. This paper is a compilation of different journals, articles and classroom discussions will focus on unifying the process of securing data or information whether it is in use, in storage or being transmitted. Promoting a change in Database Curriculum Development trends may also play a role in helping secure databases. This paper will take the approach that if one make a conscientious effort to unifying the Database Security process, which includes Database Management System (DBMS selection process, following regulatory compliances, analyzing and learning from the mistakes of others, Implementing Networking Security Technologies, and Securing the Database, may prevent database breach.

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

    Science.gov (United States)

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

    2008-01-01

    The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.

  11. Wisconsin Inventors` Network Database final report

    Energy Technology Data Exchange (ETDEWEB)

    1991-12-04

    The Wisconsin Innovation Service Center at UW-Whitewater received a DOE grant to create an Inventor`s Network Database to assist independent inventors and entrepreneurs with new product development. Since 1980, the Wisconsin Innovation Service Center (WISC) at the University of Wisconsin-Whitewater has assisted independent and small business inventors in estimating the marketability of their new product ideas and inventions. The purpose of the WISC as an economic development entity is to encourage inventors who appear to have commercially viable inventions, based on preliminary market research, to invest in the next stages of development, perhaps investigating prototype development, legal protection, or more in-depth market research. To address inventor`s information needs, WISC developed on electronic database with search capabilities by geographic region and by product category/industry. It targets both public and private resources capable of, and interested in, working with individual and small business inventors. At present, the project includes resources in Wisconsin only.

  12. CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.

    Science.gov (United States)

    Khorshid, Mohsen; Rodak, Christoph; Zavolan, Mihaela

    2011-01-01

    The stability, localization and translation rate of mRNAs are regulated by a multitude of RNA-binding proteins (RBPs) that find their targets directly or with the help of guide RNAs. Among the experimental methods for mapping RBP binding sites, cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution. However, partly due to their vast volume, the data that were so far generated in CLIP experiments have not been put in a form that enables fast and interactive exploration of binding sites. To address this need, we have developed the CLIPZ database and analysis environment. Binding site data for RBPs such as Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking and Polypyrimidine tract binding protein can be visualized at the level of the genome and of individual transcripts. Individual users can upload their own sequence data sets while being able to limit the access to these data to specific users, and analyses of the public and private data sets can be performed interactively. CLIPZ, available at http://www.clipz.unibas.ch, aims to provide an open access repository of information for post-transcriptional regulatory elements.

  13. A Bayesian Network Schema for Lessening Database Inference

    National Research Council Canada - National Science Library

    Chang, LiWu; Moskowitz, Ira S

    2001-01-01

    .... The authors introduce a formal schema for database inference analysis, based upon a Bayesian network structure, which identifies critical parameters involved in the inference problem and represents...

  14. Wireless Sensor Networks Database: Data Management and Implementation

    Directory of Open Access Journals (Sweden)

    Ping Liu

    2014-04-01

    Full Text Available As the core application of wireless sensor network technology, Data management and processing have become the research hotspot in the new database. This article studied mainly data management in wireless sensor networks, in connection with the characteristics of the data in wireless sensor networks, discussed wireless sensor network data query, integrating technology in-depth, proposed a mobile database structure based on wireless sensor network and carried out overall design and implementation for the data management system. In order to achieve the communication rules of above routing trees, network manager uses a simple maintenance algorithm of routing trees. Design ordinary node end, server end in mobile database at gathering nodes and mobile client end that can implement the system, focus on designing query manager, storage modules and synchronous module at server end in mobile database at gathering nodes.

  15. The Network Configuration of an Object Relational Database Management System

    Science.gov (United States)

    Diaz, Philip; Harris, W. C.

    2000-01-01

    The networking and implementation of the Oracle Database Management System (ODBMS) requires developers to have knowledge of the UNIX operating system as well as all the features of the Oracle Server. The server is an object relational database management system (DBMS). By using distributed processing, processes are split up between the database server and client application programs. The DBMS handles all the responsibilities of the server. The workstations running the database application concentrate on the interpretation and display of data.

  16. STITCH 2: an interaction network database for small molecules and proteins

    DEFF Research Database (Denmark)

    Kuhn, Michael; Szklarczyk, Damian; Franceschini, Andrea

    2010-01-01

    Over the last years, the publicly available knowledge on interactions between small molecules and proteins has been steadily increasing. To create a network of interactions, STITCH aims to integrate the data dispersed over the literature and various databases of biological pathways, drug......-target relationships and binding affinities. In STITCH 2, the number of relevant interactions is increased by incorporation of BindingDB, PharmGKB and the Comparative Toxicogenomics Database. The resulting network can be explored interactively or used as the basis for large-scale analyses. To facilitate links to other...... chemical databases, we adopt InChIKeys that allow identification of chemicals with a short, checksum-like string. STITCH 2.0 connects proteins from 630 organisms to over 74,000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/....

  17. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

    DEFF Research Database (Denmark)

    Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T

    2009-01-01

    JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database...... to an active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature...

  18. Database Software Selection for the Egyptian National STI Network.

    Science.gov (United States)

    Slamecka, Vladimir

    The evaluation and selection of information/data management system software for the Egyptian National Scientific and Technical (STI) Network are described. An overview of the state-of-the-art of database technology elaborates on the differences between information retrieval and database management systems (DBMS). The desirable characteristics of…

  19. Insertion algorithms for network model database management systems

    Science.gov (United States)

    Mamadolimov, Abdurashid; Khikmat, Saburov

    2017-12-01

    The network model is a database model conceived as a flexible way of representing objects and their relationships. Its distinguishing feature is that the schema, viewed as a graph in which object types are nodes and relationship types are arcs, forms partial order. When a database is large and a query comparison is expensive then the efficiency requirement of managing algorithms is minimizing the number of query comparisons. We consider updating operation for network model database management systems. We develop a new sequantial algorithm for updating operation. Also we suggest a distributed version of the algorithm.

  20. Network and Database Security: Regulatory Compliance, Network, and Database Security - A Unified Process and Goal

    OpenAIRE

    Errol A. Blake

    2007-01-01

    Database security has evolved; data security professionals have developed numerous techniques and approaches to assure data confidentiality, integrity, and availability. This paper will show that the Traditional Database Security, which has focused primarily on creating user accounts and managing user privileges to database objects are not enough to protect data confidentiality, integrity, and availability. This paper is a compilation of different journals, articles and classroom discussions ...

  1. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

    Science.gov (United States)

    Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T.; Arenillas, David; Zhao, Xiaobei; Valen, Eivind; Yusuf, Dimas; Lenhard, Boris; Wasserman, Wyeth W.; Sandelin, Albin

    2010-01-01

    JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database to date: the database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. The introduction of a yeast division brings the convenience of JASPAR to an active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family. The changes in the database set the system ready for more rapid acquisition of new high-throughput data sources. Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches. PMID:19906716

  2. SoyFN: a knowledge database of soybean functional networks.

    Science.gov (United States)

    Xu, Yungang; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Liu, Yang

    2014-01-01

    Many databases for soybean genomic analysis have been built and made publicly available, but few of them contain knowledge specifically targeting the omics-level gene-gene, gene-microRNA (miRNA) and miRNA-miRNA interactions. Here, we present SoyFN, a knowledge database of soybean functional gene networks and miRNA functional networks. SoyFN provides user-friendly interfaces to retrieve, visualize, analyze and download the functional networks of soybean genes and miRNAs. In addition, it incorporates much information about KEGG pathways, gene ontology annotations and 3'-UTR sequences as well as many useful tools including SoySearch, ID mapping, Genome Browser, eFP Browser and promoter motif scan. SoyFN is a schema-free database that can be accessed as a Web service from any modern programming language using a simple Hypertext Transfer Protocol call. The Web site is implemented in Java, JavaScript, PHP, HTML and Apache, with all major browsers supported. We anticipate that this database will be useful for members of research communities both in soybean experimental science and bioinformatics. Database URL: http://nclab.hit.edu.cn/SoyFN.

  3. ODIN. Online Database Information Network: ODIN Policy & Procedure Manual.

    Science.gov (United States)

    Townley, Charles T.; And Others

    Policies and procedures are outlined for the Online Database Information Network (ODIN), a cooperative of libraries in south-central Pennsylvania, which was organized to improve library services through technology. The first section covers organization and goals, members, and responsibilities of the administrative council and libraries. Patrons…

  4. A distributed database view of network tracking systems

    Science.gov (United States)

    Yosinski, Jason; Paffenroth, Randy

    2008-04-01

    In distributed tracking systems, multiple non-collocated trackers cooperate to fuse local sensor data into a global track picture. Generating this global track picture at a central location is fairly straightforward, but the single point of failure and excessive bandwidth requirements introduced by centralized processing motivate the development of decentralized methods. In many decentralized tracking systems, trackers communicate with their peers via a lossy, bandwidth-limited network in which dropped, delayed, and out of order packets are typical. Oftentimes the decentralized tracking problem is viewed as a local tracking problem with a networking twist; we believe this view can underestimate the network complexities to be overcome. Indeed, a subsequent 'oversight' layer is often introduced to detect and handle track inconsistencies arising from a lack of robustness to network conditions. We instead pose the decentralized tracking problem as a distributed database problem, enabling us to draw inspiration from the vast extant literature on distributed databases. Using the two-phase commit algorithm, a well known technique for resolving transactions across a lossy network, we describe several ways in which one may build a distributed multiple hypothesis tracking system from the ground up to be robust to typical network intricacies. We pay particular attention to the dissimilar challenges presented by network track initiation vs. maintenance and suggest a hybrid system that balances speed and robustness by utilizing two-phase commit for only track initiation transactions. Finally, we present simulation results contrasting the performance of such a system with that of more traditional decentralized tracking implementations.

  5. Extracting reaction networks from databases-opening Pandora's box.

    Science.gov (United States)

    Fearnley, Liam G; Davis, Melissa J; Ragan, Mark A; Nielsen, Lars K

    2014-11-01

    Large quantities of information describing the mechanisms of biological pathways continue to be collected in publicly available databases. At the same time, experiments have increased in scale, and biologists increasingly use pathways defined in online databases to interpret the results of experiments and generate hypotheses. Emerging computational techniques that exploit the rich biological information captured in reaction systems require formal standardized descriptions of pathways to extract these reaction networks and avoid the alternative: time-consuming and largely manual literature-based network reconstruction. Here, we systematically evaluate the effects of commonly used knowledge representations on the seemingly simple task of extracting a reaction network describing signal transduction from a pathway database. We show that this process is in fact surprisingly difficult, and the pathway representations adopted by various knowledge bases have dramatic consequences for reaction network extraction, connectivity, capture of pathway crosstalk and in the modelling of cell-cell interactions. Researchers constructing computational models built from automatically extracted reaction networks must therefore consider the issues we outline in this review to maximize the value of existing pathway knowledge. © The Author 2013. Published by Oxford University Press.

  6. Real-Time Ligand Binding Pocket Database Search Using Local Surface Descriptors

    Science.gov (United States)

    Chikhi, Rayan; Sael, Lee; Kihara, Daisuke

    2010-01-01

    Due to the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of a particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two dimensional pseudo-Zernike moments or the 3D Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark study employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed. PMID:20455259

  7. Handling of network and database instabilities in CORAL

    International Nuclear Information System (INIS)

    Trentadue, R; Valassi, A; Kalkhof, A

    2012-01-01

    The CORAL software is widely used by the LHC experiments for storing and accessing data using relational database technologies. CORAL provides a C++ abstraction layer that supports data persistency for several back-ends and deployment models, direct client access to Oracle servers being one of the most important use cases. Since 2010, several problems have been reported by the LHC experiments in their use of Oracle through CORAL, involving application errors, hangs or crashes after the network or the database servers became temporarily unavailable. CORAL already provided some level of handling of these instabilities, which are due to external causes and cannot be avoided, but this proved to be insufficient in some cases and to be itself the cause of other problems, such as the hangs and crashes mentioned before, in other cases. As a consequence, a major redesign of the CORAL plugins has been implemented, with the aim of making the software more robust against these database and network glitches. The new implementation ensures that CORAL automatically reconnects to Oracle databases in a transparent way whenever possible and gently terminates the application when this is not possible. Internally, this is done by resetting all relevant parameters of the underlying back-end technology (OCI, the Oracle Call Interface). This presentation reports on the status of this work at the time of the CHEP2012 conference, covering the design and implementation of these new features and the outlook for future developments in this area.

  8. CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

    Directory of Open Access Journals (Sweden)

    Baumbach Jan

    2007-11-01

    Full Text Available Abstract Background Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user can be analyzed in the context of known

  9. footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

    Science.gov (United States)

    Sebastian, Alvaro; Contreras-Moreira, Bruno

    2014-01-15

    Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases. FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value. Web site implemented in PHP,Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb.

  10. The River Network of Montenegro in the GIS Database

    Directory of Open Access Journals (Sweden)

    Goran Barović

    2017-06-01

    Full Text Available The subject of this paper is the systematization and precise identification of the structure of river networks in Montenegro in both planimetric and hypsometric dimensions, using cartometry. This includes the precise determination of the morphometric parameters of river flows, their numerical display, graphical display, and documentation. This allows for a number of analyses, for example, of individual catchments, the mutual relations of individual watercourses within a higher order catchment, and the classification of flows according to river and sea basins and their relationship to the environment. In addition, there is the potential for expanding the database further, with a view to continuous, systematic, scientific and practical follow-up in all or part of the geographic space. The cartometric analysis of the river network in Montenegro has a special scientific, and also a social value. In the geographical structure of all countries, including Montenegro, rivers occupy a central place as individual elements and integral parts of the whole. There is almost no human activity which is not related to river flows, or related phenomena and processes. The river network as part of a geographic space continues to gain in importance, and therefore studying it must connect with the other structural elements within which it functions. These are the basic relief characteristics, climate, and certain hydrographic characteristics. A complete theoretical and methodological approach to this problem forms the basis for a scientific understanding of the significance of the river network of Montenegro.

  11. Research on Construction of Road Network Database Based on Video Retrieval Technology

    Directory of Open Access Journals (Sweden)

    Wang Fengling

    2017-01-01

    Full Text Available Based on the characteristics of the video database and the basic structure of the video database and several typical video data models, the segmentation-based multi-level data model is used to describe the landscape information video database, the network database model and the road network management database system. Landscape information management system detailed design and implementation of a detailed preparation.

  12. 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

  13. The European Narcolepsy Network (EU-NN) database

    DEFF Research Database (Denmark)

    Khatami, Ramin; Luca, Gianina; Baumann, Christian R

    2016-01-01

    Narcolepsy with cataplexy is a rare disease with an estimated prevalence of 0.02% in European populations. Narcolepsy shares many features of rare disorders, in particular the lack of awareness of the disease with serious consequences for healthcare supply. Similar to other rare diseases, only a ......, identification of post-marketing medication side-effects, and will contribute to improve clinical trial designs and provide facilities to further develop phase III trials....... Narcolepsy Network is introduced. The database structure, standardization of data acquisition and quality control procedures are described, and an overview provided of the first 1079 patients from 18 European specialized centres. Due to its standardization this continuously increasing data pool is most...

  14. Convolutional neural network architectures for predicting DNA–protein binding

    Science.gov (United States)

    Zeng, Haoyang; Edwards, Matthew D.; Liu, Ge; Gifford, David K.

    2016-01-01

    Motivation: Convolutional neural networks (CNN) have outperformed conventional methods in modeling the sequence specificity of DNA–protein binding. Yet inappropriate CNN architectures can yield poorer performance than simpler models. Thus an in-depth understanding of how to match CNN architecture to a given task is needed to fully harness the power of CNNs for computational biology applications. Results: We present a systematic exploration of CNN architectures for predicting DNA sequence binding using a large compendium of transcription factor datasets. We identify the best-performing architectures by varying CNN width, depth and pooling designs. We find that adding convolutional kernels to a network is important for motif-based tasks. We show the benefits of CNNs in learning rich higher-order sequence features, such as secondary motifs and local sequence context, by comparing network performance on multiple modeling tasks ranging in difficulty. We also demonstrate how careful construction of sequence benchmark datasets, using approaches that control potentially confounding effects like positional or motif strength bias, is critical in making fair comparisons between competing methods. We explore how to establish the sufficiency of training data for these learning tasks, and we have created a flexible cloud-based framework that permits the rapid exploration of alternative neural network architectures for problems in computational biology. Availability and Implementation: All the models analyzed are available at http://cnn.csail.mit.edu. Contact: gifford@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27307608

  15. Wisconsin Inventors' Network Database final report

    Energy Technology Data Exchange (ETDEWEB)

    1991-12-04

    The Wisconsin Innovation Service Center at UW-Whitewater received a DOE grant to create an Inventor's Network Database to assist independent inventors and entrepreneurs with new product development. Since 1980, the Wisconsin Innovation Service Center (WISC) at the University of Wisconsin-Whitewater has assisted independent and small business inventors in estimating the marketability of their new product ideas and inventions. The purpose of the WISC as an economic development entity is to encourage inventors who appear to have commercially viable inventions, based on preliminary market research, to invest in the next stages of development, perhaps investigating prototype development, legal protection, or more in-depth market research. To address inventor's information needs, WISC developed on electronic database with search capabilities by geographic region and by product category/industry. It targets both public and private resources capable of, and interested in, working with individual and small business inventors. At present, the project includes resources in Wisconsin only.

  16. 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

  17. East-China Geochemistry Database (ECGD):A New Networking Database for North China Craton

    Science.gov (United States)

    Wang, X.; Ma, W.

    2010-12-01

    North China Craton is one of the best natural laboratories that research some Earth Dynamic questions[1]. Scientists made much progress in research on this area, and got vast geochemistry data, which are essential for answering many fundamental questions about the age, composition, structure, and evolution of the East China area. But the geochemical data have long been accessible only through the scientific literature and theses where they have been widely dispersed, making it difficult for the broad Geosciences community to find, access and efficiently use the full range of available data[2]. How to effectively store, manage, share and reuse the existing geochemical data in the North China Craton area? East-China Geochemistry Database(ECGD) is a networking geochemical scientific database system that has been designed based on WebGIS and relational database for the structured storage and retrieval of geochemical data and geological map information. It is integrated the functions of data retrieval, spatial visualization and online analysis. ECGD focus on three areas: 1.Storage and retrieval of geochemical data and geological map information. Research on the characters of geochemical data, including its composing and connecting of each other, we designed a relational database, which based on geochemical relational data model, to store a variety of geological sample information such as sampling locality, age, sample characteristics, reference, major elements, rare earth elements, trace elements and isotope system et al. And a web-based user-friendly interface is provided for constructing queries. 2.Data view. ECGD is committed to online data visualization by different ways, especially to view data in digital map with dynamic way. Because ECGD was integrated WebGIS technology, the query results can be mapped on digital map, which can be zoomed, translation and dot selection. Besides of view and output query results data by html, txt or xls formats, researchers also can

  18. DeepSite: protein-binding site predictor using 3D-convolutional neural networks.

    Science.gov (United States)

    Jiménez, J; Doerr, S; Martínez-Rosell, G; Rose, A S; De Fabritiis, G

    2017-10-01

    An important step in structure-based drug design consists in the prediction of druggable binding sites. Several algorithms for detecting binding cavities, those likely to bind to a small drug compound, have been developed over the years by clever exploitation of geometric, chemical and evolutionary features of the protein. Here we present a novel knowledge-based approach that uses state-of-the-art convolutional neural networks, where the algorithm is learned by examples. In total, 7622 proteins from the scPDB database of binding sites have been evaluated using both a distance and a volumetric overlap approach. Our machine-learning based method demonstrates superior performance to two other competitive algorithmic strategies. DeepSite is freely available at www.playmolecule.org. Users can submit either a PDB ID or PDB file for pocket detection to our NVIDIA GPU-equipped servers through a WebGL graphical interface. gianni.defabritiis@upf.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  19. Peptide microarrays to probe for competition for binding sites in a protein interaction network

    NARCIS (Netherlands)

    Sinzinger, M.D.S.; Ruttekolk, I.R.R.; Gloerich, J.; Wessels, H.; Chung, Y.D.; Adjobo-Hermans, M.J.W.; Brock, R.E.

    2013-01-01

    Cellular protein interaction networks are a result of the binding preferences of a particular protein and the entirety of interactors that mutually compete for binding sites. Therefore, the reconstruction of interaction networks by the accumulation of interaction networks for individual proteins

  20. 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...

  1. A Database Design and Development Case: NanoTEK Networks

    Science.gov (United States)

    Ballenger, Robert M.

    2010-01-01

    This case provides a real-world project-oriented case study for students enrolled in a management information systems, database management, or systems analysis and design course in which database design and development are taught. The case consists of a business scenario to provide background information and details of the unique operating…

  2. 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.

  3. SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

    Science.gov (United States)

    Foerster, Hartmut; Bombarely, Aureliano; Battey, James N D; Sierro, Nicolas; Ivanov, Nikolai V; Mueller, Lukas A

    2018-01-01

    Abstract SolCyc is the entry portal to pathway/genome databases (PGDBs) for major species of the Solanaceae family hosted at the Sol Genomics Network. Currently, SolCyc comprises six organism-specific PGDBs for tomato, potato, pepper, petunia, tobacco and one Rubiaceae, coffee. The metabolic networks of those PGDBs have been computationally predicted by the pathologic component of the pathway tools software using the manually curated multi-domain database MetaCyc (http://www.metacyc.org/) as reference. SolCyc has been recently extended by taxon-specific databases, i.e. the family-specific SolanaCyc database, containing only curated data pertinent to species of the nightshade family, and NicotianaCyc, a genus-specific database that stores all relevant metabolic data of the Nicotiana genus. Through manual curation of the published literature, new metabolic pathways have been created in those databases, which are complemented by the continuously updated, relevant species-specific pathways from MetaCyc. At present, SolanaCyc comprises 199 pathways and 29 superpathways and NicotianaCyc accounts for 72 pathways and 13 superpathways. Curator-maintained, taxon-specific databases such as SolanaCyc and NicotianaCyc are characterized by an enrichment of data specific to these taxa and free of falsely predicted pathways. Both databases have been used to update recently created Nicotiana-specific databases for Nicotiana tabacum, Nicotiana benthamiana, Nicotiana sylvestris and Nicotiana tomentosiformis by propagating verifiable data into those PGDBs. In addition, in-depth curation of the pathways in N.tabacum has been carried out which resulted in the elimination of 156 pathways from the 569 pathways predicted by pathway tools. Together, in-depth curation of the predicted pathway network and the supplementation with curated data from taxon-specific databases has substantially improved the curation status of the species–specific N.tabacum PGDB. The implementation of this

  4. The research of network database security technology based on web service

    Science.gov (United States)

    Meng, Fanxing; Wen, Xiumei; Gao, Liting; Pang, Hui; Wang, Qinglin

    2013-03-01

    Database technology is one of the most widely applied computer technologies, its security is becoming more and more important. This paper introduced the database security, network database security level, studies the security technology of the network database, analyzes emphatically sub-key encryption algorithm, applies this algorithm into the campus-one-card system successfully. The realization process of the encryption algorithm is discussed, this method is widely used as reference in many fields, particularly in management information system security and e-commerce.

  5. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.

    Science.gov (United States)

    Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W

    2014-01-01

    JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR-the JASPAR CORE subcollection, which contains curated, non-redundant profiles-with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods.

  6. Fish Karyome: A karyological information network database of Indian Fishes.

    Science.gov (United States)

    Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra

    2012-01-01

    'Fish Karyome', a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.

  7. A meta-database comparison from various European Research and Monitoring Networks dedicated to forest sites

    Czech Academy of Sciences Publication Activity Database

    Danielewska, A.; Clarke, N.; Olejnik, Janusz; Hansen, K.; de Vries, W.; Lundin, L.; Tuovinen, J-P.; Fischer, R.; Urbaniak, M.; Paoletti, E.

    2013-01-01

    Roč. 6, JAN 2013 (2013), s. 1-9 ISSN 1971-7458 Institutional support: RVO:67179843 Keywords : Research and Monitoring Network * Meta- database * Forest * Monitoring Subject RIV: EH - Ecology, Behaviour Impact factor: 1.150, year: 2013

  8. Research on Big Data Attribute Selection Method in Submarine Optical Fiber Network Fault Diagnosis Database

    Directory of Open Access Journals (Sweden)

    Chen Ganlang

    2017-11-01

    Full Text Available At present, in the fault diagnosis database of submarine optical fiber network, the attribute selection of large data is completed by detecting the attributes of the data, the accuracy of large data attribute selection cannot be guaranteed. In this paper, a large data attribute selection method based on support vector machines (SVM for fault diagnosis database of submarine optical fiber network is proposed. Mining large data in the database of optical fiber network fault diagnosis, and calculate its attribute weight, attribute classification is completed according to attribute weight, so as to complete attribute selection of large data. Experimental results prove that ,the proposed method can improve the accuracy of large data attribute selection in fault diagnosis database of submarine optical fiber network, and has high use value.

  9. CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks

    DEFF Research Database (Denmark)

    Abreu, Vinicius A C; Almeida, Sintia; Tiwari, Sandeep

    2015-01-01

    gene regulatory network can lead to various practical applications, creating a greater understanding of how organisms control their cellular behavior. DESCRIPTION: In this work, we present a new database, CMRegNet for the gene regulatory networks of Corynebacterium glutamicum ATCC 13032......Net to date the most comprehensive database of regulatory interactions of CMNR bacteria. The content of CMRegNet is publicly available online via a web interface found at http://lgcm.icb.ufmg.br/cmregnet ....

  10. The shortest path algorithm performance comparison in graph and relational database on a transportation network

    Directory of Open Access Journals (Sweden)

    Mario Miler

    2014-02-01

    Full Text Available In the field of geoinformation and transportation science, the shortest path is calculated on graph data mostly found in road and transportation networks. This data is often stored in various database systems. Many applications dealing with transportation network require calculation of the shortest path. The objective of this research is to compare the performance of Dijkstra shortest path calculation in PostgreSQL (with pgRouting and Neo4j graph database for the purpose of determining if there is any difference regarding the speed of the calculation. Benchmarking was done on commodity hardware using OpenStreetMap road network. The first assumption is that Neo4j graph database would be well suited for the shortest path calculation on transportation networks but this does not come without some cost. Memory proved to be an issue in Neo4j setup when dealing with larger transportation networks.

  11. Location in Mobile Networks Using Database Correlation (DCM

    Directory of Open Access Journals (Sweden)

    Michal Mada

    2008-01-01

    Full Text Available The article presents one of the methods of location (DCM, which is suitable for using in urban environments, where other methods are less accurate. The principle of this method is in comparison of measured samples of signal with samples stored in database. Next the article deals with methods for processing the data and other possibilities of correction of location.

  12. DMPD: Silica binding and toxicity in alveolar macrophages. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18226603 Silica binding and toxicity in alveolar macrophages. Hamilton RF Jr, Thaku...l) Show Silica binding and toxicity in alveolar macrophages. PubmedID 18226603 Title Silica binding and toxicity in alveolar macropha...ges. Authors Hamilton RF Jr, Thakur SA, Holian A. Public

  13. DMPD: LPS-binding proteins and receptors. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 9665271 LPS-binding proteins and receptors. Fenton MJ, Golenbock DT. J Leukoc Biol.... 1998 Jul;64(1):25-32. (.png) (.svg) (.html) (.csml) Show LPS-binding proteins and receptors. PubmedID 9665271 Title LPS-binding prot...eins and receptors. Authors Fenton MJ, Golenbock DT. Publication J Leukoc Biol. 199

  14. DMPD: Lipopolysaccharide-binding molecules: transporters, blockers and sensors. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 15241548 Lipopolysaccharide-binding molecules: transporters, blockers and sensors. ...binding molecules: transporters, blockers and sensors. PubmedID 15241548 Title Lipopolysaccharide-binding molecules: transport...Chaby R. Cell Mol Life Sci. 2004 Jul;61(14):1697-713. (.png) (.svg) (.html) (.csml) Show Lipopolysaccharide-

  15. Computer application for database management and networking of service radio physics

    International Nuclear Information System (INIS)

    Ferrando Sanchez, A.; Cabello Murillo, E.; Diaz Fuentes, R.; Castro Novais, J.; Clemente Gutierrez, F.; Casa de Juan, M. A. de la; Adaimi Hernandez, P.

    2011-01-01

    The databases in the quality control prove to be a powerful tool for recording, management and statistical process control. Developed in a Windows environment and under Access (Micros of Office) our service implements this philosophy on the canter's computer network. A computer that acts as the server provides the database to the treatment units to record quality control measures daily and incidents. To remove shortcuts stop working with data migration, possible use of duplicate and erroneous data loss because of errors in network connections, which are common problems, we proceeded to manage connections and access to databases ease of maintenance and use horn to all service personnel.

  16. Multiple k Nearest Neighbor Query Processing in Spatial Network Databases

    DEFF Research Database (Denmark)

    Xuegang, Huang; Jensen, Christian Søndergaard; Saltenis, Simonas

    2006-01-01

    This paper concerns the efficient processing of multiple k nearest neighbor queries in a road-network setting. The assumed setting covers a range of scenarios such as the one where a large population of mobile service users that are constrained to a road network issue nearest-neighbor queries...... for points of interest that are accessible via the road network. Given multiple k nearest neighbor queries, the paper proposes progressive techniques that selectively cache query results in main memory and subsequently reuse these for query processing. The paper initially proposes techniques for the case...... where an upper bound on k is known a priori and then extends the techniques to the case where this is not so. Based on empirical studies with real-world data, the paper offers insight into the circumstances under which the different proposed techniques can be used with advantage for multiple k nearest...

  17. Content-based organization of the information space in multi-database networks

    NARCIS (Netherlands)

    Papazoglou, M.; Milliner, S.

    1998-01-01

    Abstract. Rapid growth in the volume of network-available data, complexity, diversity and terminological fluctuations, at different data sources, render network-accessible information increasingly difficult to achieve. The situation is particularly cumbersome for users of multi-database systems who

  18. Analyzing GAIAN Database (GaianDB) on a Tactical Network

    Science.gov (United States)

    2015-11-30

    databases, and other files, and exposes them as 1 unified structured query language ( SQL )-compliant data source. This “store locally query anywhere...UDP server that could communicate directly with the CSRs via the CSR’s serial port. However, GAIAN has over 800,000 lines of source code. It...management, by which all would have to be modified to communicate with our server and maintain utility. Not only did we quickly realize that this

  19. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

    DEFF Research Database (Denmark)

    Bryne, J.C.; Valen, E.; Tang, M.H.E.

    2008-01-01

    JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR...... databasethe JASPAR CORE sub-databasehas increased by 12 in size, and three new specialized sub-databases have been added. New functions include clustering of matrix models by similarity, generation of random matrices by sampling from selected sets of existing models and a language-independent Web Service...

  20. Trajectory Based Optimal Segment Computation in Road Network Databases

    DEFF Research Database (Denmark)

    Li, Xiaohui; Ceikute, Vaida; Jensen, Christian S.

    2013-01-01

    Finding a location for a new facility such that the facility attracts the maximal number of customers is a challenging problem. Existing studies either model customers as static sites and thus do not consider customer movement, or they focus on theoretical aspects and do not provide solutions...... that are shown empirically to be scalable. Given a road network, a set of existing facilities, and a collection of customer route traversals, an optimal segment query returns the optimal road network segment(s) for a new facility. We propose a practical framework for computing this query, where each route...... traversal is assigned a score that is distributed among the road segments covered by the route according to a score distribution model. The query returns the road segment(s) with the highest score. To achieve low latency, it is essential to prune the very large search space. We propose two algorithms...

  1. Trajectory Based Optimal Segment Computation in Road Network Databases

    DEFF Research Database (Denmark)

    Li, Xiaohui; Ceikute, Vaida; Jensen, Christian S.

    Finding a location for a new facility such that the facility attracts the maximal number of customers is a challenging problem. Existing studies either model customers as static sites and thus do not consider customer movement, or they focus on theoretical aspects and do not provide solutions...... that are shown empirically to be scalable. Given a road network, a set of existing facilities, and a collection of customer route traversals, an optimal segment query returns the optimal road network segment(s) for a new facility. We propose a practical framework for computing this query, where each route...... traversal is assigned a score that is distributed among the road segments covered by the route according to a score distribution model. The query returns the road segment(s) with the highest score. To achieve low latency, it is essential to prune the very large search space. We propose two algorithms...

  2. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles.

    Science.gov (United States)

    Mathelier, Anthony; Fornes, Oriol; Arenillas, David J; Chen, Chih-Yu; Denay, Grégoire; Lee, Jessica; Shi, Wenqiang; Shyr, Casper; Tan, Ge; Worsley-Hunt, Rebecca; Zhang, Allen W; Parcy, François; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W

    2016-01-04

    JASPAR (http://jaspar.genereg.net) is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we expanded the JASPAR CORE collection with 494 new TF binding profiles (315 in vertebrates, 11 in nematodes, 3 in insects, 1 in fungi and 164 in plants) and updated 59 profiles (58 in vertebrates and 1 in fungi). The introduced profiles represent an 83% expansion and 10% update when compared to the previous release. We updated the structural annotation of the TF DNA binding domains (DBDs) following a published hierarchical structural classification. In addition, we introduced 130 transcription factor flexible models trained on ChIP-seq data for vertebrates, which capture dinucleotide dependencies within TF binding sites. This new JASPAR release is accompanied by a new web tool to infer JASPAR TF binding profiles recognized by a given TF protein sequence. Moreover, we provide the users with a Ruby module complementing the JASPAR API to ease programmatic access and use of the JASPAR collection of profiles. Finally, we provide the JASPAR2016 R/Bioconductor data package with the data of this release. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. 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.

  4. Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

    Science.gov (United States)

    Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C; Hoeng, Julia

    2015-01-01

    With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com © The Author(s) 2015. Published by Oxford University Press.

  5. Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

    Science.gov (United States)

    Laukens, Kris; Hollunder, Jens; Dang, Thanh Hai; De Jaeger, Geert; Kuiper, Martin; Witters, Erwin; Verschoren, Alain; Van Leemput, Koenraad

    2010-07-01

    Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file formats, or directly from external databases through specialized third party plugins. However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented. A new Cytoscape plugin 'CytoSQL' is developed to connect Cytoscape to any relational database. It allows to launch SQL ('Structured Query Language') queries from within Cytoscape, with the option to inject node or edge features of an existing network as SQL arguments, and to convert the retrieved data to Cytoscape network components. Supported by a set of case studies we demonstrate the flexibility and the power of the CytoSQL plugin in converting specific data subsets into meaningful network representations. CytoSQL offers a unified approach to let Cytoscape interact with relational databases. Thanks to the power of the SQL syntax, this tool can rapidly generate and enrich networks according to very complex criteria. The plugin is available at http://www.ptools.ua.ac.be/CytoSQL.

  6. Development of a neoclassical transport database by neural network fitting in LHD

    International Nuclear Information System (INIS)

    Wakasa, Arimitsu; Oikawa, Shun-ichi; Murakami, Sadayoshi; Yamada, Hiroshi; Yokoyama, Masayuki; Watanabe, Kiyomasa; Maassberg, Hening; Beidler, Craig D.

    2004-01-01

    A database of neoclassical transport coefficients for the Large Helical Device is developed using normalized mono-energetic diffusion coefficients evaluated by Monte Carlo simulation code; DCOM. A neural network fitting method is applied to take energy convolutions with the given distribution function, e.g. Maxwellian. The database gives the diffusion coefficients as a function of the collision frequency, the radial electric field and the minor radius position. (author)

  7. Data Linkage Graph: computation, querying and knowledge discovery of life science database networks

    Directory of Open Access Journals (Sweden)

    Lange Matthias

    2007-12-01

    Full Text Available To support the interpretation of measured molecular facts, like gene expression experiments or EST sequencing, the functional or the system biological context has to be considered. Doing so, the relationship to existing biological knowledge has to be discovered. In general, biological knowledge is worldwide represented in a network of databases. In this paper we present a method for knowledge extraction in life science databases, which prevents the scientists from screen scraping and web clicking approaches.

  8. Distributed Database Semantic Integration of Wireless Sensor Network to Access the Environmental Monitoring System

    Directory of Open Access Journals (Sweden)

    Ubaidillah Umar

    2018-06-01

    Full Text Available A wireless sensor network (WSN works continuously to gather information from sensors that generate large volumes of data to be handled and processed by applications. Current efforts in sensor networks focus more on networking and development services for a variety of applications and less on processing and integrating data from heterogeneous sensors. There is an increased need for information to become shareable across different sensors, database platforms, and applications that are not easily implemented in traditional database systems. To solve the issue of these large amounts of data from different servers and database platforms (including sensor data, a semantic sensor web service platform is needed to enable a machine to extract meaningful information from the sensor’s raw data. This additionally helps to minimize and simplify data processing and to deduce new information from existing data. This paper implements a semantic web data platform (SWDP to manage the distribution of data sensors based on the semantic database system. SWDP uses sensors for temperature, humidity, carbon monoxide, carbon dioxide, luminosity, and noise. The system uses the Sesame semantic web database for data processing and a WSN to distribute, minimize, and simplify information processing. The sensor nodes are distributed in different places to collect sensor data. The SWDP generates context information in the form of a resource description framework. The experiment results demonstrate that the SWDP is more efficient than the traditional database system in terms of memory usage and processing time.

  9. New model for distributed multimedia databases and its application to networking of museums

    Science.gov (United States)

    Kuroda, Kazuhide; Komatsu, Naohisa; Komiya, Kazumi; Ikeda, Hiroaki

    1998-02-01

    This paper proposes a new distributed multimedia data base system where the databases storing MPEG-2 videos and/or super high definition images are connected together through the B-ISDN's, and also refers to an example of the networking of museums on the basis of the proposed database system. The proposed database system introduces a new concept of the 'retrieval manager' which functions an intelligent controller so that the user can recognize a set of image databases as one logical database. A user terminal issues a request to retrieve contents to the retrieval manager which is located in the nearest place to the user terminal on the network. Then, the retrieved contents are directly sent through the B-ISDN's to the user terminal from the server which stores the designated contents. In this case, the designated logical data base dynamically generates the best combination of such a retrieving parameter as a data transfer path referring to directly or data on the basis of the environment of the system. The generated retrieving parameter is then executed to select the most suitable data transfer path on the network. Therefore, the best combination of these parameters fits to the distributed multimedia database system.

  10. An online database for informing ecological network models: http://kelpforest.ucsc.edu.

    Science.gov (United States)

    Beas-Luna, Rodrigo; Novak, Mark; Carr, Mark H; Tinker, Martin T; Black, August; Caselle, Jennifer E; Hoban, Michael; Malone, Dan; Iles, Alison

    2014-01-01

    Ecological network models and analyses are recognized as valuable tools for understanding the dynamics and resiliency of ecosystems, and for informing ecosystem-based approaches to management. However, few databases exist that can provide the life history, demographic and species interaction information necessary to parameterize ecological network models. Faced with the difficulty of synthesizing the information required to construct models for kelp forest ecosystems along the West Coast of North America, we developed an online database (http://kelpforest.ucsc.edu/) to facilitate the collation and dissemination of such information. Many of the database's attributes are novel yet the structure is applicable and adaptable to other ecosystem modeling efforts. Information for each taxonomic unit includes stage-specific life history, demography, and body-size allometries. Species interactions include trophic, competitive, facilitative, and parasitic forms. Each data entry is temporally and spatially explicit. The online data entry interface allows researchers anywhere to contribute and access information. Quality control is facilitated by attributing each entry to unique contributor identities and source citations. The database has proven useful as an archive of species and ecosystem-specific information in the development of several ecological network models, for informing management actions, and for education purposes (e.g., undergraduate and graduate training). To facilitate adaptation of the database by other researches for other ecosystems, the code and technical details on how to customize this database and apply it to other ecosystems are freely available and located at the following link (https://github.com/kelpforest-cameo/databaseui).

  11. The Fragment Network: A Chemistry Recommendation Engine Built Using a Graph Database.

    Science.gov (United States)

    Hall, Richard J; Murray, Christopher W; Verdonk, Marcel L

    2017-07-27

    The hit validation stage of a fragment-based drug discovery campaign involves probing the SAR around one or more fragment hits. This often requires a search for similar compounds in a corporate collection or from commercial suppliers. The Fragment Network is a graph database that allows a user to efficiently search chemical space around a compound of interest. The result set is chemically intuitive, naturally grouped by substitution pattern and meaningfully sorted according to the number of observations of each transformation in medicinal chemistry databases. This paper describes the algorithms used to construct and search the Fragment Network and provides examples of how it may be used in a drug discovery context.

  12. Design of special purpose database for credit cooperation bank business processing network system

    Science.gov (United States)

    Yu, Yongling; Zong, Sisheng; Shi, Jinfa

    2011-12-01

    With the popularization of e-finance in the city, the construction of e-finance is transfering to the vast rural market, and quickly to develop in depth. Developing the business processing network system suitable for the rural credit cooperative Banks can make business processing conveniently, and have a good application prospect. In this paper, We analyse the necessity of adopting special purpose distributed database in Credit Cooperation Band System, give corresponding distributed database system structure , design the specical purpose database and interface technology . The application in Tongbai Rural Credit Cooperatives has shown that system has better performance and higher efficiency.

  13. Databases as policy instruments. About extending networks as evidence-based policy

    Directory of Open Access Journals (Sweden)

    Stoevelaar Herman

    2007-12-01

    Full Text Available Abstract Background This article seeks to identify the role of databases in health policy. Access to information and communication technologies has changed traditional relationships between the state and professionals, creating new systems of surveillance and control. As a result, databases may have a profound effect on controlling clinical practice. Methods We conducted three case studies to reconstruct the development and use of databases as policy instruments. Each database was intended to be employed to control the use of one particular pharmaceutical in the Netherlands (growth hormone, antiretroviral drugs for HIV and Taxol, respectively. We studied the archives of the Dutch Health Insurance Board, conducted in-depth interviews with key informants and organized two focus groups, all focused on the use of databases both in policy circles and in clinical practice. Results Our results demonstrate that policy makers hardly used the databases, neither for cost control nor for quality assurance. Further analysis revealed that these databases facilitated self-regulation and quality assurance by (national bodies of professionals, resulting in restrictive prescription behavior amongst physicians. Conclusion The databases fulfill control functions that were formerly located within the policy realm. The databases facilitate collaboration between policy makers and physicians, since they enable quality assurance by professionals. Delegating regulatory authority downwards into a network of physicians who control the use of pharmaceuticals seems to be a good alternative for centralized control on the basis of monitoring data.

  14. Experience and Lessons learnt from running High Availability Databases on Network Attached Storage

    CERN Document Server

    Guijarro, Manuel

    2008-01-01

    The Database and Engineering Services Group of CERN's Information Technology Department supplies the Oracle Central Database services used in many activities at CERN. In order to provide High Availability and ease management for those services, a NAS (Network Attached Storage) based infrastructure has been setup. It runs several instances of the Oracle RAC (Real Application Cluster) using NFS (Network File System) as shared disk space for RAC purposes and Data hosting. It is composed of two private LANs (Local Area Network), one to provide access to the NAS filers and a second to implement the Oracle RAC private interconnect, both using Network Bonding. NAS filers are configured in partnership to prevent having single points of failure and to provide automatic NAS filer fail-over.

  15. Experience and lessons learnt from running high availability databases on network attached storage

    International Nuclear Information System (INIS)

    Guijarro, M; Gaspar, R

    2008-01-01

    The Database and Engineering Services Group of CERN's Information Technology Department supplies the Oracle Central Database services used in many activities at CERN. In order to provide High Availability and ease management for those services, a NAS (Network Attached Storage) based infrastructure has been setup. It runs several instances of the Oracle RAC (Real Application Cluster) using NFS (Network File System) as shared disk space for RAC purposes and Data hosting. It is composed of two private LANs (Local Area Network), one to provide access to the NAS filers and a second to implement the Oracle RAC private interconnect, both using Network Bonding. NAS filers are configured in partnership to prevent having single points of failure and to provide automatic NAS filer fail-over

  16. A Bayesian network approach to the database search problem in criminal proceedings

    Science.gov (United States)

    2012-01-01

    Background The ‘database search problem’, that is, the strengthening of a case - in terms of probative value - against an individual who is found as a result of a database search, has been approached during the last two decades with substantial mathematical analyses, accompanied by lively debate and centrally opposing conclusions. This represents a challenging obstacle in teaching but also hinders a balanced and coherent discussion of the topic within the wider scientific and legal community. This paper revisits and tracks the associated mathematical analyses in terms of Bayesian networks. Their derivation and discussion for capturing probabilistic arguments that explain the database search problem are outlined in detail. The resulting Bayesian networks offer a distinct view on the main debated issues, along with further clarity. Methods As a general framework for representing and analyzing formal arguments in probabilistic reasoning about uncertain target propositions (that is, whether or not a given individual is the source of a crime stain), this paper relies on graphical probability models, in particular, Bayesian networks. This graphical probability modeling approach is used to capture, within a single model, a series of key variables, such as the number of individuals in a database, the size of the population of potential crime stain sources, and the rarity of the corresponding analytical characteristics in a relevant population. Results This paper demonstrates the feasibility of deriving Bayesian network structures for analyzing, representing, and tracking the database search problem. The output of the proposed models can be shown to agree with existing but exclusively formulaic approaches. Conclusions The proposed Bayesian networks allow one to capture and analyze the currently most well-supported but reputedly counter-intuitive and difficult solution to the database search problem in a way that goes beyond the traditional, purely formulaic expressions

  17. Secbase: database module to retrieve secondary structure elements with ligand binding motifs.

    Science.gov (United States)

    Koch, Oliver; Cole, Jason; Block, Peter; Klebe, Gerhard

    2009-10-01

    Secbase is presented as a novel extension module of Relibase. It integrates the information about secondary structure elements into the retrieval facilities of Relibase. The data are accessible via the extended Relibase user interface, and integrated retrieval queries can be addressed using an extended version of Reliscript. The primary information about alpha-helices and beta-sheets is used as provided by the PDB. Furthermore, a uniform classification of all turn families, based on recent clustering methods, and a new helix assignment that is based on this turn classification has been included. Algorithms to analyze the geometric features of helices and beta-strands were also implemented. To demonstrate the performance of the Secbase implementation, some application examples are given. They provide new insights into the involvement of secondary structure elements in ligand binding. A survey of water molecules detected next to the N-terminus of helices is analyzed to show their involvement in ligand binding. Additionally, the parallel oriented NH groups at the alpha-helix N-termini provide special binding motifs to bind particular ligand functional groups with two adjacent oxygen atoms, e.g., as found in negatively charged carboxylate or phosphate groups, respectively. The present study also shows that the specific structure of the first turn of alpha-helices provides a suitable explanation for stabilizing charged structures. The magnitude of the overall helix macrodipole seems to have no or only a minor influence on binding. Furthermore, an overview of the involvement of secondary structure elements with the recognition of some important endogenous ligands such as cofactors shows some distinct preference for particular binding motifs and amino acids.

