The Design and Product of National 1:1000000 Cartographic Data of Topographic Map

NASA Astrophysics Data System (ADS)

Wang, Guizhi

2016-06-01

National administration of surveying, mapping and geoinformation started to launch the project of national fundamental geographic information database dynamic update in 2012. Among them, the 1:50000 database was updated once a year, furthermore the 1:250000 database was downsized and linkage-updated on the basis. In 2014, using the latest achievements of 1:250000 database, comprehensively update the 1:1000000 digital line graph database. At the same time, generate cartographic data of topographic map and digital elevation model data. This article mainly introduce national 1:1000000 cartographic data of topographic map, include feature content, database structure, Database-driven Mapping technology, workflow and so on.

RAID v2.0: an updated resource of RNA-associated interactions across organisms

PubMed Central

Yi, Ying; Zhao, Yue; Li, Chunhua; Zhang, Lin; Huang, Huiying; Li, Yana; Liu, Lanlan; Hou, Ping; Cui, Tianyu; Tan, Puwen; Hu, Yongfei; Zhang, Ting; Huang, Yan; Li, Xiaobo; Yu, Jia; Wang, Dong

2017-01-01

With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions is still not available for any species. Hence, we have updated the RAID database to version 2.0 (RAID v2.0, www.rna-society.org/raid/) by integrating experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID v2.0 include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60. Consequently, RAID v2.0 recruits more than 5.27 million RNA-associated interactions, including more than 4 million RNA–RNA interactions and more than 1.2 million RNA–protein interactions, referring to nearly 130 000 RNA/protein symbols across 60 species. PMID:27899615

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

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

Liu, Ling; Xiong, Yi; Gao, Hongyun

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions

DOE PAGES

Liu, Ling; Xiong, Yi; Gao, Hongyun; ...

2018-04-02

Protein–nucleic acid interactions play essential roles in various biological activities such as gene regulation, transcription, DNA repair and DNA packaging. Understanding the effects of amino acid substitutions on protein–nucleic acid binding affinities can help elucidate the molecular mechanism of protein–nucleic acid recognition. Until now, no comprehensive and updated database of quantitative binding data on alanine mutagenic effects for protein–nucleic acid interactions is publicly accessible. Thus, we developed a new database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions (dbAMEPNI). dbAMEPNI is a manually curated, literature-derived database, comprising over 577 alanine mutagenic data with experimentally determined binding affinities for protein–nucleic acidmore » complexes. Here, it contains several important parameters, such as dissociation constant (Kd), Gibbs free energy change (ΔΔG), experimental conditions and structural parameters of mutant residues. In addition, the database provides an extended dataset of 282 single alanine mutations with only qualitative data (or descriptive effects) of thermodynamic information.« less

The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection.

PubMed

Fernández-Suárez, Xosé M; Rigden, Daniel J; Galperin, Michael Y

2014-01-01

The 2014 Nucleic Acids Research Database Issue includes descriptions of 58 new molecular biology databases and recent updates to 123 databases previously featured in NAR or other journals. For convenience, the issue is now divided into eight sections that reflect major subject categories. Among the highlights of this issue are six databases of the transcription factor binding sites in various organisms and updates on such popular databases as CAZy, Database of Genomic Variants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt. There is a strong block of structural databases, which includes, among others, the new RNA Bricks database, updates on PDBe, PDBsum, ArchDB, Gene3D, ModBase, Nucleic Acid Database and the recently revived iPfam database. An update on the NCBI's MMDB describes VAST+, an improved tool for protein structure comparison. Two articles highlight the development of the Structural Classification of Proteins (SCOP) database: one describes SCOPe, which automates assignment of new structures to the existing SCOP hierarchy; the other one describes the first version of SCOP2, with its more flexible approach to classifying protein structures. This issue also includes a collection of articles on bacterial taxonomy and metagenomics, which includes updates on the List of Prokaryotic Names with Standing in Nomenclature (LPSN), Ribosomal Database Project (RDP), the Silva/LTP project and several new metagenomics resources. The NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/c/, has been expanded to 1552 databases. The entire Database Issue is freely available online on the Nucleic Acids Research website (http://nar.oxfordjournals.org/).

Comprehensive Thematic T-matrix Reference Database: a 2013-2014 Update

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Zakharova, Nadezhda T.; Khlebtsov, Nikolai G.; Wriedt, Thomas; Videen, Gorden

2014-01-01

This paper is the sixth update to the comprehensive thematic database of peer-reviewedT-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists several earlier publications not incorporated in the original database and previous updates.

RAID v2.0: an updated resource of RNA-associated interactions across organisms.

PubMed

Yi, Ying; Zhao, Yue; Li, Chunhua; Zhang, Lin; Huang, Huiying; Li, Yana; Liu, Lanlan; Hou, Ping; Cui, Tianyu; Tan, Puwen; Hu, Yongfei; Zhang, Ting; Huang, Yan; Li, Xiaobo; Yu, Jia; Wang, Dong

2017-01-04

With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions is still not available for any species. Hence, we have updated the RAID database to version 2.0 (RAID v2.0, www.rna-society.org/raid/) by integrating experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID v2.0 include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60. Consequently, RAID v2.0 recruits more than 5.27 million RNA-associated interactions, including more than 4 million RNA-RNA interactions and more than 1.2 million RNA-protein interactions, referring to nearly 130 000 RNA/protein symbols across 60 species. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

FunCoup 3.0: database of genome-wide functional coupling networks

PubMed Central

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. PMID:24185702

IRIS TOXICOLOGICAL REVIEW AND SUMMARY ...

EPA Pesticide Factsheets

EPA's assessment of the noncancer health effects and carcinogenic potential of Beryllium was added to the IRIS database in 1998. The IRIS program is updating the IRIS assessment for Beryllium. This update will incorporate health effects information published since the last assessment was prepared as well as new risk assessment methods. The IRIS assessment for Beryllium will consist of an updated Toxicological Review and IRIS Summary. The Toxicological Review is a critical review of the physicochemical and toxicokinetic properties of the chemical and its toxicity in humans and experimental systems. The assessment will present reference values for noncancer effects of Beryllium (RfD and RfC) and a cancer assessment. The Toxicological Review and IRIS Summary will be subject to internal peer consultation, Agency and Interagency review, and external scientific peer review. The final products will constitute the Agency's opinion on the toxicity of Beryllium. Beryllium is a light alkaline earth metal used in metal alloys and in high-performance products in the metallurgical, aerospace, and nuclear industries. According to the Superfund database, beryllium is found in over 300 NPL sites

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

NASA Technical Reports Server (NTRS)

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.

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

PubMed

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.

THE NASA AMES PAH IR SPECTROSCOPIC DATABASE VERSION 2.00: UPDATED CONTENT, WEB SITE, AND ON(OFF)LINE TOOLS

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

Boersma, C.; Mattioda, A. L.; Allamandola, L. J.

A significantly updated version of the NASA Ames PAH IR Spectroscopic Database, the first major revision since its release in 2010, is presented. The current version, version 2.00, contains 700 computational and 75 experimental spectra compared, respectively, with 583 and 60 in the initial release. The spectra span the 2.5-4000 μm (4000-2.5 cm{sup -1}) range. New tools are available on the site that allow one to analyze spectra in the database and compare them with imported astronomical spectra as well as a suite of IDL object classes (a collection of programs utilizing IDL's object-oriented programming capabilities) that permit offline analysismore » called the AmesPAHdbIDLSuite. Most noteworthy among the additions are the extension of the computational spectroscopic database to include a number of significantly larger polycyclic aromatic hydrocarbons (PAHs), the ability to visualize the molecular atomic motions corresponding to each vibrational mode, and a new tool that allows one to perform a non-negative least-squares fit of an imported astronomical spectrum with PAH spectra in the computational database. Finally, a methodology is described in the Appendix, and implemented using the AmesPAHdbIDLSuite, that allows the user to enforce charge balance during the fitting procedure.« less

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

PubMed Central

Rey, Maja; Weidemann, Andreas; Kania, Renate; Müller, Wolfgang

2018-01-01

Abstract SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012). (i) The website has been completely revised and (ii) allows now also free text search for kinetics data. (iii) Additional interlinkages with other databases in our field have been established; this enables users to gain directly comprehensive knowledge about the properties of enzymes and kinetics beyond SABIO-RK. (iv) Vice versa, direct access to SABIO-RK data has been implemented in several systems biology tools and workflows. (v) On request of our experimental users, the data can be exported now additionally in spreadsheet formats. (vi) The newly established SABIO-RK Curation Service allows to respond to specific data requirements. PMID:29092055

A guide to experimental particle physics literature, 1991-1996

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

Ezhela, V.V.; Filimonov, B.B.; Lugovsky, S.B.

1996-10-01

We present an indexed guide to experimental particle physics literature for the years 1991 - 1996. Approximately 4200 papers are indexed by (1) Beam/Target/Momentum (2) Reaction/Momentum/Data-Descriptor (including the final state) (3) Particle/Decay (4) Accelerator/Experiment/Detector. All indices are cross-referenced to the paper`s title and references in the ID/Reference/Title index. The information presented in this guide is also publicly available on a regularly-updated DATAGUIDE database from the World Wide Web.

A new online database of nuclear electromagnetic moments

NASA Astrophysics Data System (ADS)

Mertzimekis, Theo J.

2017-09-01

Nuclear electromagnetic (EM) moments, i.e., the magnetic dipole and the electric quadrupole moments, provide important information of nuclear structure. As in other types of experimental data available to the community, measurements of nuclear EM moments have been organized systematically in compilations since the dawn of nuclear science. However, the wealth of recent moments measurements with radioactive beams, as well as earlier existing measurements, lack an online, easy-to-access, systematically organized presence to disseminate information to researchers. In addition, available printed compilations suffer a rather long life cycle, being left behind experimental measurements published in journals or elsewhere. A new, online database (http://magneticmoments.info) focusing on nuclear EM moments has been recently developed to disseminate experimental data to the community. The database includes non-evaluated experimental data of nuclear EM moments, giving strong emphasis on frequent updates (life cycle is 3 months) and direct connection to the sources via DOI and NSR hyperlinks. It has been recently integrated in IAEA LiveChart [1], but can also be found as a standalone webapp [2]. A detailed review of the database features, as well as plans for further development and expansion in the near future is discussed.