  18. A Database of Tornado Events as Perceived by the USArray Transportable Array Network

    Science.gov (United States)

    Tytell, J. E.; Vernon, F.; Reyes, J. C.

    2015-12-01

    Over the course of the deployment of Earthscope's USArray Transportable Array (TA) network there have numerous tornado events that have occurred within the changing footprint of its network. The Array Network Facility based in San Diego, California, has compiled a database of these tornado events based on data provided by the NOAA Storm Prediction Center (SPC). The SPC data itself consists of parameters such as start-end point track data for each event, maximum EF intensities, and maximum track widths. Our database is Antelope driven and combines these data from the SPC with detailed station information from the TA network. We are now able to list all available TA stations during any specific tornado event date and also provide a single calculated "nearest" TA station per individual tornado event. We aim to provide this database as a starting resource for those with an interest in investigating tornado signatures within surface pressure and seismic response data. On a larger scale, the database may be of particular interest to the infrasound research community

  19. Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

    Science.gov (United States)

    Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

    2018-02-05

    Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Network-based statistical comparison of citation topology of bibliographic databases

    Science.gov (United States)

    Šubelj, Lovro; Fiala, Dalibor; Bajec, Marko

    2014-01-01

    Modern bibliographic databases provide the basis for scientific research and its evaluation. While their content and structure differ substantially, there exist only informal notions on their reliability. Here we compare the topological consistency of citation networks extracted from six popular bibliographic databases including Web of Science, CiteSeer and arXiv.org. The networks are assessed through a rich set of local and global graph statistics. We first reveal statistically significant inconsistencies between some of the databases with respect to individual statistics. For example, the introduced field bow-tie decomposition of DBLP Computer Science Bibliography substantially differs from the rest due to the coverage of the database, while the citation information within arXiv.org is the most exhaustive. Finally, we compare the databases over multiple graph statistics using the critical difference diagram. The citation topology of DBLP Computer Science Bibliography is the least consistent with the rest, while, not surprisingly, Web of Science is significantly more reliable from the perspective of consistency. This work can serve either as a reference for scholars in bibliometrics and scientometrics or a scientific evaluation guideline for governments and research agencies. PMID:25263231

  1. A dynamically coupled allosteric network underlies binding cooperativity in Src kinase.

    Science.gov (United States)

    Foda, Zachariah H; Shan, Yibing; Kim, Eric T; Shaw, David E; Seeliger, Markus A

    2015-01-20

    Protein tyrosine kinases are attractive drug targets because many human diseases are associated with the deregulation of kinase activity. However, how the catalytic kinase domain integrates different signals and switches from an active to an inactive conformation remains incompletely understood. Here we identify an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. Surprisingly, reactants (ATP and peptide substrates) bind with negative cooperativity to Src kinase while products (ADP and phosphopeptide) bind with positive cooperativity. We confirm the molecular details of the signal relay through the allosteric network by biochemical studies. Experiments on two additional protein tyrosine kinases indicate that the allosteric network may be largely conserved among these enzymes. Our work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity.

  2. Results on a Binding Neuron Model and Their Implications for Modified Hourglass Model for Neuronal Network

    Directory of Open Access Journals (Sweden)

    Viswanathan Arunachalam

    2013-01-01

    Full Text Available The classical models of single neuron like Hodgkin-Huxley point neuron or leaky integrate and fire neuron assume the influence of postsynaptic potentials to last till the neuron fires. Vidybida (2008 in a refreshing departure has proposed models for binding neurons in which the trace of an input is remembered only for a finite fixed period of time after which it is forgotten. The binding neurons conform to the behaviour of real neurons and are applicable in constructing fast recurrent networks for computer modeling. This paper develops explicitly several useful results for a binding neuron like the firing time distribution and other statistical characteristics. We also discuss the applicability of the developed results in constructing a modified hourglass network model in which there are interconnected neurons with excitatory as well as inhibitory inputs. Limited simulation results of the hourglass network are presented.

  3. LmSmdB: an integrated database for metabolic and gene regulatory network in Leishmania major and Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Priyanka Patel

    2016-03-01

    Full Text Available A database that integrates all the information required for biological processing is essential to be stored in one platform. We have attempted to create one such integrated database that can be a one stop shop for the essential features required to fetch valuable result. LmSmdB (L. major and S. mansoni database is an integrated database that accounts for the biological networks and regulatory pathways computationally determined by integrating the knowledge of the genome sequences of the mentioned organisms. It is the first database of its kind that has together with the network designing showed the simulation pattern of the product. This database intends to create a comprehensive canopy for the regulation of lipid metabolism reaction in the parasite by integrating the transcription factors, regulatory genes and the protein products controlled by the transcription factors and hence operating the metabolism at genetic level. Keywords: L.major, S.mansoni, Regulatory networks, Transcription factors, Database

  4. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution.

    Directory of Open Access Journals (Sweden)

    Amanda Tse

    Full Text Available Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib and promiscuous (Bosutinib, Dasatinib kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations

  5. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution

    Science.gov (United States)

    Tse, Amanda; Verkhivker, Gennady M.

    2015-01-01

    Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib) and promiscuous (Bosutinib, Dasatinib) kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations of key mediating

  6. An XML-Based Networking Method for Connecting Distributed Anthropometric Databases

    Directory of Open Access Journals (Sweden)

    H Cheng

    2007-03-01

    Full Text Available Anthropometric data are used by numerous types of organizations for health evaluation, ergonomics, apparel sizing, fitness training, and many other applications. Data have been collected and stored in electronic databases since at least the 1940s. These databases are owned by many organizations around the world. In addition, the anthropometric studies stored in these databases often employ different standards, terminology, procedures, or measurement sets. To promote the use and sharing of these databases, the World Engineering Anthropometry Resources (WEAR group was formed and tasked with the integration and publishing of member resources. It is easy to see that organizing worldwide anthropometric data into a single database architecture could be a daunting and expensive undertaking. The challenges of WEAR integration reflect mainly in the areas of distributed and disparate data, different standards and formats, independent memberships, and limited development resources. Fortunately, XML schema and web services provide an alternative method for networking databases, referred to as the Loosely Coupled WEAR Integration. A standard XML schema can be defined and used as a type of Rosetta stone to translate the anthropometric data into a universal format, and a web services system can be set up to link the databases to one another. In this way, the originators of the data can keep their data locally along with their own data management system and user interface, but their data can be searched and accessed as part of the larger data network, and even combined with the data of others. This paper will identify requirements for WEAR integration, review XML as the universal format, review different integration approaches, and propose a hybrid web services/data mart solution.

  7. Long-Term Collaboration Network Based on ClinicalTrials.gov Database in the Pharmaceutical Industry

    Directory of Open Access Journals (Sweden)

    Heyoung Yang

    2018-01-01

    Full Text Available Increasing costs, risks, and productivity problems in the pharmaceutical industry are important recent issues in the biomedical field. Open innovation is proposed as a solution to these issues. However, little statistical analysis related to collaboration in the pharmaceutical industry has been conducted so far. Meanwhile, not many cases have analyzed the clinical trials database, even though it is the information source with the widest coverage for the pharmaceutical industry. The purpose of this study is to test the clinical trials information as a probe for observing the status of the collaboration network and open innovation in the pharmaceutical industry. This study applied the social network analysis method to clinical trials data from 1980 to 2016 in ClinicalTrials.gov. Data were divided into four time periods—1980s, 1990s, 2000s, and 2010s—and the collaboration network was constructed for each time period. The characteristic of each network was investigated. The types of agencies participating in the clinical trials were classified as a university, national institute, company, or other, and the major players in the collaboration networks were identified. This study showed some phenomena related to the pharmaceutical industry that could provide clues to policymakers about open innovation. If follow-up studies were conducted, the utilization of the clinical trial database could be further expanded, which is expected to help open innovation in the pharmaceutical industry.

  8. ISOE: an international occupational exposure database and communications network for dose optimisation

    International Nuclear Information System (INIS)

    Robinson, I.F.; Lazo, E.

    1995-01-01

    The Information System on Occupational Exposure (ISOE) was launched by the Nuclear Energy Agency (NEA) of the Organisation for Economic Co-operation and Development (OECD) on 1 January 1992 to facilitate the communication of dosimetry and ALARA implementation data among nuclear facilities around the world. Members of ISOE include 51 utilities from 17 countries and regulators from 11 countries, with four regional technical centres administering the system and a Steering Group which manages the work. ISOE includes three databases and a communications network at several levels. The three databases NEA1, NEA2 and NEA3 include varying levels of details, with NEA3 being the most detailed giving task and site specific ALARA practices and experiences. Utility membership of ISOE gives full access to the databases whereas regulators have more limited access. This paper reviews the current status of participation, describes the three databases and the communications network. Some dose data showing trends in particular countries are presented as well as dose data relating to operation cycle length and outage length. The advantages of membership are described, and it is concluded that ISOE holds the potential for both dose and cost savings. (author)

  9. PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine.

    Directory of Open Access Journals (Sweden)

    Ji-Hyun Lee

    Full Text Available Despite the growing attention given to Traditional Medicine (TM worldwide, there is no well-known, publicly available, integrated bio-pharmacological Traditional Korean Medicine (TKM database for researchers in drug discovery. In this study, we have constructed PharmDB-K, which offers comprehensive information relating to TKM-associated drugs (compound, disease indication, and protein relationships. To explore the underlying molecular interaction of TKM, we integrated fourteen different databases, six Pharmacopoeias, and literature, and established a massive bio-pharmacological network for TKM and experimentally validated some cases predicted from the PharmDB-K analyses. Currently, PharmDB-K contains information about 262 TKMs, 7,815 drugs, 3,721 diseases, 32,373 proteins, and 1,887 side effects. One of the unique sets of information in PharmDB-K includes 400 indicator compounds used for standardization of herbal medicine. Furthermore, we are operating PharmDB-K via phExplorer (a network visualization software and BioMart (a data federation framework for convenient search and analysis of the TKM network. Database URL: http://pharmdb-k.org, http://biomart.i-pharm.org.

  10. Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases

    Directory of Open Access Journals (Sweden)

    Ma'ayan Avi

    2007-10-01

    Full Text Available Abstract Background In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical research literature, extracted automatically from literature using techniques such as natural language processing (NLP, generated experimentally using high-throughput methods such as yeast-2-hybrid screens, or interactions are predicted using an assortment of computational approaches. Genes or proteins identified as significantly changing in proteomic experiments, or identified as susceptibility disease genes in genomic studies, can be placed in the context of protein interaction networks in order to assign these genes and proteins to pathways and protein complexes. Results Genes2Networks is a software system that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from "seed" lists of human Entrez gene symbols. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Conclusion Genes2Networks is powerful web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of genes and proteins associated with disease processes. This system can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes.

  11. Construction and evaluation of yeast expression networks by database-guided predictions

    Directory of Open Access Journals (Sweden)

    Katharina Papsdorf

    2016-05-01

    Full Text Available DNA-Microarrays are powerful tools to obtain expression data on the genome-wide scale. We performed microarray experiments to elucidate the transcriptional networks, which are up- or down-regulated in response to the expression of toxic polyglutamine proteins in yeast. Such experiments initially generate hit lists containing differentially expressed genes. To look into transcriptional responses, we constructed networks from these genes. We therefore developed an algorithm, which is capable of dealing with very small numbers of microarrays by clustering the hits based on co-regulatory relationships obtained from the SPELL database. Here, we evaluate this algorithm according to several criteria and further develop its statistical capabilities. Initially, we define how the number of SPELL-derived co-regulated genes and the number of input hits influences the quality of the networks. We then show the ability of our networks to accurately predict further differentially expressed genes. Including these predicted genes into the networks improves the network quality and allows quantifying the predictive strength of the networks based on a newly implemented scoring method. We find that this approach is useful for our own experimental data sets and also for many other data sets which we tested from the SPELL microarray database. Furthermore, the clusters obtained by the described algorithm greatly improve the assignment to biological processes and transcription factors for the individual clusters. Thus, the described clustering approach, which will be available through the ClusterEx web interface, and the evaluation parameters derived from it represent valuable tools for the fast and informative analysis of yeast microarray data.

  12. What binds Bronisław Malinowski with social networks?

    Directory of Open Access Journals (Sweden)

    Zbigniew Meger

    2012-12-01

    Full Text Available Bronislaw Malinowski, a Polish anthropologist, ethnologist and sociologist, is the father of phatic communication. He has defined and described for the first time a phatic function of language and its importance in societies with low levels of development. As it turns, the phatic communication, which does not transfer any content, is also present today, and even - due social networks portals - comes into new stage of development. Although an impression that the phatic communication has low importance, it plays an important role in society. Also in educational activities this communication has an impact on interpersonal relationships. Through it, people better cooperate with each other and create groups of collaborating individuals. In this way are also built relationships between students and the educational institutions. They are also generated positive emotions which help in all processes of learning. Generally, the phatic communication can have a positive influence on educational processes.

  13. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

    Science.gov (United States)

    Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragon, Jaime A; van der Lee, Robin; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada R; Tan, Ge; Baranasic, Damir; Arenillas, David J; Sandelin, Albin; Vandepoele, Klaas; Lenhard, Boris; Ballester, Benoît; Wasserman, Wyeth W; Parcy, François; Mathelier, Anthony

    2018-01-04

    JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxonomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition, we have introduced 316 TFFMs (95 for vertebrates, 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally, this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Citation buidelines for nuclear data retrieved from databases resident at the Nuclear Data Centers Network

    International Nuclear Information System (INIS)

    McLane, V.

    1996-07-01

    The Nuclear Data Centers Network is a world-wide cooperation of nuclear data centers under the auspices of the International Atomic Energy Agency. The Network organizes the task of collecting, compiling, standardizing, storing, assessing, and distributing the nuclear data on an international scale. Information available at the Centers includes bibliographic, experimental, and evaluated databases for nuclear reaction data and for nuclear structure and radioactive decay data. The objective of the Network is to provide the information to users in a convenient, readily-available form. To this end, online data services have been established at three of the centers: the National Nuclear Data Center (NNDC), the Nuclear Data Section of the International Atomic Energy Agency (NDS), and the OECD Nuclear Energy Agency Data Bank (NEADB). Some information is also available at the NNDC and NEADB World Wide Web sites

  15. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lund, Ole

    2009-01-01

    this binding event. RESULTS: Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data...

  16. Application of new type of distributed multimedia databases to networked electronic museum

    Science.gov (United States)

    Kuroda, Kazuhide; Komatsu, Naohisa; Komiya, Kazumi; Ikeda, Hiroaki

    1999-01-01

    Recently, various kinds of multimedia application systems have actively been developed based on the achievement of advanced high sped communication networks, computer processing technologies, and digital contents-handling technologies. Under this background, this paper proposed a new distributed multimedia database system which can effectively perform a new function of cooperative retrieval among distributed databases. The proposed system introduces a new concept of 'Retrieval manager' which functions as an intelligent controller so that the user can recognize a set of distributed databases as one logical database. The logical database dynamically generates and performs a preferred combination of retrieving parameters on the basis of both directory data and the system environment. Moreover, a concept of 'domain' is defined in the system as a managing unit of retrieval. The retrieval can effectively be performed by cooperation of processing among multiple domains. Communication language and protocols are also defined in the system. These are used in every action for communications in the system. A language interpreter in each machine translates a communication language into an internal language used in each machine. Using the language interpreter, internal processing, such internal modules as DBMS and user interface modules can freely be selected. A concept of 'content-set' is also introduced. A content-set is defined as a package of contents. Contents in the content-set are related to each other. The system handles a content-set as one object. The user terminal can effectively control the displaying of retrieved contents, referring to data indicating the relation of the contents in the content- set. In order to verify the function of the proposed system, a networked electronic museum was experimentally built. The results of this experiment indicate that the proposed system can effectively retrieve the objective contents under the control to a number of distributed

  17. A Quality-Control-Oriented Database for a Mesoscale Meteorological Observation Network

    Science.gov (United States)

    Lussana, C.; Ranci, M.; Uboldi, F.

    2012-04-01

    In the operational context of a local weather service, data accessibility and quality related issues must be managed by taking into account a wide set of user needs. This work describes the structure and the operational choices made for the operational implementation of a database system storing data from highly automated observing stations, metadata and information on data quality. Lombardy's environmental protection agency, ARPA Lombardia, manages a highly automated mesoscale meteorological network. A Quality Assurance System (QAS) ensures that reliable observational information is collected and disseminated to the users. The weather unit in ARPA Lombardia, at the same time an important QAS component and an intensive data user, has developed a database specifically aimed to: 1) providing quick access to data for operational activities and 2) ensuring data quality for real-time applications, by means of an Automatic Data Quality Control (ADQC) procedure. Quantities stored in the archive include hourly aggregated observations of: precipitation amount, temperature, wind, relative humidity, pressure, global and net solar radiation. The ADQC performs several independent tests on raw data and compares their results in a decision-making procedure. An important ADQC component is the Spatial Consistency Test based on Optimal Interpolation. Interpolated and Cross-Validation analysis values are also stored in the database, providing further information to human operators and useful estimates in case of missing data. The technical solution adopted is based on a LAMP (Linux, Apache, MySQL and Php) system, constituting an open source environment suitable for both development and operational practice. The ADQC procedure itself is performed by R scripts directly interacting with the MySQL database. Users and network managers can access the database by using a set of web-based Php applications.

  18. RBscore&NBench: a high-level web server for nucleic acid binding residues prediction with a large-scale benchmarking database.

    Science.gov (United States)

    Miao, Zhichao; Westhof, Eric

    2016-07-08

    RBscore&NBench combines a web server, RBscore and a database, NBench. RBscore predicts RNA-/DNA-binding residues in proteins and visualizes the prediction scores and features on protein structures. The scoring scheme of RBscore directly links feature values to nucleic acid binding probabilities and illustrates the nucleic acid binding energy funnel on the protein surface. To avoid dataset, binding site definition and assessment metric biases, we compared RBscore with 18 web servers and 3 stand-alone programs on 41 datasets, which demonstrated the high and stable accuracy of RBscore. A comprehensive comparison led us to develop a benchmark database named NBench. The web server is available on: http://ahsoka.u-strasbg.fr/rbscorenbench/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Exploring the Ligand-Protein Networks in Traditional Chinese Medicine: Current Databases, Methods, and Applications

    Directory of Open Access Journals (Sweden)

    Mingzhu Zhao

    2013-01-01

    Full Text Available The traditional Chinese medicine (TCM, which has thousands of years of clinical application among China and other Asian countries, is the pioneer of the “multicomponent-multitarget” and network pharmacology. Although there is no doubt of the efficacy, it is difficult to elucidate convincing underlying mechanism of TCM due to its complex composition and unclear pharmacology. The use of ligand-protein networks has been gaining significant value in the history of drug discovery while its application in TCM is still in its early stage. This paper firstly surveys TCM databases for virtual screening that have been greatly expanded in size and data diversity in recent years. On that basis, different screening methods and strategies for identifying active ingredients and targets of TCM are outlined based on the amount of network information available, both on sides of ligand bioactivity and the protein structures. Furthermore, applications of successful in silico target identification attempts are discussed in detail along with experiments in exploring the ligand-protein networks of TCM. Finally, it will be concluded that the prospective application of ligand-protein networks can be used not only to predict protein targets of a small molecule, but also to explore the mode of action of TCM.

  20. National information network and database system of hazardous waste management in China

    Energy Technology Data Exchange (ETDEWEB)

    Ma Hongchang [National Environmental Protection Agency, Beijing (China)

    1996-12-31

    Industries in China generate large volumes of hazardous waste, which makes it essential for the nation to pay more attention to hazardous waste management. National laws and regulations, waste surveys, and manifest tracking and permission systems have been initiated. Some centralized hazardous waste disposal facilities are under construction. China`s National Environmental Protection Agency (NEPA) has also obtained valuable information on hazardous waste management from developed countries. To effectively share this information with local environmental protection bureaus, NEPA developed a national information network and database system for hazardous waste management. This information network will have such functions as information collection, inquiry, and connection. The long-term objective is to establish and develop a national and local hazardous waste management information network. This network will significantly help decision makers and researchers because it will be easy to obtain information (e.g., experiences of developed countries in hazardous waste management) to enhance hazardous waste management in China. The information network consists of five parts: technology consulting, import-export management, regulation inquiry, waste survey, and literature inquiry.

  1. [Study of algorithms to identify schizophrenia in the SNIIRAM database conducted by the REDSIAM network].

    Science.gov (United States)

    Quantin, C; Collin, C; Frérot, M; Besson, J; Cottenet, J; Corneloup, M; Soudry-Faure, A; Mariet, A-S; Roussot, A

    2017-10-01

    The aim of the REDSIAM network is to foster communication between users of French medico-administrative databases and to validate and promote analysis methods suitable for the data. Within this network, the working group "Mental and behavioral disorders" took an interest in algorithms to identify adult schizophrenia in the SNIIRAM database and inventoried identification criteria for patients with schizophrenia in these databases. The methodology was based on interviews with nine experts in schizophrenia concerning the procedures they use to identify patients with schizophrenia disorders in databases. The interviews were based on a questionnaire and conducted by telephone. The synthesis of the interviews showed that the SNIIRAM contains various tables which allow coders to identify patients suffering from schizophrenia: chronic disease status, drugs and hospitalizations. Taken separately, these criteria were not sufficient to recognize patients with schizophrenia, an algorithm should be based on all of them. Apparently, only one-third of people living with schizophrenia benefit from the longstanding disease status. Not all patients are hospitalized, and coding for diagnoses at the hospitalization, notably for short stays in medicine, surgery or obstetrics departments, is not exhaustive. As for treatment with antipsychotics, it is not specific enough as such treatments are also prescribed to patients with bipolar disorders, or even other disorders. It seems appropriate to combine these complementary criteria, while keeping in mind out-patient care (every year 80,000 patients are seen exclusively in an outpatient setting), even if these data are difficult to link with other information. Finally, the experts made three propositions for selection algorithms of patients with schizophrenia. Patients with schizophrenia can be relatively accurately identified using SNIIRAM data. Different combinations of the selected criteria must be used depending on the objectives and

  2. Five years database of landslides and floods affecting Swiss transportation networks

    Science.gov (United States)

    Voumard, Jérémie; Derron, Marc-Henri; Jaboyedoff, Michel

    2017-04-01

    Switzerland is a country threatened by a lot of natural hazards. Many events occur in built environment, affecting infrastructures, buildings or transportation networks and producing occasionally expensive damages. This is the reason why large landslides are generally well studied and monitored in Switzerland to reduce the financial and human risks. However, we have noticed a lack of data on small events which have impacted roads and railways these last years. This is why we have collect all the reported natural hazard events which have affected the Swiss transportation networks since 2012 in a database. More than 800 roads and railways closures have been recorded in five years from 2012 to 2016. These event are classified into six classes: earth flow, debris flow, rockfall, flood, avalanche and others. Data come from Swiss online press articles sorted by Google Alerts. The search is based on more than thirty keywords, in three languages (Italian, French, German). After verifying that the article relates indeed an event which has affected a road or a railways track, it is studied in details. We get finally information on about sixty attributes by event about event date, event type, event localisation, meteorological conditions as well as impacts and damages on the track and human damages. From this database, many trends over the five years of data collection can be outlined: in particular, the spatial and temporal distributions of the events, as well as their consequences in term of traffic (closure duration, deviation, etc.). Even if the database is imperfect (by the way it was built and because of the short time period considered), it highlights the not negligible impact of small natural hazard events on roads and railways in Switzerland at a national level. This database helps to better understand and quantify this events, to better integrate them in risk assessment.

  3. Extrastriatal binding of [123I]FP-CIT in the thalamus and pons: gender and age dependencies assessed in a European multicentre database of healthy controls

    International Nuclear Information System (INIS)

    Koch, Walter; Unterrainer, Marcus; Xiong, Guoming; Bartenstein, Peter; Diemling, Markus; Varrone, Andrea; Dickson, John C.; Tossici-Bolt, Livia; Sera, Terez; Asenbaum, Susanne; Booij, Jan; Kapucu, Ozlem L.; Kluge, Andreas; Ziebell, Morten; Darcourt, Jacques; Nobili, Flavio; Pagani, Marco; Hesse, Swen; Borght, Thierry Vander; Laere, Koen van; Tatsch, Klaus; La Fougere, Christian

    2014-01-01

    Apart from binding to the dopamine transporter (DAT), [ 123 I]FP-CIT shows moderate affinity for the serotonin transporter (SERT), allowing imaging of both monoamine transporters in a single imaging session in different brain areas. The aim of this study was to systematically evaluate extrastriatal binding (predominantly due to SERT) and its age and gender dependencies in a large cohort of healthy controls. SPECT data from 103 healthy controls with well-defined criteria of normality acquired at 13 different imaging centres were analysed for extrastriatal binding using volumes of interest analysis for the thalamus and the pons. Data were examined for gender and age effects as well as for potential influence of striatal DAT radiotracer binding. Thalamic binding was significantly higher than pons binding. Partial correlations showed an influence of putaminal DAT binding on measured binding in the thalamus but not on the pons. Data showed high interindividual variation in extrastriatal binding. Significant gender effects with 31 % higher binding in women than in men were observed in the thalamus, but not in the pons. An age dependency with a decline per decade (±standard error) of 8.2 ± 1.3 % for the thalamus and 6.8 ± 2.9 % for the pons was shown. The potential to evaluate extrastriatal predominant SERT binding in addition to the striatal DAT in a single imaging session was shown using a large database of [ 123 I]FP-CIT scans in healthy controls. For both the thalamus and the pons, an age-related decline in radiotracer binding was observed. Gender effects were demonstrated for binding in the thalamus only. As a potential clinical application, the data could be used as a reference to estimate SERT occupancy in addition to nigrostriatal integrity when using [ 123 I]FP-CIT for DAT imaging in patients treated with selective serotonin reuptake inhibitors. (orig.)

  4. Extrastriatal binding of [{sup 123}I]FP-CIT in the thalamus and pons: gender and age dependencies assessed in a European multicentre database of healthy controls

    Energy Technology Data Exchange (ETDEWEB)

    Koch, Walter; Unterrainer, Marcus; Xiong, Guoming; Bartenstein, Peter [University of Munich, Department of Nuclear Medicine, Munich (Germany); Diemling, Markus [Hermes Medical Solutions, Stockholm (Sweden); Varrone, Andrea [Karolinska University Hospital, Karolinska Institutet, Department of Clinical Neuroscience, Centre for Psychiatry Research, Stockholm (Sweden); Dickson, John C. [UCLH NHS Foundation Trust and University College, Institute of Nuclear Medicine, London (United Kingdom); Tossici-Bolt, Livia [University Hospitals Southampton NHS Trust, Department of Medical Physics, Southampton (United Kingdom); Sera, Terez [University of Szeged, Department of Nuclear Medicine and Euromedic Szeged, Szeged (Hungary); Asenbaum, Susanne [Medical University of Vienna, Department of Neurology, Vienna (Austria); Booij, Jan [University of Amsterdam, Department of Nuclear Medicine, Academic Medical Centre, Amsterdam (Netherlands); Kapucu, Ozlem L. [Gazi University, Department of Nuclear Medicine, Faculty of Medicine, Ankara (Turkey); Kluge, Andreas [ABX-CRO, Dresden (Germany); Ziebell, Morten [Rigshospitalet and University of Copenhagen, Neurobiology Research Unit, Copenhagen (Denmark); Darcourt, Jacques [University of Nice-Sophia Antipolis, Nuclear Medicine Department, Centre Antoine Lacassagne, Nice (France); Nobili, Flavio [University of Genoa, Clinical Neurology Unit, Department of Neuroscience (DINOGMI), Genoa (Italy); Pagani, Marco [CNR, Institute of Cognitive Sciences and Technologies, Rome (Italy); Karolinska Hospital, Department of Nuclear Medicine, Stockholm (Sweden); Hesse, Swen [University of Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Leipzig University Medical Centre, Molecular Neuroimaging IFB Adiposity Diseases, Leipzig (Germany); Borght, Thierry Vander [Universite Catholique de Louvain, Nuclear Medicine Division, CHU Dinant Godinne, Yvoir (Belgium); Laere, Koen van [University Hospital and K.U. Leuven, Nuclear Medicine, Leuven (Belgium); Tatsch, Klaus [Staedtisches Klinikum Karlsruhe, Department of Nuclear Medicine, Karlsruhe (Germany); La Fougere, Christian [University of Munich, Department of Nuclear Medicine, Munich (Germany); University of Tuebingen, Department of Nuclear Medicine, Tuebingen (Germany)

    2014-10-15

    Apart from binding to the dopamine transporter (DAT), [{sup 123}I]FP-CIT shows moderate affinity for the serotonin transporter (SERT), allowing imaging of both monoamine transporters in a single imaging session in different brain areas. The aim of this study was to systematically evaluate extrastriatal binding (predominantly due to SERT) and its age and gender dependencies in a large cohort of healthy controls. SPECT data from 103 healthy controls with well-defined criteria of normality acquired at 13 different imaging centres were analysed for extrastriatal binding using volumes of interest analysis for the thalamus and the pons. Data were examined for gender and age effects as well as for potential influence of striatal DAT radiotracer binding. Thalamic binding was significantly higher than pons binding. Partial correlations showed an influence of putaminal DAT binding on measured binding in the thalamus but not on the pons. Data showed high interindividual variation in extrastriatal binding. Significant gender effects with 31 % higher binding in women than in men were observed in the thalamus, but not in the pons. An age dependency with a decline per decade (±standard error) of 8.2 ± 1.3 % for the thalamus and 6.8 ± 2.9 % for the pons was shown. The potential to evaluate extrastriatal predominant SERT binding in addition to the striatal DAT in a single imaging session was shown using a large database of [{sup 123}I]FP-CIT scans in healthy controls. For both the thalamus and the pons, an age-related decline in radiotracer binding was observed. Gender effects were demonstrated for binding in the thalamus only. As a potential clinical application, the data could be used as a reference to estimate SERT occupancy in addition to nigrostriatal integrity when using [{sup 123}I]FP-CIT for DAT imaging in patients treated with selective serotonin reuptake inhibitors. (orig.)

  5. Application of CAPEC Lipid Property Databases in the Synthesis and Design of Biorefinery Networks

    DEFF Research Database (Denmark)

    Bertran, Maria-Ona; Cunico, Larissa; Gani, Rafiqul

    Petroleum is currently the primary raw material for the production of fuels and chemicals. Consequently, our society is highly dependent on fossil non-renewable resources. However, renewable raw materials are recently receiving increasing interest for the production of chemicals and fuels, so a n...... of biorefinery networks. The objective of this work is to show the application of databases of physical and thermodynamic properties of lipid components to the synthesis and design of biorefinery networks.......]. The wide variety and complex nature of components in biorefineries poses a challenge with respect to the synthesis and design of these types of processes. Whereas physical and thermodynamic property data or models for petroleum-based processes are widely available, most data and models for biobased...

  6. Experience and Lessons learnt from running high availability databases on Network Attached Storage

    CERN Document Server

    Guijarro, Juan Manuel; Segura Chinchilla, Nilo

    2008-01-01

    The Database and Engineering Services Group of CERN's Information Technology Department provides the Oracle based Central Data Base services used in many activities at CERN. In order to provide High Availability and ease management for those services, a NAS (Network Attached Storage) based infrastructure has been set up. It runs several instances of the Oracle RAC (Real Application Cluster) using NFS as share disk space for RAC purposes and Data hosting. It is composed of two private LAN's to provide access to the NAS file servers and Oracle RAC interconnect, both using network bonding. NAS nodes are configured in partnership to prevent having single points of failure and to provide automatic NAS fail-over. This presentation describes that infrastructure and gives some advice on how to automate its management and setup using a Fabric Management framework such as Quattor. It also covers aspects related with NAS Performance and Monitoring as well Data Backup and Archive of such facility using already existing i...

  7. A central database for the Global Terrestrial Network for Permafrost (GTN-P)

    Science.gov (United States)

    Elger, Kirsten; Lanckman, Jean-Pierre; Lantuit, Hugues; Karlsson, Ævar Karl; Johannsson, Halldór

    2013-04-01

    The Global Terrestrial Network for Permafrost (GTN-P) is the primary international observing network for permafrost sponsored by the Global Climate Observing System (GCOS) and the Global Terrestrial Observing System (GTOS), and managed by the International Permafrost Association (IPA). It monitors the Essential Climate Variable (ECV) permafrost that consists of permafrost temperature and active-layer thickness, with the long-term goal of obtaining a comprehensive view of the spatial structure, trends, and variability of changes in the active layer and permafrost. The network's two international monitoring components are (1) CALM (Circumpolar Active Layer Monitoring) and the (2) Thermal State of Permafrost (TSP), which is made of an extensive borehole-network covering all permafrost regions. Both programs have been thoroughly overhauled during the International Polar Year 2007-2008 and extended their coverage to provide a true circumpolar network stretching over both Hemispheres. GTN-P has gained considerable visibility in the science community in providing the baseline against which models are globally validated and incorporated in climate assessments. Yet it was until now operated on a voluntary basis, and is now being redesigned to meet the increasing expectations from the science community. To update the network's objectives and deliver the best possible products to the community, the IPA organized a workshop to define the user's needs and requirements for the production, archival, storage and dissemination of the permafrost data products it manages. From the beginning on, GNT-P data was "outfitted" with an open data policy with free data access via the World Wide Web. The existing data, however, is far from being homogeneous: is not yet optimized for databases, there is no framework for data reporting or archival and data documentation is incomplete. As a result, and despite the utmost relevance of permafrost in the Earth's climate system, the data has not been

  8. Detection of material property errors in handbooks and databases using artificial neural networks with hidden correlations

    Science.gov (United States)

    Zhang, Y. M.; Evans, J. R. G.; Yang, S. F.

    2010-11-01

    The authors have discovered a systematic, intelligent and potentially automatic method to detect errors in handbooks and stop their transmission using unrecognised relationships between materials properties. The scientific community relies on the veracity of scientific data in handbooks and databases, some of which have a long pedigree covering several decades. Although various outlier-detection procedures are employed to detect and, where appropriate, remove contaminated data, errors, which had not been discovered by established methods, were easily detected by our artificial neural network in tables of properties of the elements. We started using neural networks to discover unrecognised relationships between materials properties and quickly found that they were very good at finding inconsistencies in groups of data. They reveal variations from 10 to 900% in tables of property data for the elements and point out those that are most probably correct. Compared with the statistical method adopted by Ashby and co-workers [Proc. R. Soc. Lond. Ser. A 454 (1998) p. 1301, 1323], this method locates more inconsistencies and could be embedded in database software for automatic self-checking. We anticipate that our suggestion will be a starting point to deal with this basic problem that affects researchers in every field. The authors believe it may eventually moderate the current expectation that data field error rates will persist at between 1 and 5%.

  9. Analysis of functional importance of binding sites in the Drosophila gap gene network model.

    Science.gov (United States)

    Kozlov, Konstantin; Gursky, Vitaly V; Kulakovskiy, Ivan V; Dymova, Arina; Samsonova, Maria

    2015-01-01

    The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects of a good model connecting the DNA sequence information with that of a molecular phenotype (gene expression) is the selection of regulatory interactions and relevant transcription factor bindings sites. As the model may predict different levels of the functional importance of specific binding sites in different genomic and regulatory contexts, it is essential to formulate and study such models under different modeling assumptions. We elaborate a two-layer model for the Drosophila gap gene network and include in the model a combined set of transcription factor binding sites and concentration dependent regulatory interaction between gap genes hunchback and Kruppel. We show that the new variants of the model are more consistent in terms of gene expression predictions for various genetic constructs in comparison to previous work. We quantify the functional importance of binding sites by calculating their impact on gene expression in the model and calculate how these impacts correlate across all sites under different modeling assumptions. The assumption about the dual interaction between hb and Kr leads to the most consistent modeling results, but, on the other hand, may obscure existence of indirect interactions between binding sites in regulatory regions of distinct genes. The analysis confirms the previously formulated regulation concept of many weak binding sites working in concert. The model predicts a more or less uniform distribution of functionally important binding sites over the sets of experimentally characterized regulatory modules and other open chromatin domains.

  10. Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction.

    Science.gov (United States)

    Han, Youngmahn; Kim, Dongsup

    2017-12-28

    Computational scanning of peptide candidates that bind to a specific major histocompatibility complex (MHC) can speed up the peptide-based vaccine development process and therefore various methods are being actively developed. Recently, machine-learning-based methods have generated successful results by training large amounts of experimental data. However, many machine learning-based methods are generally less sensitive in recognizing locally-clustered interactions, which can synergistically stabilize peptide binding. Deep convolutional neural network (DCNN) is a deep learning method inspired by visual recognition process of animal brain and it is known to be able to capture meaningful local patterns from 2D images. Once the peptide-MHC interactions can be encoded into image-like array(ILA) data, DCNN can be employed to build a predictive model for peptide-MHC binding prediction. In this study, we demonstrated that DCNN is able to not only reliably predict peptide-MHC binding, but also sensitively detect locally-clustered interactions. Nonapeptide-HLA-A and -B binding data were encoded into ILA data. A DCNN, as a pan-specific prediction model, was trained on the ILA data. The DCNN showed higher performance than other prediction tools for the latest benchmark datasets, which consist of 43 datasets for 15 HLA-A alleles and 25 datasets for 10 HLA-B alleles. In particular, the DCNN outperformed other tools for alleles belonging to the HLA-A3 supertype. The F1 scores of the DCNN were 0.86, 0.94, and 0.67 for HLA-A*31:01, HLA-A*03:01, and HLA-A*68:01 alleles, respectively, which were significantly higher than those of other tools. We found that the DCNN was able to recognize locally-clustered interactions that could synergistically stabilize peptide binding. We developed ConvMHC, a web server to provide user-friendly web interfaces for peptide-MHC class I binding predictions using the DCNN. ConvMHC web server can be accessible via http://jumong.kaist.ac.kr:8080/convmhc

  11. An Analysis of Database Replication Technologies with Regard to Deep Space Network Application Requirements

    Science.gov (United States)

    Connell, Andrea M.

    2011-01-01

    The Deep Space Network (DSN) has three communication facilities which handle telemetry, commands, and other data relating to spacecraft missions. The network requires these three sites to share data with each other and with the Jet Propulsion Laboratory for processing and distribution. Many database management systems have replication capabilities built in, which means that data updates made at one location will be automatically propagated to other locations. This project examines multiple replication solutions, looking for stability, automation, flexibility, performance, and cost. After comparing these features, Oracle Streams is chosen for closer analysis. Two Streams environments are configured - one with a Master/Slave architecture, in which a single server is the source for all data updates, and the second with a Multi-Master architecture, in which updates originating from any of the servers will be propagated to all of the others. These environments are tested for data type support, conflict resolution, performance, changes to the data structure, and behavior during and after network or server outages. Through this experimentation, it is determined which requirements of the DSN can be met by Oracle Streams and which cannot.

  12. Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.

    Science.gov (United States)

    Balaur, Irina; Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J; Auffray, Charles

    2017-04-01

    The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/ . The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework . ibalaur@eisbm.org. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  13. Classification of Beta-lactamases and penicillin binding proteins using ligand-centric network models.

    Directory of Open Access Journals (Sweden)

    Hakime Öztürk

    Full Text Available β-lactamase mediated antibiotic resistance is an important health issue and the discovery of new β-lactam type antibiotics or β-lactamase inhibitors is an area of intense research. Today, there are about a thousand β-lactamases due to the evolutionary pressure exerted by these ligands. While β-lactamases hydrolyse the β-lactam ring of antibiotics, rendering them ineffective, Penicillin-Binding Proteins (PBPs, which share high structural similarity with β-lactamases, also confer antibiotic resistance to their host organism by acquiring mutations that allow them to continue their participation in cell wall biosynthesis. In this paper, we propose a novel approach to include ligand sharing information for classifying and clustering β-lactamases and PBPs in an effort to elucidate the ligand induced evolution of these β-lactam binding proteins. We first present a detailed summary of the β-lactamase and PBP families in the Protein Data Bank, as well as the compounds they bind to. Then, we build two different types of networks in which the proteins are represented as nodes, and two proteins are connected by an edge with a weight that depends on the number of shared identical or similar ligands. These models are analyzed under three different edge weight settings, namely unweighted, weighted, and normalized weighted. A detailed comparison of these six networks showed that the use of ligand sharing information to cluster proteins resulted in modules comprising proteins with not only sequence similarity but also functional similarity. Consideration of ligand similarity highlighted some interactions that were not detected in the identical ligand network. Analysing the β-lactamases and PBPs using ligand-centric network models enabled the identification of novel relationships, suggesting that these models can be used to examine other protein families to obtain information on their ligand induced evolutionary paths.

  14. Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach

    DEFF Research Database (Denmark)

    Buus, S.; Lauemoller, S.L.; Worning, Peder

    2003-01-01

    We have generated Artificial Neural Networks (ANN) capable of performing sensitive, quantitative predictions of peptide binding to the MHC class I molecule, HLA-A*0204. We have shown that such quantitative ANN are superior to conventional classification ANN, that have been trained to predict bind...... of an iterative feedback loop whereby advanced, computational bioinformatics optimize experimental strategy, and vice versa....

  15. Dynamically Partitionable Autoassociative Networks as a Solution to the Neural Binding Problem

    Directory of Open Access Journals (Sweden)

    Kenneth Jeffrey Hayworth

    2012-09-01

    Full Text Available An outstanding question in theoretical neuroscience is how the brain solves the neural binding problem. In vision, binding can be summarized as the ability to represent that certain properties belong to one object while other properties belong to a different object. I review the binding problem in visual and other domains, and review its simplest proposed solution – the anatomical binding hypothesis. This hypothesis has traditionally been rejected as a true solution because it seems to require a type of one-to-one wiring of neurons that would be impossible in a biological system (as opposed to an engineered system like a computer. I show that this requirement for one-to-one wiring can be loosened by carefully considering how the neural representation is actually put to use by the rest of the brain. This leads to a solution where a symbol is represented not as a particular pattern of neural activation but instead as a piece of a global stable attractor state. I introduce the Dynamically Partitionable AutoAssociative Network (DPAAN as an implementation of this solution and show how DPANNs can be used in systems which perform perceptual binding and in systems that implement syntax-sensitive rules. Finally I show how the core parts of the cognitive architecture ACT-R can be neurally implemented using a DPAAN as ACT-R’s global workspace. Because the DPAAN solution to the binding problem requires only ‘flat’ neural representations (as opposed to the phase encoded representation hypothesized in neural synchrony solutions it is directly compatible with the most well developed neural models of learning, memory, and pattern recognition.

  16. ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

    Science.gov (United States)

    Huan, Tianxiao; Sivachenko, Andrey Y; Harrison, Scott H; Chen, Jake Y

    2008-08-12

    New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed. We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges

  17. The ING Seismic Network Databank (ISND : a friendly parameters and waveform database

    Directory of Open Access Journals (Sweden)

    G. Smriglio

    1995-06-01

    Full Text Available he Istituto Nazionale di Geofisica (ING Seismic Network Database (ISND includes over 300000 arrivaI times of Italian, Mediterranean and teleseismic earthquakes from 1983 to date. This database is a useful tool for Italian and foreign seismologists ( over 1000 data requests in the first 6 months of this year. Recently (1994 the ING began storing in the ISND, the digital waveforms associated with arri,Tal times and experimen- tally allowed users to retrieve waveforms recorded by the ING acquisition system. In this paper we describe the types of data stored and the interactive and batch procedures available to obtain arrivaI times and/or asso- ciated waveforms. The ISND is reachable via telephone line, P.S.I., Internet and DecNet. Users can read and send to their E-mail address alI selected earthquakes locations, parameters, arrivaI times and associated digital waveforms (in SAC, SUDS or ASCII format. For r;aedium or large amounts of data users can ask to receive data by means of magnetic media (DAT, Video 8, floppy disk.

  18. Yeast ribonuclease III uses a network of multiple hydrogen bonds for RNA binding and cleavage.

    Science.gov (United States)

    Lavoie, Mathieu; Abou Elela, Sherif

    2008-08-19

    Members of the bacterial RNase III family recognize a variety of short structured RNAs with few common features. It is not clear how this group of enzymes supports high cleavage fidelity while maintaining a broad base of substrates. Here we show that the yeast orthologue of RNase III (Rnt1p) uses a network of 2'-OH-dependent interactions to recognize substrates with different structures. We designed a series of bipartite substrates permitting the distinction between binding and cleavage defects. Each substrate was engineered to carry a single or multiple 2'- O-methyl or 2'-fluoro ribonucleotide substitutions to prevent the formation of hydrogen bonds with a specific nucleotide or group of nucleotides. Interestingly, introduction of 2'- O-methyl ribonucleotides near the cleavage site increased the rate of catalysis, indicating that 2'-OH are not required for cleavage. Substitution of nucleotides in known Rnt1p binding site with 2'- O-methyl ribonucleotides inhibited cleavage while single 2'-fluoro ribonucleotide substitutions did not. This indicates that while no single 2'-OH is essential for Rnt1p cleavage, small changes in the substrate structure are not tolerated. Strikingly, several nucleotide substitutions greatly increased the substrate dissociation constant with little or no effect on the Michaelis-Menten constant or rate of catalysis. Together, the results indicate that Rnt1p uses a network of nucleotide interactions to identify its substrate and support two distinct modes of binding. One mode is primarily mediated by the dsRNA binding domain and leads to the formation of stable RNA/protein complex, while the other requires the presence of the nuclease and N-terminal domains and leads to RNA cleavage.

  19. FunCoup 3.0: database of genome-wide functional coupling networks.

    Science.gov (United States)

    Schmitt, Thomas; Ogris, Christoph; Sonnhammer, Erik L L

    2014-01-01

    We present an update of the FunCoup database (http://FunCoup.sbc.su.se) of functional couplings, or functional associations, between genes and gene products. Identifying these functional couplings is an important step in the understanding of higher level mechanisms performed by complex cellular processes. FunCoup distinguishes between four classes of couplings: participation in the same signaling cascade, participation in the same metabolic process, co-membership in a protein complex and physical interaction. For each of these four classes, several types of experimental and statistical evidence are combined by Bayesian integration to predict genome-wide functional coupling networks. The FunCoup framework has been completely re-implemented to allow for more frequent future updates. It contains many improvements, such as a regularization procedure to automatically downweight redundant evidences and a novel method to incorporate phylogenetic profile similarity. Several datasets have been updated and new data have been added in FunCoup 3.0. Furthermore, we have developed a new Web site, which provides powerful tools to explore the predicted networks and to retrieve detailed information about the data underlying each prediction.

  20. Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

    Science.gov (United States)

    Gerek, Z. Nevin; Ozkan, S. Banu

    2011-01-01

    The allosteric mechanism plays a key role in cellular functions of several PDZ domain proteins (PDZs) and is directly linked to pharmaceutical applications; however, it is a challenge to elaborate the nature and extent of these allosteric interactions. One solution to this problem is to explore the dynamics of PDZs, which may provide insights about how intramolecular communication occurs within a single domain. Here, we develop an advancement of perturbation response scanning (PRS) that couples elastic network models with linear response theory (LRT) to predict key residues in allosteric transitions of the two most studied PDZs (PSD-95 PDZ3 domain and hPTP1E PDZ2 domain). With PRS, we first identify the residues that give the highest mean square fluctuation response upon perturbing the binding sites. Strikingly, we observe that the residues with the highest mean square fluctuation response agree with experimentally determined residues involved in allosteric transitions. Second, we construct the allosteric pathways by linking the residues giving the same directional response upon perturbation of the binding sites. The predicted intramolecular communication pathways reveal that PSD-95 and hPTP1E have different pathways through the dynamic coupling of different residue pairs. Moreover, our analysis provides a molecular understanding of experimentally observed hidden allostery of PSD-95. We show that removing the distal third alpha helix from the binding site alters the allosteric pathway and decreases the binding affinity. Overall, these results indicate that (i) dynamics plays a key role in allosteric regulations of PDZs, (ii) the local changes in the residue interactions can lead to significant changes in the dynamics of allosteric regulations, and (iii) this might be the mechanism that each PDZ uses to tailor their binding specificities regulation. PMID:21998559

  1. Cost Function Network-based Design of Protein-Protein Interactions: predicting changes in binding affinity.

    Science.gov (United States)

    Viricel, Clément; de Givry, Simon; Schiex, Thomas; Barbe, Sophie

    2018-02-20

    Accurate and economic methods to predict change in protein binding free energy upon mutation are imperative to accelerate the design of proteins for a wide range of applications. Free energy is defined by enthalpic and entropic contributions. Following the recent progresses of Artificial Intelligence-based algorithms for guaranteed NP-hard energy optimization and partition function computation, it becomes possible to quickly compute minimum energy conformations and to reliably estimate the entropic contribution of side-chains in the change of free energy of large protein interfaces. Using guaranteed Cost Function Network algorithms, Rosetta energy functions and Dunbrack's rotamer library, we developed and assessed EasyE and JayZ, two methods for binding affinity estimation that ignore or include conformational entropic contributions on a large benchmark of binding affinity experimental measures. If both approaches outperform most established tools, we observe that side-chain conformational entropy brings little or no improvement on most systems but becomes crucial in some rare cases. as open-source Python/C ++ code at sourcesup.renater.fr/projects/easy-jayz. thomas.schiex@inra.fr and sophie.barbe@insa-toulouse.fr. Supplementary data are available at Bioinformatics online.

  2. Teradata University Network: A No Cost Web-Portal for Teaching Database, Data Warehousing, and Data-Related Subjects

    Science.gov (United States)

    Jukic, Nenad; Gray, Paul

    2008-01-01

    This paper describes the value that information systems faculty and students in classes dealing with database management, data warehousing, decision support systems, and related topics, could derive from the use of the Teradata University Network (TUN), a free comprehensive web-portal. A detailed overview of TUN functionalities and content is…

  3. Data of conformation changes by some binding - ConfC | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available pair which ID% (sequence identity) is more than 99%, and Dmax (maximum distance between Cα atoms of superimp... molecular type confName Name of binding molecules dmax Maximum distance between Cα atoms of superimposed pr

  4. Design of Korean nuclear reliability data-base network using a two-stage Bayesian concept

    International Nuclear Information System (INIS)

    Kim, T.W.; Jeong, K.S.; Chae, S.K.

    1987-01-01

    In an analysis of probabilistic risk, safety, and reliability of a nuclear power plant, the reliability data base (DB) must be established first. As the importance of the reliability data base increases, event reporting systems such as the US Nuclear Regulatory Commission's Licensee Event Report and the International Atomic Energy Agency's Incident Reporting System have been developed. In Korea, however, the systematic reliability data base is not yet available. Therefore, foreign data bases have been directly quoted in reliability analyses of Korean plants. In order to develop a reliability data base for Korean plants, the problem is which methodology is to be used, and the application limits of the selected method must be solved and clarified. After starting the commercial operation of Korea Nuclear Unit-1 (KNU-1) in 1978, six nuclear power plants have begun operation. Of these, only KNU-3 is a Canada Deuterium Uranium pressurized heavy-water reactor, and the others are all pressurized water reactors. This paper describes the proposed reliability data-base network (KNRDS) for Korean nuclear power plants in the context of two-stage Bayesian (TSB) procedure of Kaplan. It describes the concept of TSB to obtain the Korean-specific plant reliability data base, which is updated with the incorporation of both the reported generic reliability data and the operation experiences of similar plants

  5. Updates on drug-target network; facilitating polypharmacology and data integration by growth of DrugBank database.

    Science.gov (United States)

    Barneh, Farnaz; Jafari, Mohieddin; Mirzaie, Mehdi

    2016-11-01

    Network pharmacology elucidates the relationship between drugs and targets. As the identified targets for each drug increases, the corresponding drug-target network (DTN) evolves from solely reflection of the pharmaceutical industry trend to a portrait of polypharmacology. The aim of this study was to evaluate the potentials of DrugBank database in advancing systems pharmacology. We constructed and analyzed DTN from drugs and targets associations in the DrugBank 4.0 database. Our results showed that in bipartite DTN, increased ratio of identified targets for drugs augmented density and connectivity of drugs and targets and decreased modular structure. To clear up the details in the network structure, the DTNs were projected into two networks namely, drug similarity network (DSN) and target similarity network (TSN). In DSN, various classes of Food and Drug Administration-approved drugs with distinct therapeutic categories were linked together based on shared targets. Projected TSN also showed complexity because of promiscuity of the drugs. By including investigational drugs that are currently being tested in clinical trials, the networks manifested more connectivity and pictured the upcoming pharmacological space in the future years. Diverse biological processes and protein-protein interactions were manipulated by new drugs, which can extend possible target combinations. We conclude that network-based organization of DrugBank 4.0 data not only reveals the potential for repurposing of existing drugs, also allows generating novel predictions about drugs off-targets, drug-drug interactions and their side effects. Our results also encourage further effort for high-throughput identification of targets to build networks that can be integrated into disease networks. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

  6. A DNA-binding-site landscape and regulatory network analysis for NAC transcription factors in Arabidopsis thaliana

    DEFF Research Database (Denmark)

    Lindemose, Søren; Jensen, Michael Krogh; de Velde, Jan Van

    2014-01-01

    regulatory networks of 12 NAC transcription factors. Our data offer specific single-base resolution fingerprints for most TFs studied and indicate that NAC DNA-binding specificities might be predicted from their DNA-binding domain's sequence. The developed methodology, including the application......Target gene identification for transcription factors is a prerequisite for the systems wide understanding of organismal behaviour. NAM-ATAF1/2-CUC2 (NAC) transcription factors are amongst the largest transcription factor families in plants, yet limited data exist from unbiased approaches to resolve...... the DNA-binding preferences of individual members. Here, we present a TF-target gene identification workflow based on the integration of novel protein binding microarray data with gene expression and multi-species promoter sequence conservation to identify the DNA-binding specificities and the gene...

  7. Novel Strategy for Discrimination of Transcription Factor Binding Motifs Employing Mathematical Neural Network

    Science.gov (United States)

    Sugimoto, Asuka; Sumi, Takuya; Kang, Jiyoung; Tateno, Masaru

    2017-07-01

    Recognition in biological macromolecular systems, such as DNA-protein recognition, is one of the most crucial problems to solve toward understanding the fundamental mechanisms of various biological processes. Since specific base sequences of genome DNA are discriminated by proteins, such as transcription factors (TFs), finding TF binding motifs (TFBMs) in whole genome DNA sequences is currently a central issue in interdisciplinary biophysical and information sciences. In the present study, a novel strategy to create a discriminant function for discrimination of TFBMs by constituting mathematical neural networks (NNs) is proposed, together with a method to determine the boundary of signals (TFBMs) and noise in the NN-score (output) space. This analysis also leads to the mathematical limitation of discrimination in the recognition of features representing TFBMs, in an information geometrical manifold. Thus, the present strategy enables the identification of the whole space of TFBMs, right up to the noise boundary.

  8. Supplement data for conformation changes by some binding - ConfC | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ent data for conformation changes by some binding DOI 10.18908/lsdba.nbdc00400-002 Description of data contents The distance values...Bank) Data analysis method The distance values of φ and ψ between the superimposed protein structures of eac

  9. Incremental View Maintenance for Deductive Graph Databases Using Generalized Discrimination Networks

    Directory of Open Access Journals (Sweden)

    Thomas Beyhl

    2016-12-01

    Full Text Available Nowadays, graph databases are employed when relationships between entities are in the scope of database queries to avoid performance-critical join operations of relational databases. Graph queries are used to query and modify graphs stored in graph databases. Graph queries employ graph pattern matching that is NP-complete for subgraph isomorphism. Graph database views can be employed that keep ready answers in terms of precalculated graph pattern matches for often stated and complex graph queries to increase query performance. However, such graph database views must be kept consistent with the graphs stored in the graph database. In this paper, we describe how to use incremental graph pattern matching as technique for maintaining graph database views. We present an incremental maintenance algorithm for graph database views, which works for imperatively and declaratively specified graph queries. The evaluation shows that our maintenance algorithm scales when the number of nodes and edges stored in the graph database increases. Furthermore, our evaluation shows that our approach can outperform existing approaches for the incremental maintenance of graph query results.

  10. Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology.

    Science.gov (United States)

    Bakhtiarizadeh, Mohammad Reza; Moradi-Shahrbabak, Mohammad; Ebrahimi, Mansour; Ebrahimie, Esmaeil

    2014-09-07

    Due to the central roles of lipid binding proteins (LBPs) in many biological processes, sequence based identification of LBPs is of great interest. The major challenge is that LBPs are diverse in sequence, structure, and function which results in low accuracy of sequence homology based methods. Therefore, there is a need for developing alternative functional prediction methods irrespective of sequence similarity. To identify LBPs from non-LBPs, the performances of support vector machine (SVM) and neural network were compared in this study. Comprehensive protein features and various techniques were employed to create datasets. Five-fold cross-validation (CV) and independent evaluation (IE) tests were used to assess the validity of the two methods. The results indicated that SVM outperforms neural network. SVM achieved 89.28% (CV) and 89.55% (IE) overall accuracy in identification of LBPs from non-LBPs and 92.06% (CV) and 92.90% (IE) (in average) for classification of different LBPs classes. Increasing the number and the range of extracted protein features as well as optimization of the SVM parameters significantly increased the efficiency of LBPs class prediction in comparison to the only previous report in this field. Altogether, the results showed that the SVM algorithm can be run on broad, computationally calculated protein features and offers a promising tool in detection of LBPs classes. The proposed approach has the potential to integrate and improve the common sequence alignment based methods. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. An Efficient Processing of Join Queries for Sensor Networks Using Column-Oriented Databases

    OpenAIRE

    Kyung-Chang Kim

    2013-01-01

    Recently, the sensor network area is gaining attention both in the industry and academia. Many applications of sensor network such as vehicle tracking and environmental monitoring require joining sensor data scattered over the network. The main performance criterion for queries in a sensor network is to minimize the battery power consumption in each sensor node. Hence, reducing the communication cost of shipping data among sensor nodes is important since it is the main consumer of battery pow...

  12. Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach

    DEFF Research Database (Denmark)

    Buus, S.; Lauemoller, S.L.; Worning, Peder

    2003-01-01

    We have generated Artificial Neural Networks (ANN) capable of performing sensitive, quantitative predictions of peptide binding to the MHC class I molecule, HLA-A*0204. We have shown that such quantitative ANN are superior to conventional classification ANN, that have been trained to predict...

  13. A Database Query Processing Model in Peer-To-Peer Network ...

    African Journals Online (AJOL)

    Peer-to-peer databases are becoming more prevalent on the internet for sharing and distributing applications, documents, files, and other digital media. The problem associated with answering large-scale ad hoc analysis queries, aggregation queries, on these databases poses unique challenges. This paper presents an ...

  14. Investigating the Potential Impacts of Energy Production in the Marcellus Shale Region Using the Shale Network Database

    Science.gov (United States)

    Brantley, S.; Brazil, L.

    2017-12-01

    The Shale Network's extensive database of water quality observations enables educational experiences about the potential impacts of resource extraction with real data. Through tools that are open source and free to use, researchers, educators, and citizens can access and analyze the very same data that the Shale Network team has used in peer-reviewed publications about the potential impacts of hydraulic fracturing on water. The development of the Shale Network database has been made possible through efforts led by an academic team and involving numerous individuals from government agencies, citizen science organizations, and private industry. Thus far, these tools and data have been used to engage high school students, university undergraduate and graduate students, as well as citizens so that all can discover how energy production impacts the Marcellus Shale region, which includes Pennsylvania and other nearby states. This presentation will describe these data tools, how the Shale Network has used them in developing lesson plans, and the resources available to learn more.

  15. Harvesting Covert Networks: The Case Study of the iMiner Database

    DEFF Research Database (Denmark)

    Memon, Nasrullah; Wiil, Uffe Kock; Alhajj, Reda

    2011-01-01

    was incorporated in the iMiner prototype tool, which makes use of investigative data mining techniques to analyse data. This paper will present the developed framework along with the form and structure of the terrorist data in the database. Selected cases will be referenced to highlight the effectiveness of the i...... collected by intelligence agencies and government organisations is inaccessible to researchers. To counter the information scarcity, we designed and built a database of terrorist-related data and information by harvesting such data from publicly available authenticated websites. The database...

  16. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction

    Directory of Open Access Journals (Sweden)

    Lund Ole

    2009-09-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC molecule plays a central role in controlling the adaptive immune response to infections. MHC class I molecules present peptides derived from intracellular proteins to cytotoxic T cells, whereas MHC class II molecules stimulate cellular and humoral immunity through presentation of extracellularly derived peptides to helper T cells. Identification of which peptides will bind a given MHC molecule is thus of great importance for the understanding of host-pathogen interactions, and large efforts have been placed in developing algorithms capable of predicting this binding event. Results Here, we present a novel artificial neural network-based method, NN-align that allows for simultaneous identification of the MHC class II binding core and binding affinity. NN-align is trained using a novel training algorithm that allows for correction of bias in the training data due to redundant binding core representation. Incorporation of information about the residues flanking the peptide-binding core is shown to significantly improve the prediction accuracy. The method is evaluated on a large-scale benchmark consisting of six independent data sets covering 14 human MHC class II alleles, and is demonstrated to outperform other state-of-the-art MHC class II prediction methods. Conclusion The NN-align method is competitive with the state-of-the-art MHC class II peptide binding prediction algorithms. The method is publicly available at http://www.cbs.dtu.dk/services/NetMHCII-2.0.

  17. NABIC marker database: A molecular markers information network of agricultural crops.

    Science.gov (United States)

    Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

    2013-01-01

    In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

  18. FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis.

    Science.gov (United States)

    Parente, Eugenio; Cocolin, Luca; De Filippis, Francesca; Zotta, Teresa; Ferrocino, Ilario; O'Sullivan, Orla; Neviani, Erasmo; De Angelis, Maria; Cotter, Paul D; Ercolini, Danilo

    2016-02-16

    Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry. Copyright © 2015. Published by

  19. A relay network of extracellular heme-binding proteins drives C. albicans iron acquisition from hemoglobin.

    Science.gov (United States)

    Kuznets, Galit; Vigonsky, Elena; Weissman, Ziva; Lalli, Daniela; Gildor, Tsvia; Kauffman, Sarah J; Turano, Paola; Becker, Jeffrey; Lewinson, Oded; Kornitzer, Daniel

    2014-10-01

    Iron scavenging constitutes a crucial challenge for survival of pathogenic microorganisms in the iron-poor host environment. Candida albicans, like many microbial pathogens, is able to utilize iron from hemoglobin, the largest iron pool in the host's body. Rbt5 is an extracellular glycosylphosphatidylinositol (GPI)-anchored heme-binding protein of the CFEM family that facilitates heme-iron uptake by an unknown mechanism. Here, we characterize an additional C. albicans CFEM protein gene, PGA7, deletion of which elicits a more severe heme-iron utilization phenotype than deletion of RBT5. The virulence of the pga7-/- mutant is reduced in a mouse model of systemic infection, consistent with a requirement for heme-iron utilization for C. albicans pathogenicity. The Pga7 and Rbt5 proteins exhibit distinct cell wall attachment, and discrete localization within the cell envelope, with Rbt5 being more exposed than Pga7. Both proteins are shown here to efficiently extract heme from hemoglobin. Surprisingly, while Pga7 has a higher affinity for heme in vitro, we find that heme transfer can occur bi-directionally between Pga7 and Rbt5, supporting a model in which they cooperate in a heme-acquisition relay. Together, our data delineate the roles of Pga7 and Rbt5 in a cell surface protein network that transfers heme from extracellular hemoglobin to the endocytic pathway, and provide a paradigm for how receptors embedded in the cell wall matrix can mediate nutrient uptake across the fungal cell envelope.

  20. A systems biology approach to construct the gene regulatory network of systemic inflammation via microarray and databases mining

    Directory of Open Access Journals (Sweden)

    Lan Chung-Yu

    2008-09-01

    Full Text Available Abstract Background Inflammation is a hallmark of many human diseases. Elucidating the mechanisms underlying systemic inflammation has long been an important topic in basic and clinical research. When primary pathogenetic events remains unclear due to its immense complexity, construction and analysis of the gene regulatory network of inflammation at times becomes the best way to understand the detrimental effects of disease. However, it is difficult to recognize and evaluate relevant biological processes from the huge quantities of experimental data. It is hence appealing to find an algorithm which can generate a gene regulatory network of systemic inflammation from high-throughput genomic studies of human diseases. Such network will be essential for us to extract valuable information from the complex and chaotic network under diseased conditions. Results In this study, we construct a gene regulatory network of inflammation using data extracted from the Ensembl and JASPAR databases. We also integrate and apply a number of systematic algorithms like cross correlation threshold, maximum likelihood estimation method and Akaike Information Criterion (AIC on time-lapsed microarray data to refine the genome-wide transcriptional regulatory network in response to bacterial endotoxins in the context of dynamic activated genes, which are regulated by transcription factors (TFs such as NF-κB. This systematic approach is used to investigate the stochastic interaction represented by the dynamic leukocyte gene expression profiles of human subject exposed to an inflammatory stimulus (bacterial endotoxin. Based on the kinetic parameters of the dynamic gene regulatory network, we identify important properties (such as susceptibility to infection of the immune system, which may be useful for translational research. Finally, robustness of the inflammatory gene network is also inferred by analyzing the hubs and "weak ties" structures of the gene network

  1. Endocytosis of wheat germ agglutinin binding sites from the cell surface into a tubular endosomal network.

    Science.gov (United States)

    Raub, T J; Koroly, M J; Roberts, R M

    1990-04-01

    By using fluorescence and electron microscopy, the endocytic pathway encountered by cell surface components after they had bound wheat germ agglutinin (WGA) was visualized. The majority of these components are thought to consist of sialylated glycoproteins (HMWAG) that represent a subpopulation of the total cell surface proteins but most of the externally disposed plasma membrane proteins of the cell. Examination of semi-thin sections by medium- and high-voltage electron microscopy revealed the three-dimensional organization of vesicular and tubular endosomes. Binding of either fluorescein isothiocyanate-, horseradish peroxidase-, or ferritin-conjugated WGA to cells at 4 degrees C showed that the HMWAG were distributed uniformly over the cell surface. Warming of surface-labeled cells to 37 degrees C resulted in the endocytosis of WGA into peripheral endosomes via invagination of regions of both coated and uncoated membrane. The peripheral endosome appeared as isolated complexes comprising a vesicular element (300-400 nm diam.) surrounded by and continuous with tubular cisternae (45-60 nm diam.), which did not interconnect the endosomes. After 30 min or more label also became localized in a network of anastomosing tubules (45-60 nm diam.) that were located in the centrosomal region of the cell. Endocytosed WGA-HMWAG complexes did not become associated with cisternae of the Golgi apparatus, although tubular and vesicular endosomes were noted in the vicinity of the trans-Golgi region. The accumulation of WGA-HMWAG in the endosomes within the centrosomal region was inhibited when cells were incubated at 18 degrees C. None of these compartments contained acid phosphatase activity, a result that is consistent with other data that the HMWAG do not pass through lysosomes initially. The kinetics of labeling were consistent with the interpretation that recycling of most of the WGA binding surface glycoproteins occurred rapidly from early peripheral endosomes followed by the

  2. Practical Value of Food Pathogen Traceability through Building a Whole-Genome Sequencing Network and Database.

    Science.gov (United States)

    Allard, Marc W; Strain, Errol; Melka, David; Bunning, Kelly; Musser, Steven M; Brown, Eric W; Timme, Ruth

    2016-08-01

    The FDA has created a United States-based open-source whole-genome sequencing network of state, federal, international, and commercial partners. The GenomeTrakr network represents a first-of-its-kind distributed genomic food shield for characterizing and tracing foodborne outbreak pathogens back to their sources. The GenomeTrakr network is leading investigations of outbreaks of foodborne illnesses and compliance actions with more accurate and rapid recalls of contaminated foods as well as more effective monitoring of preventive controls for food manufacturing environments. An expanded network would serve to provide an international rapid surveillance system for pathogen traceback, which is critical to support an effective public health response to bacterial outbreaks. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  3. BioMart Central Portal: an open database network for the biological community

    Science.gov (United States)

    Guberman, Jonathan M.; Ai, J.; Arnaiz, O.; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J.; Di Génova, A.; Forbes, Simon; Fujisawa, T.; Gadaleta, E.; Goodstein, D. M.; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S.; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R.; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J.; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S.; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B.; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J.; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D. T.; Wong-Erasmus, Marie; Yao, L.; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

    2011-01-01

    BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. Database URL: http://central.biomart.org. PMID:21930507

  4. The Transformation of Schools' Social Networks during a Data-Based Decision Making Reform

    Science.gov (United States)

    Keuning, Trynke

    2016-01-01

    Context: Collaboration within school teams is considered to be important to build the capacity school teams need to work in a data-based way. In a school characterized by a strong collaborative culture, teachers may have more access to the knowledge and skills for analyzing data, teachers have more opportunity to discuss the performance goals to…

  5. The transformation of schools' social networks during a data-based decision making reform

    NARCIS (Netherlands)

    Keuning, Trynke; Geel, Marieke Van; Visscher, Adrie; Fox, Jean Paul; Moolenaar, Nienke M.|info:eu-repo/dai/nl/304352802

    2016-01-01

    Context: Collaboration within school teams is considered to be important to build the capacity school teams need to work in a data-based way. In a school characterized by a strong collaborative culture, teachers may have more access to the knowledge and skills for analyzing data, teachers have more

  6. Evaluating the Immunogenicity of Protein Drugs by Applying In Vitro MHC Binding Data and the Immune Epitope Database and Analysis Resource

    Directory of Open Access Journals (Sweden)

    Sinu Paul

    2013-01-01

    Full Text Available The immune system has evolved to become highly specialized in recognizing and responding to pathogens and foreign molecules. Specifically, the function of HLA class II is to ensure that a sufficient sample of peptides derived from foreign molecules is presented to T cells. This leads to an important concern in human drug development as the possible immunogenicity of biopharmaceuticals, especially those intended for chronic administration, can lead to reduced efficacy and an undesired safety profile for biological therapeutics. As part of this review, we will highlight the molecular basis of antigen presentation as a key step in the induction of T cell responses, emphasizing the events associated with peptide binding to polymorphic and polygenic HLA class II molecules. We will further review methodologies that predict HLA class II binding peptides and candidate epitopes. We will focus on tools provided by the Immune Epitope Database and Analysis Resource, discussing the basic features of different prediction methods, the objective evaluation of prediction quality, and general guidelines for practical use of these tools. Finally the use, advantages, and limitations of the methodology will be demonstrated in a review of two previous studies investigating the immunogenicity of erythropoietin and timothy grass pollen.

  7. Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks

    Science.gov (United States)

    Nishtala, Sneha; Neelamraju, Yaseswini; Janga, Sarath Chandra

    2016-05-01

    RNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks.

  8. A computer network system for mutual usage four databases of nuclear materials (Data-Free-Way)

    International Nuclear Information System (INIS)

    Fujita, M.; Kurihara, Y.; Shindou, M.; Yokoyama, N.; Tachi, Y.; Kano, S.; Iwata, S.

    1996-01-01

    Distributed database system named 'Data-Free-Way' for advanced nuclear materials has been developed by National Research Institute for Metals (NRIM), Japan Atomic Energy Research Institute (JAERI) and Power Reactor and Nuclear Fuel Development Corporation (PNC) under cooperation agreement between these three organizations. In the paper, features and functions of the system including input data are described together with method to share database among the three organizations as well as examples of the easy accessible search of material properties. Results of analysis of tensile and creep properties data on type 316 stainless steel collected by the different organizations and stored in the present system are also introduced as an example of attractive utilization of the system. Moreover, in order to consider the system in near future, some trails of WWW server of several sites in 'Data-Free-Way' to supply the information on nuclear materials to Internet are introduced. (author)

  9. BioMart Central Portal: an open database network for the biological community

    OpenAIRE

    Guberman, Jonathan M.; Ai, J.; Arnaiz, O.; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J.; Di Genova, A.; Forbes, Simon; Fujisawa, T.; Gadaleta, E.; Goodstein, D. M.

    2011-01-01

    International audience; BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common inte...

  10. Toward a standardized soil carbon database platform in the US Critical Zone Observatory Network

    Science.gov (United States)

    Filley, T. R.; Marini, L.; Todd-Brown, K. E.; Malhotra, A.; Harden, J. W.; Kumar, P.

    2017-12-01

    Within the soil carbon community of the US Critical Zone Observatory (CZO) Network, efforts are underway to promote network-level data syntheses and modeling projects and to identify barriers to data intercomparability. This represents a challenging goal given the diversity of soil carbon sampling methodologies, spatial and vertical resolution, carbon pool isolation protocols, subsequent measurement techniques, and matrix terminology. During the last annual meeting of the CZO SOC Working Group, Dec 11, 2016, it was decided that integration with, and potentially adoption of, a widely used, active, and mature data aggregation, archival, and visualization platform was the easiest route to achieve this ultimate goal. Additionally, to assess the state of deep and shallow soil C data among the CZO sites it was recommended that a comprehensive survey must be undertaken to identify data gaps and catalog the various soil sampling and analysis methodologies. The International Soil Carbon Network (ISCN) has a long history of leadership in the development of soil C data aggregation, archiving, and visualization tools and currently houses data for over 70,000 soil cores contributed from international soil carbon community. Over the past year, members of the CZO network and the ISCN have met to discuss logistics of adopting the ISCN template within the CZO. Collaborative efforts among all of the CZO site data managers, led by the Intensively Managed Landscapes CZO, will evaluate feasibility of adoption of the ISCN template, or some modification thereof, and distribution to the appropriate soil scientists for data upload and aggregation. Partnering with ISCN also ensures that soil characteristics from the US CZO are placed in a developing global soil context and paves the way for future integration of data from other international CZO networks. This poster will provide an update of this overall effort along with a summary of data products, partnering networks, and recommendations

  11. Establishment of database and network for research of stream generator and state of the art technology review

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Jae Bong; Hur, Nam Su; Moon, Seong In; Seo, Hyeong Won; Park, Bo Kyu; Park, Sung Ho; Kim, Hyung Geun [Sungkyunkwan Univ., Seoul (Korea, Republic of)

    2004-02-15

    A significant number of steam generator tubes are defective and are removed from service or repaired world widely. This wide spread damage has been caused by diverse degradation mechanisms, some of which are difficult to detect and predict. Regarding domestic nuclear power plants, also, the increase of number of operating nuclear power plants and operating periods may result in the increase of steam generator tube failure. So, it is important to carry out the integrity evaluation process to prevent the steam generator tube damage. There are two objectives of this research. The one is to make database for the research of steam generator at domestic research institution. It will increase the efficiency and capability of limited domestic research resources by sharing data and information through network organization. Also, it will enhance the current standard of integrity evaluation procedure that is considerably conservative but can be more reasonable. The second objective is to establish the standard integrity evaluation procedure for steam generator tube by reviewing state of the art technology. The research resources related to steam generator tubes are managed by the established web-based database system. The following topics are covered in this project: development of web-based network for research on steam generator tubes review of state of the art technology.

  12. Establishment of database and network for research of stream generator and state of the art technology review

    International Nuclear Information System (INIS)

    Choi, Jae Bong; Hur, Nam Su; Moon, Seong In; Seo, Hyeong Won; Park, Bo Kyu; Park, Sung Ho; Kim, Hyung Geun

    2004-02-01

    A significant number of steam generator tubes are defective and are removed from service or repaired world widely. This wide spread damage has been caused by diverse degradation mechanisms, some of which are difficult to detect and predict. Regarding domestic nuclear power plants, also, the increase of number of operating nuclear power plants and operating periods may result in the increase of steam generator tube failure. So, it is important to carry out the integrity evaluation process to prevent the steam generator tube damage. There are two objectives of this research. The one is to make database for the research of steam generator at domestic research institution. It will increase the efficiency and capability of limited domestic research resources by sharing data and information through network organization. Also, it will enhance the current standard of integrity evaluation procedure that is considerably conservative but can be more reasonable. The second objective is to establish the standard integrity evaluation procedure for steam generator tube by reviewing state of the art technology. The research resources related to steam generator tubes are managed by the established web-based database system. The following topics are covered in this project: development of web-based network for research on steam generator tubes review of state of the art technology

  13. Inferring pregnancy episodes and outcomes within a network of observational databases.

    Directory of Open Access Journals (Sweden)

    Amy Matcho

    Full Text Available Administrative claims and electronic health records are valuable resources for evaluating pharmaceutical effects during pregnancy. However, direct measures of gestational age are generally not available. Establishing a reliable approach to infer the duration and outcome of a pregnancy could improve pharmacovigilance activities. We developed and applied an algorithm to define pregnancy episodes in four observational databases: three US-based claims databases: Truven MarketScan® Commercial Claims and Encounters (CCAE, Truven MarketScan® Multi-state Medicaid (MDCD, and the Optum ClinFormatics® (Optum database and one non-US database, the United Kingdom (UK based Clinical Practice Research Datalink (CPRD. Pregnancy outcomes were classified as live births, stillbirths, abortions and ectopic pregnancies. Start dates were estimated using a derived hierarchy of available pregnancy markers, including records such as last menstrual period and nuchal ultrasound dates. Validation included clinical adjudication of 700 electronic Optum and CPRD pregnancy episode profiles to assess the operating characteristics of the algorithm, and a comparison of the algorithm's Optum pregnancy start estimates to starts based on dates of assisted conception procedures. Distributions of pregnancy outcome types were similar across all four data sources and pregnancy episode lengths found were as expected for all outcomes, excepting term lengths in episodes that used amenorrhea and urine pregnancy tests for start estimation. Validation survey results found highest agreement between reviewer chosen and algorithm operating characteristics for questions assessing pregnancy status and accuracy of outcome category with 99-100% agreement for Optum and CPRD. Outcome date agreement within seven days in either direction ranged from 95-100%, while start date agreement within seven days in either direction ranged from 90-97%. In Optum validation sensitivity analysis, a total of 73% of

  14. Inferring pregnancy episodes and outcomes within a network of observational databases

    Science.gov (United States)

    Ryan, Patrick; Fife, Daniel; Gifkins, Dina; Knoll, Chris; Friedman, Andrew

    2018-01-01

    Administrative claims and electronic health records are valuable resources for evaluating pharmaceutical effects during pregnancy. However, direct measures of gestational age are generally not available. Establishing a reliable approach to infer the duration and outcome of a pregnancy could improve pharmacovigilance activities. We developed and applied an algorithm to define pregnancy episodes in four observational databases: three US-based claims databases: Truven MarketScan® Commercial Claims and Encounters (CCAE), Truven MarketScan® Multi-state Medicaid (MDCD), and the Optum ClinFormatics® (Optum) database and one non-US database, the United Kingdom (UK) based Clinical Practice Research Datalink (CPRD). Pregnancy outcomes were classified as live births, stillbirths, abortions and ectopic pregnancies. Start dates were estimated using a derived hierarchy of available pregnancy markers, including records such as last menstrual period and nuchal ultrasound dates. Validation included clinical adjudication of 700 electronic Optum and CPRD pregnancy episode profiles to assess the operating characteristics of the algorithm, and a comparison of the algorithm’s Optum pregnancy start estimates to starts based on dates of assisted conception procedures. Distributions of pregnancy outcome types were similar across all four data sources and pregnancy episode lengths found were as expected for all outcomes, excepting term lengths in episodes that used amenorrhea and urine pregnancy tests for start estimation. Validation survey results found highest agreement between reviewer chosen and algorithm operating characteristics for questions assessing pregnancy status and accuracy of outcome category with 99–100% agreement for Optum and CPRD. Outcome date agreement within seven days in either direction ranged from 95–100%, while start date agreement within seven days in either direction ranged from 90–97%. In Optum validation sensitivity analysis, a total of 73% of

  15. Biomine: predicting links between biological entities using network models of heterogeneous databases

    Directory of Open Access Journals (Sweden)

    Eronen Lauri

    2012-06-01

    Full Text Available Abstract Background Biological databases contain large amounts of data concerning the functions and associations of genes and proteins. Integration of data from several such databases into a single repository can aid the discovery of previously unknown connections spanning multiple types of relationships and databases. Results Biomine is a system that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. We present Biomine and evaluate its performance in link prediction, where the goal is to predict pairs of nodes that will be connected in the future, based on current data. In particular, we formulate protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph. We consider and experiment with several such measures, and perform a parameter optimization procedure where different edge types are weighted to optimize link prediction accuracy. We also propose a novel method for disease-gene prioritization, defined as finding a subset of candidate genes that cluster together in the graph. We experimentally evaluate Biomine by predicting future annotations in the source databases and prioritizing lists of putative disease genes. Conclusions The experimental results show that Biomine has strong potential for predicting links when a set of selected candidate links is available. The predictions obtained using the entire Biomine dataset are shown to clearly outperform ones obtained using any single source of data alone, when different types of links are suitably weighted. In the gene prioritization task, an established reference set of disease-associated genes is useful, but the results show that under favorable

  16. Networked neuroscience : brain scans and visual knowing at the intersection of atlases and databases

    NARCIS (Netherlands)

    Beaulieu, Anne; de Rijcke, Sarah; Coopmans, Catelijne; Woolgar, Steve

    2014-01-01

    This chapter discusses the development of authoritative collections of brain scans known as “brain atlases”, focusing in particular on how such scans are constituted as authoritative visual objects. Three dimensions are identified: first, brain scans are parts of suites of networked technologies

  17. Discovering biomarkers for antidepressant response: protocol from the Canadian biomarker integration network in depression (CAN-BIND) and clinical characteristics of the first patient cohort.

    Science.gov (United States)

    Lam, Raymond W; Milev, Roumen; Rotzinger, Susan; Andreazza, Ana C; Blier, Pierre; Brenner, Colleen; Daskalakis, Zafiris J; Dharsee, Moyez; Downar, Jonathan; Evans, Kenneth R; Farzan, Faranak; Foster, Jane A; Frey, Benicio N; Geraci, Joseph; Giacobbe, Peter; Feilotter, Harriet E; Hall, Geoffrey B; Harkness, Kate L; Hassel, Stefanie; Ismail, Zahinoor; Leri, Francesco; Liotti, Mario; MacQueen, Glenda M; McAndrews, Mary Pat; Minuzzi, Luciano; Müller, Daniel J; Parikh, Sagar V; Placenza, Franca M; Quilty, Lena C; Ravindran, Arun V; Salomons, Tim V; Soares, Claudio N; Strother, Stephen C; Turecki, Gustavo; Vaccarino, Anthony L; Vila-Rodriguez, Fidel; Kennedy, Sidney H

    2016-04-16

    Major Depressive Disorder (MDD) is among the most prevalent and disabling medical conditions worldwide. Identification of clinical and biological markers ("biomarkers") of treatment response could personalize clinical decisions and lead to better outcomes. This paper describes the aims, design, and methods of a discovery study of biomarkers in antidepressant treatment response, conducted by the Canadian Biomarker Integration Network in Depression (CAN-BIND). The CAN-BIND research program investigates and identifies biomarkers that help to predict outcomes in patients with MDD treated with antidepressant medication. The primary objective of this initial study (known as CAN-BIND-1) is to identify individual and integrated neuroimaging, electrophysiological, molecular, and clinical predictors of response to sequential antidepressant monotherapy and adjunctive therapy in MDD. CAN-BIND-1 is a multisite initiative involving 6 academic health centres working collaboratively with other universities and research centres. In the 16-week protocol, patients with MDD are treated with a first-line antidepressant (escitalopram 10-20 mg/d) that, if clinically warranted after eight weeks, is augmented with an evidence-based, add-on medication (aripiprazole 2-10 mg/d). Comprehensive datasets are obtained using clinical rating scales; behavioural, dimensional, and functioning/quality of life measures; neurocognitive testing; genomic, genetic, and proteomic profiling from blood samples; combined structural and functional magnetic resonance imaging; and electroencephalography. De-identified data from all sites are aggregated within a secure neuroinformatics platform for data integration, management, storage, and analyses. Statistical analyses will include multivariate and machine-learning techniques to identify predictors, moderators, and mediators of treatment response. From June 2013 to February 2015, a cohort of 134 participants (85 outpatients with MDD and 49 healthy participants

  18. DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions.

    Directory of Open Access Journals (Sweden)

    Prashanthi Karyala

    2016-09-01

    Full Text Available Dengue virus (DENV is a human pathogen and its etiology has been widely established. There are many interactions between DENV and human proteins that have been reported in literature. However, no publicly accessible resource for efficiently retrieving the information is yet available. In this study, we mined all publicly available dengue-human interactions that have been reported in the literature into a database called DenHunt. We retrieved 682 direct interactions of human proteins with dengue viral components, 382 indirect interactions and 4120 differentially expressed human genes in dengue infected cell lines and patients. We have illustrated the importance of DenHunt by mapping the dengue-human interactions on to the host interactome and observed that the virus targets multiple host functional complexes of important cellular processes such as metabolism, immune system and signaling pathways suggesting a potential role of these interactions in viral pathogenesis. We also observed that 7 percent of the dengue virus interacting human proteins are also associated with other infectious and non-infectious diseases. Finally, the understanding that comes from such analyses could be used to design better strategies to counteract the diseases caused by dengue virus. The whole dataset has been catalogued in a searchable database, called DenHunt (http://proline.biochem.iisc.ernet.in/DenHunt/.

  19. DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions.

    Science.gov (United States)

    Karyala, Prashanthi; Metri, Rahul; Bathula, Christopher; Yelamanchi, Syam K; Sahoo, Lipika; Arjunan, Selvam; Sastri, Narayan P; Chandra, Nagasuma

    2016-09-01

    Dengue virus (DENV) is a human pathogen and its etiology has been widely established. There are many interactions between DENV and human proteins that have been reported in literature. However, no publicly accessible resource for efficiently retrieving the information is yet available. In this study, we mined all publicly available dengue-human interactions that have been reported in the literature into a database called DenHunt. We retrieved 682 direct interactions of human proteins with dengue viral components, 382 indirect interactions and 4120 differentially expressed human genes in dengue infected cell lines and patients. We have illustrated the importance of DenHunt by mapping the dengue-human interactions on to the host interactome and observed that the virus targets multiple host functional complexes of important cellular processes such as metabolism, immune system and signaling pathways suggesting a potential role of these interactions in viral pathogenesis. We also observed that 7 percent of the dengue virus interacting human proteins are also associated with other infectious and non-infectious diseases. Finally, the understanding that comes from such analyses could be used to design better strategies to counteract the diseases caused by dengue virus. The whole dataset has been catalogued in a searchable database, called DenHunt (http://proline.biochem.iisc.ernet.in/DenHunt/).

  20. Establishing the ACORN National Practitioner Database: Strategies to Recruit Practitioners to a National Practice-Based Research Network.

    Science.gov (United States)

    Adams, Jon; Steel, Amie; Moore, Craig; Amorin-Woods, Lyndon; Sibbritt, David

    2016-10-01

    The purpose of this paper is to report on the recruitment and promotion strategies employed by the Australian Chiropractic Research Network (ACORN) project aimed at helping recruit a substantial national sample of participants and to describe the features of our practice-based research network (PBRN) design that may provide key insights to others looking to establish a similar network or draw on the ACORN project to conduct sub-studies. The ACORN project followed a multifaceted recruitment and promotion strategy drawing on distinct branding, a practitioner-focused promotion campaign, and a strategically designed questionnaire and distribution/recruitment approach to attract sufficient participation from the ranks of registered chiropractors across Australia. From the 4684 chiropractors registered at the time of recruitment, the project achieved a database response rate of 36% (n = 1680), resulting in a large, nationally representative sample across age, gender, and location. This sample constitutes the largest proportional coverage of participants from any voluntary national PBRN across any single health care profession. It does appear that a number of key promotional and recruitment features of the ACORN project may have helped establish the high response rate for the PBRN, which constitutes an important sustainable resource for future national and international efforts to grow the chiropractic evidence base and research capacity. Further rigorous enquiry is needed to help evaluate the direct contribution of specific promotional and recruitment strategies in attaining high response rates from practitioner populations who may be invited to participate in future PBRNs. Copyright © 2016. Published by Elsevier Inc.