Rapid Structural Design Change Evaluation with AN Experiment Based FEM

NASA Astrophysics Data System (ADS)

Chu, C.-H.; Trethewey, M. W.

1998-04-01

The work in this paper proposes a dynamic structural design model that can be developed in a rapid fashion. The approach endeavours to produce a simplified FEM developed in conjunction with an experimental modal database. The FEM is formulated directly from the geometry and connectivity used in an experimental modal test using beam/frame elements. The model sacrifices fine detail for a rapid development time. The FEM is updated at the element level so the dynamic response replicates the experimental results closely. The physical attributes of the model are retained, making it well suited to evaluate the effect of potential design changes. The capabilities are evaluated in a series of computational and laboratory tests. First, a study is performed with a simulated cantilever beam with a variable mass and stiffness distribution. The modal characteristics serve as the updating target with random noise added to simulate experimental uncertainty. A uniformly distributed FEM is developed and updated. The results show excellent results, all natural frequencies are within 0·001% with MAC values above 0·99. Next, the method is applied to predict the dynamic changes of a hardware portal frame structure for a radical design change. Natural frequency predictions from the original FEM differ by as much as almost 18% with reasonable MAC values. The results predicted from the updated model produce excellent results when compared to the actual hardware changes, the first five modal natural frequency difference is around 5% and the corresponding mode shapes producing MAC values above 0·98.

National Solar Radiation Database 1991-2005 Update: User's Manual

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

Wilcox, S.

2007-04-01

This manual describes how to obtain and interpret the data products from the updated 1991-2005 National Solar Radiation Database (NSRDB). This is an update of the original 1961-1990 NSRDB released in 1992.

ATtRACT-a database of RNA-binding proteins and associated motifs.

PubMed

Giudice, Girolamo; Sánchez-Cabo, Fátima; Torroja, Carlos; Lara-Pezzi, Enrique

2016-01-01

RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA transport, splicing, polyadenylation and stability. Understanding the interaction between RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation in a global manner. Despite advances in recent years, a unified non-redundant resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this information is lacking. Here, we developed a database named ATtRACT (available athttp://attract.cnic.es) that compiles information on 370 RBPs and 1583 RBP consensus binding motifs, 192 of which are not present in any other database. To populate ATtRACT we (i) extracted and hand-curated experimentally validated data from CISBP-RNA, SpliceAid-F, RBPDB databases, (ii) integrated and updated the unavailable ASD database and (iii) extracted information from Protein-RNA complexes present in Protein Data Bank database through computational analyses. ATtRACT provides also efficient algorithms to search a specific motif and scan one or more RNA sequences at a time. It also allows discoveringde novomotifs enriched in a set of related sequences and compare them with the motifs included in the database.Database URL:http:// attract. cnic. es. © The Author(s) 2016. Published by Oxford University Press.

The components of working memory updating: an experimental decomposition and individual differences.

PubMed

Ecker, Ullrich K H; Lewandowsky, Stephan; Oberauer, Klaus; Chee, Abby E H

2010-01-01

Working memory updating (WMU) has been identified as a cognitive function of prime importance for everyday tasks and has also been found to be a significant predictor of higher mental abilities. Yet, little is known about the constituent processes of WMU. We suggest that operations required in a typical WMU task can be decomposed into 3 major component processes: retrieval, transformation, and substitution. We report a large-scale experiment that instantiated all possible combinations of those 3 component processes. Results show that the 3 components make independent contributions to updating performance. We additionally present structural equation models that link WMU task performance and working memory capacity (WMC) measures. These feature the methodological advancement of estimating interindividual covariation and experimental effects on mean updating measures simultaneously. The modeling results imply that WMC is a strong predictor of WMU skills in general, although some component processes-in particular, substitution skills-were independent of WMC. Hence, the reported predictive power of WMU measures may rely largely on common WM functions also measured in typical WMC tasks, although substitution skills may make an independent contribution to predicting higher mental abilities. (PsycINFO Database Record (c) 2009 APA, all rights reserved).

Development of the updated system of city underground pipelines based on Visual Studio

NASA Astrophysics Data System (ADS)

Zhang, Jianxiong; Zhu, Yun; Li, Xiangdong

2009-10-01

Our city has owned the integrated pipeline network management system with ArcGIS Engine 9.1 as the bottom development platform and with Oracle9i as basic database for storaging data. In this system, ArcGIS SDE9.1 is applied as the spatial data engine, and the system was a synthetic management software developed with Visual Studio visualization procedures development tools. As the pipeline update function of the system has the phenomenon of slower update and even sometimes the data lost, to ensure the underground pipeline data can real-time be updated conveniently and frequently, and the actuality and integrity of the underground pipeline data, we have increased a new update module in the system developed and researched by ourselves. The module has the powerful data update function, and can realize the function of inputting and outputting and rapid update volume of data. The new developed module adopts Visual Studio visualization procedures development tools, and uses access as the basic database to storage data. We can edit the graphics in AutoCAD software, and realize the database update using link between the graphics and the system. Practice shows that the update module has good compatibility with the original system, reliable and high update efficient of the database.

New spectroscopy in the HITRAN2016 database and its impact on atmospheric retrievals

NASA Astrophysics Data System (ADS)

Gordon, I.; Rothman, L. S.; Kochanov, R. V.; Tan, Y.; Toon, G. C.

2017-12-01

The HITRAN spectroscopic database is a backbone of the interpretation of spectral atmospheric retrievals and is an important input to the radiative transfer codes. The database is serving the atmospheric community for nearly half-a-century with every new edition being released every four years. The most recent release of the database is HITRAN2016 [1]. It consists of line-by-line lists, experimental absorption cross-sections, collision-induced absorption data and aerosol indices of refraction. In this presentation it will be stressed the importance of using the most recent edition of the database in the radiative transfer codes. The line-by-line lists for most of the HITRAN molecules were updated (and two new molecules added) in comparison with the previous compilation HITRAN2012 [2] that has been in use, along with some intermediate updates, since 2012. The extent of the updates ranges from updating a few lines of certain molecules to complete replacements of the lists and introduction of additional isotopologues. In addition, the amount of molecules in cross-sectional part of the database has increased dramatically from nearly 50 to over 300. The molecules covered by the HITRAN database are important in planetary remote sensing, environment monitoring (in particular, biomass burning detection), climate applications, industrial pollution tracking, atrophysics, and more. Taking advantage of the new structure and interface available at www.hitran.org [3] and the HITRAN Application Programming Interface [4] the amount of parameters has also been significantly increased, now incorporating, for instance, non-Voigt line profiles [5]; broadening by gases other than air and "self" [6]; and other phenomena, including line mixing. This is a very important novelty that needs to be properly introduced in the radiative transfer codes in order to advance accurate interpretation of the remote sensing retrievals. This work is supported by the NASA PDART (NNX16AG51G) and AURA (NNX 17AI78G) programs. References[1] I.E. Gordon et al, JQSRT in press (2017) http://doi.org/10.1016/j.jqsrt.2017.06.038. [2] L.S. Rothman et al, JQSRT 130, 4 (2013). [3] C. Hill et al, JQSRT 177, 4 (2016). [4] R.V. Kochanov et al, JQSRT 177, 15 (2016). [5] P. Wcisło et al., JQSRT 177, 75 (2016). [6] J. S. Wilzewski et al., JQSRT 168, 193 (2016).

Detection of Trace Gases in Biomass Burning Plumes via Infrared Spectroscopy: Updates and Uses of the Northwest Infrared Database (NWIR)

NASA Astrophysics Data System (ADS)

Brauer, C. S.; Johnson, T. J.; Blake, T. A.; Sharpe, S. W.; Sams, R. L.; Tonkyn, R. G.

2014-12-01

The Northwest Infrared Database (NWIR) contains quantitative, gas-phase infrared spectra of nearly 500 pure chemical species, including over 60 molecules that are known or suspected biomass-burning effluents. The data, recorded at 0.1 cm-1 resolution, are pressure broadened to one atmosphere (N2) and each 25 oC spectrum is a composite composed of a minimum of ten individual measurements. Examples from this set of measurements will be presented and experimental details will be discussed in the context of the utility of NWIR for biomass-burning studies.

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

Alekhin, S.I.; Ezhela, V.V.; Filimonov, B.B.

We present an indexed guide to the literature experimental particle physics for the years 1988--1992. About 4,000 papers are indexed by Beam/Target/Momentum, Reaction Momentum (including the final state), Final State Particle, and Accelerator/Detector/Experiment. All indices are cross-referenced to the paper`s title and reference in the ID/Reference/Title Index. The information in this guide is also publicly available from a regularly updated computer database.

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

PubMed Central

Chowdhury, Saikat; Sarkar, Ram Rup

2015-01-01

Elucidating the complexities of cell signaling pathways is of immense importance to gain understanding about various biological phenomenon, such as dynamics of gene/protein expression regulation, cell fate determination, embryogenesis and disease progression. The successful completion of human genome project has also helped experimental and theoretical biologists to analyze various important pathways. To advance this study, during the past two decades, systematic collections of pathway data from experimental studies have been compiled and distributed freely by several databases, which also integrate various computational tools for further analysis. Despite significant advancements, there exist several drawbacks and challenges, such as pathway data heterogeneity, annotation, regular update and automated image reconstructions, which motivated us to perform a thorough review on popular and actively functioning 24 cell signaling databases. Based on two major characteristics, pathway information and technical details, freely accessible data from commercial and academic databases are examined to understand their evolution and enrichment. This review not only helps to identify some novel and useful features, which are not yet included in any of the databases but also highlights their current limitations and subsequently propose the reasonable solutions for future database development, which could be useful to the whole scientific community. PMID:25632107

[Discussion of the implementation of MIMIC database in emergency medical study].

PubMed

Li, Kaiyuan; Feng, Cong; Jia, Lijing; Chen, Li; Pan, Fei; Li, Tanshi

2018-05-01

To introduce Medical Information Mart for Intensive Care (MIMIC) database and elaborate the approach of critically emergent research with big data based on the feature of MIMIC and updated studies both domestic and overseas, we put forward the feasibility and necessity of introducing medical big data to research in emergency. Then we discuss the role of MIMIC database in emergency clinical study, as well as the principles and key notes of experimental design and implementation under the medical big data circumstance. The implementation of MIMIC database in emergency medical research provides a brand new field for the early diagnosis, risk warning and prognosis of critical illness, however there are also limitations. To meet the era of big data, emergency medical database which is in accordance with our national condition is needed, which will provide new energy to the development of emergency medicine.

S2RSLDB: a comprehensive manually curated, internet-accessible database of the sigma-2 receptor selective ligands.

PubMed

Nastasi, Giovanni; Miceli, Carla; Pittalà, Valeria; Modica, Maria N; Prezzavento, Orazio; Romeo, Giuseppe; Rescifina, Antonio; Marrazzo, Agostino; Amata, Emanuele

2017-01-01

Sigma (σ) receptors are accepted as a particular receptor class consisting of two subtypes: sigma-1 (σ 1 ) and sigma-2 (σ 2 ). The two receptor subtypes have specific drug actions, pharmacological profiles and molecular characteristics. The σ 2 receptor is overexpressed in several tumor cell lines, and its ligands are currently under investigation for their role in tumor diagnosis and treatment. The σ 2 receptor structure has not been disclosed, and researchers rely on σ 2 receptor radioligand binding assay to understand the receptor's pharmacological behavior and design new lead compounds. Here we present the sigma-2 Receptor Selective Ligands Database (S2RSLDB) a manually curated database of the σ 2 receptor selective ligands containing more than 650 compounds. The database is built with chemical structure information, radioligand binding affinity data, computed physicochemical properties, and experimental radioligand binding procedures. The S2RSLDB is freely available online without account login and having a powerful search engine the user may build complex queries, sort tabulated results, generate color coded 2D and 3D graphs and download the data for additional screening. The collection here reported is extremely useful for the development of new ligands endowed of σ 2 receptor affinity, selectivity, and appropriate physicochemical properties. The database will be updated yearly and in the near future, an online submission form will be available to help with keeping the database widely spread in the research community and continually updated. The database is available at http://www.researchdsf.unict.it/S2RSLDB.

Completion of the 2006 National Land Cover Database Update for the Conterminous United States

EPA Science Inventory

Under the organization of the Multi-Resolution Land Characteristics (MRLC) Consortium, the National Land Cover Database (NLCD) has been updated to characterize both land cover and land cover change from 2001 to 2006. An updated version of NLCD 2001 (Version 2.0) is also provided....

Update to the Ground-Water Withdrawals Database for the Death Valley Regional Ground-Water Flow System, Nevada and California, 1913-2003

USGS Publications Warehouse

Moreo, Michael T.; Justet, Leigh

2008-01-01

Ground-water withdrawal estimates from 1913 through 2003 for the Death Valley regional ground-water flow system are compiled in an electronic database to support a regional, three-dimensional, transient ground-water flow model. This database updates a previously published database that compiled estimates of ground-water withdrawals for 1913-1998. The same methodology is used to construct each database. Primary differences between the 2 databases are an additional 5 years of ground-water withdrawal data, well locations in the updated database are restricted to Death Valley regional ground-water flow system model boundary, and application rates are from 0 to 1.5 feet per year lower than original estimates. The lower application rates result from revised estimates of crop consumptive use, which are based on updated estimates of potential evapotranspiration. In 2003, about 55,700 acre-feet of ground water was pumped in the DVRFS, of which 69 percent was used for irrigation, 13 percent for domestic, and 18 percent for public supply, commercial, and mining activities.

National Solar Radiation Database 1991-2010 Update: User's Manual

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

Wilcox, S. M.

This user's manual provides information on the updated 1991-2010 National Solar Radiation Database. Included are data format descriptions, data sources, production processes, and information about data uncertainty.

Wind turbine reliability database update.

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

Peters, Valerie A.; Hill, Roger Ray; Stinebaugh, Jennifer A.

2009-03-01

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

Progress on Updating the 1961-1990 National Solar Radiation Database

NASA Technical Reports Server (NTRS)

Renne, D.; Wilcox, S.; Marion, B.; George, R.; Myers, D.

2003-01-01

The 1961-1990 National Solar Radiation Data Base (NSRDB) provides a 30-year climate summary and solar characterization of 239 locations throughout the United States. Over the past several years, the National Renewable Energy Laboratory (NREL) has received numerous inquiries from a range of constituents as to whether an update of the database to include the 1990s will be developed. However, there are formidable challenges to creating an update of the serially complete station-specific database for the 1971-2000 period. During the 1990s, the National Weather Service changed its observational procedures from a human-based to an automated system, resulting in the loss of important input variables to the model used to complete the 1961-1990 NSRDB. As a result, alternative techniques are required for an update that covers the 1990s. This paper examines several alternative approaches for creating this update and describes preliminary NREL plans for implementing the update.

The Finnish disease heritage database (FinDis) update-a database for the genes mutated in the Finnish disease heritage brought to the next-generation sequencing era.

PubMed

Polvi, Anne; Linturi, Henna; Varilo, Teppo; Anttonen, Anna-Kaisa; Byrne, Myles; Fokkema, Ivo F A C; Almusa, Henrikki; Metzidis, Anthony; Avela, Kristiina; Aula, Pertti; Kestilä, Marjo; Muilu, Juha

2013-11-01

The Finnish Disease Heritage Database (FinDis) (http://findis.org) was originally published in 2004 as a centralized information resource for rare monogenic diseases enriched in the Finnish population. The FinDis database originally contained 405 causative variants for 30 diseases. At the time, the FinDis database was a comprehensive collection of data, but since 1994, a large amount of new information has emerged, making the necessity to update the database evident. We collected information and updated the database to contain genes and causative variants for 35 diseases, including six more genes and more than 1,400 additional disease-causing variants. Information for causative variants for each gene is collected under the LOVD 3.0 platform, enabling easy updating. The FinDis portal provides a centralized resource and user interface to link information on each disease and gene with variant data in the LOVD 3.0 platform. The software written to achieve this has been open-sourced and made available on GitHub (http://github.com/findis-db), allowing biomedical institutions in other countries to present their national data in a similar way, and to both contribute to, and benefit from, standardized variation data. The updated FinDis portal provides a unique resource to assist patient diagnosis, research, and the development of new cures. © 2013 WILEY PERIODICALS, INC.

Reassessment of Atomic Mobilities in fcc Cu-Ag-Sn System Aiming at Establishment of an Atomic Mobility Database in Sn-Ag-Cu-In-Sb-Bi-Pb Solder Alloys

NASA Astrophysics Data System (ADS)

Xu, Huixia; Zhang, Lijun; Cheng, Kaiming; Chen, Weimin; Du, Yong

2017-04-01

To establish an accurate atomic mobility database in solder alloys, a reassessment of atomic mobilities in the fcc (face centered cubic) Cu-Ag-Sn system was performed as reported in the present work. The work entailed initial preparation of three fcc Cu-Sn diffusion couples, which were used to determine the composition-dependent interdiffusivities at 873 K, 923 K, and 973 K, to validate the literature data and provide new experimental data at low temperatures. Then, atomic mobilities in three boundary binaries, fcc Cu-Sn, fcc Ag-Sn, and fcc Cu-Ag, were updated based on the data for various experimental diffusivities obtained from the literature and the present work, together with the available thermodynamic database for solder alloys. Finally, based on the large number of interdiffusivities recently measured from the present authors, atomic mobilities in the fcc Cu-Ag-Sn ternary system were carefully evaluated. A comprehensive comparison between various calculated/model-predicted diffusion properties and the experimental data was used to validate the reliability of the obtained atomic mobilities in ternary fcc Cu-Ag-Sn alloys.

Ontology to relational database transformation for web application development and maintenance

NASA Astrophysics Data System (ADS)

Mahmudi, Kamal; Inggriani Liem, M. M.; Akbar, Saiful

2018-03-01

Ontology is used as knowledge representation while database is used as facts recorder in a KMS (Knowledge Management System). In most applications, data are managed in a database system and updated through the application and then they are transformed to knowledge as needed. Once a domain conceptor defines the knowledge in the ontology, application and database can be generated from the ontology. Most existing frameworks generate application from its database. In this research, ontology is used for generating the application. As the data are updated through the application, a mechanism is designed to trigger an update to the ontology so that the application can be rebuilt based on the newest ontology. By this approach, a knowledge engineer has a full flexibility to renew the application based on the latest ontology without dependency to a software developer. In many cases, the concept needs to be updated when the data changed. The framework is built and tested in a spring java environment. A case study was conducted to proof the concepts.

Fast Updating National Geo-Spatial Databases with High Resolution Imagery: China's Methodology and Experience

NASA Astrophysics Data System (ADS)

Chen, J.; Wang, D.; Zhao, R. L.; Zhang, H.; Liao, A.; Jiu, J.

2014-04-01

Geospatial databases are irreplaceable national treasure of immense importance. Their up-to-dateness referring to its consistency with respect to the real world plays a critical role in its value and applications. The continuous updating of map databases at 1:50,000 scales is a massive and difficult task for larger countries of the size of more than several million's kilometer squares. This paper presents the research and technological development to support the national map updating at 1:50,000 scales in China, including the development of updating models and methods, production tools and systems for large-scale and rapid updating, as well as the design and implementation of the continuous updating workflow. The use of many data sources and the integration of these data to form a high accuracy, quality checked product were required. It had in turn required up to date techniques of image matching, semantic integration, generalization, data base management and conflict resolution. Design and develop specific software tools and packages to support the large-scale updating production with high resolution imagery and large-scale data generalization, such as map generalization, GIS-supported change interpretation from imagery, DEM interpolation, image matching-based orthophoto generation, data control at different levels. A national 1:50,000 databases updating strategy and its production workflow were designed, including a full coverage updating pattern characterized by all element topographic data modeling, change detection in all related areas, and whole process data quality controlling, a series of technical production specifications, and a network of updating production units in different geographic places in the country.