  1. PERANCANGAN MODEL NETWORK PADA MESIN DATABASE NON SPATIAL UNTUK MANUVER JARINGAN LISTRIK SEKTOR DISTRIBUSI DENGAN PL SQ

    Directory of Open Access Journals (Sweden)

    I Made Sukarsa

    2009-06-01

    Full Text Available Saat ini aplikasi di bidang SIG telah banyak yang dikembangkan berbasis mesin DBMS (Database Management System non spatial sehingga mampu mendukung model penyajian data secara client server dan menangani data dalam jumlah yang besar. Salah satunya telah dikembangkan untuk menangani data jaringan listrik.Kenyataannya, mesin-mesin DBMS belum dilengkapi dengan kemampuan untuk melakukan analisis network seperti manuver jaringan dan merupakan dasar untuk pengembangan berbagai aplikasi lainnya. Oleh karena itu,perlu dikembangkan suatu model network untuk manuver jaringan listrik dengan berbagai kekhasannya.Melalui beberapa tahapan penelitian yang dilakukan, telah dapat dikembangkan suatu model network yangdapat digunakan untuk menangani manuver jaringan. Model ini dibangun dengan memperhatikan kepentingan pengintegrasian dengan sistem eksisting dengan meminimalkan adanya perubahan pada aplikasi eksisting.Pemilihan implementasi berbasis PL SQL (Pragrammable Language Structure Query Language akan memberikan berbagai keuntungan termasuk unjuk kerja sistem. Model ini telah diujikan untuk simulasi pemadaman,menghitung perubahan struktur pembebanan jaringan dan dapat dikembangkan untuk analisis sistem tenaga listrik seperti rugi-rugi, load flow dan sebagainya sehingga pada akhirnya aplikasi SIG akan mampu mensubstitusi danmengatasi kelemahan aplikasi analisis sistem tenaga yang banyak dipakai saat ini seperti EDSA (Electrical DesignSystem Anaysis .

  2. Network of TAMCNS: Identifying Influence Regions Within the GCSS-MC Database

    Science.gov (United States)

    2017-06-01

    friendship. You made spending many hours at NPS an enjoyable experience. In particular, I want to acknowledge Dan for his assistance with math and LaTeX...Hall, 2001. [7] K. H. Rosen, Discrete Mathematics and Its Applications, 7th ed. New York, NY: McGraw-Hill, 2012. [8] D. Ortiz-Arroyo, “Discovering sets...observations/whats-a-voxel-and-what-can-it-tell-us-a-primer-on-fmri/ [28] A. Beveridge and J. Shan, “Network of thrones,” Math Horizons, vol. 23, no. 4

  3. SISSY: An example of a multi-threaded, networked, object-oriented databased application

    International Nuclear Information System (INIS)

    Scipioni, B.; Liu, D.; Song, T.

    1993-05-01

    The Systems Integration Support SYstem (SISSY) is presented and its capabilities and techniques are discussed. It is fully automated data collection and analysis system supporting the SSCL's systems analysis activities as they relate to the Physics Detector and Simulation Facility (PDSF). SISSY itself is a paradigm of effective computing on the PDSF. It uses home-grown code (C++), network programming (RPC, SNMP), relational (SYBASE) and object-oriented (ObjectStore) DBMSs, UNIX operating system services (IRIX threads, cron, system utilities, shells scripts, etc.), and third party software applications (NetCentral Station, Wingz, DataLink) all of which act together as a single application to monitor and analyze the PDSF

  4. RNA binding protein RNPC1 inhibits breast cancer cells metastasis via activating STARD13-correlated ceRNA network.

    Science.gov (United States)

    Zhang, Zhiting; Guo, Qianqian; Zhang, Shufang; Xiang, Chenxi; Guo, Xinwei; Zhang, Feng; Gao, Lanlan; Ni, Haiwei; Xi, Tao; Zheng, Lufeng

    2018-05-07

    RNA binding proteins (RBPs) are pivotal post-transcriptional regulators. RNPC1, an RBP, acts as a tumor suppressor through binding and regulating the expression of target genes in cancer cells. This study disclosed that RNPC1 expression was positively correlated with breast cancer patients' relapse free and overall survival, and RNPC1suppressed breast cancer cells metastasis. Mechanistically, RNPC1 promoting a competing endogenous network (ceRNA) crosstalk between STARD13, CDH5, HOXD10, and HOXD1 (STARD13-correlated ceRNA network) that we previously confirmed in breast cancer cells through stabilizing the transcripts and thus facilitating the expression of these four genes in breast cancer cells. Furthermore, RNPC1 overexpression restrained the promotion of STARD13, CDH5, HOXD10, and HOXD1 knockdown on cell metastasis. Notably, RNPC1 expression was positively correlated with CDH5, HOXD1 and HOXD10 expression in breast cancer tissues, and attenuated adriamycin resistance. Taken together, these results identified that RNPC1 could inhibit breast cancer cells metastasis via promoting STARD13-correlated ceRNA network.

  5. SPAN: A Network Providing Integrated, End-to-End, Sensor-to-Database Solutions for Environmental Sciences

    Science.gov (United States)

    Benzel, T.; Cho, Y. H.; Deschon, A.; Gullapalli, S.; Silva, F.

    2009-12-01

    In recent years, advances in sensor network technology have shown great promise to revolutionize environmental data collection. Still, wide spread adoption of these systems by domain experts has been lacking, and these have remained the purview of the engineers who design them. While there are many data logging options for basic data collection in the field currently, scientists are often required to visit the deployment sites to retrieve their data and manually import it into spreadsheets. Some advanced commercial software systems do allow scientists to collect data remotely, but most of these systems only allow point-to-point access, and require proprietary hardware. Furthermore, these commercial solutions preclude the use of sensors from other manufacturers or integration with internet based database repositories and compute engines. Therefore, scientists often must download and manually reformat their data before uploading it to the repositories if they wish to share their data. We present an open-source, low-cost, extensible, turnkey solution called Sensor Processing and Acquisition Network (SPAN) which provides a robust and flexible sensor network service. At the deployment site, SPAN leverages low-power generic embedded processors to integrate variety of commercially available sensor hardware to the network of environmental observation systems. By bringing intelligence close to the sensed phenomena, we can remotely control configuration and re-use, establish rules to trigger sensor activity, manage power requirements, and control the two-way flow of sensed data as well as control information to the sensors. Key features of our design include (1) adoption of a hardware agnostic architecture: our solutions are compatible with several programmable platforms, sensor systems, communication devices and protocols. (2) information standardization: our system supports several popular communication protocols and data formats, and (3) extensible data support: our

  6. Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network.

    Science.gov (United States)

    Culyba, Matthew J; Kubiak, Jeffrey M; Mo, Charlie Y; Goulian, Mark; Kohli, Rahul M

    2018-06-01

    Biochemical pathways are often genetically encoded as simple transcription regulation networks, where one transcription factor regulates the expression of multiple genes in a pathway. The relative timing of each promoter's activation and shut-off within the network can impact physiology. In the DNA damage repair pathway (known as the SOS response) of Escherichia coli, approximately 40 genes are regulated by the LexA repressor. After a DNA damaging event, LexA degradation triggers SOS gene transcription, which is temporally separated into subsets of 'early', 'middle', and 'late' genes. Although this feature plays an important role in regulating the SOS response, both the range of this separation and its underlying mechanism are not experimentally defined. Here we show that, at low doses of DNA damage, the timing of promoter activities is not separated. Instead, timing differences only emerge at higher levels of DNA damage and increase as a function of DNA damage dose. To understand mechanism, we derived a series of synthetic SOS gene promoters which vary in LexA-operator binding kinetics, but are otherwise identical, and then studied their activity over a large dose-range of DNA damage. In distinction to established models based on rapid equilibrium assumptions, the data best fit a kinetic model of repressor occupancy at promoters, where the drop in cellular LexA levels associated with higher doses of DNA damage leads to non-equilibrium binding kinetics of LexA at operators. Operators with slow LexA binding kinetics achieve their minimal occupancy state at later times than operators with fast binding kinetics, resulting in a time separation of peak promoter activity between genes. These data provide insight into this remarkable feature of the SOS pathway by demonstrating how a single transcription factor can be employed to control the relative timing of each gene's transcription as a function of stimulus dose.

  7. Vitamin K3 disrupts the microtubule networks by binding to tubulin: a novel mechanism of its antiproliferative activity.

    Science.gov (United States)

    Acharya, Bipul R; Choudhury, Diptiman; Das, Amlan; Chakrabarti, Gopal

    2009-07-28

    Vitamin K3 (2-methyl-1,4-naphthoquinone), also known as menadione, is the synthetic precursor of all the naturally occurring vitamin K in the body. Vitamin K is necessary for the production of prothrombin and five other blood-clotting factors in humans. We have examined the effects of menadione on cellular microtubules ex vivo as well as its binding with purified tubulin and microtubules in vitro. Cell viability experiments using human cervical epithelial cancer cells (HeLa) and human oral epithelial cancer cells (KB) indicated that the IC(50) values for menadione are 25.6 +/- 0.6 and 64.3 +/- 0.36 microM, respectively, in those cells. Mendione arrests HeLa cells in mitosis. Immunofluorescence studies using an anti-alpha-tubulin antibody showed a significant irreversible depolymeriztion of the interphase microtubule network and spindle microtubule in a dose-dependent manner. In vitro polymerization of purified tubulin into microtubules is inhibited by menadione with an IC(50) value of 47 +/- 0.65 microM. The binding of menadione with tubulin was studied using menadione fluorescence and intrinsic tryptophan fluorescence of tubulin. Binding of menadione to tubulin is slow, taking 35 min for equilibration at 25 degrees C. The association reaction kinetics is biphasic in nature, and the association rate constants for fast and slow phases are 189.12 +/- 17 and 32.44 +/- 21 M(-1) s(-1) at 25 degrees C, respectively. The stoichiometry of menadione binding to tubulin is 1:1 (molar ratio) with a dissociation constant from 2.44 +/- 0.34 to 3.65 +/- 0.25 microM at 25 degrees C. Menadione competes for the colchicine binding site with a K(i) of 2.5 muM as determined from a modified Dixon plot. The obtained data suggested that menadione binds at the colchicine binding site to tubulin. Thus, we can conclude one novel mechanism of inhibition of cancer cell proliferation by menadione is through tubulin binding.

  8. Database management for an electrical distribution network of intermediate complexity CERN

    CERN Document Server

    De Ruschi, Daniele; Burdet, Georges

    2010-01-01

    This thesis is submitted as the final work for the degree of Master of Science in Engineering of Information that has been taken by the writer at at University of Bergamo, Italy. The report is based on the work conducted by the writer from September 2009 throughout June 2010 on a project assignment given by the department of Engineering Electrical Control at CERN Genève The work performed is a contribution to the GESMAR system of CERN. GESMAR is a CERN made complex platform for support and management of electric network. In this work is developed an information system for an ETL process. The report presents the design, implementation and evaluation made, prototypes of applications which take advantages of new information inserted in GESMAR are also presented.

  9. Ties that Bind: A Social Network Approach To Understanding Student Integration and Persistence.

    Science.gov (United States)

    Thomas, Scott L.

    2000-01-01

    This study used a social network paradigm to examine college student integration of 329 college freshmen at a private liberal arts college. Analysis of the structural aspects of students' on-campus associations found differential effects of various social network characteristics on student commitment and persistence. (DB)

  10. The ties that bind: the networked performance of gender, sexuality, and friendship on Myspace

    NARCIS (Netherlands)

    van Doorn, N.

    2010-01-01

    Although the body of research on social network sites (SNSs) continues to increase, scholarship in this relatively new field has largely neglected the gendered dimensions of networked interaction on SNSs. Through an empirical analysis of users’ comment exchanges, this study demonstrates how a group

  11. Data-Based Energy Efficient Clustered Routing Protocol for Wireless Sensors Networks – Tabuk Flood Monitoring System Case Study

    Directory of Open Access Journals (Sweden)

    Ammar Babiker

    2017-10-01

    Full Text Available Energy efficiency has been considered as the most important issue in wireless sensor networks. As in many applications, wireless sensors are scattered in a wide harsh area, where the battery replacement or charging will be quite difficult and it is the most important challenge. Therefore, the design of energy saving mechanism becomes mandatory in most recent research. In this paper, a new energy efficient clustered routing protocol is proposed: the proposed protocol is based on analyzing the data collected from the sensors in a base-station. Based on this analysis the cluster head will be selected as the one with the most useful data. Then, a variable time slot is specified to each sensor to minimize the transmission of repetitive and un-useful data. The proposed protocol Data-Based Energy Efficient Clustered Routing Protocol for Wireless Sensors Networks (DCRP was compared with the famous energy efficient LEACH protocol and also with one of the recent energy efficient routing protocols named Position Responsive Routing Protocol (PRRP. DCRP has been used in monitoring the floods in Tabuk area –Saudi Arabia. It shows comparatively better results.

  12. Liver Transplantation for Urea Cycle Disorders: Analysis of the United Network for Organ Sharing Database.

    Science.gov (United States)

    Yu, L; Rayhill, S C; Hsu, E K; Landis, C S

    2015-10-01

    Urea cycle disorders (UCD) are caused by rare inherited defects in the urea cycle enzymes leading to diminished ability to convert ammonia to urea in the liver. The resulting excess of circulating ammonia can lead to central nervous system toxicity and irreversible neurologic damage. Most cases are identified in children. However, UCDs can also be diagnosed in adulthood, and liver transplant is occasionally required. We examined the UNOS database to evaluate outcomes in adult and pediatric patients who underwent liver transplant as treatment for a UCD. We identified 265 pediatric and 13 adult patients who underwent liver transplant for a UCD between 1987 and 2010. The majority (68%) of these patients were transplanted before age 5 years. Ornithine transcarbamylase (OTC) deficiency was the most common UCD in both adults and children who underwent transplant. UCD patients who underwent liver transplant were younger, more likely to be male (67%), had lower pediatric end-stage liver disease/model for end-stage liver disease scores, and were more likely to be Caucasian or Asian compared with all other patients transplanted during the same time period. UCD patients did not have an increased utilization of living donor transplantation in this US cohort. Univariate and multivariate risk factor analyses were performed and did not reveal any significant factors that were predictive of post-transplant death or graft loss. Excellent outcomes were seen in both children and adults with UCDs who underwent transplant with overall 1-, 5-, and 10-year survivals of 93%, 89%, and 87%, respectively. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Patterns of severe injury in pediatric car crash victims: Crash Injury Research Engineering Network database.

    Science.gov (United States)

    Brown, J Kristine; Jing, Yuezhou; Wang, Stewart; Ehrlich, Peter F

    2006-02-01

    Motor vehicle crashes (MVCs) account for 50% of pediatric trauma. Safety improvements are typically tested with child crash dummies using an in vitro model. The Crash Injury Research Engineering Network (CIREN) provides an in vivo validation process. Previous research suggest that children in lateral crashes or front-seat locations have higher Injury Severity Scale scores and lower Glasgow Coma Scale scores than those in frontal-impact crashes. However, specific injury patterns and crash characteristics have not been characterized. Data were collected from the CIREN multidisciplinary crash reconstruction network (10 pediatric trauma centers). Injuries were examined with regard to crash direction (frontal/lateral), restraint use, seat location, and change in velocity at impact (DeltaV). Injuries were limited to Abbreviated Injury Scale (AIS) scores of 3 or higher and included head, thoracic, abdominal, pelvic, spine, and long bone (orthopedic) injuries. Standard age groupings (0-4, 5-9, 10-14, and 15-18 years) were used. Statistical analyses used Fisher's Exact test and multiple logistic regressions. Four hundred seventeen MVCs with 2500 injuries were analyzed (males = 219, females = 198). Controlling for DeltaV and age, children in lateral-impact crashes (n = 232) were significantly more likely to suffer severe injuries to the head and thorax as compared with children in frontal crashes (n = 185), who were more likely to suffer severe spine and orthopedic injuries. Children in a front-seat (n = 236) vs those in a back-seat (n = 169) position had more injuries to the thoracic (27% vs 17%), abdominal (21% vs 13%), pelvic (11% vs 1%), and orthopedic (28% vs 10%) regions (P < .05 for all). Seat belts were protective for pelvic (5% vs 12% unbelted) and orthopedic (15% vs 40%) injuries (odds ratio = 3, P < .01 for both). A reproducible pattern of injury is noted for children involved in lateral-impact crashes characterized by head and chest injuries. The Injury Severity

  14. Predicting the binding patterns of hub proteins: a study using yeast protein interaction networks.

    Directory of Open Access Journals (Sweden)

    Carson M Andorf

    Full Text Available Protein-protein interactions are critical to elucidating the role played by individual proteins in important biological pathways. Of particular interest are hub proteins that can interact with large numbers of partners and often play essential roles in cellular control. Depending on the number of binding sites, protein hubs can be classified at a structural level as singlish-interface hubs (SIH with one or two binding sites, or multiple-interface hubs (MIH with three or more binding sites. In terms of kinetics, hub proteins can be classified as date hubs (i.e., interact with different partners at different times or locations or party hubs (i.e., simultaneously interact with multiple partners.Our approach works in 3 phases: Phase I classifies if a protein is likely to bind with another protein. Phase II determines if a protein-binding (PB protein is a hub. Phase III classifies PB proteins as singlish-interface versus multiple-interface hubs and date versus party hubs. At each stage, we use sequence-based predictors trained using several standard machine learning techniques.Our method is able to predict whether a protein is a protein-binding protein with an accuracy of 94% and a correlation coefficient of 0.87; identify hubs from non-hubs with 100% accuracy for 30% of the data; distinguish date hubs/party hubs with 69% accuracy and area under ROC curve of 0.68; and SIH/MIH with 89% accuracy and area under ROC curve of 0.84. Because our method is based on sequence information alone, it can be used even in settings where reliable protein-protein interaction data or structures of protein-protein complexes are unavailable to obtain useful insights into the functional and evolutionary characteristics of proteins and their interactions.We provide a web server for our three-phase approach: http://hybsvm.gdcb.iastate.edu.

  15. Ripples Make Waves: Binding Structured Activity and Plasticity in Hippocampal Networks

    Directory of Open Access Journals (Sweden)

    Josef H. L. P. Sadowski

    2011-01-01

    Full Text Available Establishing novel episodic memories and stable spatial representations depends on an exquisitely choreographed, multistage process involving the online encoding and offline consolidation of sensory information, a process that is largely dependent on the hippocampus. Each step is influenced by distinct neural network states that influence the pattern of activation across cellular assemblies. In recent years, the occurrence of hippocampal sharp wave ripple (SWR oscillations has emerged as a potentially vital network phenomenon mediating the steps between encoding and consolidation, both at a cellular and network level by promoting the rapid replay and reactivation of recent activity patterns. Such events facilitate memory formation by optimising the conditions for synaptic plasticity to occur between contingent neural elements. In this paper, we explore the ways in which SWRs and other network events can bridge the gap between spatiomnemonic processing at cellular/synaptic and network levels in the hippocampus.

  16. Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks.

    Directory of Open Access Journals (Sweden)

    Mathilde de Taffin

    Full Text Available Collier, the single Drosophila COE (Collier/EBF/Olf-1 transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous and eyes-absent (eya is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles.

  17. Genome-Wide Mapping of Collier In Vivo Binding Sites Highlights Its Hierarchical Position in Different Transcription Regulatory Networks

    Science.gov (United States)

    Dubois, Laurence; Bataillé, Laetitia; Painset, Anaïs; Le Gras, Stéphanie; Jost, Bernard; Crozatier, Michèle; Vincent, Alain

    2015-01-01

    Collier, the single Drosophila COE (Collier/EBF/Olf-1) transcription factor, is required in several developmental processes, including head patterning and specification of muscle and neuron identity during embryogenesis. To identify direct Collier (Col) targets in different cell types, we used ChIP-seq to map Col binding sites throughout the genome, at mid-embryogenesis. In vivo Col binding peaks were associated to 415 potential direct target genes. Gene Ontology analysis revealed a strong enrichment in proteins with DNA binding and/or transcription-regulatory properties. Characterization of a selection of candidates, using transgenic CRM-reporter assays, identified direct Col targets in dorso-lateral somatic muscles and specific neuron types in the central nervous system. These data brought new evidence that Col direct control of the expression of the transcription regulators apterous and eyes-absent (eya) is critical to specifying neuronal identities. They also showed that cross-regulation between col and eya in muscle progenitor cells is required for specification of muscle identity, revealing a new parallel between the myogenic regulatory networks operating in Drosophila and vertebrates. Col regulation of eya, both in specific muscle and neuronal lineages, may illustrate one mechanism behind the evolutionary diversification of Col biological roles. PMID:26204530

  18. Histone and RNA-binding protein interaction creates crosstalk network for regulation of alternative splicing.

    Science.gov (United States)

    Kim, Yong-Eun; Park, Chungoo; Kim, Kyoon Eon; Kim, Kee K

    2018-04-30

    Alternative splicing is an essential process in eukaryotes, as it increases the complexity of gene expression by generating multiple proteins from a single pre-mRNA. However, information on the regulatory mechanisms for alternative splicing is lacking, because splicing occurs over a short period via the transient interactions of proteins within functional complexes of the spliceosome. Here, we investigated in detail the molecular mechanisms connecting alternative splicing with epigenetic mechanisms. We identified interactions between histone proteins and splicing factors such as Rbfox2, Rbfox3, and splicing factor proline and glutamine rich protein (SFPQ) by in vivo crosslinking and immunoprecipitation. Furthermore, we confirmed that splicing factors were bound to specific modified residues of histone proteins. Additionally, changes in histone methylation due to histone methyltransferase inhibitor treatment notably affected alternative splicing in selected genes. Therefore, we suggested that there may be crosstalk mechanisms connecting histone modifications and RNA-binding proteins that increase the local concentration of RNA-binding proteins in alternative exon loci of nucleosomes by binding specific modified histone proteins, leading to alternative splicing. This crosstalk mechanism may play a major role in epigenetic processes such as histone modification and the regulation of alternative splicing. Copyright © 2018 Elsevier Inc. All rights reserved.

  19. Historical database for estimating flows in a water supply network; Base de datos historica para estimacion de caudales en una red de abastecimiento de agua

    Energy Technology Data Exchange (ETDEWEB)

    Menendez Martinez, A.; Ariel Gomez Gutierrez, A.; Alvarez Ramos, I.; Biscarri Trivino, F. [Universidad de Sevilla (Spain)

    2000-07-01

    Monitoring the flows managed by water supply companies involves processing huge amounts of data. These data also have to correspond to the topology of the network in a way that is consistent with the data collection time. The specific purpose database described in this article was developed to meet such requirements. (Author) 4 refs.

  20. Coordinating Mobile Databases: A System Demonstration

    OpenAIRE

    Zaihrayeu, Ilya; Giunchiglia, Fausto

    2004-01-01

    In this paper we present the Peer Database Management System (PDBMS). This system runs on top of the standard database management system, and it allows it to connect its database with other (peer) databases on the network. A particularity of our solution is that PDBMS allows for conventional database technology to be effectively operational in mobile settings. We think of database mobility as a database network, where databases appear and disappear spontaneously and their network access point...

  1. Development and Implementation of a Segment/Junction Box Level Database for the ITS Fiber Optic Conduit Network

    Science.gov (United States)

    2012-03-01

    This project initiated the development of a computerized database of ITS facilities, including conduits, junction : boxes, cameras, connections, etc. The current system consists of a database of conduit sections of various lengths. : Over the length ...

  2. Input vector optimization of feed-forward neural networks for fitting ab initio potential-energy databases

    Science.gov (United States)

    Malshe, M.; Raff, L. M.; Hagan, M.; Bukkapatnam, S.; Komanduri, R.

    2010-05-01

    The variation in the fitting accuracy of neural networks (NNs) when used to fit databases comprising potential energies obtained from ab initio electronic structure calculations is investigated as a function of the number and nature of the elements employed in the input vector to the NN. Ab initio databases for H2O2, HONO, Si5, and H2CCHBr were employed in the investigations. These systems were chosen so as to include four-, five-, and six-body systems containing first, second, third, and fourth row elements with a wide variety of chemical bonding and whose conformations cover a wide range of structures that occur under high-energy machining conditions and in chemical reactions involving cis-trans isomerizations, six different types of two-center bond ruptures, and two different three-center dissociation reactions. The ab initio databases for these systems were obtained using density functional theory/B3LYP, MP2, and MP4 methods with extended basis sets. A total of 31 input vectors were investigated. In each case, the elements of the input vector were chosen from interatomic distances, inverse powers of the interatomic distance, three-body angles, and dihedral angles. Both redundant and nonredundant input vectors were investigated. The results show that among all the input vectors investigated, the set employed in the Z-matrix specification of the molecular configurations in the electronic structure calculations gave the lowest NN fitting accuracy for both Si5 and vinyl bromide. The underlying reason for this result appears to be the discontinuity present in the dihedral angle for planar geometries. The use of trigometric functions of the angles as input elements produced significantly improved fitting accuracy as this choice eliminates the discontinuity. The most accurate fitting was obtained when the elements of the input vector were taken to have the form Rij-n, where the Rij are the interatomic distances. When the Levenberg-Marquardt procedure was modified

  3. Integration of Genome-Wide TF Binding and Gene Expression Data to Characterize Gene Regulatory Networks in Plant Development.

    Science.gov (United States)

    Chen, Dijun; Kaufmann, Kerstin

    2017-01-01

    Key transcription factors (TFs) controlling the morphogenesis of flowers and leaves have been identified in the model plant Arabidopsis thaliana. Recent genome-wide approaches based on chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) enable systematic identification of genome-wide TF binding sites (TFBSs) of these regulators. Here, we describe a computational pipeline for analyzing ChIP-seq data to identify TFBSs and to characterize gene regulatory networks (GRNs) with applications to the regulatory studies of flower development. In particular, we provide step-by-step instructions on how to download, analyze, visualize, and integrate genome-wide data in order to construct GRNs for beginners of bioinformatics. The practical guide presented here is ready to apply to other similar ChIP-seq datasets to characterize GRNs of interest.

  4. A network-flow based valve-switching aware binding algorithm for flow-based microfluidic biochips

    DEFF Research Database (Denmark)

    Tseng, Kai-Han; You, Sheng-Chi; Minhass, Wajid Hassan

    2013-01-01

    -flow based resource binding algorithm based on breadth-first search (BFS) and minimum cost maximum flow (MCMF) in architectural-level synthesis. The experimental results show that our methodology not only makes significant reduction of valve-switching activities but also diminishes the application completion......Designs of flow-based microfluidic biochips are receiving much attention recently because they replace conventional biological automation paradigm and are able to integrate different biochemical analysis functions on a chip. However, as the design complexity increases, a flow-based microfluidic...... biochip needs more chip-integrated micro-valves, i.e., the basic unit of fluid-handling functionality, to manipulate the fluid flow for biochemical applications. Moreover, frequent switching of micro-valves results in decreased reliability. To minimize the valve-switching activities, we develop a network...

  5. The ties that bind: a network approach to creating a programme in faculty development.

    Science.gov (United States)

    Baker, Lindsay; Reeves, Scott; Egan-Lee, Eileen; Leslie, Karen; Silver, Ivan

    2010-02-01

    Current trends in medical education reflect the changing health care environment. An increasingly large and diverse student population, a move to more distributed models of education, greater community involvement and an emphasis on social accountability, interprofessional education and student-centred approaches to learning necessitate new approaches to faculty development to help faculty members respond effectively to this rapidly changing landscape. Drawing upon the tenets of network theory and the broader organisational literature, we propose a 'fishhook' model of faculty development programme formation. The model is based on seven key factors which supported the successful formation of a centralised programme for faculty development that addressed many of the contemporary issues in medical education. These factors include: environmental readiness; commitment and vision of a mobiliser; recruitment of key stakeholders and leaders to committees; formation of a collaborative network structure; accumulation of networking capital; legitimacy, and flexibility. Our aim in creating this model is to provide a guide for other medical schools to consider when developing similar programmes. The model can be adapted to reflect the local goals, settings and cultures of other medical education contexts.

  6. DRD2 genotype-based variation of default mode network activity and of its relationship with striatal DAT binding.

    Science.gov (United States)

    Sambataro, Fabio; Fazio, Leonardo; Taurisano, Paolo; Gelao, Barbara; Porcelli, Annamaria; Mancini, Marina; Sinibaldi, Lorenzo; Ursini, Gianluca; Masellis, Rita; Caforio, Grazia; Di Giorgio, Annabella; Niccoli-Asabella, Artor; Popolizio, Teresa; Blasi, Giuseppe; Bertolino, Alessandro

    2013-01-01

    The default mode network (DMN) comprises a set of brain regions with "increased" activity during rest relative to cognitive processing. Activity in the DMN is associated with functional connections with the striatum and dopamine (DA) levels in this brain region. A functional single-nucleotide polymorphism within the dopamine D2 receptor gene (DRD2, rs1076560 G > T) shifts splicing of the 2 D2 isoforms, D2 short and D2 long, and has been associated with striatal DA signaling as well as with cognitive processing. However, the effects of this polymorphism on DMN have not been explored. The aim of this study was to evaluate the effects of rs1076560 on DMN and striatal connectivity and on their relationship with striatal DA signaling. Twenty-eight subjects genotyped for rs1076560 underwent functional magnetic resonance imaging during a working memory task and 123 55 I-Fluoropropyl-2-beta-carbomethoxy-3-beta(4-iodophenyl) nortropan Single Photon Emission Computed Tomography ([(123)I]-FP-CIT SPECT) imaging (a measure of dopamine transporter [DAT] binding). Spatial group-independent component (IC) analysis was used to identify DMN and striatal ICs. Within the anterior DMN IC, GG subjects had relatively greater connectivity in medial prefrontal cortex (MPFC), which was directly correlated with striatal DAT binding. Within the posterior DMN IC, GG subjects had reduced connectivity in posterior cingulate relative to T carriers. Additionally, rs1076560 genotype predicted connectivity differences within a striatal network, and these changes were correlated with connectivity in MPFC and posterior cingulate within the DMN. These results suggest that genetically determined D2 receptor signaling is associated with DMN connectivity and that these changes are correlated with striatal function and presynaptic DA signaling.

  7. The protein network surrounding the human telomere repeat binding factors TRF1, TRF2, and POT1.

    Directory of Open Access Journals (Sweden)

    Richard J Giannone

    2010-08-01

    Full Text Available Telomere integrity (including telomere length and capping is critical in overall genomic stability. Telomere repeat binding factors and their associated proteins play vital roles in telomere length regulation and end protection. In this study, we explore the protein network surrounding telomere repeat binding factors, TRF1, TRF2, and POT1 using dual-tag affinity purification in combination with multidimensional protein identification technology liquid chromatography--tandem mass spectrometry (MudPIT LC-MS/MS. After control subtraction and data filtering, we found that TRF2 and POT1 co-purified all six members of the telomere protein complex, while TRF1 identified five of six components at frequencies that lend evidence towards the currently accepted telomere architecture. Many of the known TRF1 or TRF2 interacting proteins were also identified. Moreover, putative associating partners identified for each of the three core components fell into functional categories such as DNA damage repair, ubiquitination, chromosome cohesion, chromatin modification/remodeling, DNA replication, cell cycle and transcription regulation, nucleotide metabolism, RNA processing, and nuclear transport. These putative protein-protein associations may participate in different biological processes at telomeres or, intriguingly, outside telomeres.

  8. 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...

  9. A single charge in the actin binding domain of fascin can independently tune the linear and non-linear response of an actin bundle network.

    Science.gov (United States)

    Maier, M; Müller, K W; Heussinger, C; Köhler, S; Wall, W A; Bausch, A R; Lieleg, O

    2015-05-01

    Actin binding proteins (ABPs) not only set the structure of actin filament assemblies but also mediate the frequency-dependent viscoelastic moduli of cross-linked and bundled actin networks. Point mutations in the actin binding domain of those ABPs can tune the association and dissociation dynamics of the actin/ABP bond and thus modulate the network mechanics both in the linear and non-linear response regime. We here demonstrate how the exchange of a single charged amino acid in the actin binding domain of the ABP fascin triggers such a modulation of the network rheology. Whereas the overall structure of the bundle networks is conserved, the transition point from strain-hardening to strain-weakening sensitively depends on the cross-linker off-rate and the applied shear rate. Our experimental results are consistent both with numerical simulations of a cross-linked bundle network and a theoretical description of the bundle network mechanics which is based on non-affine bending deformations and force-dependent cross-link dynamics.

  10. Multi-categorical deep learning neural network to classify retinal images: A pilot study employing small database.

    Science.gov (United States)

    Choi, Joon Yul; Yoo, Tae Keun; Seo, Jeong Gi; Kwak, Jiyong; Um, Terry Taewoong; Rim, Tyler Hyungtaek

    2017-01-01

    Deep learning emerges as a powerful tool for analyzing medical images. Retinal disease detection by using computer-aided diagnosis from fundus image has emerged as a new method. We applied deep learning convolutional neural network by using MatConvNet for an automated detection of multiple retinal diseases with fundus photographs involved in STructured Analysis of the REtina (STARE) database. Dataset was built by expanding data on 10 categories, including normal retina and nine retinal diseases. The optimal outcomes were acquired by using a random forest transfer learning based on VGG-19 architecture. The classification results depended greatly on the number of categories. As the number of categories increased, the performance of deep learning models was diminished. When all 10 categories were included, we obtained results with an accuracy of 30.5%, relative classifier information (RCI) of 0.052, and Cohen's kappa of 0.224. Considering three integrated normal, background diabetic retinopathy, and dry age-related macular degeneration, the multi-categorical classifier showed accuracy of 72.8%, 0.283 RCI, and 0.577 kappa. In addition, several ensemble classifiers enhanced the multi-categorical classification performance. The transfer learning incorporated with ensemble classifier of clustering and voting approach presented the best performance with accuracy of 36.7%, 0.053 RCI, and 0.225 kappa in the 10 retinal diseases classification problem. First, due to the small size of datasets, the deep learning techniques in this study were ineffective to be applied in clinics where numerous patients suffering from various types of retinal disorders visit for diagnosis and treatment. Second, we found that the transfer learning incorporated with ensemble classifiers can improve the classification performance in order to detect multi-categorical retinal diseases. Further studies should confirm the effectiveness of algorithms with large datasets obtained from hospitals.

  11. DMPD: Function of lipopolysaccharide (LPS)-binding protein (LBP) and CD14, thereceptor for LPS/LBP complexes: a short review. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available eptor for LPS/LBP complexes: a short review. Schumann RR. Res Immunol. 1992 Jan;143(1):11-5. (.png) (.svg) (...ride (LPS)-binding protein (LBP) and CD14, thereceptor for LPS/LBP complexes: a short review. Authors Schuma.../LBP complexes: a short review. PubmedID 1373512 Title Function of lipopolysaccha....html) (.csml) Show Function of lipopolysaccharide (LPS)-binding protein (LBP) and CD14, thereceptor for LPS

  12. Abnormal binding and disruption in large scale networks involved in human partial seizures

    Directory of Open Access Journals (Sweden)

    Bartolomei Fabrice

    2013-12-01

    Full Text Available There is a marked increase in the amount of electrophysiological and neuroimaging works dealing with the study of large scale brain connectivity in the epileptic brain. Our view of the epileptogenic process in the brain has largely evolved over the last twenty years from the historical concept of “epileptic focus” to a more complex description of “Epileptogenic networks” involved in the genesis and “propagation” of epileptic activities. In particular, a large number of studies have been dedicated to the analysis of intracerebral EEG signals to characterize the dynamic of interactions between brain areas during temporal lobe seizures. These studies have reported that large scale functional connectivity is dramatically altered during seizures, particularly during temporal lobe seizure genesis and development. Dramatic changes in neural synchrony provoked by epileptic rhythms are also responsible for the production of ictal symptoms or changes in patient’s behaviour such as automatisms, emotional changes or consciousness alteration. Beside these studies dedicated to seizures, large-scale network connectivity during the interictal state has also been investigated not only to define biomarkers of epileptogenicity but also to better understand the cognitive impairments observed between seizures.

  13. rSNPBase 3.0: an updated database of SNP-related regulatory elements, element-gene pairs and SNP-based gene regulatory networks.

    Science.gov (United States)

    Guo, Liyuan; Wang, Jing

    2018-01-04

    Here, we present the updated rSNPBase 3.0 database (http://rsnp3.psych.ac.cn), which provides human SNP-related regulatory elements, element-gene pairs and SNP-based regulatory networks. This database is the updated version of the SNP regulatory annotation database rSNPBase and rVarBase. In comparison to the last two versions, there are both structural and data adjustments in rSNPBase 3.0: (i) The most significant new feature is the expansion of analysis scope from SNP-related regulatory elements to include regulatory element-target gene pairs (E-G pairs), therefore it can provide SNP-based gene regulatory networks. (ii) Web function was modified according to data content and a new network search module is provided in the rSNPBase 3.0 in addition to the previous regulatory SNP (rSNP) search module. The two search modules support data query for detailed information (related-elements, element-gene pairs, and other extended annotations) on specific SNPs and SNP-related graphic networks constructed by interacting transcription factors (TFs), miRNAs and genes. (3) The type of regulatory elements was modified and enriched. To our best knowledge, the updated rSNPBase 3.0 is the first data tool supports SNP functional analysis from a regulatory network prospective, it will provide both a comprehensive understanding and concrete guidance for SNP-related regulatory studies. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Investigating the Potential Impacts of Energy Production in the Marcellus Shale Region Using the Shale Network Database and CUAHSI-Supported Data Tools

    Science.gov (United States)

    Brazil, L.

    2017-12-01

    The Shale Network's extensive database of water quality observations enables educational experiences about the potential impacts of resource extraction with real data. Through open source tools that are developed and maintained by the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI), researchers, educators, and citizens can access and analyze the very same data that the Shale Network team has used in peer-reviewed publications about the potential impacts of hydraulic fracturing on water. The development of the Shale Network database has been made possible through collection efforts led by an academic team and involving numerous individuals from government agencies, citizen science organizations, and private industry. Thus far, CUAHSI-supported data tools have been used to engage high school students, university undergraduate and graduate students, as well as citizens so that all can discover how energy production impacts the Marcellus Shale region, which includes Pennsylvania and other nearby states. This presentation will describe these data tools, how the Shale Network has used them in developing educational material, and the resources available to learn more.

  15. Age and sex differences in oxytocin and vasopressin V1a receptor binding densities in the rat brain: focus on the social decision-making network.

    Science.gov (United States)

    Smith, Caroline J W; Poehlmann, Max L; Li, Sara; Ratnaseelan, Aarane M; Bredewold, Remco; Veenema, Alexa H

    2017-03-01

    Oxytocin (OT) and vasopressin (AVP) regulate various social behaviors via activation of the OT receptor (OTR) and the AVP V1a receptor (V1aR) in the brain. Social behavior often differs across development and between the sexes, yet our understanding of age and sex differences in brain OTR and V1aR binding remains incomplete. Here, we provide an extensive analysis of OTR and V1aR binding density throughout the brain in juvenile and adult male and female rats, with a focus on regions within the social decision-making network. OTR and V1aR binding density were higher in juveniles than in adults in regions associated with reward and socio-spatial memory and higher in adults than in juveniles in key regions of the social decision-making network and in cortical regions. We discuss possible implications of these shifts in OTR and V1aR binding density for the age-specific regulation of social behavior. Furthermore, sex differences in OTR and V1aR binding density were less numerous than age differences. The direction of these sex differences was region-specific for OTR but consistently higher in females than in males for V1aR. Finally, almost all sex differences in OTR and V1aR binding density were already present in juveniles and occurred in regions with denser binding in adults compared to juveniles. Possible implications of these sex differences for the sex-specific regulation of behavior, as well potential underlying mechanisms, are discussed. Overall, these findings provide an important framework for testing age- and sex-specific roles of OTR and V1aR in the regulation of social behavior.

  16. DMPD: Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation inrespiratory disease. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18031251 Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation inrespiratory...l) (.csml) Show Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation inrespiratory dis...utrophilic inflammation inrespiratory disease. Authors Sabroe I, Whyte MK. Publication Biochem Soc Trans. 20

  17. [Establishment of the database of the 3D facial models for the plastic surgery based on network].

    Science.gov (United States)

    Liu, Zhe; Zhang, Hai-Lin; Zhang, Zheng-Guo; Qiao, Qun

    2008-07-01

    To collect the three-dimensional (3D) facial data of 30 facial deformity patients by the 3D scanner and establish a professional database based on Internet. It can be helpful for the clinical intervention. The primitive point data of face topography were collected by the 3D scanner. Then the 3D point cloud was edited by reverse engineering software to reconstruct the 3D model of the face. The database system was divided into three parts, including basic information, disease information and surgery information. The programming language of the web system is Java. The linkages between every table of the database are credibility. The query operation and the data mining are convenient. The users can visit the database via the Internet and use the image analysis system to observe the 3D facial models interactively. In this paper we presented a database and a web system adapt to the plastic surgery of human face. It can be used both in clinic and in basic research.

  18. Neurovascular Network Explorer 1.0: a database of 2-photon single-vessel diameter measurements with MATLAB(®) graphical user interface.

    Science.gov (United States)

    Sridhar, Vishnu B; Tian, Peifang; Dale, Anders M; Devor, Anna; Saisan, Payam A

    2014-01-01

    We present a database client software-Neurovascular Network Explorer 1.0 (NNE 1.0)-that uses MATLAB(®) based Graphical User Interface (GUI) for interaction with a database of 2-photon single-vessel diameter measurements from our previous publication (Tian et al., 2010). These data are of particular interest for modeling the hemodynamic response. NNE 1.0 is downloaded by the user and then runs either as a MATLAB script or as a standalone program on a Windows platform. The GUI allows browsing the database according to parameters specified by the user, simple manipulation and visualization of the retrieved records (such as averaging and peak-normalization), and export of the results. Further, we provide NNE 1.0 source code. With this source code, the user can database their own experimental results, given the appropriate data structure and naming conventions, and thus share their data in a user-friendly format with other investigators. NNE 1.0 provides an example of seamless and low-cost solution for sharing of experimental data by a regular size neuroscience laboratory and may serve as a general template, facilitating dissemination of biological results and accelerating data-driven modeling approaches.

  19. Interpenetrating metal-organic and inorganic 3D networks: a computer-aided systematic investigation. Part II [1]. Analysis of the Inorganic Crystal Structure Database (ICSD)

    International Nuclear Information System (INIS)

    Baburin, I.A.; Blatov, V.A.; Carlucci, L.; Ciani, G.; Proserpio, D.M.

    2005-01-01

    Interpenetration in metal-organic and inorganic networks has been investigated by a systematic analysis of the crystallographic structural databases. We have used a version of TOPOS (a package for multipurpose crystallochemical analysis) adapted for searching for interpenetration and based on the concept of Voronoi-Dirichlet polyhedra and on the representation of a crystal structure as a reduced finite graph. In this paper, we report comprehensive lists of interpenetrating inorganic 3D structures from the Inorganic Crystal Structure Database (ICSD), inclusive of 144 Collection Codes for equivalent interpenetrating nets, analyzed on the basis of their topologies. Distinct Classes, corresponding to the different modes in which individual identical motifs can interpenetrate, have been attributed to the entangled structures. Interpenetrating nets of different nature as well as interpenetrating H-bonded nets were also examined

  20. Artificial Neural Networks for differential diagnosis of breast lesions in MR-Mammography: A systematic approach addressing the influence of network architecture on diagnostic performance using a large clinical database

    International Nuclear Information System (INIS)

    Dietzel, Matthias; Baltzer, Pascal A.T.; Dietzel, Andreas; Zoubi, Ramy; Gröschel, Tobias; Burmeister, Hartmut P.; Bogdan, Martin; Kaiser, Werner A.

    2012-01-01

    Rationale and objectives: Differential diagnosis of lesions in MR-Mammography (MRM) remains a complex task. The aim of this MRM study was to design and to test robustness of Artificial Neural Network architectures to predict malignancy using a large clinical database. Materials and methods: For this IRB-approved investigation standardized protocols and study design were applied (T1w-FLASH; 0.1 mmol/kgBW Gd-DTPA; T2w-TSE; histological verification after MRM). All lesions were evaluated by two experienced (>500 MRM) radiologists in consensus. In every lesion, 18 previously published descriptors were assessed and documented in the database. An Artificial Neural Network (ANN) was developed to process this database (The-MathWorks/Inc., feed-forward-architecture/resilient back-propagation-algorithm). All 18 descriptors were set as input variables, whereas histological results (malignant vs. benign) was defined as classification variable. Initially, the ANN was optimized in terms of “Training Epochs” (TE), “Hidden Layers” (HL), “Learning Rate” (LR) and “Neurons” (N). Robustness of the ANN was addressed by repeated evaluation cycles (n: 9) with receiver operating characteristics (ROC) analysis of the results applying 4-fold Cross Validation. The best network architecture was identified comparing the corresponding Area under the ROC curve (AUC). Results: Histopathology revealed 436 benign and 648 malignant lesions. Enhancing the level of complexity could not increase diagnostic accuracy of the network (P: n.s.). The optimized ANN architecture (TE: 20, HL: 1, N: 5, LR: 1.2) was accurate (mean-AUC 0.888; P: <0.001) and robust (CI: 0.885–0.892; range: 0.880–0.898). Conclusion: The optimized neural network showed robust performance and high diagnostic accuracy for prediction of malignancy on unknown data.

  1. Artificial Neural Networks for differential diagnosis of breast lesions in MR-Mammography: a systematic approach addressing the influence of network architecture on diagnostic performance using a large clinical database.