MedlinePlus FAQ: How Often MedlinePlus is Updated

MedlinePlus

... System Pharmacists is updated monthly. Natural Medicines Comprehensive Database Consumer Version is updated quarterly. Medical Encyclopedia: Updated monthly. ... Guidelines Viewers & Players MedlinePlus Connect for ...

REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding.

PubMed

Mizutani, Hisashi; Sugawara, Hideaki; Buckle, Ashley M; Sangawa, Takeshi; Miyazono, Ken-Ichi; Ohtsuka, Jun; Nagata, Koji; Shojima, Tomoki; Nosaki, Shohei; Xu, Yuqun; Wang, Delong; Hu, Xiao; Tanokura, Masaru; Yura, Kei

2017-04-24

More than 7000 papers related to "protein refolding" have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource - "REFOLDdb" that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest. We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17 th , 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/ . REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.

Expediting topology data gathering for the TOPDB database.

PubMed

Dobson, László; Langó, Tamás; Reményi, István; Tusnády, Gábor E

2015-01-01

The Topology Data Bank of Transmembrane Proteins (TOPDB, http://topdb.enzim.ttk.mta.hu) contains experimentally determined topology data of transmembrane proteins. Recently, we have updated TOPDB from several sources and utilized a newly developed topology prediction algorithm to determine the most reliable topology using the results of experiments as constraints. In addition to collecting the experimentally determined topology data published in the last couple of years, we gathered topographies defined by the TMDET algorithm using 3D structures from the PDBTM. Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database. Moreover, a new algorithm was developed to integrate scattered topology data from various publicly available databases and a new method was introduced to measure the reliability of predicted topologies. We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method. Altogether, more than 52,000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

MIPS: analysis and annotation of proteins from whole genomes

PubMed Central

Mewes, H. W.; Amid, C.; Arnold, R.; Frishman, D.; Güldener, U.; Mannhaupt, G.; Münsterkötter, M.; Pagel, P.; Strack, N.; Stümpflen, V.; Warfsmann, J.; Ruepp, A.

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein–protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de). PMID:14681354

MIPS: analysis and annotation of proteins from whole genomes.

PubMed

Mewes, H W; Amid, C; Arnold, R; Frishman, D; Güldener, U; Mannhaupt, G; Münsterkötter, M; Pagel, P; Strack, N; Stümpflen, V; Warfsmann, J; Ruepp, A

2004-01-01

The Munich Information Center for Protein Sequences (MIPS-GSF), Neuherberg, Germany, provides protein sequence-related information based on whole-genome analysis. The main focus of the work is directed toward the systematic organization of sequence-related attributes as gathered by a variety of algorithms, primary information from experimental data together with information compiled from the scientific literature. MIPS maintains automatically generated and manually annotated genome-specific databases, develops systematic classification schemes for the functional annotation of protein sequences and provides tools for the comprehensive analysis of protein sequences. This report updates the information on the yeast genome (CYGD), the Neurospora crassa genome (MNCDB), the database of complete cDNAs (German Human Genome Project, NGFN), the database of mammalian protein-protein interactions (MPPI), the database of FASTA homologies (SIMAP), and the interface for the fast retrieval of protein-associated information (QUIPOS). The Arabidopsis thaliana database, the rice database, the plant EST databases (MATDB, MOsDB, SPUTNIK), as well as the databases for the comprehensive set of genomes (PEDANT genomes) are described elsewhere in the 2003 and 2004 NAR database issues, respectively. All databases described, and the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de).

National Water Quality Standards Database (NWQSD)

EPA Pesticide Factsheets

The National Water Quality Standards Database (WQSDB) provides access to EPA and state water quality standards (WQS) information in text, tables, and maps. This data source was last updated in December 2007 and will no longer be updated.

Literature searches on Ayurveda: An update.

PubMed

Aggithaya, Madhur G; Narahari, Saravu R

2015-01-01

The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. To update on Ayurveda literature search and strategy to retrieve maximum publications. Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Five among 46 databases are now relevant - AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. "The Researches in Ayurveda" and "Ayurvedic Research Database" (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches.

Building Change Detection from LIDAR Point Cloud Data Based on Connected Component Analysis

NASA Astrophysics Data System (ADS)

Awrangjeb, M.; Fraser, C. S.; Lu, G.

2015-08-01

Building data are one of the important data types in a topographic database. Building change detection after a period of time is necessary for many applications, such as identification of informal settlements. Based on the detected changes, the database has to be updated to ensure its usefulness. This paper proposes an improved building detection technique, which is a prerequisite for many building change detection techniques. The improved technique examines the gap between neighbouring buildings in the building mask in order to avoid under segmentation errors. Then, a new building change detection technique from LIDAR point cloud data is proposed. Buildings which are totally new or demolished are directly added to the change detection output. However, for demolished or extended building parts, a connected component analysis algorithm is applied and for each connected component its area, width and height are estimated in order to ascertain if it can be considered as a demolished or new building part. Finally, a graphical user interface (GUI) has been developed to update detected changes to the existing building map. Experimental results show that the improved building detection technique can offer not only higher performance in terms of completeness and correctness, but also a lower number of undersegmentation errors as compared to its original counterpart. The proposed change detection technique produces no omission errors and thus it can be exploited for enhanced automated building information updating within a topographic database. Using the developed GUI, the user can quickly examine each suggested change and indicate his/her decision with a minimum number of mouse clicks.

A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

PubMed Central

2014-01-01

Background Constraint-based models of Escherichia coli metabolic flux have played a key role in computational studies of cellular metabolism at the genome scale. We sought to develop a next-generation constraint-based E. coli model that achieved improved phenotypic prediction accuracy while being frequently updated and easy to use. We also sought to compare model predictions with experimental data to highlight open questions in E. coli biology. Results We present EcoCyc–18.0–GEM, a genome-scale model of the E. coli K–12 MG1655 metabolic network. The model is automatically generated from the current state of EcoCyc using the MetaFlux software, enabling the release of multiple model updates per year. EcoCyc–18.0–GEM encompasses 1445 genes, 2286 unique metabolic reactions, and 1453 unique metabolites. We demonstrate a three-part validation of the model that breaks new ground in breadth and accuracy: (i) Comparison of simulated growth in aerobic and anaerobic glucose culture with experimental results from chemostat culture and simulation results from the E. coli modeling literature. (ii) Essentiality prediction for the 1445 genes represented in the model, in which EcoCyc–18.0–GEM achieves an improved accuracy of 95.2% in predicting the growth phenotype of experimental gene knockouts. (iii) Nutrient utilization predictions under 431 different media conditions, for which the model achieves an overall accuracy of 80.7%. The model’s derivation from EcoCyc enables query and visualization via the EcoCyc website, facilitating model reuse and validation by inspection. We present an extensive investigation of disagreements between EcoCyc–18.0–GEM predictions and experimental data to highlight areas of interest to E. coli modelers and experimentalists, including 70 incorrect predictions of gene essentiality on glucose, 80 incorrect predictions of gene essentiality on glycerol, and 83 incorrect predictions of nutrient utilization. Conclusion Significant advantages can be derived from the combination of model organism databases and flux balance modeling represented by MetaFlux. Interpretation of the EcoCyc database as a flux balance model results in a highly accurate metabolic model and provides a rigorous consistency check for information stored in the database. PMID:24974895

Update of the Diatom EST Database: a new tool for digital transcriptomics

PubMed Central

Maheswari, Uma; Mock, Thomas; Armbrust, E. Virginia; Bowler, Chris

2009-01-01

The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130 000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77 000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3. PMID:19029140

Update of KDBI: Kinetic Data of Bio-molecular Interaction database

PubMed Central

Kumar, Pankaj; Han, B. C.; Shi, Z.; Jia, J.; Wang, Y. P.; Zhang, Y. T.; Liang, L.; Liu, Q. F.; Ji, Z. L.; Chen, Y. Z.

2009-01-01

Knowledge of the kinetics of biomolecular interactions is important for facilitating the study of cellular processes and underlying molecular events, and is essential for quantitative study and simulation of biological systems. Kinetic Data of Bio-molecular Interaction database (KDBI) has been developed to provide information about experimentally determined kinetic data of protein–protein, protein–nucleic acid, protein–ligand, nucleic acid–ligand binding or reaction events described in the literature. To accommodate increasing demand for studying and simulating biological systems, numerous improvements and updates have been made to KDBI, including new ways to access data by pathway and molecule names, data file in System Biology Markup Language format, more efficient search engine, access to published parameter sets of simulation models of 63 pathways, and 2.3-fold increase of data (19 263 entries of 10 532 distinctive biomolecular binding and 11 954 interaction events, involving 2635 proteins/protein complexes, 847 nucleic acids, 1603 small molecules and 45 multi-step processes). KDBI is publically available at http://bidd.nus.edu.sg/group/kdbi/kdbi.asp. PMID:18971255

77 FR 71089 - Pilot Loading of Aeronautical Database Updates

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-29

... the use of newer systems and data-transfer mechanisms such as those employing wireless technology. In... which enables wireless updating of systems and databases. The current regulation does not accommodate... maintenance); Recordkeeping requirements; Training for pilots; Technological advancements in data-transfer...

Partial Updating of TSCA Inventory DataBase; Production and Site Reports; Final Rule

EPA Pesticide Factsheets

A partial updating of the TSCA inventory database. The final rule requires manufacturers and importers of certain chemical substances included on the TSCA Chemical Substances Inventory to report current data on the production volume, plant site, etc.