    Science.gov (United States)

    Dietzel, Matthias; Baltzer, Pascal A T; Dietzel, Andreas; Zoubi, Ramy; Gröschel, Tobias; Burmeister, Hartmut P; Bogdan, Martin; Kaiser, Werner A

    2012-07-01

    Differential diagnosis of lesions in MR-Mammography (MRM) remains a complex task. The aim of this MRM study was to design and to test robustness of Artificial Neural Network architectures to predict malignancy using a large clinical database. For this IRB-approved investigation standardized protocols and study design were applied (T1w-FLASH; 0.1 mmol/kgBW Gd-DTPA; T2w-TSE; histological verification after MRM). All lesions were evaluated by two experienced (>500 MRM) radiologists in consensus. In every lesion, 18 previously published descriptors were assessed and documented in the database. An Artificial Neural Network (ANN) was developed to process this database (The-MathWorks/Inc., feed-forward-architecture/resilient back-propagation-algorithm). All 18 descriptors were set as input variables, whereas histological results (malignant vs. benign) was defined as classification variable. Initially, the ANN was optimized in terms of "Training Epochs" (TE), "Hidden Layers" (HL), "Learning Rate" (LR) and "Neurons" (N). Robustness of the ANN was addressed by repeated evaluation cycles (n: 9) with receiver operating characteristics (ROC) analysis of the results applying 4-fold Cross Validation. The best network architecture was identified comparing the corresponding Area under the ROC curve (AUC). Histopathology revealed 436 benign and 648 malignant lesions. Enhancing the level of complexity could not increase diagnostic accuracy of the network (P: n.s.). The optimized ANN architecture (TE: 20, HL: 1, N: 5, LR: 1.2) was accurate (mean-AUC 0.888; P: <0.001) and robust (CI: 0.885-0.892; range: 0.880-0.898). The optimized neural network showed robust performance and high diagnostic accuracy for prediction of malignancy on unknown data. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  2. The ties that bind? Social networks of nursing staff and staff’s behaviour towards residents with dementia.

    NARCIS (Netherlands)

    Beek, A.P.A. van; Wagner, C.; Frijters, D.H.M.; Ribbe, M.W.; Groenewegen, P.P.

    2013-01-01

    This study investigated social networks of nursing staff and staff's behaviour towards residents with dementia. We focused on two types of networks: communication networks among staff, and networks between nursing staff and relatives/acquaintances of residents. Data was collected in 37 long-term

  3. Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers.

    Science.gov (United States)

    Eguchi, Asuka; Lee, Garrett O; Wan, Fang; Erwin, Graham S; Ansari, Aseem Z

    2014-09-15

    Transcription factors control the fate of a cell by regulating the expression of genes and regulatory networks. Recent successes in inducing pluripotency in terminally differentiated cells as well as directing differentiation with natural transcription factors has lent credence to the efforts that aim to direct cell fate with rationally designed transcription factors. Because DNA-binding factors are modular in design, they can be engineered to target specific genomic sequences and perform pre-programmed regulatory functions upon binding. Such precision-tailored factors can serve as molecular tools to reprogramme or differentiate cells in a targeted manner. Using different types of engineered DNA binders, both regulatory transcriptional controls of gene networks, as well as permanent alteration of genomic content, can be implemented to study cell fate decisions. In the present review, we describe the current state of the art in artificial transcription factor design and the exciting prospect of employing artificial DNA-binding factors to manipulate the transcriptional networks as well as epigenetic landscapes that govern cell fate.

  4. National Transportation Atlas Databases : 2012.

    Science.gov (United States)

    2012-01-01

    The National Transportation Atlas Databases 2012 (NTAD2012) is a set of nationwide geographic databases of transportation facilities, transportation networks, and associated infrastructure. These datasets include spatial information for transportatio...

  5. National Transportation Atlas Databases : 2011.

    Science.gov (United States)

    2011-01-01

    The National Transportation Atlas Databases 2011 (NTAD2011) is a set of nationwide geographic databases of transportation facilities, transportation networks, and associated infrastructure. These datasets include spatial information for transportatio...

  6. National Transportation Atlas Databases : 2009.

    Science.gov (United States)

    2009-01-01

    The National Transportation Atlas Databases 2009 (NTAD2009) is a set of nationwide geographic databases of transportation facilities, transportation networks, and associated infrastructure. These datasets include spatial information for transportatio...

  7. National Transportation Atlas Databases : 2010.

    Science.gov (United States)

    2010-01-01

    The National Transportation Atlas Databases 2010 (NTAD2010) is a set of nationwide geographic databases of transportation facilities, transportation networks, and associated infrastructure. These datasets include spatial information for transportatio...

  8. Tradeoffs in distributed databases

    OpenAIRE

    Juntunen, R. (Risto)

    2016-01-01

    Abstract In a distributed database data is spread throughout the network into separated nodes with different DBMS systems (Date, 2000). According to CAP-theorem three database properties — consistency, availability and partition tolerance cannot be achieved simultaneously in distributed database systems. Two of these properties can be achieved but not all three at the same time (Brewer, 2000). Since this theorem there has b...

  9. Computer application for database management and networking of service radio physics; Aplicacion informatica para la gestion de bases de datos y conexiones en red de un servicio de radiofisica

    Energy Technology Data Exchange (ETDEWEB)

    Ferrando Sanchez, A.; Cabello Murillo, E.; Diaz Fuentes, R.; Castro Novais, J.; Clemente Gutierrez, F.; Casa de Juan, M. A. de la; Adaimi Hernandez, P.

    2011-07-01

    The databases in the quality control prove to be a powerful tool for recording, management and statistical process control. Developed in a Windows environment and under Access (Microsoft Office) our service implements this philosophy on the centers computer network. A computer that acts as the server provides the database to the treatment units to record quality control measures daily and incidents. To remove shortcuts stop working with data migration, possible use of duplicate and erroneous data loss because of errors in network connections, which are common problems, we proceeded to manage connections and access to databases ease of maintenance and use horn to all service personnel.

  10. DMPD: Glucocorticoids and the innate immune system: crosstalk with the toll-likereceptor signaling network. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17576036 Glucocorticoids and the innate immune system: crosstalk with the toll-like...07 May 13. (.png) (.svg) (.html) (.csml) Show Glucocorticoids and the innate immune system: crosstalk with t...nd the innate immune system: crosstalk with the toll-likereceptor signaling network. Authors Chinenov Y, Rog

  11. Relational nuclear databases upon the MSU INP CDFE Web-site and Nuclear Data Centres Network CDFE activities. P7

    International Nuclear Information System (INIS)

    Boboshin, I.N.; Varlamov, V.V.; Ivanov, E.M.; Ivanov, S.V.; Peskov, N.N.; Stepanov, M.E.; Chesnokov, V.V.

    2001-01-01

    This report contains only the short review of the work carried out by the CDFE concerning the IAEA Nuclear Reaction Data Centres Network activities for the period of time from the IAEA Advisory Group Meeting (15-19 May 2000, Obninsk, Russia) till May 2001 and the description of the main results obtained

  12. Ties That Bind: A Social Network Approach to Understanding Student Integration and Persistence. ASHE Annual Meeting Paper.

    Science.gov (United States)

    Thomas, Scott L.

    This study examined the social networks of college students and how such networks affect student commitment and persistence. The study's theoretical framework was based on application of the social network paradigm to Tinto's Student Integration Model, in which a student's initial commitment is modified over time as a result of the student's…

  13. The GTN-P Data Management System: A central database for permafrost monitoring parameters of the Global Terrestrial Network for Permafrost (GTN-P) and beyond

    Science.gov (United States)

    Lanckman, Jean-Pierre; Elger, Kirsten; Karlsson, Ævar Karl; Johannsson, Halldór; Lantuit, Hugues

    2013-04-01

    Permafrost is a direct indicator of climate change and has been identified as Essential Climate Variable (ECV) by the global observing community. The monitoring of permafrost temperatures, active-layer thicknesses and other parameters has been performed for several decades already, but it was brought together within the Global Terrestrial Network for Permafrost (GTN-P) in the 1990's only, including the development of measurement protocols to provide standardized data. GTN-P is the primary international observing network for permafrost sponsored by the Global Climate Observing System (GCOS) and the Global Terrestrial Observing System (GTOS), and managed by the International Permafrost Association (IPA). All GTN-P data was outfitted with an "open data policy" with free data access via the World Wide Web. The existing data, however, is far from being homogeneous: it is not yet optimized for databases, there is no framework for data reporting or archival and data documentation is incomplete. As a result, and despite the utmost relevance of permafrost in the Earth's climate system, the data has not been used by as many researchers as intended by the initiators of the programs. While the monitoring of many other ECVs has been tackled by organized international networks (e.g. FLUXNET), there is still no central database for all permafrost-related parameters. The European Union project PAGE21 created opportunities to develop this central database for permafrost monitoring parameters of GTN-P during the duration of the project and beyond. The database aims to be the one location where the researcher can find data, metadata, and information of all relevant parameters for a specific site. Each component of the Data Management System (DMS), including parameters, data levels and metadata formats were developed in cooperation with the GTN-P and the IPA. The general framework of the GTN-P DMS is based on an object oriented model (OOM), open for as many parameters as possible, and

  14. An Aerosol Extinction-to-Backscatter Ratio Database Derived from the NASA Micro-Pulse Lidar Network: Applications for Space-based Lidar Observations

    Science.gov (United States)

    Welton, Ellsworth J.; Campbell, James R.; Spinhime, James D.; Berkoff, Timothy A.; Holben, Brent; Tsay, Si-Chee; Bucholtz, Anthony

    2004-01-01

    Backscatter lidar signals are a function of both backscatter and extinction. Hence, these lidar observations alone cannot separate the two quantities. The aerosol extinction-to-backscatter ratio, S, is the key parameter required to accurately retrieve extinction and optical depth from backscatter lidar observations of aerosol layers. S is commonly defined as 4*pi divided by the product of the single scatter albedo and the phase function at 180-degree scattering angle. Values of S for different aerosol types are not well known, and are even more difficult to determine when aerosols become mixed. Here we present a new lidar-sunphotometer S database derived from Observations of the NASA Micro-Pulse Lidar Network (MPLNET). MPLNET is a growing worldwide network of eye-safe backscatter lidars co-located with sunphotometers in the NASA Aerosol Robotic Network (AERONET). Values of S for different aerosol species and geographic regions will be presented. A framework for constructing an S look-up table will be shown. Look-up tables of S are needed to calculate aerosol extinction and optical depth from space-based lidar observations in the absence of co-located AOD data. Applications for using the new S look-up table to reprocess aerosol products from NASA's Geoscience Laser Altimeter System (GLAS) will be discussed.

  15. TheCellMap.org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network.

    Science.gov (United States)

    Usaj, Matej; Tan, Yizhao; Wang, Wen; VanderSluis, Benjamin; Zou, Albert; Myers, Chad L; Costanzo, Michael; Andrews, Brenda; Boone, Charles

    2017-05-05

    Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap.org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae In particular, TheCellMap.org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner. Copyright © 2017 Usaj et al.

  16. Numerical databases in marine biology

    Digital Repository Service at National Institute of Oceanography (India)

    Sarupria, J.S.; Bhargava, R.M.S.

    stream_size 9 stream_content_type text/plain stream_name Natl_Workshop_Database_Networking_Mar_Biol_1991_45.pdf.txt stream_source_info Natl_Workshop_Database_Networking_Mar_Biol_1991_45.pdf.txt Content-Encoding ISO-8859-1 Content-Type... text/plain; charset=ISO-8859-1 ...

  17. Automated classification of seismic sources in a large database: a comparison of Random Forests and Deep Neural Networks.

    Science.gov (United States)

    Hibert, Clement; Stumpf, André; Provost, Floriane; Malet, Jean-Philippe

    2017-04-01

    In the past decades, the increasing quality of seismic sensors and capability to transfer remotely large quantity of data led to a fast densification of local, regional and global seismic networks for near real-time monitoring of crustal and surface processes. This technological advance permits the use of seismology to document geological and natural/anthropogenic processes (volcanoes, ice-calving, landslides, snow and rock avalanches, geothermal fields), but also led to an ever-growing quantity of seismic data. This wealth of seismic data makes the construction of complete seismicity catalogs, which include earthquakes but also other sources of seismic waves, more challenging and very time-consuming as this critical pre-processing stage is classically done by human operators and because hundreds of thousands of seismic signals have to be processed. To overcome this issue, the development of automatic methods for the processing of continuous seismic data appears to be a necessity. The classification algorithm should satisfy the need of a method that is robust, precise and versatile enough to be deployed to monitor the seismicity in very different contexts. In this study, we evaluate the ability of machine learning algorithms for the analysis of seismic sources at the Piton de la Fournaise volcano being Random Forest and Deep Neural Network classifiers. We gather a catalog of more than 20,000 events, belonging to 8 classes of seismic sources. We define 60 attributes, based on the waveform, the frequency content and the polarization of the seismic waves, to parameterize the seismic signals recorded. We show that both algorithms provide similar positive classification rates, with values exceeding 90% of the events. When trained with a sufficient number of events, the rate of positive identification can reach 99%. These very high rates of positive identification open the perspective of an operational implementation of these algorithms for near-real time monitoring of

  18. Strengthening the Ties That Bind: Integrating Undergraduate Liberal and Professional Study. Report of the Professional Preparation Network.

    Science.gov (United States)

    Stark, Joan S.; Lowther, Malcolm A.

    The integration of undergraduate liberal and professional education is discussed in the following chapters: (1) "A Call to Action"; (2) "Binding Values, Changing Times and Curricular Balance"; (3) "Seizing Opportunities for Excellence"; (4) "Defining the Educated Professional"; (5) "Extending a Constructive Debate"; and (6) "A New Spirit of…

  19. 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

  20. A normalization method for combination of laboratory test results from different electronic healthcare databases in a distributed research network.

    Science.gov (United States)

    Yoon, Dukyong; Schuemie, Martijn J; Kim, Ju Han; Kim, Dong Ki; Park, Man Young; Ahn, Eun Kyoung; Jung, Eun-Young; Park, Dong Kyun; Cho, Soo Yeon; Shin, Dahye; Hwang, Yeonsoo; Park, Rae Woong

    2016-03-01

    Distributed research networks (DRNs) afford statistical power by integrating observational data from multiple partners for retrospective studies. However, laboratory test results across care sites are derived using different assays from varying patient populations, making it difficult to simply combine data for analysis. Additionally, existing normalization methods are not suitable for retrospective studies. We normalized laboratory results from different data sources by adjusting for heterogeneous clinico-epidemiologic characteristics of the data and called this the subgroup-adjusted normalization (SAN) method. Subgroup-adjusted normalization renders the means and standard deviations of distributions identical under population structure-adjusted conditions. To evaluate its performance, we compared SAN with existing methods for simulated and real datasets consisting of blood urea nitrogen, serum creatinine, hematocrit, hemoglobin, serum potassium, and total bilirubin. Various clinico-epidemiologic characteristics can be applied together in SAN. For simplicity of comparison, age and gender were used to adjust population heterogeneity in this study. In simulations, SAN had the lowest standardized difference in means (SDM) and Kolmogorov-Smirnov values for all tests (p normalization performed better than normalization using other methods. The SAN method is applicable in a DRN environment and should facilitate analysis of data integrated across DRN partners for retrospective observational studies. Copyright © 2015 John Wiley & Sons, Ltd.

  1. ORACLE DATABASE SECURITY

    OpenAIRE

    Cristina-Maria Titrade

    2011-01-01

    This paper presents some security issues, namely security database system level, data level security, user-level security, user management, resource management and password management. Security is a constant concern in the design and database development. Usually, there are no concerns about the existence of security, but rather how large it should be. A typically DBMS has several levels of security, in addition to those offered by the operating system or network. Typically, a DBMS has user a...

  2. 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.

  3. 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 such...

  4. 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…

  5. The transcriptional regulatory network mediated by banana (Musa acuminata) dehydration-responsive element binding (MaDREB) transcription factors in fruit ripening.

    Science.gov (United States)

    Kuang, Jian-Fei; Chen, Jian-Ye; Liu, Xun-Cheng; Han, Yan-Chao; Xiao, Yun-Yi; Shan, Wei; Tang, Yang; Wu, Ke-Qiang; He, Jun-Xian; Lu, Wang-Jin

    2017-04-01

    Fruit ripening is a complex, genetically programmed process involving the action of critical transcription factors (TFs). Despite the established significance of dehydration-responsive element binding (DREB) TFs in plant abiotic stress responses, the involvement of DREBs in fruit ripening is yet to be determined. Here, we identified four genes encoding ripening-regulated DREB TFs in banana (Musa acuminata), MaDREB1, MaDREB2, MaDREB3, and MaDREB4, and demonstrated that they play regulatory roles in fruit ripening. We showed that MaDREB1-MaDREB4 are nucleus-localized, induced by ethylene and encompass transcriptional activation activities. We performed a genome-wide chromatin immunoprecipitation and high-throughput sequencing (ChIP-Seq) experiment for MaDREB2 and identified 697 genomic regions as potential targets of MaDREB2. MaDREB2 binds to hundreds of loci with diverse functions and its binding sites are distributed in the promoter regions proximal to the transcriptional start site (TSS). Most of the MaDREB2-binding targets contain the conserved (A/G)CC(G/C)AC motif and MaDREB2 appears to directly regulate the expression of a number of genes involved in fruit ripening. In combination with transcriptome profiling (RNA sequencing) data, our results indicate that MaDREB2 may serve as both transcriptional activator and repressor during banana fruit ripening. In conclusion, our study suggests a hierarchical regulatory model of fruit ripening in banana and that the MaDREB TFs may act as transcriptional regulators in the regulatory network. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  6. Asn792 participates in the hydrogen bond network around the K+-binding pocket of gastric H,K-ATPase.

    NARCIS (Netherlands)

    Swarts, H.G.P.; Koenderink, J.B.; Willems, P.H.G.M.; Krieger, E.; Pont, J.J.H.H.M. de

    2005-01-01

    Asn792 present in M5 of gastric H,K-ATPase is highly conserved within the P-type ATPase family. A direct role in K+ binding was postulated for Na,K-ATPase but was not found in a recent model for gastric H,K-ATPase (Koenderink, J. B., Swarts, H. G. P., Willems, P. H. G. M., Krieger, E., and De Pont,

  7. Ties That Bind: The Practice of Social Networks. Number Two in a Series of Reports on Social Networks from The Annie E. Casey Foundation

    Science.gov (United States)

    Bailey, Terri J.

    2006-01-01

    This report documents the Annie E. Casey Foundation's effort to learn from families, communities and organizations around the country about their experiences with social network strategies and approaches. Using the voices and experiences of the families and organizations visited, the report summarizes findings from these visits and helps lay the…

  8. Investigation of naphthofuran moiety as potential dual inhibitor against BACE-1 and GSK-3β: molecular dynamics simulations, binding energy, and network analysis to identify first-in-class dual inhibitors against Alzheimer's disease.

    Science.gov (United States)

    Kumar, Akhil; Srivastava, Gaurava; Srivastava, Swati; Verma, Seema; Negi, Arvind S; Sharma, Ashok

    2017-08-01

    BACE-1 and GSK-3β are potential therapeutic drug targets for Alzheimer's disease. Recently, both the targets received attention for designing dual inhibitors for Alzheimer's disease. Until now, only two-scaffold triazinone and curcumin have been reported as BACE-1 and GSK-3β dual inhibitors. Docking, molecular dynamics, clustering, binding energy, and network analysis of triazinone derivatives with BACE-1 and GSK-3β was performed to get molecular insight into the first reported dual inhibitor. Further, we designed and evaluated a naphthofuran series for its ability to inhibit BACE-1 and GSK-3β with the computational approaches. Docking study of naphthofuran series showed a good binding affinity towards both the targets. Molecular dynamics, binding energy, and network analysis were performed to compare their binding with the targets and amino acids responsible for binding. Naphthofuran series derivatives showed good interaction within the active site residues of both of the targets. Hydrogen bond occupancy and binding energy suggested strong binding with the targets. Dual-inhibitor binding was mostly governed by the hydrophobic interactions for both of the targets. Per residue energy decomposition and network analysis identified the key residues involved in the binding and inhibiting BACE-1 and GSK-3β. The results indicated that naphthofuran series derivative 11 may be a promising first-in-class dual inhibitor against BACE-1 and GSK-3β. This naphthofuran series may be further explored to design better dual inhibitors. Graphical abstract Naphthofuran derivative as a dual inhibitor for BACE-1 and GSK-3β.

  9. 經由校園網路存取圖書館光碟資料庫之研究 Studies on Multiuser Access Library CD-ROM Database via Campus Network

    Directory of Open Access Journals (Sweden)

    Ruey-shun Chen

    1992-06-01

    Full Text Available 無Library CD-ROM with its enormous storage, retrieval capabilities and reasonable price. It has been gradually replacing some of its printed counterpart. But one of the greatest limitation on the use of stand-alone CD-ROM workstation is that only one user can access the CD-ROM database at a time. This paper is proposed a new method to solve this problem. The method use personal computer via standard network system Ethernet high speed fiber network FADDY and standard protocol TCP/IP can access library CD-ROM database and perform a practical CD-ROM campus network system. Its advantage reduce redundant CD-ROM purchase fee and reduce damage by handed in and out and allows multiuser to access the same CD-ROM disc simultaneously.

  10. The International Haemovigilance Network Database for the Surveillance of Adverse Reactions and Events in Donors and Recipients of Blood Components: technical issues and results.

    Science.gov (United States)

    Politis, C; Wiersum, J C; Richardson, C; Robillard, P; Jorgensen, J; Renaudier, P; Faber, J-C; Wood, E M

    2016-11-01

    The International Haemovigilance Network's ISTARE is an online database for surveillance of all adverse reactions (ARs) and adverse events (AEs) associated with donation of blood and transfusion of blood components, irrespective of severity or the harm caused. ISTARE aims to unify the collection and sharing of information with a view to harmonizing best practices for haemovigilance systems around the world. Adverse reactionss and adverse events are recorded by blood component, type of reaction, severity and imputability to transfusion, using internationally agreed standard definitions. From 2006 to 2012, 125 national sets of annual aggregated data were received from 25 countries, covering 132.8 million blood components issued. The incidence of all ARs was 77.5 per 100 000 components issued, of which 25% were severe (19.1 per 100 000). Of 349 deaths (0.26 per 100 000), 58% were due to the three ARs related to the respiratory system: transfusion-associated circulatory overload (TACO, 27%), transfusion-associated acute lung injury (TRALI, 19%) and transfusion-associated dyspnoea (TAD, 12%). Cumulatively, 594 477 donor complications were reported (rate 660 per 100 000), of which 2.9% were severe. ISTARE is a well-established surveillance tool offering important contributions to international efforts to maximize transfusion safety. © 2016 International Society of Blood Transfusion.

  11. Comparing deep neural network and other machine learning algorithms for stroke prediction in a large-scale population-based electronic medical claims database.

    Science.gov (United States)

    Chen-Ying Hung; Wei-Chen Chen; Po-Tsun Lai; Ching-Heng Lin; Chi-Chun Lee

    2017-07-01

    Electronic medical claims (EMCs) can be used to accurately predict the occurrence of a variety of diseases, which can contribute to precise medical interventions. While there is a growing interest in the application of machine learning (ML) techniques to address clinical problems, the use of deep-learning in healthcare have just gained attention recently. Deep learning, such as deep neural network (DNN), has achieved impressive results in the areas of speech recognition, computer vision, and natural language processing in recent years. However, deep learning is often difficult to comprehend due to the complexities in its framework. Furthermore, this method has not yet been demonstrated to achieve a better performance comparing to other conventional ML algorithms in disease prediction tasks using EMCs. In this study, we utilize a large population-based EMC database of around 800,000 patients to compare DNN with three other ML approaches for predicting 5-year stroke occurrence. The result shows that DNN and gradient boosting decision tree (GBDT) can result in similarly high prediction accuracies that are better compared to logistic regression (LR) and support vector machine (SVM) approaches. Meanwhile, DNN achieves optimal results by using lesser amounts of patient data when comparing to GBDT method.

  12. PipY, a Member of the Conserved COG0325 Family of PLP-Binding Proteins, Expands the Cyanobacterial Nitrogen Regulatory Network

    Directory of Open Access Journals (Sweden)

    José I. Labella

    2017-07-01

    Full Text Available Synechococcus elongatus PCC 7942 is a paradigmatic model organism for nitrogen regulation in cyanobacteria. Expression of genes involved in nitrogen assimilation is positively regulated by the 2-oxoglutarate receptor and global transcriptional regulator NtcA. Maximal activation requires the subsequent binding of the co-activator PipX. PII, a protein found in all three domains of life as an integrator of signals of the nitrogen and carbon balance, binds to PipX to counteract NtcA activity at low 2-oxoglutarate levels. PII-PipX complexes can also bind to the transcriptional regulator PlmA, whose regulon remains unknown. Here we expand the nitrogen regulatory network to PipY, encoded by the bicistronic operon pipXY in S. elongatus. Work with PipY, the cyanobacterial member of the widespread family of COG0325 proteins, confirms the conserved roles in vitamin B6 and amino/keto acid homeostasis and reveals new PLP-related phenotypes, including sensitivity to antibiotics targeting essential PLP-holoenzymes or synthetic lethality with cysK. In addition, the related phenotypes of pipY and pipX mutants are consistent with genetic interactions in the contexts of survival to PLP-targeting antibiotics and transcriptional regulation. We also showed that PipY overexpression increased the length of S. elongatus cells. Taken together, our results support a universal regulatory role for COG0325 proteins, paving the way to a better understanding of these proteins and of their connections with other biological processes.

  13. Predicting binding within disordered protein regions to structurally characterised peptide-binding domains.

    Directory of Open Access Journals (Sweden)

    Waqasuddin Khan

    Full Text Available Disordered regions of proteins often bind to structured domains, mediating interactions within and between proteins. However, it is difficult to identify a priori the short disordered regions involved in binding. We set out to determine if docking such peptide regions to peptide binding domains would assist in these predictions.We assembled a redundancy reduced dataset of SLiM (Short Linear Motif containing proteins from the ELM database. We selected 84 sequences which had an associated PDB structures showing the SLiM bound to a protein receptor, where the SLiM was found within a 50 residue region of the protein sequence which was predicted to be disordered. First, we investigated the Vina docking scores of overlapping tripeptides from the 50 residue SLiM containing disordered regions of the protein sequence to the corresponding PDB domain. We found only weak discrimination of docking scores between peptides involved in binding and adjacent non-binding peptides in this context (AUC 0.58.Next, we trained a bidirectional recurrent neural network (BRNN using as input the protein sequence, predicted secondary structure, Vina docking score and predicted disorder score. The results were very promising (AUC 0.72 showing that multiple sources of information can be combined to produce results which are clearly superior to any single source.We conclude that the Vina docking score alone has only modest power to define the location of a peptide within a larger protein region known to contain it. However, combining this information with other knowledge (using machine learning methods clearly improves the identification of peptide binding regions within a protein sequence. This approach combining docking with machine learning is primarily a predictor of binding to peptide-binding sites, and is not intended as a predictor of specificity of binding to particular receptors.

  14. DSSTOX STRUCTURE-SEARCHABLE PUBLIC TOXICITY DATABASE NETWORK: CURRENT PROGRESS AND NEW INITIATIVES TO IMPROVE CHEMO-BIOINFORMATICS CAPABILITIES

    Science.gov (United States)

    The EPA DSSTox website (http://www/epa.gov/nheerl/dsstox) publishes standardized, structure-annotated toxicity databases, covering a broad range of toxicity disciplines. Each DSSTox database features documentation written in collaboration with the source authors and toxicity expe...

  15. Federal databases

    International Nuclear Information System (INIS)

    Welch, M.J.; Welles, B.W.

    1988-01-01

    Accident statistics on all modes of transportation are available as risk assessment analytical tools through several federal agencies. This paper reports on the examination of the accident databases by personal contact with the federal staff responsible for administration of the database programs. This activity, sponsored by the Department of Energy through Sandia National Laboratories, is an overview of the national accident data on highway, rail, air, and marine shipping. For each mode, the definition or reporting requirements of an accident are determined and the method of entering the accident data into the database is established. Availability of the database to others, ease of access, costs, and who to contact were prime questions to each of the database program managers. Additionally, how the agency uses the accident data was of major interest

  16. National Transportation Atlas Databases : 2013.

    Science.gov (United States)

    2013-01-01

    The National Transportation Atlas Databases 2013 (NTAD2013) is a set of nationwide geographic datasets of transportation facilities, transportation networks, associated infrastructure, and other political and administrative entities. These datasets i...

  17. National Transportation Atlas Databases : 2015.

    Science.gov (United States)

    2015-01-01

    The National Transportation Atlas Databases 2015 (NTAD2015) is a set of nationwide geographic datasets of transportation facilities, transportation networks, associated infrastructure, and other political and administrative entities. These datasets i...

  18. National Transportation Atlas Databases : 2014.

    Science.gov (United States)

    2014-01-01

    The National Transportation Atlas Databases 2014 (NTAD2014) is a set of nationwide geographic datasets of transportation facilities, transportation networks, associated infrastructure, and other political and administrative entities. These datasets i...

  19. The Global Terrestrial Network for Permafrost Database: metadata statistics and prospective analysis on future permafrost temperature and active layer depth monitoring site distribution

    Science.gov (United States)

    Biskaborn, B. K.; Lanckman, J.-P.; Lantuit, H.; Elger, K.; Streletskiy, D. A.; Cable, W. L.; Romanovsky, V. E.

    2015-03-01

    The Global Terrestrial Network for Permafrost (GTN-P) provides the first dynamic database associated with the Thermal State of Permafrost (TSP) and the Circumpolar Active Layer Monitoring (CALM) programs, which extensively collect permafrost temperature and active layer thickness data from Arctic, Antarctic and Mountain permafrost regions. The purpose of the database is to establish an "early warning system" for the consequences of climate change in permafrost regions and to provide standardized thermal permafrost data to global models. In this paper we perform statistical analysis of the GTN-P metadata aiming to identify the spatial gaps in the GTN-P site distribution in relation to climate-effective environmental parameters. We describe the concept and structure of the Data Management System in regard to user operability, data transfer and data policy. We outline data sources and data processing including quality control strategies. Assessment of the metadata and data quality reveals 63% metadata completeness at active layer sites and 50% metadata completeness for boreholes. Voronoi Tessellation Analysis on the spatial sample distribution of boreholes and active layer measurement sites quantifies the distribution inhomogeneity and provides potential locations of additional permafrost research sites to improve the representativeness of thermal monitoring across areas underlain by permafrost. The depth distribution of the boreholes reveals that 73% are shallower than 25 m and 27% are deeper, reaching a maximum of 1 km depth. Comparison of the GTN-P site distribution with permafrost zones, soil organic carbon contents and vegetation types exhibits different local to regional monitoring situations on maps. Preferential slope orientation at the sites most likely causes a bias in the temperature monitoring and should be taken into account when using the data for global models. The distribution of GTN-P sites within zones of projected temperature change show a high

  20. 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

  1. Refactoring databases evolutionary database design

    CERN Document Server

    Ambler, Scott W

    2006-01-01

    Refactoring has proven its value in a wide range of development projects–helping software professionals improve system designs, maintainability, extensibility, and performance. Now, for the first time, leading agile methodologist Scott Ambler and renowned consultant Pramodkumar Sadalage introduce powerful refactoring techniques specifically designed for database systems. Ambler and Sadalage demonstrate how small changes to table structures, data, stored procedures, and triggers can significantly enhance virtually any database design–without changing semantics. You’ll learn how to evolve database schemas in step with source code–and become far more effective in projects relying on iterative, agile methodologies. This comprehensive guide and reference helps you overcome the practical obstacles to refactoring real-world databases by covering every fundamental concept underlying database refactoring. Using start-to-finish examples, the authors walk you through refactoring simple standalone databas...

  2. SCOWLP classification: Structural comparison and analysis of protein binding regions

    Directory of Open Access Journals (Sweden)

    Anders Gerd

    2008-01-01

    Full Text Available Abstract Background Detailed information about protein interactions is critical for our understanding of the principles governing protein recognition mechanisms. The structures of many proteins have been experimentally determined in complex with different ligands bound either in the same or different binding regions. Thus, the structural interactome requires the development of tools to classify protein binding regions. A proper classification may provide a general view of the regions that a protein uses to bind others and also facilitate a detailed comparative analysis of the interacting information for specific protein binding regions at atomic level. Such classification might be of potential use for deciphering protein interaction networks, understanding protein function, rational engineering and design. Description Protein binding regions (PBRs might be ideally described as well-defined separated regions that share no interacting residues one another. However, PBRs are often irregular, discontinuous and can share a wide range of interacting residues among them. The criteria to define an individual binding region can be often arbitrary and may differ from other binding regions within a protein family. Therefore, the rational behind protein interface classification should aim to fulfil the requirements of the analysis to be performed. We extract detailed interaction information of protein domains, peptides and interfacial solvent from the SCOWLP database and we classify the PBRs of each domain family. For this purpose, we define a similarity index based on the overlapping of interacting residues mapped in pair-wise structural alignments. We perform our classification with agglomerative hierarchical clustering using the complete-linkage method. Our classification is calculated at different similarity cut-offs to allow flexibility in the analysis of PBRs, feature especially interesting for those protein families with conflictive binding regions

  3. Neurostimulation options for failed back surgery syndrome: The need for rational and objective measurements. Proposal of an international clinical network using an integrated database and health economic analysis: the PROBACK network.

    Science.gov (United States)

    Rigoard, P; Slavin, K

    2015-03-01

    In the context of failed back surgery syndrome (FBSS) treatment, the current practice in neurostimulation varies from center-to-center and most clinical decisions are based on an individual diagnosis. Neurostimulation evaluation tools and pain relief assessment are of major concern, as they now constitute one of the main biases of clinical trials. Moreover, the proliferation of technological devices, in a fertile and unsatisfied market, fosters and only furthers the confusion. There are three options available to apply scientific debates to our daily neurostimulation practice: intentional ignorance, standardized evidence-based practice or alternative data mining approach. In view of the impossibility of conducting multiple randomized clinical trials comparing various devices, one by one, the proposed concept would be to redefine the indications and the respective roles of the various spinal cord and peripheral nerve stimulation devices with large-scale computational modeling/data mining approach, by conducting a multicenter prospective database registry, supported by a clinician's global network called "PROBACK". We chose to specifically analyze 6 parameters: device coverage performance/coverage selectivity/persistence of the long-term electrical response (technical criteria) and comparative mapping of patient pain relief/persistence of the long-term clinical response/safety and complications occurrence (clinical criteria). Two types of analysis will be performed: immediate analysis (including cost analysis) and computational analysis, i.e. demonstration of the robustness of certain correlations of variables, in order to extract response predictors. By creating an international prospective database, the purpose of the PROBACK project was to set up a process of extraction and comparative analysis of data derived from the selection, implantation and follow-up of FBSS patients candidates for implanted neurostimulation. This evaluation strategy should help to change

  4. Regional variations of basal cell carcinoma incidence in the U.K. using The Health Improvement Network database (2004-10).

    Science.gov (United States)

    Musah, A; Gibson, J E; Leonardi-Bee, J; Cave, M R; Ander, E L; Bath-Hextall, F

    2013-11-01

    Basal cell carcinoma (BCC) is one of the most common types of nonmelanoma skin cancer affecting the white population; however, little is known about how the incidence varies across the U.K. To determine the variation in BCC throughout the U.K. Data from 2004 to 2010 were obtained from The Health Improvement Network database. European and world age-standardized incidence rates (EASRs and WASRs, respectively) were obtained for country-level estimates and levels of socioeconomic deprivation, while strategic health-authority-level estimates were directly age and sex standardized to the U.K. standard population. Incidence-rate ratios were estimated using multivariable Poisson regression models. The overall EASR and WASR of BCC in the U.K. were 98.6 per 100,000 person-years and 66.9 per 100,000 person-years, respectively. Regional-level incidence rates indicated a significant geographical variation in the distribution of BCC, which was more pronounced in the southern parts of the country. The South East Coast had the highest BCC rate followed by South Central, Wales and the South West. Incidence rates were substantially higher in the least deprived groups and we observed a trend of decreasing incidence with increasing levels of deprivation (P < 0.001). Finally, in terms of age groups, the largest annual increase was observed among those aged 30-49 years. Basal cell carcinoma is an increasing health problem in the U.K.; the southern regions of the U.K. and those in the least deprived groups had a higher incidence of BCC. Our findings indicate an increased incidence of BCC for younger age groups below 49 years. © 2013 British Association of Dermatologists.

  5. Impact of Socioeconomic Status on Patients Supported With a Left Ventricular Assist Device: An Analysis of the UNOS Database (United Network for Organ Sharing).

    Science.gov (United States)

    Clerkin, Kevin J; Garan, Arthur Reshad; Wayda, Brian; Givens, Raymond C; Yuzefpolskaya, Melana; Nakagawa, Shunichi; Takeda, Koji; Takayama, Hiroo; Naka, Yoshifumi; Mancini, Donna M; Colombo, Paolo C; Topkara, Veli K

    2016-10-01

    Low socioeconomic status (SES) is a known risk factor for heart failure, mortality among those with heart failure, and poor post heart transplant (HT) outcomes. This study sought to determine whether SES is associated with decreased waitlist survival while on left ventricular assist device (LVADs) support and after HT. A total of 3361 adult patients bridged to primary HT with an LVAD between May 2004 and April 2014 were identified in the UNOS database (United Network for Organ Sharing). SES was measured using the Agency for Healthcare Research and Quality SES index using data from the 2014 American Community Survey. In the study cohort, SES did not have an association with the combined end point of death or delisting on LVAD support (P=0.30). In a cause-specific unadjusted model, those in the top (hazard ratio, 1.55; 95% confidence interval, 1.14-2.11; P=0.005) and second greatest SES quartile (hazard ratio 1.50; 95% confidence interval, 1.10-2.04; P=0.01) had an increased risk of death on device support compared with the lowest SES quartile. Adjusting for clinical risk factors mitigated the increased risk. There was no association between SES and complications. Post-HT survival, both crude and adjusted, was decreased for patients in the lowest quartile of SES index compared with all other SES quartiles. Freedom from waitlist death or delisting was not affected by SES. Patients with a higher SES had an increased unadjusted risk of waitlist mortality during LVAD support, which was mitigated by adjusting for increased comorbid conditions. Low SES was associated with worse post-HT outcomes. Further study is needed to confirm and understand a differential effect of SES on post-transplant outcomes that was not seen during LVAD support before HT. © 2016 American Heart Association, Inc.

  6. Incidence, treatment and recurrence of endometriosis in a UK-based population analysis using data from The Health Improvement Network and the Hospital Episode Statistics database.

    Science.gov (United States)

    Cea Soriano, Lucia; López-Garcia, Esther; Schulze-Rath, Renate; Garcia Rodríguez, Luis A

    2017-10-01

    This retrospective study used medical records from The Health Improvement Network (THIN) and Hospital Episode Statistics (HES) database to evaluate endometriosis (incidence, treatment and need for recurrent invasive procedures) in the general UK population. Women aged 12-54 years between January 2000 and December 2010, with a Read code for endometriosis, were identified in THIN. Cases were validated by manual review of free-text comments in medical records and responses to physician questionnaires. False-negative cases were identified among women with Read codes for hysterectomy or dysmenorrhea. Prescriptions of medical therapies for endometriosis were identified in THIN. Cases of single and recurrent invasive procedures were identified in women with medical records in both THIN and HES. Overall, 5087 women had a Read code for endometriosis, corresponding to an incidence of 1.02 (95% confidence interval [CI]: 0.99-1.05) per 1000 person-years. After case validation, the estimate was 1.46 (95% CI: 1.43-1.50) per 1000 person-years. Medical therapy was prescribed to 55.5% of women with endometriosis in the first year after diagnosis. In total, 48.3% of women received invasive treatment during the study period; approximately one-fifth of these women required further invasive treatment, mainly in the 3 years after the index procedure. Using Read codes as the only method to identify women with endometriosis underestimates incidence. Over half of women with recorded endometriosis are prescribed medical therapy in the first year after diagnosis. Women with diagnosed endometriosis are at risk of requiring recurrent invasive procedures.

  7. 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...

  8. Snowstorm Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Snowstorm Database is a collection of over 500 snowstorms dating back to 1900 and updated operationally. Only storms having large areas of heavy snowfall (10-20...

  9. 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 1,...

  10. 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....

  11. The magnet database system

    International Nuclear Information System (INIS)

    Baggett, P.; Delagi, N.; Leedy, R.; Marshall, W.; Robinson, S.L.; Tompkins, J.C.

    1991-01-01

    This paper describes the current status of MagCom, a central database of SSC magnet information that is available to all magnet scientists via network connections. The database has been 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 help magnet scientists to track and control the production process and to correlate the performance of magnets with the properties of their constituents

  12. Experiment Databases

    Science.gov (United States)

    Vanschoren, Joaquin; Blockeel, Hendrik

    Next to running machine learning algorithms based on inductive queries, much can be learned by immediately querying the combined results of many prior studies. Indeed, all around the globe, thousands of machine learning experiments are being executed on a daily basis, generating a constant stream of empirical information on machine learning techniques. While the information contained in these experiments might have many uses beyond their original intent, results are typically described very concisely in papers and discarded afterwards. If we properly store and organize these results in central databases, they can be immediately reused for further analysis, thus boosting future research. In this chapter, we propose the use of experiment databases: databases designed to collect all the necessary details of these experiments, and to intelligently organize them in online repositories to enable fast and thorough analysis of a myriad of collected results. They constitute an additional, queriable source of empirical meta-data based on principled descriptions of algorithm executions, without reimplementing the algorithms in an inductive database. As such, they engender a very dynamic, collaborative approach to experimentation, in which experiments can be freely shared, linked together, and immediately reused by researchers all over the world. They can be set up for personal use, to share results within a lab or to create open, community-wide repositories. Here, we provide a high-level overview of their design, and use an existing experiment database to answer various interesting research questions about machine learning algorithms and to verify a number of recent studies.

  13. A Generic Data Harmonization Process for Cross-linked Research and Network Interaction. Construction and Application for the Lung Cancer Phenotype Database of the German Center for Lung Research.

    Science.gov (United States)

    Firnkorn, D; Ganzinger, M; Muley, T; Thomas, M; Knaup, P

    2015-01-01

    Joint data analysis is a key requirement in medical research networks. Data are available in heterogeneous formats at each network partner and their harmonization is often rather complex. The objective of our paper is to provide a generic approach for the harmonization process in research networks. We applied the process when harmonizing data from three sites for the Lung Cancer Phenotype Database within the German Center for Lung Research. We developed a spreadsheet-based solution as tool to support the harmonization process for lung cancer data and a data integration procedure based on Talend Open Studio. The harmonization process consists of eight steps describing a systematic approach for defining and reviewing source data elements and standardizing common data elements. The steps for defining common data elements and harmonizing them with local data definitions are repeated until consensus is reached. Application of this process for building the phenotype database led to a common basic data set on lung cancer with 285 structured parameters. The Lung Cancer Phenotype Database was realized as an i2b2 research data warehouse. Data harmonization is a challenging task requiring informatics skills as well as domain knowledge. Our approach facilitates data harmonization by providing guidance through a uniform process that can be applied in a wide range of projects.

  14. DMPD: The involvement of the interleukin-1 receptor-associated kinases (IRAKs) incellular signaling networks controlling inflammation. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available ncellular signaling networks controlling inflammation. Ringwood L, Li L. Cytokine. 2008 Apr;42(1):1-7. Epub ...ases (IRAKs) incellular signaling networks controlling inflammation. PubmedID 182...49132 Title The involvement of the interleukin-1 receptor-associated kinases (IRAKs) incellular signaling networks controlling

  15. Database Perspectives on Blockchains

    OpenAIRE

    Cohen, Sara; Zohar, Aviv

    2018-01-01

    Modern blockchain systems are a fresh look at the paradigm of distributed computing, applied under assumptions of large-scale public networks. They can be used to store and share information without a trusted central party. There has been much effort to develop blockchain systems for a myriad of uses, ranging from cryptocurrencies to identity control, supply chain management, etc. None of this work has directly studied the fundamental database issues that arise when using blockchains as the u...

  16. Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network.

    Science.gov (United States)

    Varrault, Annie; Dantec, Christelle; Le Digarcher, Anne; Chotard, Laëtitia; Bilanges, Benoit; Parrinello, Hugues; Dubois, Emeric; Rialle, Stéphanie; Severac, Dany; Bouschet, Tristan; Journot, Laurent

    2017-10-13

    PLAGL1/ZAC1 undergoes parental genomic imprinting, is paternally expressed, and is a member of the imprinted gene network (IGN). It encodes a zinc finger transcription factor with anti-proliferative activity and is a candidate tumor suppressor gene on 6q24 whose expression is frequently lost in various neoplasms. Conversely, gain of PLAGL1 function is responsible for transient neonatal diabetes mellitus, a rare genetic disease that results from defective pancreas development. In the present work, we showed that Plagl1 up-regulation was not associated with DNA damage-induced cell cycle arrest. It was rather associated with physiological cell cycle exit that occurred with contact inhibition, growth factor withdrawal, or cell differentiation. To gain insights into Plagl1 mechanism of action, we identified Plagl1 target genes by combining chromatin immunoprecipitation and genome-wide transcriptomics in transfected cell lines. Plagl1-elicited gene regulation correlated with multiple binding to the proximal promoter region through a GC-rich motif. Plagl1 target genes included numerous genes involved in signaling, cell adhesion, and extracellular matrix composition, including collagens. Plagl1 targets also included 22% of the 409 genes that make up the IGN. Altogether, this work identified Plagl1 as a transcription factor that coordinated the regulation of a subset of IGN genes and controlled extracellular matrix composition. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Basic database performance tuning - developer's perspective

    CERN Document Server

    Kwiatek, Michal

    2008-01-01

    This lecture discusses selected database performance issues from the developer's point of view: connection overhead, bind variables and SQL injection, making most of the optimizer with up-to-date statistics, reading execution plans. Prior knowledge of SQL is expected.

  18. Maintaining the Database for Information Object Analysis, Intent, Dissemination and Enhancement (IOAIDE) and the US Army Research Laboratory Campus Sensor Network (ARL CSN)

    Science.gov (United States)

    2017-01-01

    operations as well as basic knowledge of Microsoft Structured Query Language Server Management Studio (2014 or 2016). 15. SUBJECT TERMS Microsoft SQL ...designed and is maintained with Microsoft SQL Server Management Studio. The basic requirements for the IOAIDE/ARL CSN database development and... SQL server (2014 or 2016) installed. All images in this report were generated using Windows 10. The IOAIDE/ARL CSN database could reside on the

  19. Networking

    OpenAIRE

    Rauno Lindholm, Daniel; Boisen Devantier, Lykke; Nyborg, Karoline Lykke; Høgsbro, Andreas; Fries, de; Skovlund, Louise

    2016-01-01

    The purpose of this project was to examine what influencing factor that has had an impact on the presumed increasement of the use of networking among academics on the labour market and how it is expressed. On the basis of the influence from globalization on the labour market it can be concluded that the globalization has transformed the labour market into a market based on the organization of networks. In this new organization there is a greater emphasis on employees having social qualificati...

  20. DMPD: Translational mini-review series on Toll-like receptors: networks regulated byToll-like receptors mediate innate and adaptive immunity. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17223959 Translational mini-review series on Toll-like receptors: networks regulate...ol. 2007 Feb;147(2):199-207. (.png) (.svg) (.html) (.csml) Show Translational mini-review series on Toll-lik... immunity. PubmedID 17223959 Title Translational mini-review series on Toll-like receptors: networks regulat

  1. First diagnosis and management of incontinence in older people with and without dementia in primary care: a cohort study using The Health Improvement Network primary care database.

    Directory of Open Access Journals (Sweden)

    Robert L Grant

    2013-08-01

    Full Text Available Dementia is one of the most disabling and burdensome diseases. Incontinence in people with dementia is distressing, adds to carer burden, and influences decisions to relocate people to care homes. Successful and safe management of incontinence in people with dementia presents additional challenges. The aim of this study was to investigate the rates of first diagnosis in primary care of urinary and faecal incontinence among people aged 60-89 with dementia, and the use of medication or indwelling catheters for urinary incontinence.We extracted data on 54,816 people aged 60-89 with dementia and an age-gender stratified sample of 205,795 people without dementia from 2001 to 2010 from The Health Improvement Network (THIN, a United Kingdom primary care database. THIN includes data on patients and primary care consultations but does not identify care home residents. Rate ratios were adjusted for age, sex, and co-morbidity using multilevel Poisson regression. The rates of first diagnosis per 1,000 person-years at risk (95% confidence interval for urinary incontinence in the dementia cohort, among men and women, respectively, were 42.3 (40.9-43.8 and 33.5 (32.6-34.5. In the non-dementia cohort, the rates were 19.8 (19.4-20.3 and 18.6 (18.2-18.9. The rates of first diagnosis for faecal incontinence in the dementia cohort were 11.1 (10.4-11.9 and 10.1 (9.6-10.6. In the non-dementia cohort, the rates were 3.1 (2.9-3.3 and 3.6 (3.5-3.8. The adjusted rate ratio for first diagnosis of urinary incontinence was 3.2 (2.7-3.7 in men and 2.7 (2.3-3.2 in women, and for faecal incontinence was 6.0 (5.1-7.0 in men and 4.5 (3.8-5.2 in women. The adjusted rate ratio for pharmacological treatment of urinary incontinence was 2.2 (1.4-3.7 for both genders, and for indwelling urinary catheters was 1.6 (1.3-1.9 in men and 2.3 (1.9-2.8 in women.Compared with those without a dementia diagnosis, those with a dementia diagnosis have approximately three times the rate of

  2. Database of Information technology resources

    OpenAIRE

    Barzda, Erlandas

    2005-01-01

    The subject of this master work is the internet information resource database. This work also handles the problems of old information systems which do not meet the new contemporary requirements. The aim is to create internet information system, based on object-oriented technologies and tailored to computer users’ needs. The internet information database system helps computers administrators to get the all needed information about computers network elements and easy to register all changes int...

  3. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  4. Knitting Relational Documentary Networks: The Database Meta-Documentary Filming Revolution as a paradigm of bringing interactive audio-visual archives alive

    NARCIS (Netherlands)

    Wiehl, Anna

    2016-01-01

    abstractOne phenomenon in the emerging field of digital documentary are experiments with rhizomatic interfaces and database-logics to bring audio-visual archives 'alive'. A paradigm hereof is Filming Revolution (2015), an interactive platform which gathers and interlinks films of the uprisings in

  5. The magnet database system

    International Nuclear Information System (INIS)

    Ball, M.J.; Delagi, N.; Horton, B.; Ivey, J.C.; Leedy, R.; Li, X.; Marshall, B.; Robinson, S.L.; Tompkins, J.C.

    1992-01-01

    The Test Department of the Magnet Systems Division of the Superconducting Super Collider Laboratory (SSCL) is developing a central database of SSC magnet information that will be available to all magnet scientists at the SSCL or elsewhere, via network connections. The database contains information on the magnets' major components, configuration information (specifying which individual items were used in each cable, coil, and magnet), measurements made at major fabrication stages, and the test results on completed magnets. These data will facilitate the correlation of magnet performance with the properties of its constituents. Recent efforts have focused on the development of procedures for user-friendly access to the data, including displays in the format of the production open-quotes travelerclose quotes data sheets, standard summary reports, and a graphical interface for ad hoc queues and plots

  6. Physical database design using Oracle

    CERN Document Server

    Burleson, Donald K

    2004-01-01

    INTRODUCTION TO ORACLE PHYSICAL DESIGNPrefaceRelational Databases and Physical DesignSystems Analysis and Physical Database DesignIntroduction to Logical Database DesignEntity/Relation ModelingBridging between Logical and Physical ModelsPhysical Design Requirements Validation PHYSICAL ENTITY DESIGN FOR ORACLEData Relationships and Physical DesignMassive De-Normalization: STAR Schema DesignDesigning Class HierarchiesMaterialized Views and De-NormalizationReferential IntegrityConclusionORACLE HARDWARE DESIGNPlanning the Server EnvironmentDesigning the Network Infrastructure for OracleOracle Netw

  7. The magnet components database system

    International Nuclear Information System (INIS)

    Baggett, M.J.; Leedy, R.; Saltmarsh, C.; Tompkins, J.C.

    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

  8. The magnet components database system

    International Nuclear Information System (INIS)

    Baggett, M.J.; Leedy, R.; Saltmarsh, C.; Tompkins, J.C.

    1990-01-01

    The philosophy, structure, and usage of 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. The 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., 9 figs

  9. 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.

  10. ETMB-RBF: discrimination of metal-binding sites in electron transporters based on RBF networks with PSSM profiles and significant amino acid pairs.

    Science.gov (United States)

    Ou, Yu-Yen; Chen, Shu-An; Wu, Sheng-Cheng

    2013-01-01

    Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation-reduction reactions. In these oxidation-reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain. We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins. We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88. We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins.

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

    International Nuclear Information System (INIS)

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

    2003-01-01

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

  12. SmallSat Database

    Science.gov (United States)

    Petropulos, Dolores; Bittner, David; Murawski, Robert; Golden, Bert

    2015-01-01

    The SmallSat has an unrealized potential in both the private industry and in the federal government. Currently over 70 companies, 50 universities and 17 governmental agencies are involved in SmallSat research and development. In 1994, the U.S. Army Missile and Defense mapped the moon using smallSat imagery. Since then Smart Phones have introduced this imagery to the people of the world as diverse industries watched this trend. The deployment cost of smallSats is also greatly reduced compared to traditional satellites due to the fact that multiple units can be deployed in a single mission. Imaging payloads have become more sophisticated, smaller and lighter. In addition, the growth of small technology obtained from private industries has led to the more widespread use of smallSats. This includes greater revisit rates in imagery, significantly lower costs, the ability to update technology more frequently and the ability to decrease vulnerability of enemy attacks. The popularity of smallSats show a changing mentality in this fast paced world of tomorrow. What impact has this created on the NASA communication networks now and in future years? In this project, we are developing the SmallSat Relational Database which can support a simulation of smallSats within the NASA SCaN Compatability Environment for Networks and Integrated Communications (SCENIC) Modeling and Simulation Lab. The NASA Space Communications and Networks (SCaN) Program can use this modeling to project required network support needs in the next 10 to 15 years. The SmallSat Rational Database could model smallSats just as the other SCaN databases model the more traditional larger satellites, with a few exceptions. One being that the smallSat Database is designed to be built-to-order. The SmallSat database holds various hardware configurations that can be used to model a smallSat. It will require significant effort to develop as the research material can only be populated by hand to obtain the unique data

  13. Webcam network and image database for studies of phenological changes of vegetation and snow cover in Finland, image time series from 2014 to 2016

    Science.gov (United States)

    Peltoniemi, Mikko; Aurela, Mika; Böttcher, Kristin; Kolari, Pasi; Loehr, John; Karhu, Jouni; Linkosalmi, Maiju; Melih Tanis, Cemal; Tuovinen, Juha-Pekka; Nadir Arslan, Ali

    2018-01-01

    In recent years, monitoring of the status of ecosystems using low-cost web (IP) or time lapse cameras has received wide interest. With broad spatial coverage and high temporal resolution, networked cameras can provide information about snow cover and vegetation status, serve as ground truths to Earth observations and be useful for gap-filling of cloudy areas in Earth observation time series. Networked cameras can also play an important role in supplementing laborious phenological field surveys and citizen science projects, which also suffer from observer-dependent observation bias. We established a network of digital surveillance cameras for automated monitoring of phenological activity of vegetation and snow cover in the boreal ecosystems of Finland. Cameras were mounted at 14 sites, each site having 1-3 cameras. Here, we document the network, basic camera information and access to images in the permanent data repository (http://www.zenodo.org/communities/phenology_camera/). Individual DOI-referenced image time series consist of half-hourly images collected between 2014 and 2016 (https://doi.org/10.5281/zenodo.1066862). Additionally, we present an example of a colour index time series derived from images from two contrasting sites.

  14. Relational nuclear databases upon the MSU INP CDFE Web-site and Nuclear Data Centres Network CDFE activities. P7[Centre for Photonuclear Experiments Data, Moscow, Russian Federation

    Energy Technology Data Exchange (ETDEWEB)

    Boboshin, I N; Varlamov, V V; Ivanov, E M; Ivanov, S V; Peskov, N N; Stepanov, M E; Chesnokov, V V [Centre for Photonuclear Experiments Data, Moscow (Russian Federation)

    2001-07-01

    This report contains only the short review of the work carried out by the CDFE concerning the IAEA Nuclear Reaction Data Centres Network activities for the period of time from the IAEA Advisory Group Meeting (15-19 May 2000, Obninsk, Russia) till May 2001 and the description of the main results obtained.

  15. Webcam network and image database for studies of phenological changes of vegetation and snow cover in Finland, image time series from 2014 to 2016

    Directory of Open Access Journals (Sweden)

    M. Peltoniemi

    2018-01-01

    Full Text Available In recent years, monitoring of the status of ecosystems using low-cost web (IP or time lapse cameras has received wide interest. With broad spatial coverage and high temporal resolution, networked cameras can provide information about snow cover and vegetation status, serve as ground truths to Earth observations and be useful for gap-filling of cloudy areas in Earth observation time series. Networked cameras can also play an important role in supplementing laborious phenological field surveys and citizen science projects, which also suffer from observer-dependent observation bias. We established a network of digital surveillance cameras for automated monitoring of phenological activity of vegetation and snow cover in the boreal ecosystems of Finland. Cameras were mounted at 14 sites, each site having 1–3 cameras. Here, we document the network, basic camera information and access to images in the permanent data repository (http://www.zenodo.org/communities/phenology_camera/. Individual DOI-referenced image time series consist of half-hourly images collected between 2014 and 2016 (https://doi.org/10.5281/zenodo.1066862. Additionally, we present an example of a colour index time series derived from images from two contrasting sites.

  16. Investigating core genetic-and-epigenetic cell cycle networks for stemness and carcinogenic mechanisms, and cancer drug design using big database mining and genome-wide next-generation sequencing data.

    Science.gov (United States)

    Li, Cheng-Wei; Chen, Bor-Sen

    2016-10-01

    Recent studies have demonstrated that cell cycle plays a central role in development and carcinogenesis. Thus, the use of big databases and genome-wide high-throughput data to unravel the genetic and epigenetic mechanisms underlying cell cycle progression in stem cells and cancer cells is a matter of considerable interest. Real genetic-and-epigenetic cell cycle networks (GECNs) of embryonic stem cells (ESCs) and HeLa cancer cells were constructed by applying system modeling, system identification, and big database mining to genome-wide next-generation sequencing data. Real GECNs were then reduced to core GECNs of HeLa cells and ESCs by applying principal genome-wide network projection. In this study, we investigated potential carcinogenic and stemness mechanisms for systems cancer drug design by identifying common core and specific GECNs between HeLa cells and ESCs. Integrating drug database information with the specific GECNs of HeLa cells could lead to identification of multiple drugs for cervical cancer treatment with minimal side-effects on the genes in the common core. We found that dysregulation of miR-29C, miR-34A, miR-98, and miR-215; and methylation of ANKRD1, ARID5B, CDCA2, PIF1, STAMBPL1, TROAP, ZNF165, and HIST1H2AJ in HeLa cells could result in cell proliferation and anti-apoptosis through NFκB, TGF-β, and PI3K pathways. We also identified 3 drugs, methotrexate, quercetin, and mimosine, which repressed the activated cell cycle genes, ARID5B, STK17B, and CCL2, in HeLa cells with minimal side-effects.

  17. Reduction in camera-specific variability in [{sup 123}I]FP-CIT SPECT outcome measures by image reconstruction optimized for multisite settings: impact on age-dependence of the specific binding ratio in the ENC-DAT database of healthy controls

    Energy Technology Data Exchange (ETDEWEB)

    Buchert, Ralph; Lange, Catharina [Charite - Universitaetsmedizin Berlin, Department of Nuclear Medicine, Berlin (Germany); Kluge, Andreas; Bronzel, Marcus [ABX-CRO advanced pharmaceutical services Forschungsgesellschaft m.b.H., Dresden (Germany); Tossici-Bolt, Livia [University Hospital Southampton NHS Foundation Trust, Department of Medical Physics, Southampton (United Kingdom); Dickson, John [University College London Hospital NHS Foundation Trust, Institute of Nuclear Medicine, London (United Kingdom); Asenbaum, Susanne [Medical University of Vienna, Department of Nuclear Medicine, Vienna (Austria); Booij, Jan [University of Amsterdam, Department of Nuclear Medicine, Academic Medical Centre, Amsterdam (Netherlands); Kapucu, L. Oezlem Atay [Gazi University, Department of Nuclear Medicine, Faculty of Medicine, Ankara (Turkey); Svarer, Claus [Rigshospitalet and University of Copenhagen, Neurobiology Research Unit, Copenhagen (Denmark); Koulibaly, Pierre-Malick [University of Nice-Sophia Antipolis, Nuclear Medicine Department, Centre Antoine Lacassagne, Nice (France); Nobili, Flavio [University of Genoa, Department of Neuroscience (DINOGMI), Clinical Neurology Unit, Genoa (Italy); Pagani, Marco [CNR, Institute of Cognitive Sciences and Technologies, Rome (Italy); Karolinska Hospital, Department of Nuclear Medicine, Stockholm (Sweden); Sabri, Osama [University of Leipzig, Department of Nuclear Medicine, Leipzig (Germany); Sera, Terez [University of Szeged, Department of Nuclear Medicine and Euromedic Szeged, Szeged (Hungary); Tatsch, Klaus [Municipal Hospital of Karlsruhe Inc, Department of Nuclear Medicine, Karlsruhe (Germany); Borght, Thierry vander [CHU Namur, IREC, Nuclear Medicine Division, Universite catholique de Louvain, Yvoir (Belgium); Laere, Koen van [University Hospital and K.U. Leuven, Nuclear Medicine, Leuven (Belgium); Varrone, Andrea [Karolinska University Hospital, Department of Clinical Neuroscience, Centre for Psychiatry Research, Karolinska Institutet, Stockholm (Sweden); Iida, Hidehiro [National Cerebral and Cardiovascular Center - Research Institute, Osaka (Japan)

    2016-07-15

    Quantitative estimates of dopamine transporter availability, determined with [{sup 123}I]FP-CIT SPECT, depend on the SPECT equipment, including both hardware and (reconstruction) software, which limits their use in multicentre research and clinical routine. This study tested a dedicated reconstruction algorithm for its ability to reduce camera-specific intersubject variability in [{sup 123}I]FP-CIT SPECT. The secondary aim was to evaluate binding in whole brain (excluding striatum) as a reference for quantitative analysis. Of 73 healthy subjects from the European Normal Control Database of [{sup 123}I]FP-CIT recruited at six centres, 70 aged between 20 and 82 years were included. SPECT images were reconstructed using the QSPECT software package which provides fully automated detection of the outer contour of the head, camera-specific correction for scatter and septal penetration by transmission-dependent convolution subtraction, iterative OSEM reconstruction including attenuation correction, and camera-specific ''to kBq/ml'' calibration. LINK and HERMES reconstruction were used for head-to-head comparison. The specific striatal [{sup 123}I]FP-CIT binding ratio (SBR) was computed using the Southampton method with binding in the whole brain, occipital cortex or cerebellum as the reference. The correlation between SBR and age was used as the primary quality measure. The fraction of SBR variability explained by age was highest (1) with QSPECT, independently of the reference region, and (2) with whole brain as the reference, independently of the reconstruction algorithm. QSPECT reconstruction appears to be useful for reduction of camera-specific intersubject variability of [{sup 123}I]FP-CIT SPECT in multisite and single-site multicamera settings. Whole brain excluding striatal binding as the reference provides more stable quantitative estimates than occipital or cerebellar binding. (orig.)

  18. Extending Database Integration Technology

    National Research Council Canada - National Science Library

    Buneman, Peter

    1999-01-01

    Formal approaches to the semantics of databases and database languages can have immediate and practical consequences in extending database integration technologies to include a vastly greater range...

  19. The AMMA database

    Science.gov (United States)

    Boichard, Jean-Luc; Brissebrat, Guillaume; Cloche, Sophie; Eymard, Laurence; Fleury, Laurence; Mastrorillo, Laurence; Moulaye, Oumarou; Ramage, Karim

    2010-05-01

    The AMMA project includes aircraft, ground-based and ocean measurements, an intensive use of satellite data and diverse modelling studies. Therefore, the AMMA database aims at storing a great amount and a large variety of data, and at providing the data as rapidly and safely as possible to the AMMA research community. In order to stimulate the exchange of information and collaboration between researchers from different disciplines or using different tools, the database provides a detailed description of the products and uses standardized formats. The AMMA database contains: - AMMA field campaigns datasets; - historical data in West Africa from 1850 (operational networks and previous scientific programs); - satellite products from past and future satellites, (re-)mapped on a regular latitude/longitude grid and stored in NetCDF format (CF Convention); - model outputs from atmosphere or ocean operational (re-)analysis and forecasts, and from research simulations. The outputs are processed as the satellite products are. Before accessing the data, any user has to sign the AMMA data and publication policy. This chart only covers the use of data in the framework of scientific objectives and categorically excludes the redistribution of data to third parties and the usage for commercial applications. Some collaboration between data producers and users, and the mention of the AMMA project in any publication is also required. The AMMA database and the associated on-line tools have been fully developed and are managed by two teams in France (IPSL Database Centre, Paris and OMP, Toulouse). Users can access data of both data centres using an unique web portal. This website is composed of different modules : - Registration: forms to register, read and sign the data use chart when an user visits for the first time - Data access interface: friendly tool allowing to build a data extraction request by selecting various criteria like location, time, parameters... The request can

  20. Management system of instrument database

    International Nuclear Information System (INIS)

    Zhang Xin

    1997-01-01

    The author introduces a management system of instrument database. This system has been developed using with Foxpro on network. The system has some characters such as clear structure, easy operation, flexible and convenient query, as well as the data safety and reliability

  1. Establishing a Dynamic Database of Blue and Fin Whale Locations from Recordings at the IMS CTBTO hydro-acoustic network. The Baleakanta Project

    Science.gov (United States)

    Le Bras, R. J.; Kuzma, H.

    2013-12-01

    Falling as they do into the frequency range of continuously recording hydrophones (15-100Hz), blue and fin whale songs are a significant source of noise on the hydro-acoustic monitoring array of the International Monitoring System (IMS) of the Comprehensive Nuclear Test Ban Treaty Organization (CTBTO). One researcher's noise, however, can be a very interesting signal in another field of study. The aim of the Baleakanta Project (www.baleakanta.org) is to flag and catalogue these songs, using the azimuth and slowness of the signal measured at multiple hydrophones to solve for the approximate location of singing whales. Applying techniques borrowed from human speaker identification, it may even be possible to recognize the songs of particular individuals. The result will be a dynamic database of whale locations and songs with known individuals noted. This database will be of great value to marine biologists studying cetaceans, as there is no existing dataset which spans the globe over many years (more than 15 years of data have been collected by the IMS). Current whale song datasets from other sources are limited to detections made on small, temporary listening devices. The IMS song catalogue will make it possible to study at least some aspects of the global migration patterns of whales, changes in their songs over time, and the habits of individuals. It is believed that about 10 blue whale 'cultures' exist with distinct vocal patterns; the IMS song catalogue will test that number. Results and a subset of the database (delayed in time to mitigate worries over whaling and harassment of the animals) will be released over the web. A traveling museum exhibit is planned which will not only educate the public about whale songs, but will also make the CTBTO and its achievements more widely known. As a testament to the public's enduring fascination with whales, initial funding for this project has been crowd-sourced through an internet campaign.

  2. Secure Distributed Databases Using Cryptography

    Directory of Open Access Journals (Sweden)

    Ion IVAN

    2006-01-01

    Full Text Available The computational encryption is used intensively by different databases management systems for ensuring privacy and integrity of information that are physically stored in files. Also, the information is sent over network and is replicated on different distributed systems. It is proved that a satisfying level of security is achieved if the rows and columns of tables are encrypted independently of table or computer that sustains the data. Also, it is very important that the SQL - Structured Query Language query requests and responses to be encrypted over the network connection between the client and databases server. All this techniques and methods must be implemented by the databases administrators, designer and developers in a consistent security policy.

  3. Database design using entity-relationship diagrams

    CERN Document Server

    Bagui, Sikha

    2011-01-01

    Data, Databases, and the Software Engineering ProcessDataBuilding a DatabaseWhat is the Software Engineering Process?Entity Relationship Diagrams and the Software Engineering Life Cycle          Phase 1: Get the Requirements for the Database          Phase 2: Specify the Database          Phase 3: Design the DatabaseData and Data ModelsFiles, Records, and Data ItemsMoving from 3 × 5 Cards to ComputersDatabase Models     The Hierarchical ModelThe Network ModelThe Relational ModelThe Relational Model and Functional DependenciesFundamental Relational DatabaseRelational Database and SetsFunctional

  4. NATIONAL TRANSPORTATION ATLAS DATABASE: RAILROADS 2011

    Data.gov (United States)

    Kansas Data Access and Support Center — The Rail Network is a comprehensive database of the nation's railway system at the 1:100,000 scale or better. The data set covers all 50 States plus the District of...

  5. Developmental and Reproductive Toxicology Database (DART)

    Data.gov (United States)

    U.S. Department of Health & Human Services — A bibliographic database on the National Library of Medicine's (NLM) Toxicology Data Network (TOXNET) with references to developmental and reproductive toxicology...

  6. Guide to the Durham-Rutherford high energy physics databases

    International Nuclear Information System (INIS)

    Gault, F.D.; Lotts, A.P.; Read, B.J.; Crawford, R.L.; Roberts, R.G.

    1979-12-01

    New databases and graphics facilities are added in this edition of the guide. It explains, with examples, how to retrieve tabulated experimental scattering data from databases on the Rutherford Laboratory computer network. (author)

  7. 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

  8. An Adaptive Database Intrusion Detection System

    Science.gov (United States)

    Barrios, Rita M.

    2011-01-01

    Intrusion detection is difficult to accomplish when attempting to employ current methodologies when considering the database and the authorized entity. It is a common understanding that current methodologies focus on the network architecture rather than the database, which is not an adequate solution when considering the insider threat. Recent…

  9. Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Ou, Yu-Yen

    2016-07-30

    Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respiration, they require a pathway to keep and transfer electrons (i.e., the electron transport chain). Due to oxidation-reduction reactions, the electron transport chain produces a transmembrane proton electrochemical gradient. In case protons flow back through this membrane, this mechanical energy is converted into chemical energy by ATP synthase. The convert process is involved in producing ATP which provides energy in a lot of cellular processes. In the electron transport chain process, flavin adenine dinucleotide (FAD) is one of the most vital molecules for carrying and transferring electrons. Therefore, predicting FAD binding sites in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. We used an independent data set to evaluate the performance of the proposed method, which had an accuracy of 69.84 %. We compared the performance of the proposed method in analyzing two newly discovered electron transport protein sequences with that of the general FAD binding predictor presented by Mishra and Raghava and determined that the accuracy of the proposed method improved by 9-45 % and its Matthew's correlation coefficient was 0.14-0.5. Furthermore, the proposed method enabled reducing the number of false positives significantly and can provide useful information for biologists. We developed a method that is based on PSSM profiles and SAAPs for identifying FAD binding sites in newly discovered electron transport protein sequences. This approach achieved a significant improvement after we added SAAPs to PSSM features to analyze FAD binding proteins in the electron transport chain. The proposed method can serve as an effective tool for predicting FAD binding sites in electron

  10. A Sandia telephone database system

    Energy Technology Data Exchange (ETDEWEB)

    Nelson, S.D.; Tolendino, L.F.

    1991-08-01

    Sandia National Laboratories, Albuquerque, may soon have more responsibility for the operation of its own telephone system. The processes that constitute providing telephone service can all be improved through the use of a central data information system. We studied these processes, determined the requirements for a database system, then designed the first stages of a system that meets our needs for work order handling, trouble reporting, and ISDN hardware assignments. The design was based on an extensive set of applications that have been used for five years to manage the Sandia secure data network. The system utilizes an Ingres database management system and is programmed using the Application-By-Forms tools.

  11. Technical Network

    CERN Multimedia

    2007-01-01

    In order to optimise the management of the Technical Network (TN), to facilitate understanding of the purpose of devices connected to the TN and to improve security incident handling, the Technical Network Administrators and the CNIC WG have asked IT/CS to verify the "description" and "tag" fields of devices connected to the TN. Therefore, persons responsible for systems connected to the TN will receive e-mails from IT/CS asking them to add the corresponding information in the network database at "network-cern-ch". Thank you very much for your cooperation. The Technical Network Administrators & the CNIC WG

  12. Mathematics for Databases

    NARCIS (Netherlands)

    ir. Sander van Laar

    2007-01-01

    A formal description of a database consists of the description of the relations (tables) of the database together with the constraints that must hold on the database. Furthermore the contents of a database can be retrieved using queries. These constraints and queries for databases can very well be

  13. Databases and their application

    NARCIS (Netherlands)

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

    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

  14. DOT Online Database

    Science.gov (United States)

    Page Home Table of Contents Contents Search Database Search Login Login Databases Advisory Circulars accessed by clicking below: Full-Text WebSearch Databases Database Records Date Advisory Circulars 2092 5 data collection and distribution policies. Document Database Website provided by MicroSearch

  15. Databases for INDUS-1 and INDUS-2

    International Nuclear Information System (INIS)

    Merh, Bhavna N.; Fatnani, Pravin

    2003-01-01

    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)

  16. From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

    Science.gov (United States)

    Kılıç, Sefa; Sagitova, Dinara M; Wolfish, Shoshannah; Bely, Benoit; Courtot, Mélanie; Ciufo, Stacy; Tatusova, Tatiana; O'Donovan, Claire; Chibucos, Marcus C; Martin, Maria J; Erill, Ivan

    2016-01-01

    Domain-specific databases are essential resources for the biomedical community, leveraging expert knowledge to curate published literature and provide access to referenced data and knowledge. The limited scope of these databases, however, poses important challenges on their infrastructure, visibility, funding and usefulness to the broader scientific community. CollecTF is a community-oriented database documenting experimentally validated transcription factor (TF)-binding sites in the Bacteria domain. In its quest to become a community resource for the annotation of transcriptional regulatory elements in bacterial genomes, CollecTF aims to move away from the conventional data-repository paradigm of domain-specific databases. Through the adoption of well-established ontologies, identifiers and collaborations, CollecTF has progressively become also a portal for the annotation and submission of information on transcriptional regulatory elements to major biological sequence resources (RefSeq, UniProtKB and the Gene Ontology Consortium). This fundamental change in database conception capitalizes on the domain-specific knowledge of contributing communities to provide high-quality annotations, while leveraging the availability of stable information hubs to promote long-term access and provide high-visibility to the data. As a submission portal, CollecTF generates TF-binding site information through direct annotation of RefSeq genome records, definition of TF-based regulatory networks in UniProtKB entries and submission of functional annotations to the Gene Ontology. As a database, CollecTF provides enhanced search and browsing, targeted data exports, binding motif analysis tools and integration with motif discovery and search platforms. This innovative approach will allow CollecTF to focus its limited resources on the generation of high-quality information and the provision of specialized access to the data.Database URL: http://www.collectf.org/. © The Author(s) 2016

  17. Dietary Supplement Ingredient Database

    Science.gov (United States)

    ... and US Department of Agriculture Dietary Supplement Ingredient Database Toggle navigation Menu Home About DSID Mission Current ... values can be saved to build a small database or add to an existing database for national, ...

  18. Energy Consumption Database

    Science.gov (United States)

    Consumption Database The California Energy Commission has created this on-line database for informal reporting ) classifications. The database also provides easy downloading of energy consumption data into Microsoft Excel (XLSX

  19. 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...

  20. 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...

  1. NoSQL databases

    OpenAIRE

    Mrozek, Jakub

    2012-01-01

    This thesis deals with database systems referred to as NoSQL databases. In the second chapter, I explain basic terms and the theory of database systems. A short explanation is dedicated to database systems based on the relational data model and the SQL standardized query language. Chapter Three explains the concept and history of the NoSQL databases, and also presents database models, major features and the use of NoSQL databases in comparison with traditional database systems. In the fourth ...

  2. Secure Distributed Databases Using Cryptography

    OpenAIRE

    Ion IVAN; Cristian TOMA

    2006-01-01

    The computational encryption is used intensively by different databases management systems for ensuring privacy and integrity of information that are physically stored in files. Also, the information is sent over network and is replicated on different distributed systems. It is proved that a satisfying level of security is achieved if the rows and columns of tables are encrypted independently of table or computer that sustains the data. Also, it is very important that the SQL - Structured Que...

  3. Cyanide binding to hexacoordinate cyanobacterial hemoglobins: hydrogen-bonding network and heme pocket rearrangement in ferric H117A Synechocystis hemoglobin.

    Science.gov (United States)

    Vu, B Christie; Nothnagel, Henry J; Vuletich, David A; Falzone, Christopher J; Lecomte, Juliette T J

    2004-10-05

    The truncated hemoglobin (Hb) from the cyanobacterium Synechocystis sp. PCC 6803 is a bis-histidyl hexacoordinate complex in the absence of exogenous ligands. This protein can form a covalent cross-link between His117 in the H-helix and the heme 2-vinyl group. Cross-linking, the physiological importance of which has not been established, is avoided with the His117Ala substitution. In the present work, H117A Hb was used to explore exogenous ligand binding to the heme group. NMR and thermal denaturation data showed that the replacement was of little consequence to the structural and thermodynamic properties of ferric Synechocystis Hb. It did, however, decelerate the association of cyanide ions with the heme iron. Full complexation required hours, instead of minutes, of incubation at optical and NMR concentrations. At neutral pH and in the presence of excess cyanide, binding occurred with a first-order dependence on cyanide concentration, eliminating distal histidine decoordination as the rate-limiting step. The cyanide complex of the H117A variant was characterized for the conformational changes occurring as the histidine on the distal side, His46 (E10), was displaced. Extensive rearrangement allowed Tyr22 (B10) to insert in the heme pocket and Gln43 (E7) and Gln47 (E11) to come in contact with it. H-bond formation to the bound cyanide was identified in solution with the use of (1)H(2)O/(2)H(2)O mixtures. Cyanide binding also resulted in a change in the ratio of heme orientational isomers, in a likely manifestation of heme environment reshaping. Similar observations were made with the related Synechococcus sp. PCC 7002 H117A Hb, except that cyanide binding was rapid in this protein. In both cases, the (15)N chemical shift of bound cyanide was reminiscent of that in peroxidases and the orientation of the proximal histidine was as in other truncated Hbs. The ensemble of the data provided insight into the structural cooperativity of the heme pocket scaffold and pointed

  4. Being First Matters: Topographical Representational Similarity Analysis of ERP Signals Reveals Separate Networks for Audiovisual Temporal Binding Depending on the Leading Sense.

    Science.gov (United States)

    Cecere, Roberto; Gross, Joachim; Willis, Ashleigh; Thut, Gregor

    2017-05-24

    In multisensory integration, processing in one sensory modality is enhanced by complementary information from other modalities. Intersensory timing is crucial in this process because only inputs reaching the brain within a restricted temporal window are perceptually bound. Previous research in the audiovisual field has investigated various features of the temporal binding window, revealing asymmetries in its size and plasticity depending on the leading input: auditory-visual (AV) or visual-auditory (VA). Here, we tested whether separate neuronal mechanisms underlie this AV-VA dichotomy in humans. We recorded high-density EEG while participants performed an audiovisual simultaneity judgment task including various AV-VA asynchronies and unisensory control conditions (visual-only, auditory-only) and tested whether AV and VA processing generate different patterns of brain activity. After isolating the multisensory components of AV-VA event-related potentials (ERPs) from the sum of their unisensory constituents, we ran a time-resolved topographical representational similarity analysis (tRSA) comparing the AV and VA ERP maps. Spatial cross-correlation matrices were built from real data to index the similarity between the AV and VA maps at each time point (500 ms window after stimulus) and then correlated with two alternative similarity model matrices: AV maps = VA maps versus AV maps ≠ VA maps The tRSA results favored the AV maps ≠ VA maps model across all time points, suggesting that audiovisual temporal binding (indexed by synchrony perception) engages different neural pathways depending on the leading sense. The existence of such dual route supports recent theoretical accounts proposing that multiple binding mechanisms are implemented in the brain to accommodate different information parsing strategies in auditory and visual sensory systems. SIGNIFICANCE STATEMENT Intersensory timing is a crucial aspect of multisensory integration, determining whether and how

  5. PreBIND and Textomy – mining the biomedical literature for protein-protein interactions using a support vector machine

    Directory of Open Access Journals (Sweden)

    Baskin Berivan

    2003-03-01

    Full Text Available Abstract Background The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND seeks to capture these data in a machine-readable format. We hypothesized that the formidable task-size of backfilling the database could be reduced by using Support Vector Machine technology to first locate interaction information in the literature. We present an information extraction system that was designed to locate protein-protein interaction data in the literature and present these data to curators and the public for review and entry into BIND. Results Cross-validation estimated the support vector machine's test-set precision, accuracy and recall for classifying abstracts describing interaction information was 92%, 90% and 92% respectively. We estimated that the system would be able to recall up to 60% of all non-high throughput interactions present in another yeast-protein interaction database. Finally, this system was applied to a real-world curation problem and its use was found to reduce the task duration by 70% thus saving 176 days. Conclusions Machine learning methods are useful as tools to direct interaction and pathway database back-filling; however, this potential can only be realized if these techniques are coupled with human review and entry into a factual database such as BIND. The PreBIND system described here is available to the public at http://bind.ca. Current capabilities allow searching for human, mouse and yeast protein-interaction information.

  6. Solute-vacancy binding in aluminum

    International Nuclear Information System (INIS)

    Wolverton, C.

    2007-01-01

    Previous efforts to understand solute-vacancy binding in aluminum alloys have been hampered by a scarcity of reliable, quantitative experimental measurements. Here, we report a large database of solute-vacancy binding energies determined from first-principles density functional calculations. The calculated binding energies agree well with accurate measurements where available, and provide an accurate predictor of solute-vacancy binding in other systems. We find: (i) some common solutes in commercial Al alloys (e.g., Cu and Mg) possess either very weak (Cu), or even repulsive (Mg), binding energies. Hence, we assert that some previously reported large binding energies for these solutes are erroneous. (ii) Large binding energies are found for Sn, Cd and In, confirming the proposed mechanism for the reduced natural aging in Al-Cu alloys containing microalloying additions of these solutes. (iii) In addition, we predict that similar reduction in natural aging should occur with additions of Si, Ge and Au. (iv) Even larger binding energies are found for other solutes (e.g., Pb, Bi, Sr, Ba), but these solutes possess essentially no solubility in Al. (v) We have explored the physical effects controlling solute-vacancy binding in Al. We find that there is a strong correlation between binding energy and solute size, with larger solute atoms possessing a stronger binding with vacancies. (vi) Most transition-metal 3d solutes do not bind strongly with vacancies, and some are even energetically strongly repelled from vacancies, particularly for the early 3d solutes, Ti and V

  7. In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

    Directory of Open Access Journals (Sweden)

    Kristopher J. L. Irizarry

    2016-01-01

    Full Text Available Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1 that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons.

  8. PrimateLit Database

    Science.gov (United States)

    Primate Info Net Related Databases NCRR PrimateLit: A bibliographic database for primatology Top of any problems with this service. We welcome your feedback. The PrimateLit database is no longer being Resources, National Institutes of Health. The database is a collaborative project of the Wisconsin Primate

  9. Technical Network

    CERN Multimedia

    2007-01-01

    In order to optimize the management of the Technical Network (TN), to ease the understanding and purpose of devices connected to the TN, and to improve security incident handling, the Technical Network Administrators and the CNIC WG have asked IT/CS to verify the "description" and "tag" fields of devices connected to the TN. Therefore, persons responsible for systems connected to the TN will receive email notifications from IT/CS asking them to add the corresponding information in the network database. Thank you very much for your cooperation. The Technical Network Administrators & the CNIC WG

  10. 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.

  11. KALIMER database development

    International Nuclear Information System (INIS)

    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

  12. Study on managing EPICS database using ORACLE

    International Nuclear Information System (INIS)

    Liu Shu; Wang Chunhong; Zhao Jijiu

    2007-01-01

    EPICS is used as a development toolkit of BEPCII control system. The core of EPICS is a distributed database residing in front-end machines. The distributed database is usually created by tools such as VDCT and text editor in the host, then loaded to front-end target IOCs through the network. In BEPCII control system there are about 20,000 signals, which are distributed in more than 20 IOCs. All the databases are developed by device control engineers using VDCT or text editor. There's no uniform tools providing transparent management. The paper firstly presents the current status on EPICS database management issues in many labs. Secondly, it studies EPICS database and the interface between ORACLE and EPICS database. finally, it introduces the software development and application is BEPCII control system. (authors)

  13. 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

  14. An Interoperable Cartographic Database

    OpenAIRE

    Slobodanka Ključanin; Zdravko Galić

    2007-01-01

    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 t...

  15. Software listing: CHEMTOX database

    International Nuclear Information System (INIS)

    Moskowitz, P.D.

    1993-01-01

    Initially launched in 1983, the CHEMTOX Database was among the first microcomputer databases containing hazardous chemical information. The database is used in many industries and government agencies in more than 17 countries. Updated quarterly, the CHEMTOX Database provides detailed environmental and safety information on 7500-plus hazardous substances covered by dozens of regulatory and advisory sources. This brief listing describes the method of accessing data and provides ordering information for those wishing to obtain the CHEMTOX Database

  16. LIBP-Pred: web server for lipid binding proteins using structural network parameters; PDB mining of human cancer biomarkers and drug targets in parasites and bacteria.

    Science.gov (United States)

    González-Díaz, Humberto; Munteanu, Cristian R; Postelnicu, Lucian; Prado-Prado, Francisco; Gestal, Marcos; Pazos, Alejandro

    2012-03-01

    Lipid-Binding Proteins (LIBPs) or Fatty Acid-Binding Proteins (FABPs) play an important role in many diseases such as different types of cancer, kidney injury, atherosclerosis, diabetes, intestinal ischemia and parasitic infections. Thus, the computational methods that can predict LIBPs based on 3D structure parameters became a goal of major importance for drug-target discovery, vaccine design and biomarker selection. In addition, the Protein Data Bank (PDB) contains 3000+ protein 3D structures with unknown function. This list, as well as new experimental outcomes in proteomics research, is a very interesting source to discover relevant proteins, including LIBPs. However, to the best of our knowledge, there are no general models to predict new LIBPs based on 3D structures. We developed new Quantitative Structure-Activity Relationship (QSAR) models based on 3D electrostatic parameters of 1801 different proteins, including 801 LIBPs. We calculated these electrostatic parameters with the MARCH-INSIDE software and they correspond to the entire protein or to specific protein regions named core, inner, middle, and surface. We used these parameters as inputs to develop a simple Linear Discriminant Analysis (LDA) classifier to discriminate 3D structure of LIBPs from other proteins. We implemented this predictor in the web server named LIBP-Pred, freely available at , along with other important web servers of the Bio-AIMS portal. The users can carry out an automatic retrieval of protein structures from PDB or upload their custom protein structural models from their disk created with LOMETS server. We demonstrated the PDB mining option performing a predictive study of 2000+ proteins with unknown function. Interesting results regarding the discovery of new Cancer Biomarkers in humans or drug targets in parasites have been discussed here in this sense.

  17. The network researchers' network

    DEFF Research Database (Denmark)

    Henneberg, Stephan C.; Jiang, Zhizhong; Naudé, Peter

    2009-01-01

    The Industrial Marketing and Purchasing (IMP) Group is a network of academic researchers working in the area of business-to-business marketing. The group meets every year to discuss and exchange ideas, with a conference having been held every year since 1984 (there was no meeting in 1987). In thi......The Industrial Marketing and Purchasing (IMP) Group is a network of academic researchers working in the area of business-to-business marketing. The group meets every year to discuss and exchange ideas, with a conference having been held every year since 1984 (there was no meeting in 1987......). In this paper, based upon the papers presented at the 22 conferences held to date, we undertake a Social Network Analysis in order to examine the degree of co-publishing that has taken place between this group of researchers. We identify the different components in this database, and examine the large main...

  18. Determination of fat, moisture, and protein in meat and meat products by using the FOSS FoodScan Near-Infrared Spectrophotometer with FOSS Artificial Neural Network Calibration Model and Associated Database: collaborative study.

    Science.gov (United States)

    Anderson, Shirley

    2007-01-01

    A collaborative study was conducted to evaluate the repeatability and reproducibility of the FOSS FoodScan near-infrared spectrophotometer with artificial neural network calibration model and database for the determination of fat, moisture, and protein in meat and meat products. Representative samples were homogenized by grinding according to AOAC Official Method 983.18. Approximately 180 g ground sample was placed in a 140 mm round sample dish, and the dish was placed in the FoodScan. The operator ID was entered, the meat product profile within the software was selected, and the scanning process was initiated by pressing the "start" button. Results were displayed for percent (g/100 g) fat, moisture, and protein. Ten blind duplicate samples were sent to 15 collaborators in the United States. The within-laboratory (repeatability) relative standard deviation (RSD(r)) ranged from 0.22 to 2.67% for fat, 0.23 to 0.92% for moisture, and 0.35 to 2.13% for protein. The between-laboratories (reproducibility) relative standard deviation (RSD(R)) ranged from 0.52 to 6.89% for fat, 0.39 to 1.55% for moisture, and 0.54 to 5.23% for protein. The method is recommended for Official First Action.

  19. Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis

    Science.gov (United States)

    Malhotra, Deepti; Portales-Casamar, Elodie; Singh, Anju; Srivastava, Siddhartha; Arenillas, David; Happel, Christine; Shyr, Casper; Wakabayashi, Nobunao; Kensler, Thomas W.; Wasserman, Wyeth W.; Biswal, Shyam

    2010-01-01

    The Nrf2 (nuclear factor E2 p45-related factor 2) transcription factor responds to diverse oxidative and electrophilic environmental stresses by circumventing repression by Keap1, translocating to the nucleus, and activating cytoprotective genes. Nrf2 responses provide protection against chemical carcinogenesis, chronic inflammation, neurodegeneration, emphysema, asthma and sepsis in murine models. Nrf2 regulates the expression of a plethora of genes that detoxify oxidants and electrophiles and repair or remove damaged macromolecules, such as through proteasomal processing. However, many direct targets of Nrf2 remain undefined. Here, mouse embryonic fibroblasts (MEF) with either constitutive nuclear accumulation (Keap1−/−) or depletion (Nrf2−/−) of Nrf2 were utilized to perform chromatin-immunoprecipitation with parallel sequencing (ChIP-Seq) and global transcription profiling. This unique Nrf2 ChIP-Seq dataset is highly enriched for Nrf2-binding motifs. Integrating ChIP-Seq and microarray analyses, we identified 645 basal and 654 inducible direct targets of Nrf2, with 244 genes at the intersection. Modulated pathways in stress response and cell proliferation distinguish the inducible and basal programs. Results were confirmed in an in vivo stress model of cigarette smoke-exposed mice. This study reveals global circuitry of the Nrf2 stress response emphasizing Nrf2 as a central node in cell survival response. PMID:20460467

  20. Database Description - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name PSCDB Alternative n...rial Science and Technology (AIST) Takayuki Amemiya E-mail: Database classification Structure Databases - Protein structure Database...554-D558. External Links: Original website information Database maintenance site Graduate School of Informat...available URL of Web services - Need for user registration Not available About This Database Database Descri...ption Download License Update History of This Database Site Policy | Contact Us Database Description - PSCDB | LSDB Archive ...