Domain fusion analysis by applying relational algebra to protein sequence and domain databases

PubMed Central

Truong, Kevin; Ikura, Mitsuhiko

2003-01-01

Background Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. Results This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at . Conclusion As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time. PMID:12734020

Upgrades to the TPSX Material Properties Database

NASA Technical Reports Server (NTRS)

Squire, T. H.; Milos, F. S.; Partridge, Harry (Technical Monitor)

2001-01-01

The TPSX Material Properties Database is a web-based tool that serves as a database for properties of advanced thermal protection materials. TPSX provides an easy user interface for retrieving material property information in a variety of forms, both graphical and text. The primary purpose and advantage of TPSX is to maintain a high quality source of often used thermal protection material properties in a convenient, easily accessible form, for distribution to government and aerospace industry communities. Last year a major upgrade to the TPSX web site was completed. This year, through the efforts of researchers at several NASA centers, the Office of the Chief Engineer awarded funds to update and expand the databases in TPSX. The FY01 effort focuses on updating correcting the Ames and Johnson thermal protection materials databases. In this session we will summarize the improvements made to the web site last year, report on the status of the on-going database updates, describe the planned upgrades for FY02 and FY03, and provide a demonstration of TPSX.

Updated folate data in the Dutch Food Composition Database and implications for intake estimates

PubMed Central

Westenbrink, Susanne; Jansen-van der Vliet, Martine; van Rossum, Caroline

2012-01-01

Background and objective Nutrient values are influenced by the analytical method used. Food folate measured by high performance liquid chromatography (HPLC) or by microbiological assay (MA) yield different results, with in general higher results from MA than from HPLC. This leads to the question of how to deal with different analytical methods in compiling standardised and internationally comparable food composition databases? A recent inventory on folate in European food composition databases indicated that currently MA is more widely used than HPCL. Since older Dutch values are produced by HPLC and newer values by MA, analytical methods and procedures for compiling folate data in the Dutch Food Composition Database (NEVO) were reconsidered and folate values were updated. This article describes the impact of this revision of folate values in the NEVO database as well as the expected impact on the folate intake assessment in the Dutch National Food Consumption Survey (DNFCS). Design The folate values were revised by replacing HPLC with MA values from recent Dutch analyses. Previously MA folate values taken from foreign food composition tables had been recalculated to the HPLC level, assuming a 27% lower value from HPLC analyses. These recalculated values were replaced by the original MA values. Dutch HPLC and MA values were compared to each other. Folate intake was assessed for a subgroup within the DNFCS to estimate the impact of the update. Results In the updated NEVO database nearly all folate values were produced by MA or derived from MA values which resulted in an average increase of 24%. The median habitual folate intake in young children was increased by 11–15% using the updated folate values. Conclusion The current approach for folate in NEVO resulted in more transparency in data production and documentation and higher comparability among European databases. Results of food consumption surveys are expected to show higher folate intakes when using the updated values. PMID:22481900

Archival and Dissemination of the U.S. and Canadian Experimental Nuclear Reaction Data (EXFOR Project)

NASA Astrophysics Data System (ADS)

Pritychenko, Boris; Hlavac, Stanislav; Schwerer, Otto; Zerkin, Viktor

2017-09-01

The Exchange Format (EXFOR) or experimental nuclear reaction database and the associated Web interface provide access to the wealth of low- and intermediate-energy nuclear reaction physics data. This resource includes numerical data sets and bibliographical information for more than 22,000 experiments since the beginning of nuclear science. Analysis of the experimental data sets, recovery and archiving will be discussed. Examples of the recent developments of the data renormalization, uploads and inverse reaction calculations for nuclear science and technology applications will be presented. The EXFOR database, updated monthly, provides an essential support for nuclear data evaluation, application development and research activities. It is publicly available at the National Nuclear Data Center website http://www.nndc.bnl.gov/exfor and the International Atomic Energy Agency mirror site http://www-nds.iaea.org/exfor. This work was sponsored in part by the Office of Nuclear Physics, Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-98CH10886 with Brookha ven Science Associates, LLC.

Semi Automated Land Cover Layer Updating Process Utilizing Spectral Analysis and GIS Data Fusion

NASA Astrophysics Data System (ADS)

Cohen, L.; Keinan, E.; Yaniv, M.; Tal, Y.; Felus, A.; Regev, R.

2018-04-01

Technological improvements made in recent years of mass data gathering and analyzing, influenced the traditional methods of updating and forming of the national topographic database. It has brought a significant increase in the number of use cases and detailed geo information demands. Processes which its purpose is to alternate traditional data collection methods developed in many National Mapping and Cadaster Agencies. There has been significant progress in semi-automated methodologies aiming to facilitate updating of a topographic national geodatabase. Implementation of those is expected to allow a considerable reduction of updating costs and operation times. Our previous activity has focused on building automatic extraction (Keinan, Zilberstein et al, 2015). Before semiautomatic updating method, it was common that interpreter identification has to be as detailed as possible to hold most reliable database eventually. When using semi-automatic updating methodologies, the ability to insert human insights based knowledge is limited. Therefore, our motivations were to reduce the created gap by allowing end-users to add their data inputs to the basic geometric database. In this article, we will present a simple Land cover database updating method which combines insights extracted from the analyzed image, and a given spatial data of vector layers. The main stages of the advanced practice are multispectral image segmentation and supervised classification together with given vector data geometric fusion while maintaining the principle of low shape editorial work to be done. All coding was done utilizing open source software components.

Highlights of the HITRAN2016 database

NASA Astrophysics Data System (ADS)

Gordon, I.; Rothman, L. S.; Hill, C.; Kochanov, R. V.; Tan, Y.

2016-12-01

The HITRAN2016 database will be released just before the AGU meeting. It is a titanic effort of world-wide collaboration between experimentalists, theoreticians and atmospheric scientists, who measure, calculate and validate the HITRAN data. The line-by-line lists for almost all of the HITRAN molecules were updated in comparison with the previous compilation HITRAN2012 [1] that has been in use, along with some intermediate updates, since 2012. The extent of the updates ranges from updating a few lines of certain molecules to complete replacements of the lists and introduction of additional isotopologues. Many more vibrational bands were added to the database, extending the spectral coverage and completeness of the datasets. For several molecules, including H2O, CO2 and CH4, the extent of the updates is so complex that separate task groups were assembled to make strategic decisions about the choices of sources for various parameters in different spectral regions. The amount of parameters has also been significantly increased, now incorporating, for instance, non-Voigt line profiles [2]; broadening by gases other than air and "self" [3]; and other phenomena, including line mixing. In addition, the amount of cross-sectional sets in the database has increased dramatically and includes many recent experiments as well as adaptation of the existing databases that were not in HITRAN previously (for instance the PNNL database [4]). The HITRAN2016 edition takes full advantage of the new structure and interface available at www.hitran.org [5] and the HITRAN Application Programming Interface [6]. This poster will provide a summary of the updates, emphasizing details of some of the most important or dramatic improvements. The users of the database will have an opportunity to discuss the updates relevant to their research and request a demonstration on how to work with the database. This work is supported by the NASA PATM (NNX13AI59G), PDART (NNX16AG51G) and AURA (NNX14AI55G) programs. References[1] L.S. Rothman et al, JQSRT 130, 4 (2013). [2] P. Wcisło et al., JQSRT 177, 75 (2016). [3] J. S. Wilzewski et al., JQSRT 168, 193 (2016). [4] S.W. Sharpe et al, Appl Spectrosc 58, 1452 (2004). [5] C. Hill et al, JQSRT 177, 4 (2016). [6] R.V. Kochanov et al, JQSRT 177, 15 (2016).

Literature searches on Ayurveda: An update

PubMed Central

Aggithaya, Madhur G.; Narahari, Saravu R.

2015-01-01

Introduction: The journals that publish on Ayurveda are increasingly indexed by popular medical databases in recent years. However, many Eastern journals are not indexed biomedical journal databases such as PubMed. Literature searches for Ayurveda continue to be challenging due to the nonavailability of active, unbiased dedicated databases for Ayurvedic literature. In 2010, authors identified 46 databases that can be used for systematic search of Ayurvedic papers and theses. This update reviewed our previous recommendation and identified current and relevant databases. Aims: To update on Ayurveda literature search and strategy to retrieve maximum publications. Methods: Author used psoriasis as an example to search previously listed databases and identify new. The population, intervention, control, and outcome table included keywords related to psoriasis and Ayurvedic terminologies for skin diseases. Current citation update status, search results, and search options of previous databases were assessed. Eight search strategies were developed. Hundred and five journals, both biomedical and Ayurveda, which publish on Ayurveda, were identified. Variability in databases was explored to identify bias in journal citation. Results: Five among 46 databases are now relevant – AYUSH research portal, Annotated Bibliography of Indian Medicine, Digital Helpline for Ayurveda Research Articles (DHARA), PubMed, and Directory of Open Access Journals. Search options in these databases are not uniform, and only PubMed allows complex search strategy. “The Researches in Ayurveda” and “Ayurvedic Research Database” (ARD) are important grey resources for hand searching. About 44/105 (41.5%) journals publishing Ayurvedic studies are not indexed in any database. Only 11/105 (10.4%) exclusive Ayurveda journals are indexed in PubMed. Conclusion: AYUSH research portal and DHARA are two major portals after 2010. It is mandatory to search PubMed and four other databases because all five carry citations from different groups of journals. The hand searching is important to identify Ayurveda publications that are not indexed elsewhere. Availability information of citations in Ayurveda libraries from National Union Catalogue of Scientific Serials in India if regularly updated will improve the efficacy of hand searching. A grey database (ARD) contains unpublished PG/Ph.D. theses. The AYUSH portal, DHARA (funded by Ministry of AYUSH), and ARD should be merged to form single larger database to limit Ayurveda literature searches. PMID:27313409

Updated and revised neutron reaction data for 237Np

NASA Astrophysics Data System (ADS)

Chen, Guochang; Wang, Jimin; Cao, Wentian; Tang, Guoyou; Yu, Baosheng

2017-09-01

Nuclear data with high accuracy for minor actinides play an important role in nuclear technology applications, including reactor design and operation, fuel cycle, estimation of the amount of minor actinides in high burn-up reactors and the minor actinides transmutation. Based on the evaluated experimental data, the updated and revised evaluation of a full set of n+237Np nuclear data from 10-5 eV ˜ 20 MeV are carried out and recommended. Mainly revised quantities are neutron multiplicities from fission reaction, inelastic, fission, (n, 2n) and (n, γ) reaction cross sections as well as angular distribution and so on. The promising results are obtained when the renewal evaluated data of 237Np will be used to instead of the evaluated data in CENDL-3.1 database.