  1. Aspects of the design of distributed databases

    OpenAIRE

    Burlacu Irina-Andreea

    2011-01-01

    Distributed data - data, processed by a system, can be distributed among several computers, but it is accessible from any of them. A distributed database design problem is presented that involves the development of a global model, a fragmentation, and a data allocation. The student is given a conceptual entity-relationship model for the database and a description of the transactions and a generic network environment. A stepwise solution approach to this problem is shown, based on mean value a...

  2. Directory of IAEA databases

    International Nuclear Information System (INIS)

    1991-11-01

    The first edition of the Directory of IAEA Databases is intended to describe the computerized information sources available to IAEA staff members. It contains a listing of all databases produced at the IAEA, together with information on their availability

  3. Native Health Research Database

    Science.gov (United States)

    ... Indian Health Board) Welcome to the Native Health Database. Please enter your search terms. Basic Search Advanced ... To learn more about searching the Native Health Database, click here. Tutorial Video The NHD has made ...

  4. 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 imaging.

  5. E3 Staff Database

    Data.gov (United States)

    US Agency for International Development — E3 Staff database is maintained by E3 PDMS (Professional Development & Management Services) office. The database is Mysql. It is manually updated by E3 staff as...

  6. NIRS database of the original research database

    International Nuclear Information System (INIS)

    Morita, Kyoko

    1991-01-01

    Recently, library staffs arranged and compiled the original research papers that have been written by researchers for 33 years since National Institute of Radiological Sciences (NIRS) established. This papers describes how the internal database of original research papers has been created. This is a small sample of hand-made database. This has been cumulating by staffs who have any knowledge about computer machine or computer programming. (author)

  7. 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.

  8. Aviation Safety Issues Database

    Science.gov (United States)

    Morello, Samuel A.; Ricks, Wendell R.

    2009-01-01

    The aviation safety issues database was instrumental in the refinement and substantiation of the National Aviation Safety Strategic Plan (NASSP). The issues database is a comprehensive set of issues from an extremely broad base of aviation functions, personnel, and vehicle categories, both nationally and internationally. Several aviation safety stakeholders such as the Commercial Aviation Safety Team (CAST) have already used the database. This broader interest was the genesis to making the database publically accessible and writing this report.

  9. Automated Oracle database testing

    CERN Multimedia

    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.

  10. Inleiding database-systemen

    NARCIS (Netherlands)

    Pels, H.J.; Lans, van der R.F.; Pels, H.J.; Meersman, R.A.

    1993-01-01

    Dit artikel introduceert de voornaamste begrippen die een rol spelen rond databases en het geeft een overzicht van de doelstellingen, de functies en de componenten van database-systemen. Hoewel de functie van een database intuitief vrij duidelijk is, is het toch een in technologisch opzicht complex

  11. IAEA Illicit Trafficking Database (ITDB)

    International Nuclear Information System (INIS)

    2010-01-01

    The IAEA Illicit Trafficking Database (ITDB) was established in 1995 as a unique network of points of contact connecting 100 states and several international organizations. Information collected from official sources supplemented by open-source reports. The 1994 - GC 38, resolution intensifies the activities through which the Agency is currently supporting Member States in this field. Member states were notified of completed database in 1995 and invited to participate. The purpose of the I TDB is to facilitate exchange of authoritative information among States on incidents of illicit trafficking and other related unauthorized activities involving nuclear and other radioactive materials; to collect, maintain and analyse information on such incidents with a view to identifying common threats, trends, and patterns; use this information for internal planning and prioritisation and provide this information to member states and to provide a reliable source of basic information on such incidents to the media, when appropriate

  12. Database Description - RMOS | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name RMOS Alternative nam...arch Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Microarray Data and other Gene Expression Database...s Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The Ric...19&lang=en Whole data download - Referenced database Rice Expression Database (RED) Rice full-length cDNA Database... (KOME) Rice Genome Integrated Map Database (INE) Rice Mutant Panel Database (Tos17) Rice Genome Annotation Database

  13. PSCID List - PSCDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data ...t.zip File URL: ftp://ftp.biosciencedbc.jp/archive/pscdb/LATEST/pscdb_pscid_list.zip File size: 24.4 KB Simp...nd-binding sites About This Database Database Description Download License Update History of This Database Site Policy | Contact Us PSCID List - PSCDB | LSDB Archive ...

  14. Concurrency control in distributed database systems

    CERN Document Server

    Cellary, W; Gelenbe, E

    1989-01-01

    Distributed Database Systems (DDBS) may be defined as integrated database systems composed of autonomous local databases, geographically distributed and interconnected by a computer network.The purpose of this monograph is to present DDBS concurrency control algorithms and their related performance issues. The most recent results have been taken into consideration. A detailed analysis and selection of these results has been made so as to include those which will promote applications and progress in the field. The application of the methods and algorithms presented is not limited to DDBSs but a

  15. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    Energy Technology Data Exchange (ETDEWEB)

    Gangi Setty, Thanuja [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Cho, Christine [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Govindappa, Sowmya [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Apicella, Michael A. [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Ramaswamy, S., E-mail: ramas@instem.res.in [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India)

    2014-07-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.

  16. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    International Nuclear Information System (INIS)

    Gangi Setty, Thanuja; Cho, Christine; Govindappa, Sowmya; Apicella, Michael A.; Ramaswamy, S.

    2014-01-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states

  17. A KINETIC DATABASE FOR ASTROCHEMISTRY (KIDA)

    International Nuclear Information System (INIS)

    Wakelam, V.; Pavone, B.; Hébrard, E.; Hersant, F.; Herbst, E.; Loison, J.-C.; Chandrasekaran, V.; Bergeat, A.; Smith, I. W. M.; Adams, N. G.; Bacchus-Montabonel, M.-C.; Béroff, K.; Bierbaum, V. M.; Chabot, M.; Dalgarno, A.; Van Dishoeck, E. F.; Faure, A.; Geppert, W. D.; Gerlich, D.; Galli, D.

    2012-01-01

    We present a novel chemical database for gas-phase astrochemistry. Named the KInetic Database for Astrochemistry (KIDA), this database consists of gas-phase reactions with rate coefficients and uncertainties that will be vetted to the greatest extent possible. Submissions of measured and calculated rate coefficients are welcome, and will be studied by experts before inclusion into the database. Besides providing kinetic information for the interstellar medium, KIDA is planned to contain such data for planetary atmospheres and for circumstellar envelopes. Each year, a subset of the reactions in the database (kida.uva) will be provided as a network for the simulation of the chemistry of dense interstellar clouds with temperatures between 10 K and 300 K. We also provide a code, named Nahoon, to study the time-dependent gas-phase chemistry of zero-dimensional and one-dimensional interstellar sources.

  18. 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. 

  19. Keyword Search in Databases

    CERN Document Server

    Yu, Jeffrey Xu; Chang, Lijun

    2009-01-01

    It has become highly desirable to provide users with flexible ways to query/search information over databases as simple as keyword search like Google search. This book surveys the recent developments on keyword search over databases, and focuses on finding structural information among objects in a database using a set of keywords. Such structural information to be returned can be either trees or subgraphs representing how the objects, that contain the required keywords, are interconnected in a relational database or in an XML database. The structural keyword search is completely different from

  20. Nuclear power economic database

    International Nuclear Information System (INIS)

    Ding Xiaoming; Li Lin; Zhao Shiping

    1996-01-01

    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

  1. Interconnecting heterogeneous database management systems

    Science.gov (United States)

    Gligor, V. D.; Luckenbaugh, G. L.

    1984-01-01

    It is pointed out that there is still a great need for the development of improved communication between remote, heterogeneous database management systems (DBMS). Problems regarding the effective communication between distributed DBMSs are primarily related to significant differences between local data managers, local data models and representations, and local transaction managers. A system of interconnected DBMSs which exhibit such differences is called a network of distributed, heterogeneous DBMSs. In order to achieve effective interconnection of remote, heterogeneous DBMSs, the users must have uniform, integrated access to the different DBMs. The present investigation is mainly concerned with an analysis of the existing approaches to interconnecting heterogeneous DBMSs, taking into account four experimental DBMS projects.

  2. PRODORIC2: the bacterial gene regulation database in 2018

    Science.gov (United States)

    Dudek, Christian-Alexander; Hartlich, Juliane; Brötje, David; Jahn, Dieter

    2018-01-01

    Abstract Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PRODORIC2 is more intuitive and user-friendly. Besides significant technical improvements, the new update offers more than 1000 new transcription factor binding sites and 110 new position weight matrices for genome-wide pattern searches with the Virtual Footprint tool. Moreover, binding sites deduced from high-throughput experiments were included. Data for 6 new bacterial species including bacteria of the Rhodobacteraceae family were added. Finally, a comprehensive collection of sigma- and transcription factor data for the nosocomial pathogen Clostridium difficile is now part of the database. PRODORIC2 is publicly available at http://www.prodoric2.de. PMID:29136200

  3. Database Description - RPD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ase Description General information of database Database name RPD Alternative name Rice Proteome Database...titute of Crop Science, National Agriculture and Food Research Organization Setsuko Komatsu E-mail: Database... classification Proteomics Resources Plant databases - Rice Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database... description Rice Proteome Database contains information on protei...and entered in the Rice Proteome Database. The database is searchable by keyword,

  4. Database Description - JSNP | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name JSNP Alternative nam...n Science and Technology Agency Creator Affiliation: Contact address E-mail : Database...sapiens Taxonomy ID: 9606 Database description A database of about 197,000 polymorphisms in Japanese populat...1):605-610 External Links: Original website information Database maintenance site Institute of Medical Scien...er registration Not available About This Database Database Description Download License Update History of This Database

  5. Database Description - ASTRA | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name ASTRA Alternative n...tics Journal Search: Contact address Database classification Nucleotide Sequence Databases - Gene structure,...3702 Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description The database represents classified p...(10):1211-6. External Links: Original website information Database maintenance site National Institute of Ad... for user registration Not available About This Database Database Description Dow

  6. Database Description - RED | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ase Description General information of database Database name RED Alternative name Rice Expression Database...enome Research Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice Database classifi...cation Microarray, Gene Expression Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database descripti... Article title: Rice Expression Database: the gateway to rice functional genomics...nt Science (2002) Dec 7 (12):563-564 External Links: Original website information Database maintenance site

  7. Database Description - PLACE | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name PLACE Alternative name A Database...Kannondai, Tsukuba, Ibaraki 305-8602, Japan National Institute of Agrobiological Sciences E-mail : Databas...e classification Plant databases Organism Taxonomy Name: Tracheophyta Taxonomy ID: 58023 Database...99, Vol.27, No.1 :297-300 External Links: Original website information Database maintenance site National In...- Need for user registration Not available About This Database Database Descripti

  8. Data mining the EXFOR database

    International Nuclear Information System (INIS)

    Brown, David; Herman, Michal; Hirdt, John

    2014-01-01

    The EXFOR database contains the largest collection of experimental nuclear reaction data available as well as this data's bibliographic information and experimental details. We created an undirected graph from the EXFOR datasets with graph nodes representing single observables and graph links representing the connections of various types between these observables. This graph is an abstract representation of the connections in EXFOR, similar to graphs of social networks, authorship networks, etc. Analysing this abstract graph, we are able to address very specific questions such as: i) What observables are being used as reference measurements by the experimental community? ii) Are these observables given the attention needed by various standards organisations? iii) Are there classes of observables that are not connected to these reference measurements? In addressing these questions, we propose several (mostly cross-section) observables that should be evaluated and made into reaction reference standards. (authors)

  9. Database Description - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Arabidopsis Phenome Database Database Description General information of database Database n... BioResource Center Hiroshi Masuya Database classification Plant databases - Arabidopsis thaliana Organism T...axonomy Name: Arabidopsis thaliana Taxonomy ID: 3702 Database description The Arabidopsis thaliana phenome i...heir effective application. We developed the new Arabidopsis Phenome Database integrating two novel database...seful materials for their experimental research. The other, the “Database of Curated Plant Phenome” focusing

  10. The Yersinia enterocolitica type three secretion chaperone SycO is integrated into the Yop regulatory network and binds to the Yop secretion protein YscM1

    Directory of Open Access Journals (Sweden)

    Heesemann Jürgen

    2007-07-01

    Full Text Available Abstract Background Pathogenic yersiniae (Y. pestis, Y. pseudotuberculosis, Y. enterocolitica share a virulence plasmid encoding a type three secretion system (T3SS. This T3SS comprises more than 40 constituents. Among these are the transport substrates called Yops (Yersinia outer proteins, the specific Yop chaperones (Sycs, and the Ysc (Yop secretion proteins which form the transport machinery. The effectors YopO and YopP are encoded on an operon together with SycO, the chaperone of YopO. The characterization of SycO is the focus of this study. Results We have established the large-scale production of recombinant SycO in its outright form. We confirm that Y. enterocolitica SycO forms homodimers which is typical for Syc chaperones. SycO overproduction in Y. enterocolitica decreases secretion of Yops into the culture supernatant suggesting a regulatory role of SycO in type III secretion. We demonstrate that in vitro SycO interacts with YscM1, a negative regulator of Yop expression in Y. enterocolitica. However, the SycO overproduction phenotype was not mediated by YscM1, YscM2, YopO or YopP as revealed by analysis of isogenic deletion mutants. Conclusion We present evidence that SycO is integrated into the regulatory network of the Yersinia T3SS. Our picture of the Yersinia T3SS interactome is supplemented by identification of the SycO/YscM1 interaction. Further, our results suggest that at least one additional interaction partner of SycO has to be identified.

  11. HCVpro: Hepatitis C virus protein interaction database

    KAUST Repository

    Kwofie, Samuel K.

    2011-12-01

    It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs. The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/. © 2011 Elsevier B.V.

  12. The Immune Epitope Database 2.0

    DEFF Research Database (Denmark)

    Hoof, Ilka; Vita, R; Zarebski, L

    2010-01-01

    The Immune Epitope Database (IEDB, www.iedb.org) provides a catalog of experimentally characterized B and T cell epitopes, as well as data on Major Histocompatibility Complex (MHC) binding and MHC ligand elution experiments. The database represents the molecular structures recognized by adaptive...... immune receptors and the experimental contexts in which these molecules were determined to be immune epitopes. Epitopes recognized in humans, nonhuman primates, rodents, pigs, cats and all other tested species are included. Both positive and negative experimental results are captured. Over the course...

  13. Experience in running relational databases on clustered storage

    CERN Document Server

    Aparicio, Ruben Gaspar

    2015-01-01

    For past eight years, CERN IT Database group has based its backend storage on NAS (Network-Attached Storage) architecture, providing database access via NFS (Network File System) protocol. In last two and half years, our storage has evolved from a scale-up architecture to a scale-out one. This paper describes our setup and a set of functionalities providing key features to other services like Database on Demand [1] or CERN Oracle backup and recovery service. It also outlines possible trend of evolution that, storage for databases could follow.

  14. 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...

  15. 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.

  16. National Database of Geriatrics

    DEFF Research Database (Denmark)

    Kannegaard, Pia Nimann; Vinding, Kirsten L; Hare-Bruun, Helle

    2016-01-01

    AIM OF DATABASE: The aim of the National Database of Geriatrics is to monitor the quality of interdisciplinary diagnostics and treatment of patients admitted to a geriatric hospital unit. STUDY POPULATION: The database population consists of patients who were admitted to a geriatric hospital unit....... Geriatric patients cannot be defined by specific diagnoses. A geriatric patient is typically a frail multimorbid elderly patient with decreasing functional ability and social challenges. The database includes 14-15,000 admissions per year, and the database completeness has been stable at 90% during the past......, percentage of discharges with a rehabilitation plan, and the part of cases where an interdisciplinary conference has taken place. Data are recorded by doctors, nurses, and therapists in a database and linked to the Danish National Patient Register. DESCRIPTIVE DATA: Descriptive patient-related data include...

  17. Adaptive evolution of transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Berg Johannes

    2004-10-01

    Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

  18. Computational 2D Materials Database

    DEFF Research Database (Denmark)

    Rasmussen, Filip Anselm; Thygesen, Kristian Sommer

    2015-01-01

    We present a comprehensive first-principles study of the electronic structure of 51 semiconducting monolayer transition-metal dichalcogenides and -oxides in the 2H and 1T hexagonal phases. The quasiparticle (QP) band structures with spin-orbit coupling are calculated in the G(0)W(0) approximation...... and used as input to a 2D hydrogenic model to estimate exciton binding energies. Throughout the paper we focus on trends and correlations in the electronic structure rather than detailed analysis of specific materials. All the computed data is available in an open database......., and comparison is made with different density functional theory descriptions. Pitfalls related to the convergence of GW calculations for two-dimensional (2D) materials are discussed together with possible solutions. The monolayer band edge positions relative to vacuum are used to estimate the band alignment...

  19. Specialist Bibliographic Databases

    OpenAIRE

    Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A.; Trukhachev, Vladimir I.; Kostyukova, Elena I.; Gerasimov, Alexey N.; Kitas, George D.

    2016-01-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and d...

  20. 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.

  1. Foundations of database systems : an introductory tutorial

    NARCIS (Netherlands)

    Paredaens, J.; Paredaens, J.; Tenenbaum, L. A.

    1994-01-01

    A very short overview is given of the principles of databases. The entity relationship model is used to define the conceptual base. Furthermore file management, the hierarchical model, the network model, the relational model and the object oriented model are discussed During the second world war,

  2. Database setup insuring radiopharmaceuticals traceability

    International Nuclear Information System (INIS)

    Robert, N.; Salmon, F.; Clermont-Gallerande, H. de; Celerier, C.

    2002-01-01

    Having to organize radiopharmacy and to insure proper traceability of radiopharmaceutical medicines brings numerous problems, especially for the departments which are not assisted with global management network systems. Our work has been to find a solution enabling to use high street software to cover those needs. We have set up a PC database run by the Microsoft software ACCESS 97. Its use consists in: saving data related to generators, isotopes and kits reception and deletion, as well as the results of quality control; transferring data collected from the software that is connected to the activimeter (elutions and preparations registers, prescription book). By relating all the saved data, ACCESS enables to mix all information in order to proceed requests. At this stage, it is possible to edit all regular registers (prescription book, generator and radionuclides follow-up, blood derived medicines traceability) and to quickly retrieve patients who have received a particular radiopharmaceutical, or the radiopharmaceutical that has been given to a particular patient. This user-friendly database provides a considerable support to nuclear medicine department that don't possess any network management for their radiopharmaceutical activity. (author)

  3. Database Description - SAHG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name SAHG Alternative nam...h: Contact address Chie Motono Tel : +81-3-3599-8067 E-mail : Database classification Structure Databases - ...e databases - Protein properties Organism Taxonomy Name: Homo sapiens Taxonomy ID: 9606 Database description... Links: Original website information Database maintenance site The Molecular Profiling Research Center for D...stration Not available About This Database Database Description Download License Update History of This Database Site Policy | Contact Us Database Description - SAHG | LSDB Archive ...

  4. Intermodal Passenger Connectivity Database -

    Data.gov (United States)

    Department of Transportation — The Intermodal Passenger Connectivity Database (IPCD) is a nationwide data table of passenger transportation terminals, with data on the availability of connections...

  5. 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)...

  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. 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 block...

  8. 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

  9. 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.

  10. 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.

  11. Towards Sensor Database Systems

    DEFF Research Database (Denmark)

    Bonnet, Philippe; Gehrke, Johannes; Seshadri, Praveen

    2001-01-01

    . These systems lack flexibility because data is extracted in a predefined way; also, they do not scale to a large number of devices because large volumes of raw data are transferred regardless of the queries that are submitted. In our new concept of sensor database system, queries dictate which data is extracted...... from the sensors. In this paper, we define the concept of sensor databases mixing stored data represented as relations and sensor data represented as time series. Each long-running query formulated over a sensor database defines a persistent view, which is maintained during a given time interval. We...... also describe the design and implementation of the COUGAR sensor database system....

  12. 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....

  13. 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 block...

  14. Database Description - RMG | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ase Description General information of database Database name RMG Alternative name ...raki 305-8602, Japan National Institute of Agrobiological Sciences E-mail : Database... classification Nucleotide Sequence Databases Organism Taxonomy Name: Oryza sativa Japonica Group Taxonomy ID: 39947 Database...rnal: Mol Genet Genomics (2002) 268: 434–445 External Links: Original website information Database...available URL of Web services - Need for user registration Not available About This Database Database Descri

  15. Database Description - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name KOME Alternative nam... Sciences Plant Genome Research Unit Shoshi Kikuchi E-mail : Database classification Plant databases - Rice ...Organism Taxonomy Name: Oryza sativa Taxonomy ID: 4530 Database description Information about approximately ...Hayashizaki Y, Kikuchi S. Journal: PLoS One. 2007 Nov 28; 2(11):e1235. External Links: Original website information Database...OS) Rice mutant panel database (Tos17) A Database of Plant Cis-acting Regulatory

  16. Update History of This Database - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Arabidopsis Phenome Database Update History of This Database Date Update contents 2017/02/27 Arabidopsis Phenome Data...base English archive site is opened. - Arabidopsis Phenome Database (http://jphenom...e.info/?page_id=95) is opened. About This Database Database Description Download License Update History of This Database... Site Policy | Contact Us Update History of This Database - Arabidopsis Phenome Database | LSDB Archive ...

  17. Update History of This Database - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us SKIP Stemcell Database Update History of This Database Date Update contents 2017/03/13 SKIP Stemcell Database... English archive site is opened. 2013/03/29 SKIP Stemcell Database ( https://www.skip.med.k...eio.ac.jp/SKIPSearch/top?lang=en ) is opened. About This Database Database Description Download License Update History of This Databa...se Site Policy | Contact Us Update History of This Database - SKIP Stemcell Database | LSDB Archive ...

  18. Update History of This Database - Yeast Interacting Proteins Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Yeast Interacting Proteins Database Update History of This Database Date Update contents 201...0/03/29 Yeast Interacting Proteins Database English archive site is opened. 2000/12/4 Yeast Interacting Proteins Database...( http://itolab.cb.k.u-tokyo.ac.jp/Y2H/ ) is released. About This Database Database Description... Download License Update History of This Database Site Policy | Contact Us Update History of This Database... - Yeast Interacting Proteins Database | LSDB Archive ...

  19. Download - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Trypanosomes Database Download First of all, please read the license of this database. Data ...1.4 KB) Simple search and download Downlaod via FTP FTP server is sometimes jammed. If it is, access [here]. About This Database Data...base Description Download License Update History of This Database Site Policy | Contact Us Download - Trypanosomes Database | LSDB Archive ...

  20. 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.

  1. Directory of IAEA databases

    International Nuclear Information System (INIS)

    1992-12-01

    This second edition of the Directory of IAEA Databases has been prepared within the Division of Scientific and Technical Information (NESI). Its main objective is to describe the computerized information sources available to staff members. This directory contains all databases produced at the IAEA, including databases stored on the mainframe, LAN's and PC's. All IAEA Division Directors have been requested to register the existence of their databases with NESI. For the second edition database owners were requested to review the existing entries for their databases and answer four additional questions. The four additional questions concerned the type of database (e.g. Bibliographic, Text, Statistical etc.), the category of database (e.g. Administrative, Nuclear Data etc.), the available documentation and the type of media used for distribution. In the individual entries on the following pages the answers to the first two questions (type and category) is always listed, but the answers to the second two questions (documentation and media) is only listed when information has been made available

  2. HIV Structural Database

    Science.gov (United States)

    SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

  3. Balkan Vegetation Database

    NARCIS (Netherlands)

    Vassilev, Kiril; Pedashenko, Hristo; Alexandrova, Alexandra; Tashev, Alexandar; Ganeva, Anna; Gavrilova, Anna; Gradevska, Asya; Assenov, Assen; Vitkova, Antonina; Grigorov, Borislav; Gussev, Chavdar; Filipova, Eva; Aneva, Ina; Knollová, Ilona; Nikolov, Ivaylo; Georgiev, Georgi; Gogushev, Georgi; Tinchev, Georgi; Pachedjieva, Kalina; Koev, Koycho; Lyubenova, Mariyana; Dimitrov, Marius; Apostolova-Stoyanova, Nadezhda; Velev, Nikolay; Zhelev, Petar; Glogov, Plamen; Natcheva, Rayna; Tzonev, Rossen; Boch, Steffen; Hennekens, Stephan M.; Georgiev, Stoyan; Stoyanov, Stoyan; Karakiev, Todor; Kalníková, Veronika; Shivarov, Veselin; Russakova, Veska; Vulchev, Vladimir

    2016-01-01

    The Balkan Vegetation Database (BVD; GIVD ID: EU-00-019; http://www.givd.info/ID/EU-00- 019) is a regional database that consists of phytosociological relevés from different vegetation types from six countries on the Balkan Peninsula (Albania, Bosnia and Herzegovina, Bulgaria, Kosovo, Montenegro

  4. World Database of Happiness

    NARCIS (Netherlands)

    R. Veenhoven (Ruut)

    1995-01-01

    textabstractABSTRACT The World Database of Happiness is an ongoing register of research on subjective appreciation of life. Its purpose is to make the wealth of scattered findings accessible, and to create a basis for further meta-analytic studies. The database involves four sections:
    1.

  5. Dictionary as Database.

    Science.gov (United States)

    Painter, Derrick

    1996-01-01

    Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

  6. Fire test database

    International Nuclear Information System (INIS)

    Lee, J.A.

    1989-01-01

    This paper describes a project recently completed for EPRI by Impell. The purpose of the project was to develop a reference database of fire tests performed on non-typical fire rated assemblies. The database is designed for use by utility fire protection engineers to locate test reports for power plant fire rated assemblies. As utilities prepare to respond to Information Notice 88-04, the database will identify utilities, vendors or manufacturers who have specific fire test data. The database contains fire test report summaries for 729 tested configurations. For each summary, a contact is identified from whom a copy of the complete fire test report can be obtained. Five types of configurations are included: doors, dampers, seals, wraps and walls. The database is computerized. One version for IBM; one for Mac. Each database is accessed through user-friendly software which allows adding, deleting, browsing, etc. through the database. There are five major database files. One each for the five types of tested configurations. The contents of each provides significant information regarding the test method and the physical attributes of the tested configuration. 3 figs

  7. 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.

  8. Consumer Product Category Database

    Science.gov (United States)

    The Chemical and Product Categories database (CPCat) catalogs the use of over 40,000 chemicals and their presence in different consumer products. The chemical use information is compiled from multiple sources while product information is gathered from publicly available Material Safety Data Sheets (MSDS). EPA researchers are evaluating the possibility of expanding the database with additional product and use information.

  9. Database in Artificial Intelligence.

    Science.gov (United States)

    Wilkinson, Julia

    1986-01-01

    Describes a specialist bibliographic database of literature in the field of artificial intelligence created by the Turing Institute (Glasgow, Scotland) using the BRS/Search information retrieval software. The subscription method for end-users--i.e., annual fee entitles user to unlimited access to database, document provision, and printed awareness…

  10. NoSQL database scaling

    OpenAIRE

    Žardin, Norbert

    2017-01-01

    NoSQL database scaling is a decision, where system resources or financial expenses are traded for database performance or other benefits. By scaling a database, database performance and resource usage might increase or decrease, such changes might have a negative impact on an application that uses the database. In this work it is analyzed how database scaling affect database resource usage and performance. As a results, calculations are acquired, using which database scaling types and differe...

  11. IAEA nuclear databases for applications

    International Nuclear Information System (INIS)

    Schwerer, Otto

    2003-01-01

    The Nuclear Data Section (NDS) of the International Atomic Energy Agency (IAEA) provides nuclear data services to scientists on a worldwide scale with particular emphasis on developing countries. More than 100 data libraries are made available cost-free by Internet, CD-ROM and other media. These databases are used for practically all areas of nuclear applications as well as basic research. An overview is given of the most important nuclear reaction and nuclear structure databases, such as EXFOR, CINDA, ENDF, NSR, ENSDF, NUDAT, and of selected special purpose libraries such as FENDL, RIPL, RNAL, the IAEA Photonuclear Data Library, and the IAEA charged-particle cross section database for medical radioisotope production. The NDS also coordinates two international nuclear data centre networks and is involved in data development activities (to create new or improve existing data libraries when the available data are inadequate) and in technology transfer to developing countries, e.g. through the installation and support of the mirror web site of the IAEA Nuclear Data Services at IPEN (operational since March 2000) and by organizing nuclear-data related workshops. By encouraging their participation in IAEA Co-ordinated Research Projects and also by compiling their experimental results in databases such as EXFOR, the NDS helps to make developing countries' contributions to nuclear science visible and conveniently available. The web address of the IAEA Nuclear Data Services is http://www.nds.iaea.org and the NDS mirror service at IPEN (Brasil) can be accessed at http://www.nds.ipen.br/ (author)

  12. 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...

  13. Mycobacteriophage genome database.

    Science.gov (United States)

    Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

    2011-01-01

    Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

  14. 數據資料庫 Numeric Databases

    Directory of Open Access Journals (Sweden)

    Mei-ling Wang Chen

    1989-03-01

    Full Text Available 無In 1979, the International Communication Bureau of R.O.C. connected some U.S. information service centers through the international telecommunication network. Since then, there are Dialog, ORBIT & BRS introduced into this country. However, the users are interested in the bibliographic databases and seldomly know the non-bibliographic databases or the numeric databases. This article mainly describes the numeric database about its definition & characteristics, comparison with bibliographic databases, its producers. Service systems & users, data element, a brief introduction by the subject, its problem and future, Iibrary role and the present use status in the R.O.C.

  15. Analysis of commercial and public bioactivity databases.

    Science.gov (United States)

    Tiikkainen, Pekka; Franke, Lutz

    2012-02-27

    Activity data for small molecules are invaluable in chemoinformatics. Various bioactivity databases exist containing detailed information of target proteins and quantitative binding data for small molecules extracted from journals and patents. In the current work, we have merged several public and commercial bioactivity databases into one bioactivity metabase. The molecular presentation, target information, and activity data of the vendor databases were standardized. The main motivation of the work was to create a single relational database which allows fast and simple data retrieval by in-house scientists. Second, we wanted to know the amount of overlap between databases by commercial and public vendors to see whether the former contain data complementing the latter. Third, we quantified the degree of inconsistency between data sources by comparing data points derived from the same scientific article cited by more than one vendor. We found that each data source contains unique data which is due to different scientific articles cited by the vendors. When comparing data derived from the same article we found that inconsistencies between the vendors are common. In conclusion, using databases of different vendors is still useful since the data overlap is not complete. It should be noted that this can be partially explained by the inconsistencies and errors in the source data.

  16. Benchmarking database performance for genomic data.

    Science.gov (United States)

    Khushi, Matloob

    2015-06-01

    Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene annotations are common research needs. The data can be saved in a database system for easy management, however, there is no comprehensive database built-in algorithm at present to identify overlapping regions. Therefore I have developed a novel region-mapping (RegMap) SQL-based algorithm to perform genomic operations and have benchmarked the performance of different databases. Benchmarking identified that PostgreSQL extracts overlapping regions much faster than MySQL. Insertion and data uploads in PostgreSQL were also better, although general searching capability of both databases was almost equivalent. In addition, using the algorithm pair-wise, overlaps of >1000 datasets of transcription factor binding sites and histone marks, collected from previous publications, were reported and it was found that HNF4G significantly co-locates with cohesin subunit STAG1 (SA1).Inc. © 2015 Wiley Periodicals, Inc.

  17. Database Description - SKIP Stemcell Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us SKIP Stemcell Database Database Description General information of database Database name SKIP Stemcell Database...rsity Journal Search: Contact address http://www.skip.med.keio.ac.jp/en/contact/ Database classification Human Genes and Diseases Dat...abase classification Stemcell Article Organism Taxonomy Name: Homo sapiens Taxonomy ID: 9606 Database...ks: Original website information Database maintenance site Center for Medical Genetics, School of medicine, ...lable Web services Not available URL of Web services - Need for user registration Not available About This Database Database

  18. Hazard Analysis Database Report

    Energy Technology Data Exchange (ETDEWEB)

    GAULT, G.W.

    1999-10-13

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

  19. Database for propagation models

    Science.gov (United States)

    Kantak, Anil V.

    1991-07-01

    A propagation researcher or a systems engineer who intends to use the results of a propagation experiment is generally faced with various database tasks such as the selection of the computer software, the hardware, and the writing of the programs to pass the data through the models of interest. This task is repeated every time a new experiment is conducted or the same experiment is carried out at a different location generating different data. Thus the users of this data have to spend a considerable portion of their time learning how to implement the computer hardware and the software towards the desired end. This situation may be facilitated considerably if an easily accessible propagation database is created that has all the accepted (standardized) propagation phenomena models approved by the propagation research community. Also, the handling of data will become easier for the user. Such a database construction can only stimulate the growth of the propagation research it if is available to all the researchers, so that the results of the experiment conducted by one researcher can be examined independently by another, without different hardware and software being used. The database may be made flexible so that the researchers need not be confined only to the contents of the database. Another way in which the database may help the researchers is by the fact that they will not have to document the software and hardware tools used in their research since the propagation research community will know the database already. The following sections show a possible database construction, as well as properties of the database for the propagation research.

  20. 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.

  1. 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....

  2. JICST Factual Database(2)

    Science.gov (United States)

    Araki, Keisuke

    The computer programme, which builds atom-bond connection tables from nomenclatures, is developed. Chemical substances with their nomenclature and varieties of trivial names or experimental code numbers are inputted. The chemical structures of the database are stereospecifically stored and are able to be searched and displayed according to stereochemistry. Source data are from laws and regulations of Japan, RTECS of US and so on. The database plays a central role within the integrated fact database service of JICST and makes interrelational retrieval possible.

  3. Report on Approaches to Database Translation. Final Report.

    Science.gov (United States)

    Gallagher, Leonard; Salazar, Sandra

    This report describes approaches to database translation (i.e., transferring data and data definitions from a source, either a database management system (DBMS) or a batch file, to a target DBMS), and recommends a method for representing the data structures of newly-proposed network and relational data models in a form suitable for database…

  4. ISSUES IN MOBILE DISTRIBUTED REAL TIME DATABASES: PERFORMANCE AND REVIEW

    OpenAIRE

    VISHNU SWAROOP,; Gyanendra Kumar Gupta,; UDAI SHANKER

    2011-01-01

    Increase in handy and small electronic devices in computing fields; it makes the computing more popularand useful in business. Tremendous advances in wireless networks and portable computing devices have led to development of mobile computing. Support of real time database system depending upon thetiming constraints, due to availability of data distributed database, and ubiquitous computing pull the mobile database concept, which emerges them in a new form of technology as mobile distributed ...

  5. Combination of a geolocation database access with infrastructure sensing in TV bands

    OpenAIRE

    Dionísio, Rogério; Ribeiro, Jorge; Marques, Paulo; Rodriguez, Jonathan

    2014-01-01

    This paper describes the implementation and the technical specifications of a geolocation database assisted by a spectrum-monitoring outdoor network. The geolocation database is populated according to Electronic Communications Committee (ECC) report 186 methodology. The application programming interface (API) between the sensor network and the geolocation database implements an effective and secure connection to successfully gather sensing data and sends it to the geolocation database for ...

  6. Livestock Anaerobic Digester Database

    Science.gov (United States)

    The Anaerobic Digester Database provides basic information about anaerobic digesters on livestock farms in the United States, organized in Excel spreadsheets. It includes projects that are under construction, operating, or shut down.

  7. Toxicity Reference Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Toxicity Reference Database (ToxRefDB) contains approximately 30 years and $2 billion worth of animal studies. ToxRefDB allows scientists and the interested...

  8. Dissolution Methods Database

    Data.gov (United States)

    U.S. Department of Health & Human Services — For a drug product that does not have a dissolution test method in the United States Pharmacopeia (USP), the FDA Dissolution Methods Database provides information on...

  9. OTI Activity Database

    Data.gov (United States)

    US Agency for International Development — OTI's worldwide activity database is a simple and effective information system that serves as a program management, tracking, and reporting tool. In each country,...

  10. ARTI Refrigerant Database

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-05-27

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

  11. Marine Jurisdictions Database

    National Research Council Canada - National Science Library

    Goldsmith, Roger

    1998-01-01

    The purpose of this project was to take the data gathered for the Maritime Claims chart and create a Maritime Jurisdictions digital database suitable for use with oceanographic mission planning objectives...

  12. Medicaid CHIP ESPC Database

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Environmental Scanning and Program Characteristic (ESPC) Database is in a Microsoft (MS) Access format and contains Medicaid and CHIP data, for the 50 states and...

  13. Records Management Database

    Data.gov (United States)

    US Agency for International Development — The Records Management Database is tool created in Microsoft Access specifically for USAID use. It contains metadata in order to access and retrieve the information...

  14. Reach Address Database (RAD)

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Reach Address Database (RAD) stores the reach address of each Water Program feature that has been linked to the underlying surface water features (streams,...

  15. Household Products Database: Pesticides

    Science.gov (United States)

    ... of Products Manufacturers Ingredients About the Database FAQ Product ... control bulbs carpenter ants caterpillars crabgrass control deer dogs dogs/cats fertilizer w/insecticide fertilizer w/weed ...

  16. Mouse Phenome Database (MPD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Mouse Phenome Database (MPD) has characterizations of hundreds of strains of laboratory mice to facilitate translational discoveries and to assist in selection...

  17. Consumer Product Category Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Chemical and Product Categories database (CPCat) catalogs the use of over 40,000 chemicals and their presence in different consumer products. The chemical use...

  18. Drycleaner Database - Region 7

    Data.gov (United States)

    U.S. Environmental Protection Agency — THIS DATA ASSET NO LONGER ACTIVE: This is metadata documentation for the Region 7 Drycleaner Database (R7DryClnDB) which tracks all Region7 drycleaners who notify...

  19. National Assessment Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Assessment Database stores and tracks state water quality assessment decisions, Total Maximum Daily Loads (TMDLs) and other watershed plans designed to...

  20. IVR RSA Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This database contains trip-level reports submitted by vessels participating in Research Set-Aside projects with IVR reporting requirements.

  1. Rat Genome Database (RGD)

    Data.gov (United States)

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

  2. The CAPEC Database

    DEFF Research Database (Denmark)

    Nielsen, Thomas Lund; Abildskov, Jens; Harper, Peter Mathias

    2001-01-01

    in the compound. This classification makes the CAPEC database a very useful tool, for example, in the development of new property models, since properties of chemically similar compounds are easily obtained. A program with efficient search and retrieval functions of properties has been developed.......The Computer-Aided Process Engineering Center (CAPEC) database of measured data was established with the aim to promote greater data exchange in the chemical engineering community. The target properties are pure component properties, mixture properties, and special drug solubility data....... The database divides pure component properties into primary, secondary, and functional properties. Mixture properties are categorized in terms of the number of components in the mixture and the number of phases present. The compounds in the database have been classified on the basis of the functional groups...

  3. Danish Urogynaecological Database

    DEFF Research Database (Denmark)

    Hansen, Ulla Darling; Gradel, Kim Oren; Larsen, Michael Due

    2016-01-01

    , complications if relevant, implants used if relevant, 3-6-month postoperative recording of symptoms, if any. A set of clinical quality indicators is being maintained by the steering committee for the database and is published in an annual report which also contains extensive descriptive statistics. The database......The Danish Urogynaecological Database is established in order to ensure high quality of treatment for patients undergoing urogynecological surgery. The database contains details of all women in Denmark undergoing incontinence surgery or pelvic organ prolapse surgery amounting to ~5,200 procedures...... has a completeness of over 90% of all urogynecological surgeries performed in Denmark. Some of the main variables have been validated using medical records as gold standard. The positive predictive value was above 90%. The data are used as a quality monitoring tool by the hospitals and in a number...

  4. The Danish Urogynaecological Database

    DEFF Research Database (Denmark)

    Guldberg, Rikke; Brostrøm, Søren; Hansen, Jesper Kjær

    2013-01-01

    in the DugaBase from 1 January 2009 to 31 October 2010, using medical records as a reference. RESULTS: A total of 16,509 urogynaecological procedures were registered in the DugaBase by 31 December 2010. The database completeness has increased by calendar time, from 38.2 % in 2007 to 93.2 % in 2010 for public......INTRODUCTION AND HYPOTHESIS: The Danish Urogynaecological Database (DugaBase) is a nationwide clinical database established in 2006 to monitor, ensure and improve the quality of urogynaecological surgery. We aimed to describe its establishment and completeness and to validate selected variables....... This is the first study based on data from the DugaBase. METHODS: The database completeness was calculated as a comparison between urogynaecological procedures reported to the Danish National Patient Registry and to the DugaBase. Validity was assessed for selected variables from a random sample of 200 women...

  5. Danish Pancreatic Cancer Database

    DEFF Research Database (Denmark)

    Fristrup, Claus; Detlefsen, Sönke; Palnæs Hansen, Carsten

    2016-01-01

    : Death is monitored using data from the Danish Civil Registry. This registry monitors the survival status of the Danish population, and the registration is virtually complete. All data in the database are audited by all participating institutions, with respect to baseline characteristics, key indicators......AIM OF DATABASE: The Danish Pancreatic Cancer Database aims to prospectively register the epidemiology, diagnostic workup, diagnosis, treatment, and outcome of patients with pancreatic cancer in Denmark at an institutional and national level. STUDY POPULATION: Since May 1, 2011, all patients...... with microscopically verified ductal adenocarcinoma of the pancreas have been registered in the database. As of June 30, 2014, the total number of patients registered was 2,217. All data are cross-referenced with the Danish Pathology Registry and the Danish Patient Registry to ensure the completeness of registrations...

  6. Food Habits Database (FHDBS)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NEFSC Food Habits Database has two major sources of data. The first, and most extensive, is the standard NEFSC Bottom Trawl Surveys Program. During these...

  7. Functionally Graded Materials Database

    Science.gov (United States)

    Kisara, Katsuto; Konno, Tomomi; Niino, Masayuki

    2008-02-01

    Functionally Graded Materials Database (hereinafter referred to as FGMs Database) was open to the society via Internet in October 2002, and since then it has been managed by the Japan Aerospace Exploration Agency (JAXA). As of October 2006, the database includes 1,703 research information entries with 2,429 researchers data, 509 institution data and so on. Reading materials such as "Applicability of FGMs Technology to Space Plane" and "FGMs Application to Space Solar Power System (SSPS)" were prepared in FY 2004 and 2005, respectively. The English version of "FGMs Application to Space Solar Power System (SSPS)" is now under preparation. This present paper explains the FGMs Database, describing the research information data, the sitemap and how to use it. From the access analysis, user access results and users' interests are discussed.

  8. Tethys Acoustic Metadata Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Tethys database houses the metadata associated with the acoustic data collection efforts by the Passive Acoustic Group. These metadata include dates, locations...

  9. NLCD 2011 database

    Data.gov (United States)

    U.S. Environmental Protection Agency — National Land Cover Database 2011 (NLCD 2011) is the most recent national land cover product created by the Multi-Resolution Land Characteristics (MRLC) Consortium....

  10. Medicare Coverage Database

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Medicare Coverage Database (MCD) contains all National Coverage Determinations (NCDs) and Local Coverage Determinations (LCDs), local articles, and proposed NCD...

  11. Household Products Database

    Data.gov (United States)

    U.S. Department of Health & Human Services — This database links over 4,000 consumer brands to health effects from Material Safety Data Sheets (MSDS) provided by the manufacturers and allows scientists and...

  12. Global Volcano Locations Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — NGDC maintains a database of over 1,500 volcano locations obtained from the Smithsonian Institution Global Volcanism Program, Volcanoes of the World publication. The...

  13. 1988 Spitak Earthquake Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The 1988 Spitak Earthquake database is an extensive collection of geophysical and geological data, maps, charts, images and descriptive text pertaining to the...

  14. Uranium Location Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — A GIS compiled locational database in Microsoft Access of ~15,000 mines with uranium occurrence or production, primarily in the western United States. The metadata...

  15. INIST: databases reorientation

    International Nuclear Information System (INIS)

    Bidet, J.C.