The Biomolecular Interaction Network Database and related tools 2005 update

PubMed Central

Alfarano, C.; Andrade, C. E.; Anthony, K.; Bahroos, N.; Bajec, M.; Bantoft, K.; Betel, D.; Bobechko, B.; Boutilier, K.; Burgess, E.; Buzadzija, K.; Cavero, R.; D'Abreo, C.; Donaldson, I.; Dorairajoo, D.; Dumontier, M. J.; Dumontier, M. R.; Earles, V.; Farrall, R.; Feldman, H.; Garderman, E.; Gong, Y.; Gonzaga, R.; Grytsan, V.; Gryz, E.; Gu, V.; Haldorsen, E.; Halupa, A.; Haw, R.; Hrvojic, A.; Hurrell, L.; Isserlin, R.; Jack, F.; Juma, F.; Khan, A.; Kon, T.; Konopinsky, S.; Le, V.; Lee, E.; Ling, S.; Magidin, M.; Moniakis, J.; Montojo, J.; Moore, S.; Muskat, B.; Ng, I.; Paraiso, J. P.; Parker, B.; Pintilie, G.; Pirone, R.; Salama, J. J.; Sgro, S.; Shan, T.; Shu, Y.; Siew, J.; Skinner, D.; Snyder, K.; Stasiuk, R.; Strumpf, D.; Tuekam, B.; Tao, S.; Wang, Z.; White, M.; Willis, R.; Wolting, C.; Wong, S.; Wrong, A.; Xin, C.; Yao, R.; Yates, B.; Zhang, S.; Zheng, K.; Pawson, T.; Ouellette, B. F. F.; Hogue, C. W. V.

2005-01-01

The Biomolecular Interaction Network Database (BIND) (http://bind.ca) archives biomolecular interaction, reaction, complex and pathway information. Our aim is to curate the details about molecular interactions that arise from published experimental research and to provide this information, as well as tools to enable data analysis, freely to researchers worldwide. BIND data are curated into a comprehensive machine-readable archive of computable information and provides users with methods to discover interactions and molecular mechanisms. BIND has worked to develop new methods for visualization that amplify the underlying annotation of genes and proteins to facilitate the study of molecular interaction networks. BIND has maintained an open database policy since its inception in 1999. Data growth has proceeded at a tremendous rate, approaching over 100 000 records. New services provided include a new BIND Query and Submission interface, a Standard Object Access Protocol service and the Small Molecule Interaction Database (http://smid.blueprint.org) that allows users to determine probable small molecule binding sites of new sequences and examine conserved binding residues. PMID:15608229

The NASA Ames PAH IR Spectroscopic Database: Computational Version 3.00 with Updated Content and the Introduction of Multiple Scaling Factors

NASA Astrophysics Data System (ADS)

Bauschlicher, Charles W., Jr.; Ricca, A.; Boersma, C.; Allamandola, L. J.

2018-02-01

Version 3.00 of the library of computed spectra in the NASA Ames PAH IR Spectroscopic Database (PAHdb) is described. Version 3.00 introduces the use of multiple scale factors, instead of the single scaling factor used previously, to align the theoretical harmonic frequencies with the experimental fundamentals. The use of multiple scale factors permits the use of a variety of basis sets; this allows new PAH species to be included in the database, such as those containing oxygen, and yields an improved treatment of strained species and those containing nitrogen. In addition, the computed spectra of 2439 new PAH species have been added. The impact of these changes on the analysis of an astronomical spectrum through database-fitting is considered and compared with a fit using Version 2.00 of the library of computed spectra. Finally, astronomical constraints are defined for the PAH spectral libraries in PAHdb.

An update on Experimental and Clinical Psychopharmacology: Something old, something new, something borrowed, something green?

PubMed

Stoops, William W

2018-02-01

In this editorial, the author provides an update on Experimental and Clinical Psychopharmacology in several areas. First, the journal will continue to accept original research reports and full reviews as it has in past years. The author hopes to still receive outstanding manuscripts in the journal's primary areas of strength, such as clinical research on alcohol use and cigarette smoking. The journal will also continue to publish an annual special issue on a current topic in the field. Second, the journal now accepts brief communications, brief reviews, and case reports. The authors sees these new formats as opportunities to publish cutting edge, novel findings that may not be suitable as original research reports or full reviews-such work would previously not have fit with the journal. Third, the author has borrowed an idea from colleagues who serve as editors for other journals in the field: the addition of an editorial fellowship at Experimental and Clinical Psychopharmacology . Finally, the "something green" part of the title refers to the new, bright green cover color of the print version of the journal. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Questions and Answers for Reporting for the 2006 Partial Updating of the TSCA Chemical Inventory Database: Inorganic Chemicals Addendum

EPA Pesticide Factsheets

This document addresses specific questions related to reporting inorganic chemicals under the IUR and is an addendum to the Questions and Answers for Reporting for the 2006 Partial Updating of the TSCA Chemical Inventory Database (Questions and Answers Document).

Update of NDL’s list of key foods based on the 2007-2008 WWEIA-NHANES

USDA-ARS?s Scientific Manuscript database

The Nutrient Data Laboratory is responsible for developing authoritative nutrient databases that contain a wide range of food composition values of the nation's food supply. This requires updating and revising the USDA Nutrient Database for Standard Reference (SR) and developing various special int...

Performance analysis of different database in new internet mapping system

NASA Astrophysics Data System (ADS)

Yao, Xing; Su, Wei; Gao, Shuai

2017-03-01

In the Mapping System of New Internet, Massive mapping entries between AID and RID need to be stored, added, updated, and deleted. In order to better deal with the problem when facing a large number of mapping entries update and query request, the Mapping System of New Internet must use high-performance database. In this paper, we focus on the performance of Redis, SQLite, and MySQL these three typical databases, and the results show that the Mapping System based on different databases can adapt to different needs according to the actual situation.

Updating a Searchable Database of Dropout Prevention Programs and Policies in Nine Low-Income Urban School Districts in the Northeast and Islands Region. REL Technical Brief. REL 2012-No. 020

ERIC Educational Resources Information Center

Myint-U, Athi; O'Donnell, Lydia; Phillips, Dawna

2012-01-01

This technical brief describes updates to a database of dropout prevention programs and policies in 2006/07 created by the Regional Education Laboratory (REL) Northeast and Islands and described in the Issues & Answers report, "Piloting a searchable database of dropout prevention programs in nine low-income urban school districts in the…

The 2018 Nucleic Acids Research database issue and the online molecular biology database collection.

PubMed

Rigden, Daniel J; Fernández, Xosé M

2018-01-04

The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest. In the area of metabolism, HMDB and Reactome both report new features while PULDB appears in NAR for the first time. This issue also contains reports on genomics resources including Ensembl, the UCSC Genome Browser and ENCODE. Update papers from the IUPHAR/BPS Guide to Pharmacology and DrugBank are highlights of the drug and drug target section while a number of proteomics databases including proteomicsDB are also covered. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 138 entries, adding 88 new resources and eliminating 47 discontinued URLs, bringing the current total to 1737 databases. It is available at http://www.oxfordjournals.org/nar/database/c/. © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

Integration of Narrative Processing, Data Fusion, and Database Updating Techniques in an Automated System.

DTIC Science & Technology

1981-10-29

are implemented, respectively, in the files "W-Update," "W-combine" and RW-Copy," listed in the appendix. The appendix begins with a typescript of an...the typescript ) and the copying process (steps 45 and 46) are shown as human actions in the typescript , but can be performed easily by a "master...for Natural Language, M. Marcus, MIT Press, 1980. I 29 APPENDIX: DATABASE UPDATING EXPERIMENT 30 CONTENTS Typescript of an experiment in Rosie

76 FR 64859 - Pilot Loading of Navigation and Terrain Awareness Database Updates

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-19

... category the task of updating databases used in self-contained, front-panel or pedestal-mounted navigation... Rule This rulemaking would allow pilots of all certificated aircraft equipped with self-contained... verification, or by errors in ATC assignments which may occur during redirection of the flight. Both types of...

The UCSC Genome Browser database: extensions and updates 2013.

PubMed

Meyer, Laurence R; Zweig, Ann S; Hinrichs, Angie S; Karolchik, Donna; Kuhn, Robert M; Wong, Matthew; Sloan, Cricket A; Rosenbloom, Kate R; Roe, Greg; Rhead, Brooke; Raney, Brian J; Pohl, Andy; Malladi, Venkat S; Li, Chin H; Lee, Brian T; Learned, Katrina; Kirkup, Vanessa; Hsu, Fan; Heitner, Steve; Harte, Rachel A; Haeussler, Maximilian; Guruvadoo, Luvina; Goldman, Mary; Giardine, Belinda M; Fujita, Pauline A; Dreszer, Timothy R; Diekhans, Mark; Cline, Melissa S; Clawson, Hiram; Barber, Galt P; Haussler, David; Kent, W James

2013-01-01

The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database of genomic sequence and annotations for a wide variety of organisms. The Browser is an integrated tool set for visualizing, comparing, analysing and sharing both publicly available and user-generated genomic datasets. As of September 2012, genomic sequence and a basic set of annotation 'tracks' are provided for 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms, yeast and sea hare. In the past year 19 new genome assemblies have been added, and we anticipate releasing another 28 in early 2013. Further, a large number of annotation tracks have been either added, updated by contributors or remapped to the latest human reference genome. Among these are an updated UCSC Genes track for human and mouse assemblies. We have also introduced several features to improve usability, including new navigation menus. This article provides an update to the UCSC Genome Browser database, which has been previously featured in the Database issue of this journal.

LEPER: Library of Experimental PhasE Relations

NASA Astrophysics Data System (ADS)

Davis, F.; Gordon, S.; Mukherjee, S.; Hirschmann, M.; Ghiorso, M.

2006-12-01

The Library of Experimental PhasE Relations (LEPER) seeks to compile published experimental determinations of magmatic phase equilibria and provide those data on the web with a searchable and downloadable interface. Compiled experimental data include the conditions and durations of experiments, the bulk compositions of experimental charges, and the identity, compositions and proportions of phases observed, and, where available, estimates of experimental and analytical uncertainties. Also included are metadata such as the type of experimental device, capsule material, and method(s) of quantitative analysis. The database may be of use to practicing experimentalists as well as the wider Earth science community. Experimentalists may find the data useful for planning new experiments and will easily be able to compare their results to the full body of previous experimentnal data. Geologists may use LEPER to compare rocks sampled in the field with experiments performed on similar bulk composition or with experiments that produced similar-composition product phases. Modelers may use LEPER to parameterize partial melting of various lithologies. One motivation for compiling LEPER is for calibration of updated and revised versions of MELTS, however, it is hoped that the availability of LEPER will facilitate formulation and calibration of additional thermodynamic or empirical models of magmatic phase relations and phase equilibria, geothermometers and more. Data entry for LEPER is occuring presently: As of August, 2006, >6200 experiments have been entered, chiefly from work published between 1997 and 2005. A prototype web interface has been written and beta release on the web is anticipated in Fall, 2006. Eventually, experimentalists will be able to submit their new experimental data to the database via the web. At present, the database contains only data pertaining to the phase equilibria of silicate melts, but extension to other experimental data involving other fluids or sub-solidus phase equilibria may be contemplated. Also, the data are at present limited to natural or near-natural systems, but in the future, extension to synthetic (i.e., CMAS, etc.) systems is also possible. Each would depend in part on whether there is community demand for such databases. A trace element adjunct to LEPER is presently in planning stages.

DGIdb 3.0: a redesign and expansion of the drug-gene interaction database.

PubMed

Cotto, Kelsy C; Wagner, Alex H; Feng, Yang-Yang; Kiwala, Susanna; Coffman, Adam C; Spies, Gregory; Wollam, Alex; Spies, Nicholas C; Griffith, Obi L; Griffith, Malachi

2018-01-04

The drug-gene interaction database (DGIdb, www.dgidb.org) consolidates, organizes and presents drug-gene interactions and gene druggability information from papers, databases and web resources. DGIdb normalizes content from 30 disparate sources and allows for user-friendly advanced browsing, searching and filtering for ease of access through an intuitive web user interface, application programming interface (API) and public cloud-based server image. DGIdb v3.0 represents a major update of the database. Nine of the previously included 24 sources were updated. Six new resources were added, bringing the total number of sources to 30. These updates and additions of sources have cumulatively resulted in 56 309 interaction claims. This has also substantially expanded the comprehensive catalogue of druggable genes and anti-neoplastic drug-gene interactions included in the DGIdb. Along with these content updates, v3.0 has received a major overhaul of its codebase, including an updated user interface, preset interaction search filters, consolidation of interaction information into interaction groups, greatly improved search response times and upgrading the underlying web application framework. In addition, the expanded API features new endpoints which allow users to extract more detailed information about queried drugs, genes and drug-gene interactions, including listings of PubMed IDs, interaction type and other interaction metadata.

CyanoBase: the cyanobacteria genome database update 2010.

PubMed

Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

2010-01-01

CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in various formats with other tools, seamlessly.

Domain fusion analysis by applying relational algebra to protein sequence and domain databases.

PubMed

Truong, Kevin; Ikura, Mitsuhiko

2003-05-06

Domain fusion analysis is a useful method to predict functionally linked proteins that may be involved in direct protein-protein interactions or in the same metabolic or signaling pathway. As separate domain databases like BLOCKS, PROSITE, Pfam, SMART, PRINTS-S, ProDom, TIGRFAMs, and amalgamated domain databases like InterPro continue to grow in size and quality, a computational method to perform domain fusion analysis that leverages on these efforts will become increasingly powerful. This paper proposes a computational method employing relational algebra to find domain fusions in protein sequence databases. The feasibility of this method was illustrated on the SWISS-PROT+TrEMBL sequence database using domain predictions from the Pfam HMM (hidden Markov model) database. We identified 235 and 189 putative functionally linked protein partners in H. sapiens and S. cerevisiae, respectively. From scientific literature, we were able to confirm many of these functional linkages, while the remainder offer testable experimental hypothesis. Results can be viewed at http://calcium.uhnres.utoronto.ca/pi. As the analysis can be computed quickly on any relational database that supports standard SQL (structured query language), it can be dynamically updated along with the sequence and domain databases, thereby improving the quality of predictions over time.

Insertion algorithms for network model database management systems

NASA Astrophysics Data System (ADS)

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.

An Updating System for the Gridded Population Database of China Based on Remote Sensing, GIS and Spatial Database Technologies.

PubMed

Yang, Xiaohuan; Huang, Yaohuan; Dong, Pinliang; Jiang, Dong; Liu, Honghui

2009-01-01

The spatial distribution of population is closely related to land use and land cover (LULC) patterns on both regional and global scales. Population can be redistributed onto geo-referenced square grids according to this relation. In the past decades, various approaches to monitoring LULC using remote sensing and Geographic Information Systems (GIS) have been developed, which makes it possible for efficient updating of geo-referenced population data. A Spatial Population Updating System (SPUS) is developed for updating the gridded population database of China based on remote sensing, GIS and spatial database technologies, with a spatial resolution of 1 km by 1 km. The SPUS can process standard Moderate Resolution Imaging Spectroradiometer (MODIS L1B) data integrated with a Pattern Decomposition Method (PDM) and an LULC-Conversion Model to obtain patterns of land use and land cover, and provide input parameters for a Population Spatialization Model (PSM). The PSM embedded in SPUS is used for generating 1 km by 1 km gridded population data in each population distribution region based on natural and socio-economic variables. Validation results from finer township-level census data of Yishui County suggest that the gridded population database produced by the SPUS is reliable.

SATRAT: Staphylococcus aureus transcript regulatory network analysis tool.

PubMed

Gopal, Tamilselvi; Nagarajan, Vijayaraj; Elasri, Mohamed O

2015-01-01

Staphylococcus aureus is a commensal organism that primarily colonizes the nose of healthy individuals. S. aureus causes a spectrum of infections that range from skin and soft-tissue infections to fatal invasive diseases. S. aureus uses a large number of virulence factors that are regulated in a coordinated fashion. The complex regulatory mechanisms have been investigated in numerous high-throughput experiments. Access to this data is critical to studying this pathogen. Previously, we developed a compilation of microarray experimental data to enable researchers to search, browse, compare, and contrast transcript profiles. We have substantially updated this database and have built a novel exploratory tool-SATRAT-the S. aureus transcript regulatory network analysis tool, based on the updated database. This tool is capable of performing deep searches using a query and generating an interactive regulatory network based on associations among the regulators of any query gene. We believe this integrated regulatory network analysis tool would help researchers explore the missing links and identify novel pathways that regulate virulence in S. aureus. Also, the data model and the network generation code used to build this resource is open sourced, enabling researchers to build similar resources for other bacterial systems.

Comprehensive T-matrix Reference Database: A 2009-2011 Update

NASA Technical Reports Server (NTRS)

Zakharova, Nadezhda T.; Videen, G.; Khlebtsov, Nikolai G.

2012-01-01

The T-matrix method is one of the most versatile and efficient theoretical techniques widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of peer-reviewed T-matrix publications compiled by us previously and includes the publications that appeared since 2009. It also lists several earlier publications not included in the original database.

CyanoBase: the cyanobacteria genome database update 2010

PubMed Central

Nakao, Mitsuteru; Okamoto, Shinobu; Kohara, Mitsuyo; Fujishiro, Tsunakazu; Fujisawa, Takatomo; Sato, Shusei; Tabata, Satoshi; Kaneko, Takakazu; Nakamura, Yasukazu

2010-01-01

CyanoBase (http://genome.kazusa.or.jp/cyanobase) is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and mutant information. In this version, we updated these datasets and improved the navigation and the visual display of the data views. In addition, a web service API now enables users to retrieve the data in various formats with other tools, seamlessly. PMID:19880388

Active fault databases: building a bridge between earthquake geologists and seismic hazard practitioners, the case of the QAFI v.3 database

NASA Astrophysics Data System (ADS)

García-Mayordomo, Julián; Martín-Banda, Raquel; Insua-Arévalo, Juan M.; Álvarez-Gómez, José A.; Martínez-Díaz, José J.; Cabral, João

2017-08-01

Active fault databases are a very powerful and useful tool in seismic hazard assessment, particularly when singular faults are considered seismogenic sources. Active fault databases are also a very relevant source of information for earth scientists, earthquake engineers and even teachers or journalists. Hence, active fault databases should be updated and thoroughly reviewed on a regular basis in order to keep a standard quality and uniformed criteria. Desirably, active fault databases should somehow indicate the quality of the geological data and, particularly, the reliability attributed to crucial fault-seismic parameters, such as maximum magnitude and recurrence interval. In this paper we explain how we tackled these issues during the process of updating and reviewing the Quaternary Active Fault Database of Iberia (QAFI) to its current version 3. We devote particular attention to describing the scheme devised for classifying the quality and representativeness of the geological evidence of Quaternary activity and the accuracy of the slip rate estimation in the database. Subsequently, we use this information as input for a straightforward rating of the level of reliability of maximum magnitude and recurrence interval fault seismic parameters. We conclude that QAFI v.3 is a much better database than version 2 either for proper use in seismic hazard applications or as an informative source for non-specialized users. However, we already envision new improvements for a future update.

Updated Palaeotsunami Database for Aotearoa/New Zealand

NASA Astrophysics Data System (ADS)

Gadsby, M. R.; Goff, J. R.; King, D. N.; Robbins, J.; Duesing, U.; Franz, T.; Borrero, J. C.; Watkins, A.