    1995-01-01

    INIST is a CNRS (Centre National de la Recherche Scientifique) laboratory devoted to the treatment of scientific and technical informations and to the management of these informations compiled in a database. Reorientation of the database content has been proposed in 1994 to increase the transfer of research towards enterprises and services, to develop more automatized accesses to the informations, and to create a quality assurance plan. The catalog of publications comprises 5800 periodical titles (1300 for fundamental research and 4500 for applied research). A science and technology multi-thematic database will be created in 1995 for the retrieval of applied and technical informations. ''Grey literature'' (reports, thesis, proceedings..) and human and social sciences data will be added to the base by the use of informations selected in the existing GRISELI and Francis databases. Strong modifications are also planned in the thematic cover of Earth sciences and will considerably reduce the geological information content. (J.S.). 1 tab

  16. Fine Arts Database (FAD)

    Data.gov (United States)

    General Services Administration — The Fine Arts Database records information on federally owned art in the control of the GSA; this includes the location, current condition and information on artists.

  17. Kansas Cartographic Database (KCD)

    Data.gov (United States)

    Kansas Data Access and Support Center — The Kansas Cartographic Database (KCD) is an exact digital representation of selected features from the USGS 7.5 minute topographic map series. Features that are...

  18. Developments in diffraction databases

    International Nuclear Information System (INIS)

    Jenkins, R.

    1999-01-01

    Full text: There are a number of databases available to the diffraction community. Two of the more important of these are the Powder Diffraction File (PDF) maintained by the International Centre for Diffraction Data (ICDD), and the Inorganic Crystal Structure Database (ICSD) maintained by Fachsinformationzentrum (FIZ, Karlsruhe). In application, the PDF has been used as an indispensable tool in phase identification and identification of unknowns. The ICSD database has extensive and explicit reference to the structures of compounds: atomic coordinates, space group and even thermal vibration parameters. A similar database, but for organic compounds, is maintained by the Cambridge Crystallographic Data Centre. These databases are often used as independent sources of information. However, little thought has been given on how to exploit the combined properties of structural database tools. A recently completed agreement between ICDD and FIZ, plus ICDD and Cambridge, provides a first step in complementary use of the PDF and the ICSD databases. The focus of this paper (as indicated below) is to examine ways of exploiting the combined properties of both databases. In 1996, there were approximately 76,000 entries in the PDF and approximately 43,000 entries in the ICSD database. The ICSD database has now been used to calculate entries in the PDF. Thus, to derive d-spacing and peak intensity data requires the synthesis of full diffraction patterns, i.e., we use the structural data in the ICSD database and then add instrumental resolution information. The combined data from PDF and ICSD can be effectively used in many ways. For example, we can calculate PDF data for an ideally random crystal distribution and also in the absence of preferred orientation. Again, we can use systematic studies of intermediate members in solid solutions series to help produce reliable quantitative phase analyses. In some cases, we can study how solid solution properties vary with composition and

  19. Database Replication Prototype

    OpenAIRE

    Vandewall, R.

    2000-01-01

    This report describes the design of a Replication Framework that facilitates the implementation and com-parison of database replication techniques. Furthermore, it discusses the implementation of a Database Replication Prototype and compares the performance measurements of two replication techniques based on the Atomic Broadcast communication primitive: pessimistic active replication and optimistic active replication. The main contributions of this report can be split into four parts....

  20. Database on Wind Characteristics

    DEFF Research Database (Denmark)

    Højstrup, J.; Ejsing Jørgensen, Hans; Lundtang Petersen, Erik

    1999-01-01

    his report describes the work and results of the project: Database on Wind Characteristics which was sponsered partly by the European Commision within the framework of JOULE III program under contract JOR3-CT95-0061......his report describes the work and results of the project: Database on Wind Characteristics which was sponsered partly by the European Commision within the framework of JOULE III program under contract JOR3-CT95-0061...

  1. Database computing in HEP

    International Nuclear Information System (INIS)

    Day, C.T.; Loken, S.; MacFarlane, J.F.; May, E.; Lifka, D.; Lusk, E.; Price, L.E.; Baden, A.

    1992-01-01

    The major SSC experiments are expected to produce up to 1 Petabyte of data per year each. Once the primary reconstruction is completed by farms of inexpensive processors. I/O becomes a major factor in further analysis of the data. We believe that the application of database techniques can significantly reduce the I/O performed in these analyses. We present examples of such I/O reductions in prototype based on relational and object-oriented databases of CDF data samples

  2. Update History of This Database - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Trypanosomes Database Update History of This Database Date Update contents 2014/05/07 The co...ntact information is corrected. The features and manner of utilization of the database are corrected. 2014/02/04 Trypanosomes Databas...e English archive site is opened. 2011/04/04 Trypanosomes Database ( http://www.tan...paku.org/tdb/ ) is opened. About This Database Database Description Download Lice...nse Update History of This Database Site Policy | Contact Us Update History of This Database - Trypanosomes Database | LSDB Archive ...

  3. DATABASES DEVELOPED IN INDIA FOR BIOLOGICAL SCIENCES

    Directory of Open Access Journals (Sweden)

    Gitanjali Yadav

    2017-09-01

    Full Text Available The complexity of biological systems requires use of a variety of experimental methods with ever increasing sophistication to probe various cellular processes at molecular and atomic resolution. The availability of technologies for determining nucleic acid sequences of genes and atomic resolution structures of biomolecules prompted development of major biological databases like GenBank and PDB almost four decades ago. India was one of the few countries to realize early, the utility of such databases for progress in modern biology/biotechnology. Department of Biotechnology (DBT, India established Biotechnology Information System (BTIS network in late eighties. Starting with the genome sequencing revolution at the turn of the century, application of high-throughput sequencing technologies in biology and medicine for analysis of genomes, transcriptomes, epigenomes and microbiomes have generated massive volumes of sequence data. BTIS network has not only provided state of the art computational infrastructure to research institutes and universities for utilizing various biological databases developed abroad in their research, it has also actively promoted research and development (R&D projects in Bioinformatics to develop a variety of biological databases in diverse areas. It is encouraging to note that, a large number of biological databases or data driven software tools developed in India, have been published in leading peer reviewed international journals like Nucleic Acids Research, Bioinformatics, Database, BMC, PLoS and NPG series publication. Some of these databases are not only unique, they are also highly accessed as reflected in number of citations. Apart from databases developed by individual research groups, BTIS has initiated consortium projects to develop major India centric databases on Mycobacterium tuberculosis, Rice and Mango, which can potentially have practical applications in health and agriculture. Many of these biological

  4. Specialist Bibliographic Databases.

    Science.gov (United States)

    Gasparyan, Armen Yuri; Yessirkepov, Marlen; Voronov, Alexander A; Trukhachev, Vladimir I; Kostyukova, Elena I; Gerasimov, Alexey N; Kitas, George D

    2016-05-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls.

  5. Specialist Bibliographic Databases

    Science.gov (United States)

    2016-01-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

  6. Recent improvements to Binding MOAD: a resource for protein–ligand binding affinities and structures

    Science.gov (United States)

    Ahmed, Aqeel; Smith, Richard D.; Clark, Jordan J.; Dunbar, James B.; Carlson, Heather A.

    2015-01-01

    For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein–ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23 269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. PMID:25378330

  7. Recent improvements to Binding MOAD: a resource for protein-ligand binding affinities and structures.

    Science.gov (United States)

    Ahmed, Aqeel; Smith, Richard D; Clark, Jordan J; Dunbar, James B; Carlson, Heather A

    2015-01-01

    For over 10 years, Binding MOAD (Mother of All Databases; http://www.BindingMOAD.org) has been one of the largest resources for high-quality protein-ligand complexes and associated binding affinity data. Binding MOAD has grown at the rate of 1994 complexes per year, on average. Currently, it contains 23,269 complexes and 8156 binding affinities. Our annual updates curate the data using a semi-automated literature search of the references cited within the PDB file, and we have recently upgraded our website and added new features and functionalities to better serve Binding MOAD users. In order to eliminate the legacy application server of the old platform and to accommodate new changes, the website has been completely rewritten in the LAMP (Linux, Apache, MySQL and PHP) environment. The improved user interface incorporates current third-party plugins for better visualization of protein and ligand molecules, and it provides features like sorting, filtering and filtered downloads. In addition to the field-based searching, Binding MOAD now can be searched by structural queries based on the ligand. In order to remove redundancy, Binding MOAD records are clustered in different families based on 90% sequence identity. The new Binding MOAD, with the upgraded platform, features and functionalities, is now equipped to better serve its users. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. A Database for Decision-Making in Training and Distributed Learning Technology

    National Research Council Canada - National Science Library

    Stouffer, Virginia

    1998-01-01

    .... A framework for incorporating data about distributed learning courseware into the existing training database was devised and a plan for a national electronic courseware redistribution network was recommended...

  9. Database Description - TMFunction | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available sidue (or mutant) in a protein. The experimental data are collected from the literature both by searching th...the sequence database, UniProt, structural database, PDB, and literature database

  10. Total iron binding capacity

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003489.htm Total iron binding capacity To use the sharing features on this page, please enable JavaScript. Total iron binding capacity (TIBC) is a blood test to ...

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

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name RPSD Alternative nam...e Rice Protein Structure Database DOI 10.18908/lsdba.nbdc00749-000 Creator Creator Name: Toshimasa Yamazaki ... Ibaraki 305-8602, Japan National Institute of Agrobiological Sciences Toshimasa Yamazaki E-mail : Databas...e classification Structure Databases - Protein structure Organism Taxonomy Name: Or...or name(s): Journal: External Links: Original website information Database maintenance site National Institu

  12. PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database.

    Science.gov (United States)

    Huang, Weiliang; Brewer, Luke K; Jones, Jace W; Nguyen, Angela T; Marcu, Ana; Wishart, David S; Oglesby-Sherrouse, Amanda G; Kane, Maureen A; Wilks, Angela

    2018-01-04

    The Pseudomonas aeruginosaMetabolome Database (PAMDB, http://pseudomonas.umaryland.edu) is a searchable, richly annotated metabolite database specific to P. aeruginosa. P. aeruginosa is a soil organism and significant opportunistic pathogen that adapts to its environment through a versatile energy metabolism network. Furthermore, P. aeruginosa is a model organism for the study of biofilm formation, quorum sensing, and bioremediation processes, each of which are dependent on unique pathways and metabolites. The PAMDB is modelled on the Escherichia coli (ECMDB), yeast (YMDB) and human (HMDB) metabolome databases and contains >4370 metabolites and 938 pathways with links to over 1260 genes and proteins. The database information was compiled from electronic databases, journal articles and mass spectrometry (MS) metabolomic data obtained in our laboratories. For each metabolite entered, we provide detailed compound descriptions, names and synonyms, structural and physiochemical information, nuclear magnetic resonance (NMR) and MS spectra, enzymes and pathway information, as well as gene and protein sequences. The database allows extensive searching via chemical names, structure and molecular weight, together with gene, protein and pathway relationships. The PAMBD and its future iterations will provide a valuable resource to biologists, natural product chemists and clinicians in identifying active compounds, potential biomarkers and clinical diagnostics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Some Considerations about Modern Database Machines

    Directory of Open Access Journals (Sweden)

    Manole VELICANU

    2010-01-01

    Full Text Available Optimizing the two computing resources of any computing system - time and space - has al-ways been one of the priority objectives of any database. A current and effective solution in this respect is the computer database. Optimizing computer applications by means of database machines has been a steady preoccupation of researchers since the late seventies. Several information technologies have revolutionized the present information framework. Out of these, those which have brought a major contribution to the optimization of the databases are: efficient handling of large volumes of data (Data Warehouse, Data Mining, OLAP – On Line Analytical Processing, the improvement of DBMS – Database Management Systems facilities through the integration of the new technologies, the dramatic increase in computing power and the efficient use of it (computer networks, massive parallel computing, Grid Computing and so on. All these information technologies, and others, have favored the resumption of the research on database machines and the obtaining in the last few years of some very good practical results, as far as the optimization of the computing resources is concerned.

  14. Nuclear integrated database and design advancement system

    International Nuclear Information System (INIS)

    Ha, Jae Joo; Jeong, Kwang Sub; Kim, Seung Hwan; Choi, Sun Young.

    1997-01-01

    The objective of NuIDEAS is to computerize design processes through an integrated database by eliminating the current work style of delivering hardcopy documents and drawings. The major research contents of NuIDEAS are the advancement of design processes by computerization, the establishment of design database and 3 dimensional visualization of design data. KSNP (Korea Standard Nuclear Power Plant) is the target of legacy database and 3 dimensional model, so that can be utilized in the next plant design. In the first year, the blueprint of NuIDEAS is proposed, and its prototype is developed by applying the rapidly revolutionizing computer technology. The major results of the first year research were to establish the architecture of the integrated database ensuring data consistency, and to build design database of reactor coolant system and heavy components. Also various softwares were developed to search, share and utilize the data through networks, and the detailed 3 dimensional CAD models of nuclear fuel and heavy components were constructed, and walk-through simulation using the models are developed. This report contains the major additions and modifications to the object oriented database and associated program, using methods and Javascript.. (author). 36 refs., 1 tab., 32 figs

  15. Database Description - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name DGBY Alternative name Database...EL: +81-29-838-8066 E-mail: Database classification Microarray Data and other Gene Expression Databases Orga...nism Taxonomy Name: Saccharomyces cerevisiae Taxonomy ID: 4932 Database descripti...-called phenomics). We uploaded these data on this website which is designated DGBY(Database for Gene expres...ma J, Ando A, Takagi H. Journal: Yeast. 2008 Mar;25(3):179-90. External Links: Original website information Database

  16. Lectindb: a plant lectin database.

    Science.gov (United States)

    Chandra, Nagasuma R; Kumar, Nirmal; Jeyakani, Justin; Singh, Desh Deepak; Gowda, Sharan B; Prathima, M N

    2006-10-01

    Lectins, a class of carbohydrate-binding proteins, are now widely recognized to play a range of crucial roles in many cell-cell recognition events triggering several important cellular processes. They encompass different members that are diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities, and specificities as well as their larger biological roles and potential applications. It is not surprising, therefore, that the vast amount of experimental data on lectins available in the literature is so diverse, that it becomes difficult and time consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. To achieve an effective use of all the data toward understanding the function and their possible applications, an organization of these seemingly independent data into a common framework is essential. An integrated knowledge base ( Lectindb, http://nscdb.bic.physics.iisc.ernet.in ) together with appropriate analytical tools has therefore been developed initially for plant lectins by collating and integrating diverse data. The database has been implemented using MySQL on a Linux platform and web-enabled using PERL-CGI and Java tools. Data for each lectin pertain to taxonomic, biochemical, domain architecture, molecular sequence, and structural details as well as carbohydrate and hence blood group specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value not only for basic studies in lectin biology but also for basic studies in pursuing several applications in biotechnology, immunology, and clinical practice, using these molecules.

  17. Human Performance Event Database

    International Nuclear Information System (INIS)

    Trager, E. A.

    1998-01-01

    The purpose of this paper is to describe several aspects of a Human Performance Event Database (HPED) that is being developed by the Nuclear Regulatory Commission. These include the background, the database structure and basis for the structure, the process for coding and entering event records, the results of preliminary analyses of information in the database, and plans for the future. In 1992, the Office for Analysis and Evaluation of Operational Data (AEOD) within the NRC decided to develop a database for information on human performance during operating events. The database was needed to help classify and categorize the information to help feedback operating experience information to licensees and others. An NRC interoffice working group prepared a list of human performance information that should be reported for events and the list was based on the Human Performance Investigation Process (HPIP) that had been developed by the NRC as an aid in investigating events. The structure of the HPED was based on that list. The HPED currently includes data on events described in augmented inspection team (AIT) and incident investigation team (IIT) reports from 1990 through 1996, AEOD human performance studies from 1990 through 1993, recent NRR special team inspections, and licensee event reports (LERs) that were prepared for the events. (author)

  18. The CUTLASS database facilities

    International Nuclear Information System (INIS)

    Jervis, P.; Rutter, P.

    1988-09-01

    The enhancement of the CUTLASS database management system to provide improved facilities for data handling is seen as a prerequisite to its effective use for future power station data processing and control applications. This particularly applies to the larger projects such as AGR data processing system refurbishments, and the data processing systems required for the new Coal Fired Reference Design stations. In anticipation of the need for improved data handling facilities in CUTLASS, the CEGB established a User Sub-Group in the early 1980's to define the database facilities required by users. Following the endorsement of the resulting specification and a detailed design study, the database facilities have been implemented as an integral part of the CUTLASS system. This paper provides an introduction to the range of CUTLASS Database facilities, and emphasises the role of Database as the central facility around which future Kit 1 and (particularly) Kit 6 CUTLASS based data processing and control systems will be designed and implemented. (author)

  19. ADANS database specification

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-01-16

    The purpose of the Air Mobility Command (AMC) Deployment Analysis System (ADANS) Database Specification (DS) is to describe the database organization and storage allocation and to provide the detailed data model of the physical design and information necessary for the construction of the parts of the database (e.g., tables, indexes, rules, defaults). The DS includes entity relationship diagrams, table and field definitions, reports on other database objects, and a description of the ADANS data dictionary. ADANS is the automated system used by Headquarters AMC and the Tanker Airlift Control Center (TACC) for airlift planning and scheduling of peacetime and contingency operations as well as for deliberate planning. ADANS also supports planning and scheduling of Air Refueling Events by the TACC and the unit-level tanker schedulers. ADANS receives input in the form of movement requirements and air refueling requests. It provides a suite of tools for planners to manipulate these requirements/requests against mobility assets and to develop, analyze, and distribute schedules. Analysis tools are provided for assessing the products of the scheduling subsystems, and editing capabilities support the refinement of schedules. A reporting capability provides formatted screen, print, and/or file outputs of various standard reports. An interface subsystem handles message traffic to and from external systems. The database is an integral part of the functionality summarized above.

  20. Database Description - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Trypanosomes Database Database Description General information of database Database name Trypanosomes Database...stitute of Genetics Research Organization of Information and Systems Yata 1111, Mishima, Shizuoka 411-8540, JAPAN E mail: Database...y Name: Trypanosoma Taxonomy ID: 5690 Taxonomy Name: Homo sapiens Taxonomy ID: 9606 Database description The... Article title: Author name(s): Journal: External Links: Original website information Database maintenance s...DB (Protein Data Bank) KEGG PATHWAY Database DrugPort Entry list Available Query search Available Web servic

  1. Open Geoscience Database

    Science.gov (United States)

    Bashev, A.

    2012-04-01

    Currently there is an enormous amount of various geoscience databases. Unfortunately the only users of the majority of the databases are their elaborators. There are several reasons for that: incompaitability, specificity of tasks and objects and so on. However the main obstacles for wide usage of geoscience databases are complexity for elaborators and complication for users. The complexity of architecture leads to high costs that block the public access. The complication prevents users from understanding when and how to use the database. Only databases, associated with GoogleMaps don't have these drawbacks, but they could be hardly named "geoscience" Nevertheless, open and simple geoscience database is necessary at least for educational purposes (see our abstract for ESSI20/EOS12). We developed a database and web interface to work with them and now it is accessible at maps.sch192.ru. In this database a result is a value of a parameter (no matter which) in a station with a certain position, associated with metadata: the date when the result was obtained; the type of a station (lake, soil etc); the contributor that sent the result. Each contributor has its own profile, that allows to estimate the reliability of the data. The results can be represented on GoogleMaps space image as a point in a certain position, coloured according to the value of the parameter. There are default colour scales and each registered user can create the own scale. The results can be also extracted in *.csv file. For both types of representation one could select the data by date, object type, parameter type, area and contributor. The data are uploaded in *.csv format: Name of the station; Lattitude(dd.dddddd); Longitude(ddd.dddddd); Station type; Parameter type; Parameter value; Date(yyyy-mm-dd). The contributor is recognised while entering. This is the minimal set of features that is required to connect a value of a parameter with a position and see the results. All the complicated data

  2. The LHCb configuration database

    CERN Document Server

    Abadie, Lana; Gaspar, Clara; Jacobsson, Richard; Jost, Beat; Neufeld, Niko

    2005-01-01

    The Experiment Control System (ECS) will handle the monitoring, configuration and operation of all the LHCb experimental equipment. All parameters required to configure electronics equipment under the control of the ECS will reside in a configuration database. The database will contain two kinds of information: 1.\tConfiguration properties about devices such as hardware addresses, geographical location, and operational parameters associated with particular running modes (dynamic properties). 2.\tConnectivity between devices : this consists of describing the output and input connections of a device (static properties). The representation of these data using tables must be complete so that it can provide all the required information to the ECS and must cater for all the subsystems. The design should also guarantee a fast response time, even if a query results in a large volume of data being loaded from the database into the ECS. To fulfil these constraints, we apply the following methodology: Determine from the d...

  3. 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.

  4. Tibetan Magmatism Database

    Science.gov (United States)

    Chapman, James B.; Kapp, Paul

    2017-11-01

    A database containing previously published geochronologic, geochemical, and isotopic data on Mesozoic to Quaternary igneous rocks in the Himalayan-Tibetan orogenic system are presented. The database is intended to serve as a repository for new and existing igneous rock data and is publicly accessible through a web-based platform that includes an interactive map and data table interface with search, filtering, and download options. To illustrate the utility of the database, the age, location, and ɛHft composition of magmatism from the central Gangdese batholith in the southern Lhasa terrane are compared. The data identify three high-flux events, which peak at 93, 50, and 15 Ma. They are characterized by inboard arc migration and a temporal and spatial shift to more evolved isotopic compositions.

  5. 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.

  6. The Danish Sarcoma Database

    DEFF Research Database (Denmark)

    Jørgensen, Peter Holmberg; Lausten, Gunnar Schwarz; Pedersen, Alma B

    2016-01-01

    AIM: The aim of the database is to gather information about sarcomas treated in Denmark in order to continuously monitor and improve the quality of sarcoma treatment in a local, a national, and an international perspective. STUDY POPULATION: Patients in Denmark diagnosed with a sarcoma, both...... skeletal and ekstraskeletal, are to be registered since 2009. MAIN VARIABLES: The database contains information about appearance of symptoms; date of receiving referral to a sarcoma center; date of first visit; whether surgery has been performed elsewhere before referral, diagnosis, and treatment; tumor...... of Diseases - tenth edition codes and TNM Classification of Malignant Tumours, and date of death (after yearly coupling to the Danish Civil Registration System). Data quality and completeness are currently secured. CONCLUSION: The Danish Sarcoma Database is population based and includes sarcomas occurring...

  7. Danish Gynecological Cancer Database

    DEFF Research Database (Denmark)

    Sørensen, Sarah Mejer; Bjørn, Signe Frahm; Jochumsen, Kirsten Marie

    2016-01-01

    AIM OF DATABASE: The Danish Gynecological Cancer Database (DGCD) is a nationwide clinical cancer database and its aim is to monitor the treatment quality of Danish gynecological cancer patients, and to generate data for scientific purposes. DGCD also records detailed data on the diagnostic measures...... data forms as follows: clinical data, surgery, pathology, pre- and postoperative care, complications, follow-up visits, and final quality check. DGCD is linked with additional data from the Danish "Pathology Registry", the "National Patient Registry", and the "Cause of Death Registry" using the unique...... Danish personal identification number (CPR number). DESCRIPTIVE DATA: Data from DGCD and registers are available online in the Statistical Analysis Software portal. The DGCD forms cover almost all possible clinical variables used to describe gynecological cancer courses. The only limitation...

  8. RODOS database adapter

    International Nuclear Information System (INIS)

    Xie Gang

    1995-11-01

    Integrated data management is an essential aspect of many automatical information systems such as RODOS, a real-time on-line decision support system for nuclear emergency management. In particular, the application software must provide access management to different commercial database systems. This report presents the tools necessary for adapting embedded SQL-applications to both HP-ALLBASE/SQL and CA-Ingres/SQL databases. The design of the database adapter and the concept of RODOS embedded SQL syntax are discussed by considering some of the most important features of SQL-functions and the identification of significant differences between SQL-implementations. Finally fully part of the software developed and the administrator's and installation guides are described. (orig.) [de

  9. The Danish Depression Database

    DEFF Research Database (Denmark)

    Videbech, Poul Bror Hemming; Deleuran, Anette

    2016-01-01

    AIM OF DATABASE: The purpose of the Danish Depression Database (DDD) is to monitor and facilitate the improvement of the quality of the treatment of depression in Denmark. Furthermore, the DDD has been designed to facilitate research. STUDY POPULATION: Inpatients as well as outpatients...... with depression, aged above 18 years, and treated in the public psychiatric hospital system were enrolled. MAIN VARIABLES: Variables include whether the patient has been thoroughly somatically examined and has been interviewed about the psychopathology by a specialist in psychiatry. The Hamilton score as well...... as an evaluation of the risk of suicide are measured before and after treatment. Whether psychiatric aftercare has been scheduled for inpatients and the rate of rehospitalization are also registered. DESCRIPTIVE DATA: The database was launched in 2011. Every year since then ~5,500 inpatients and 7,500 outpatients...

  10. 600 MW nuclear power database

    International Nuclear Information System (INIS)

    Cao Ruiding; Chen Guorong; Chen Xianfeng; Zhang Yishu

    1996-01-01

    600 MW Nuclear power database, based on ORACLE 6.0, consists of three parts, i.e. nuclear power plant database, nuclear power position database and nuclear power equipment database. In the database, there are a great deal of technique data and picture of nuclear power, provided by engineering designing units and individual. The database can give help to the designers of nuclear power

  11. Survey on utilization of database for research and development of global environmental industry technology; Chikyu kankyo sangyo gijutsu kenkyu kaihatsu no tame no database nado no riyo ni kansuru chosa

    Energy Technology Data Exchange (ETDEWEB)

    1993-03-01

    To optimize networks and database systems for promotion of the industry technology development contributing to the solution of the global environmental problem, studies are made on reusable information resource and its utilization methods. As reusable information resource, there are external database and network system for researchers` information exchange and for computer use. The external database includes commercial database and academic database. As commercial database, 6 agents and 13 service systems are selected. As academic database, there are NACSIS-IR and the database which is connected with INTERNET in the U.S. These are used in connection with the UNIX academic research network called INTERNET. For connection with INTERNET, a commercial UNIX network service called IIJ which starts service in April 1993 can be used. However, personal computer communication network is used for the time being. 6 figs., 4 tabs.

  12. The Neotoma Paleoecology Database

    Science.gov (United States)

    Grimm, E. C.; Ashworth, A. C.; Barnosky, A. D.; Betancourt, J. L.; Bills, B.; Booth, R.; Blois, J.; Charles, D. F.; Graham, R. W.; Goring, S. J.; Hausmann, S.; Smith, A. J.; Williams, J. W.; Buckland, P.

    2015-12-01

    The Neotoma Paleoecology Database (www.neotomadb.org) is a multiproxy, open-access, relational database that includes fossil data for the past 5 million years (the late Neogene and Quaternary Periods). Modern distributional data for various organisms are also being made available for calibration and paleoecological analyses. The project is a collaborative effort among individuals from more than 20 institutions worldwide, including domain scientists representing a spectrum of Pliocene-Quaternary fossil data types, as well as experts in information technology. Working groups are active for diatoms, insects, ostracodes, pollen and plant macroscopic remains, testate amoebae, rodent middens, vertebrates, age models, geochemistry and taphonomy. Groups are also active in developing online tools for data analyses and for developing modules for teaching at different levels. A key design concept of NeotomaDB is that stewards for various data types are able to remotely upload and manage data. Cooperatives for different kinds of paleo data, or from different regions, can appoint their own stewards. Over the past year, much progress has been made on development of the steward software-interface that will enable this capability. The steward interface uses web services that provide access to the database. More generally, these web services enable remote programmatic access to the database, which both desktop and web applications can use and which provide real-time access to the most current data. Use of these services can alleviate the need to download the entire database, which can be out-of-date as soon as new data are entered. In general, the Neotoma web services deliver data either from an entire table or from the results of a view. Upon request, new web services can be quickly generated. Future developments will likely expand the spatial and temporal dimensions of the database. NeotomaDB is open to receiving new datasets and stewards from the global Quaternary community

  13. The Danish Sarcoma Database

    Directory of Open Access Journals (Sweden)

    Jorgensen PH

    2016-10-01

    Full Text Available Peter Holmberg Jørgensen,1 Gunnar Schwarz Lausten,2 Alma B Pedersen3 1Tumor Section, Department of Orthopedic Surgery, Aarhus University Hospital, Aarhus, 2Tumor Section, Department of Orthopedic Surgery, Rigshospitalet, Copenhagen, 3Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark Aim: The aim of the database is to gather information about sarcomas treated in Denmark in order to continuously monitor and improve the quality of sarcoma treatment in a local, a national, and an international perspective. Study population: Patients in Denmark diagnosed with a sarcoma, both skeletal and ekstraskeletal, are to be registered since 2009. Main variables: The database contains information about appearance of symptoms; date of receiving referral to a sarcoma center; date of first visit; whether surgery has been performed elsewhere before referral, diagnosis, and treatment; tumor characteristics such as location, size, malignancy grade, and growth pattern; details on treatment (kind of surgery, amount of radiation therapy, type and duration of chemotherapy; complications of treatment; local recurrence and metastases; and comorbidity. In addition, several quality indicators are registered in order to measure the quality of care provided by the hospitals and make comparisons between hospitals and with international standards. Descriptive data: Demographic patient-specific data such as age, sex, region of living, comorbidity, World Health Organization's International Classification of Diseases – tenth edition codes and TNM Classification of Malignant Tumours, and date of death (after yearly coupling to the Danish Civil Registration System. Data quality and completeness are currently secured. Conclusion: The Danish Sarcoma Database is population based and includes sarcomas occurring in Denmark since 2009. It is a valuable tool for monitoring sarcoma incidence and quality of treatment and its improvement, postoperative

  14. C# Database Basics

    CERN Document Server

    Schmalz, Michael

    2012-01-01

    Working with data and databases in C# certainly can be daunting if you're coming from VB6, VBA, or Access. With this hands-on guide, you'll shorten the learning curve considerably as you master accessing, adding, updating, and deleting data with C#-basic skills you need if you intend to program with this language. No previous knowledge of C# is necessary. By following the examples in this book, you'll learn how to tackle several database tasks in C#, such as working with SQL Server, building data entry forms, and using data in a web service. The book's code samples will help you get started

  15. Danish Palliative Care Database

    DEFF Research Database (Denmark)

    Grønvold, Mogens; Adsersen, Mathilde; Hansen, Maiken Bang

    2016-01-01

    Aims: The aim of the Danish Palliative Care Database (DPD) is to monitor, evaluate, and improve the clinical quality of specialized palliative care (SPC) (ie, the activity of hospital-based palliative care teams/departments and hospices) in Denmark. Study population: The study population is all...... patients were registered in DPD during the 5 years 2010–2014. Of those registered, 96% had cancer. Conclusion: DPD is a national clinical quality database for SPC having clinically relevant variables and high data and patient completeness....

  16. 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.

  17. The Danish Anaesthesia Database

    DEFF Research Database (Denmark)

    Antonsen, Kristian; Rosenstock, Charlotte Vallentin; Lundstrøm, Lars Hyldborg

    2016-01-01

    AIM OF DATABASE: The aim of the Danish Anaesthesia Database (DAD) is the nationwide collection of data on all patients undergoing anesthesia. Collected data are used for quality assurance, quality development, and serve as a basis for research projects. STUDY POPULATION: The DAD was founded in 2004....... In addition, an annual DAD report is a benchmark for departments nationwide. CONCLUSION: The DAD is covering the anesthetic process for the majority of patients undergoing anesthesia in Denmark. Data in the DAD are increasingly used for both quality and research projects....

  18. MARKS ON ART database

    DEFF Research Database (Denmark)

    van Vlierden, Marieke; Wadum, Jørgen; Wolters, Margreet

    2016-01-01

    Mestermærker, monogrammer og kvalitetsmærker findes ofte præget eller stemplet på kunstværker fra 1300-1700. En illustreret database med denne typer mræker er under etablering på Nederlands Kunsthistoriske Institut (RKD) i Den Haag.......Mestermærker, monogrammer og kvalitetsmærker findes ofte præget eller stemplet på kunstværker fra 1300-1700. En illustreret database med denne typer mræker er under etablering på Nederlands Kunsthistoriske Institut (RKD) i Den Haag....

  19. Yucca Mountain digital database

    International Nuclear Information System (INIS)

    Daudt, C.R.; Hinze, W.J.

    1992-01-01

    This paper discusses the Yucca Mountain Digital Database (DDB) which is a digital, PC-based geographical database of geoscience-related characteristics of the proposed high-level waste (HLW) repository site of Yucca Mountain, Nevada. It was created to provide the US Nuclear Regulatory Commission's (NRC) Advisory Committee on Nuclear Waste (ACNW) and its staff with a visual perspective of geological, geophysical, and hydrological features at the Yucca Mountain site as discussed in the Department of Energy's (DOE) pre-licensing reports

  20. ARTI refrigerant database

    Energy Technology Data Exchange (ETDEWEB)

    Calm, J.M.

    1998-03-15

    The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to thermophysical properties, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alternative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air conditioning and refrigeration equipment. It also references documents addressing compatibility of refrigerants and lubricants with other materials.

  1. Surgery Risk Assessment (SRA) Database

    Data.gov (United States)

    Department of Veterans Affairs — The Surgery Risk Assessment (SRA) database is part of the VA Surgical Quality Improvement Program (VASQIP). This database contains assessments of selected surgical...

  2. 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 dissemination. Structure and functionality of chemical databases are considered. The typical kinds of information found in a chemical database are considered-identification, structural, and associated data. Functionality of chemical databases is presented, with examples of search and access types. More details...... 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....

  3. PEP725 Pan European Phenological Database

    Science.gov (United States)

    Koch, E.; Adler, S.; Lipa, W.; Ungersböck, M.; Zach-Hermann, S.

    2010-09-01

    Europe is in the fortunate situation that it has a long tradition in phenological networking: the history of collecting phenological data and using them in climatology has its starting point in 1751 when Carl von Linné outlined in his work Philosophia Botanica methods for compiling annual plant calendars of leaf opening, flowering, fruiting and leaf fall together with climatological observations "so as to show how areas differ". Recently in most European countries, phenological observations have been carried out routinely for more than 50 years by different governmental and non governmental organisations and following different observation guidelines, the data stored at different places in different formats. This has been really hampering pan European studies as one has to address many network operators to get access to the data before one can start to bring them in a uniform style. From 2004 to 2009 the COST-action 725 established a European wide data set of phenological observations. But the deliverables of this COST action was not only the common phenological database and common observation guidelines - COST725 helped to trigger a revival of some old networks and to establish new ones as for instance in Sweden. At the end of 2009 the COST action the database comprised about 8 million data in total from 15 European countries plus the data from the International Phenological Gardens IPG. In January 2010 PEP725 began its work as follow up project with funding from EUMETNET the network of European meteorological services and of ZAMG the Austrian national meteorological service. PEP725 not only will take over the part of maintaining, updating the COST725 database, but also to bring in phenological data from the time before 1951, developing better quality checking procedures and ensuring an open access to the database. An attractive webpage will make phenology and climate impacts on vegetation more visible in the public enabling a monitoring of vegetation development.

  4. Complex Networks

    CERN Document Server

    Evsukoff, Alexandre; González, Marta

    2013-01-01

    In the last decade we have seen the emergence of a new inter-disciplinary field focusing on the understanding of networks which are dynamic, large, open, and have a structure sometimes called random-biased. The field of Complex Networks is helping us better understand many complex phenomena such as the spread of  deseases, protein interactions, social relationships, to name but a few. Studies in Complex Networks are gaining attention due to some major scientific breakthroughs proposed by network scientists helping us understand and model interactions contained in large datasets. In fact, if we could point to one event leading to the widespread use of complex network analysis is the availability of online databases. Theories of Random Graphs from Erdös and Rényi from the late 1950s led us to believe that most networks had random characteristics. The work on large online datasets told us otherwise. Starting with the work of Barabási and Albert as well as Watts and Strogatz in the late 1990s, we now know th...

  5. Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein.

    Science.gov (United States)

    Bertaccini, Edward J; Lindahl, Erik; Sixma, Titia; Trudell, James R

    2008-04-01

    Recent crystal structures of the acetylcholine binding protein (AChBP) have revealed surprisingly small structural alterations upon ligand binding. Here we investigate the extent to which ligand binding may affect receptor dynamics. AChBP is a homologue of the extracellular component of ligand-gated ion channels (LGICs). We have previously used an elastic network normal-mode analysis to propose a gating mechanism for the LGICs and to suggest the effects of various ligands on such motions. However, the difficulties with elastic network methods lie in their inability to account for the modest effects of a small ligand or mutation on ion channel motion. Here, we report the successful application of an elastic network normal mode technique to measure the effects of large ligand binding on receptor dynamics. The present calculations demonstrate a clear alteration in the native symmetric motions of a protein due to the presence of large protein cobratoxin ligands. In particular, normal-mode analysis revealed that cobratoxin binding to this protein significantly dampened the axially symmetric motion of the AChBP that may be associated with channel gating in the full nAChR. The results suggest that alterations in receptor dynamics could be a general feature of ligand binding.

  6. Spatial database for intersections.

    Science.gov (United States)

    2015-08-01

    Deciding which intersections in the state of Kentucky warrant safety improvements requires a comprehensive inventory : with information on every intersection in the public roadway network. The Kentucky Transportation Cabinet (KYTC) : had previously c...

  7. Random Walks and Diffusions on Graphs and Databases An Introduction

    CERN Document Server

    Blanchard, Philippe

    2011-01-01

    Most networks and databases that humans have to deal with contain large, albeit finite number of units. Their structure, for maintaining functional consistency of the components, is essentially not random and calls for a precise quantitative description of relations between nodes (or data units) and all network components. This book is an introduction, for both graduate students and newcomers to the field, to the theory of graphs and random walks on such graphs. The methods based on random walks and diffusions for exploring the structure of finite connected graphs and databases are reviewed (Markov chain analysis). This provides the necessary basis for consistently discussing a number of applications such diverse as electric resistance networks, estimation of land prices, urban planning, linguistic databases, music, and gene expression regulatory networks.

  8. License - Trypanosomes Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us Trypanoso... Attribution-Share Alike 2.1 Japan . If you use data from this database, please be sure attribute this database as follows: Trypanoso...nse Update History of This Database Site Policy | Contact Us License - Trypanosomes Database | LSDB Archive ...

  9. MARC and Relational Databases.

    Science.gov (United States)

    Llorens, Jose; Trenor, Asuncion

    1993-01-01

    Discusses the use of MARC format in relational databases and addresses problems of incompatibilities. A solution is presented that is in accordance with Open Systems Interconnection (OSI) standards and is based on experiences at the library of the Universidad Politecnica de Valencia (Spain). (four references) (EA)

  10. Teaching Historians with Databases.

    Science.gov (United States)

    Burton, Vernon

    1993-01-01

    Asserts that, although pressures to publish have detracted from the quality of teaching at the college level, recent innovations in educational technology have created opportunities for instructional improvement. Describes the use of computer-assisted instruction and databases in college-level history courses. (CFR)

  11. Literature database aid

    International Nuclear Information System (INIS)

    Wanderer, J.A.

    1991-01-01

    The booklet is to help with the acquisition of original literature either after a conventional literature search or in particular after a database search. It bridges the gap between abbreviated (short) and original (long) titel. This, together with information on the holdings of technical/scientific libraries, facilitates document delivery. 1500 short titles are listed alphabetically. (orig.) [de

  12. Oversigt over databaser

    DEFF Research Database (Denmark)

    Krogh Graversen, Brian

    Dette er en oversigt over registre, som kan anvendes til at beslyse situationen og udviklingen på det sociale område. Oversigten er anden fase i et dataprojekt, som har til formål at etablere en database, som kan danne basis for en løbende overvågning, udredning, evaluering og forskning på det...

  13. LHCb distributed conditions database

    International Nuclear Information System (INIS)

    Clemencic, M

    2008-01-01

    The LHCb Conditions Database project provides the necessary tools to handle non-event time-varying data. The main users of conditions are reconstruction and analysis processes, which are running on the Grid. To allow efficient access to the data, we need to use a synchronized replica of the content of the database located at the same site as the event data file, i.e. the LHCb Tier1. The replica to be accessed is selected from information stored on LFC (LCG File Catalog) and managed with the interface provided by the LCG developed library CORAL. The plan to limit the submission of jobs to those sites where the required conditions are available will also be presented. LHCb applications are using the Conditions Database framework on a production basis since March 2007. We have been able to collect statistics on the performance and effectiveness of both the LCG library COOL (the library providing conditions handling functionalities) and the distribution framework itself. Stress tests on the CNAF hosted replica of the Conditions Database have been performed and the results will be summarized here

  14. Database Programming Languages

    DEFF Research Database (Denmark)

    This volume contains the proceedings of the 11th International Symposium on Database Programming Languages (DBPL 2007), held in Vienna, Austria, on September 23-24, 2007. DBPL 2007 was one of 15 meetings co-located with VLBD (the International Conference on Very Large Data Bases). DBPL continues...

  15. From database to normbase

    NARCIS (Netherlands)

    Stamper, R.K.; Liu, Kecheng; Liu, K.; Kolkman, M.; Kolkman, M.; Klarenberg, P.; Ades, Y.; van Slooten, C.; van Slooten, F.; Ades, Y.

    1991-01-01

    After the database concept, we are ready for the normbase concept. The object is to decouple organizational and technical knowledge that are now mixed inextricably together in the application programs we write today. The underlying principle is to find a way of specifying a social system as a system

  16. Database on wind characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, K.S. [The Technical Univ. of Denmark (Denmark); Courtney, M.S. [Risoe National Lab., (Denmark)

    1999-08-01

    The organisations that participated in the project consists of five research organisations: MIUU (Sweden), ECN (The Netherlands), CRES (Greece), DTU (Denmark), Risoe (Denmark) and one wind turbine manufacturer: Vestas Wind System A/S (Denmark). The overall goal was to build a database consisting of a large number of wind speed time series and create tools for efficiently searching through the data to select interesting data. The project resulted in a database located at DTU, Denmark with online access through the Internet. The database contains more than 50.000 hours of measured wind speed measurements. A wide range of wind climates and terrain types are represented with significant amounts of time series. Data have been chosen selectively with a deliberate over-representation of high wind and complex terrain cases. This makes the database ideal for wind turbine design needs but completely unsuitable for resource studies. Diversity has also been an important aim and this is realised with data from a large range of terrain types; everything from offshore to mountain, from Norway to Greece. (EHS)

  17. Database Description - SSBD | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available base Description General information of database Database name SSBD Alternative nam...ss 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan, RIKEN Quantitative Biology Center Shuichi Onami E-mail: Database... classification Other Molecular Biology Databases Database classification Dynamic databa...elegans Taxonomy ID: 6239 Taxonomy Name: Escherichia coli Taxonomy ID: 562 Database description Systems Scie...i Onami Journal: Bioinformatics/April, 2015/Volume 31, Issue 7 External Links: Original website information Database

  18. Database Description - GETDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available abase Description General information of database Database name GETDB Alternative n...ame Gal4 Enhancer Trap Insertion Database DOI 10.18908/lsdba.nbdc00236-000 Creator Creator Name: Shigeo Haya... Chuo-ku, Kobe 650-0047 Tel: +81-78-306-3185 FAX: +81-78-306-3183 E-mail: Database classification Expression... Invertebrate genome database Organism Taxonomy Name: Drosophila melanogaster Taxonomy ID: 7227 Database des...riginal website information Database maintenance site Drosophila Genetic Resource

  19. JDD, Inc. Database

    Science.gov (United States)

    Miller, David A., Jr.

    2004-01-01

    JDD Inc, is a maintenance and custodial contracting company whose mission is to provide their clients in the private and government sectors "quality construction, construction management and cleaning services in the most efficient and cost effective manners, (JDD, Inc. Mission Statement)." This company provides facilities support for Fort Riley in Fo,rt Riley, Kansas and the NASA John H. Glenn Research Center at Lewis Field here in Cleveland, Ohio. JDD, Inc. is owned and operated by James Vaughn, who started as painter at NASA Glenn and has been working here for the past seventeen years. This summer I worked under Devan Anderson, who is the safety manager for JDD Inc. in the Logistics and Technical Information Division at Glenn Research Center The LTID provides all transportation, secretarial, security needs and contract management of these various services for the center. As a safety manager, my mentor provides Occupational Health and Safety Occupation (OSHA) compliance to all JDD, Inc. employees and handles all other issues (Environmental Protection Agency issues, workers compensation, safety and health training) involving to job safety. My summer assignment was not as considered "groundbreaking research" like many other summer interns have done in the past, but it is just as important and beneficial to JDD, Inc. I initially created a database using a Microsoft Excel program to classify and categorize data pertaining to numerous safety training certification courses instructed by our safety manager during the course of the fiscal year. This early portion of the database consisted of only data (training field index, employees who were present at these training courses and who was absent) from the training certification courses. Once I completed this phase of the database, I decided to expand the database and add as many dimensions to it as possible. Throughout the last seven weeks, I have been compiling more data from day to day operations and been adding the

  20. Database Description - Open TG-GATEs Pathological Image Database | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Open TG-GATEs Pathological Image Database Database Description General information of database Database... name Open TG-GATEs Pathological Image Database Alternative name - DOI 10.18908/lsdba.nbdc00954-0...iomedical Innovation 7-6-8, Saito-asagi, Ibaraki-city, Osaka 567-0085, Japan TEL:81-72-641-9826 Email: Database... classification Toxicogenomics Database Organism Taxonomy Name: Rattus norvegi... Article title: Author name(s): Journal: External Links: Original website information Database