2016-12-01

The updated configuration, design, and implementation of a national palaeotsunami (pre-historic tsunami) database for Aotearoa/New Zealand (A/NZ) is near completion. This tool enables correlation of events along different stretches of the NZ coastline, provides information on frequency and extent of local, regional and distant-source tsunamis, and delivers detailed information on the science and proxies used to identify the deposits. In A/NZ a plethora of data, scientific research and experience surrounds palaeotsunami deposits, but much of this information has been difficult to locate, has variable reporting standards, and lacked quality assurance. The original database was created by Professor James Goff while working at the National Institute of Water & Atmospheric Research in A/NZ, but has subsequently been updated during his tenure at the University of New South Wales. The updating and establishment of the national database was funded by the Ministry of Civil Defence and Emergency Management (MCDEM), led by Environment Canterbury Regional Council, and supported by all 16 regions of A/NZ's local government. Creation of a single database has consolidated a wide range of published and unpublished research contributions from many science providers on palaeotsunamis in A/NZ. The information is now easily accessible and quality assured and allows examination of frequency, extent and correlation of events. This provides authoritative scientific support for coastal-marine planning and risk management. The database will complement the GNS New Zealand Historical Database, and contributes to a heightened public awareness of tsunami by being a "one-stop-shop" for information on past tsunami impacts. There is scope for this to become an international database, enabling the pacific-wide correlation of large events, as well as identifying smaller regional ones. The Australian research community has already expressed an interest, and the database is also compatible with a similar one currently under development in Japan. Expressions of interest in collaborating with the A/NZ team to expand the database are invited from other Pacific nations.

The 2015 edition of the GEISA spectroscopic database

NASA Astrophysics Data System (ADS)

Jacquinet-Husson, N.; Armante, R.; Scott, N. A.; Chédin, A.; Crépeau, L.; Boutammine, C.; Bouhdaoui, A.; Crevoisier, C.; Capelle, V.; Boonne, C.; Poulet-Crovisier, N.; Barbe, A.; Chris Benner, D.; Boudon, V.; Brown, L. R.; Buldyreva, J.; Campargue, A.; Coudert, L. H.; Devi, V. M.; Down, M. J.; Drouin, B. J.; Fayt, A.; Fittschen, C.; Flaud, J.-M.; Gamache, R. R.; Harrison, J. J.; Hill, C.; Hodnebrog, Ø.; Hu, S.-M.; Jacquemart, D.; Jolly, A.; Jiménez, E.; Lavrentieva, N. N.; Liu, A.-W.; Lodi, L.; Lyulin, O. M.; Massie, S. T.; Mikhailenko, S.; Müller, H. S. P.; Naumenko, O. V.; Nikitin, A.; Nielsen, C. J.; Orphal, J.; Perevalov, V. I.; Perrin, A.; Polovtseva, E.; Predoi-Cross, A.; Rotger, M.; Ruth, A. A.; Yu, S. S.; Sung, K.; Tashkun, S. A.; Tennyson, J.; Tyuterev, Vl. G.; Vander Auwera, J.; Voronin, B. A.; Makie, A.

2016-09-01

The GEISA database (Gestion et Etude des Informations Spectroscopiques Atmosphériques: Management and Study of Atmospheric Spectroscopic Information) has been developed and maintained by the http://ara.abct.lmd.polytechnique.fr. The "line parameters database" contains 52 molecular species (118 isotopologues) and transitions in the spectral range from 10-6 to 35,877.031 cm-1, representing 5,067,351 entries, against 3,794,297 in GEISA-2011. Among the previously existing molecules, 20 molecular species have been updated. A new molecule (SO3) has been added. HDO, isotopologue of H2O, is now identified as an independent molecular species. Seven new isotopologues have been added to the GEISA-2015 database. The "cross section sub-database" has been enriched by the addition of 43 new molecular species in its infrared part, 4 molecules (ethane, propane, acetone, acetonitrile) are also updated; they represent 3% of the update. A new section is added, in the near-infrared spectral region, involving 7 molecular species: CH3CN, CH3I, CH3O2, H2CO, HO2, HONO, NH3. The "microphysical and optical properties of atmospheric aerosols sub-database" has been updated for the first time since 2003. It contains more than 40 species originating from NCAR and 20 from the http://eodg.atm.ox.ac.uk/ARIA/introduction_nocol.html. As for the previous versions, this new release of GEISA and associated management software facilities are implemented and freely accessible on the http://cds-espri.ipsl.fr/etherTypo/?id=950.

Recent updates and developments to plant genome size databases

PubMed Central

Garcia, Sònia; Leitch, Ilia J.; Anadon-Rosell, Alba; Canela, Miguel Á.; Gálvez, Francisco; Garnatje, Teresa; Gras, Airy; Hidalgo, Oriane; Johnston, Emmeline; Mas de Xaxars, Gemma; Pellicer, Jaume; Siljak-Yakovlev, Sonja; Vallès, Joan; Vitales, Daniel; Bennett, Michael D.

2014-01-01

Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols. PMID:24288377

Teleform scannable data entry: an efficient method to update a community-based medical record? Community care coordination network Database Group.

PubMed Central

Guerette, P.; Robinson, B.; Moran, W. P.; Messick, C.; Wright, M.; Wofford, J.; Velez, R.

1995-01-01

Community-based multi-disciplinary care of chronically ill individuals frequently requires the efforts of several agencies and organizations. The Community Care Coordination Network (CCCN) is an effort to establish a community-based clinical database and electronic communication system to facilitate the exchange of pertinent patient data among primary care, community-based and hospital-based providers. In developing a primary care based electronic record, a method is needed to update records from the field or remote sites and agencies and yet maintain data quality. Scannable data entry with fixed fields, optical character recognition and verification was compared to traditional keyboard data entry to determine the relative efficiency of each method in updating the CCCN database. PMID:8563414

OriDB, the DNA replication origin database updated and extended.

PubMed

Siow, Cheuk C; Nieduszynska, Sian R; Müller, Carolin A; Nieduszynski, Conrad A

2012-01-01

OriDB (http://www.oridb.org/) is a database containing collated genome-wide mapping studies of confirmed and predicted replication origin sites. The original database collated and curated Saccharomyces cerevisiae origin mapping studies. Here, we report that the OriDB database and web site have been revamped to improve user accessibility to curated data sets, to greatly increase the number of curated origin mapping studies, and to include the collation of replication origin sites in the fission yeast Schizosaccharomyces pombe. The revised database structure underlies these improvements and will facilitate further expansion in the future. The updated OriDB for S. cerevisiae is available at http://cerevisiae.oridb.org/ and for S. pombe at http://pombe.oridb.org/.

PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank.

PubMed

Tusnády, Gábor E; Dosztányi, Zsuzsanna; Simon, István

2005-01-01

PDB_TM is a database for transmembrane proteins with known structures. It aims to collect all transmembrane proteins that are deposited in the protein structure database (PDB) and to determine their membrane-spanning regions. These assignments are based on the TMDET algorithm, which uses only structural information to locate the most likely position of the lipid bilayer and to distinguish between transmembrane and globular proteins. This algorithm was applied to all PDB entries and the results were collected in the PDB_TM database. By using TMDET algorithm, the PDB_TM database can be automatically updated every week, keeping it synchronized with the latest PDB updates. The PDB_TM database is available at http://www.enzim.hu/PDB_TM.

Text mining for metabolic pathways, signaling cascades, and protein networks.

PubMed

Hoffmann, Robert; Krallinger, Martin; Andres, Eduardo; Tamames, Javier; Blaschke, Christian; Valencia, Alfonso

2005-05-10

The complexity of the information stored in databases and publications on metabolic and signaling pathways, the high throughput of experimental data, and the growing number of publications make it imperative to provide systems to help the researcher navigate through these interrelated information resources. Text-mining methods have started to play a key role in the creation and maintenance of links between the information stored in biological databases and its original sources in the literature. These links will be extremely useful for database updating and curation, especially if a number of technical problems can be solved satisfactorily, including the identification of protein and gene names (entities in general) and the characterization of their types of interactions. The first generation of openly accessible text-mining systems, such as iHOP (Information Hyperlinked over Proteins), provides additional functions to facilitate the reconstruction of protein interaction networks, combine database and text information, and support the scientist in the formulation of novel hypotheses. The next challenge is the generation of comprehensive information regarding the general function of signaling pathways and protein interaction networks.

Comprehensive T-Matrix Reference Database: A 2007-2009 Update

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Zakharova, Nadia T.; Videen, Gorden; Khlebtsov, Nikolai G.; Wriedt, Thomas

2010-01-01

The T-matrix method is among the most versatile, efficient, and widely used theoretical techniques for the numerically exact computation of electromagnetic scattering by homogeneous and composite particles, clusters of particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper presents an update to the comprehensive database of T-matrix publications compiled by us previously and includes the publications that appeared since 2007. It also lists several earlier publications not included in the original database.

Digital images in the map revision process

NASA Astrophysics Data System (ADS)

Newby, P. R. T.

Progress towards the adoption of digital (or softcopy) photogrammetric techniques for database and map revision is reviewed. Particular attention is given to the Ordnance Survey of Great Britain, the author's former employer, where digital processes are under investigation but have not yet been introduced for routine production. Developments which may lead to increasing automation of database update processes appear promising, but because of the cost and practical problems associated with managing as well as updating large digital databases, caution is advised when considering the transition to softcopy photogrammetry for revision tasks.

GlycomeDB – integration of open-access carbohydrate structure databases

PubMed Central

Ranzinger, René; Herget, Stephan; Wetter, Thomas; von der Lieth, Claus-Wilhelm

2008-01-01

Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource. PMID:18803830

77 FR 24925 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-26

... CES Personnel Information System database of NIFA. This database is updated annually from data provided by 1862 and 1890 land-grant universities. This database is maintained by the Agricultural Research... reviewer. NIFA maintains a database of potential reviewers. Information in the database is used to match...

Sharing mutants and experimental information prepublication using FgMutantDb (https://scabusa.org/FgMutantDb).

PubMed

Baldwin, Thomas T; Basenko, Evelina; Harb, Omar; Brown, Neil A; Urban, Martin; Hammond-Kosack, Kim E; Bregitzer, Phil P

2018-06-01

There is no comprehensive storage for generated mutants of Fusarium graminearum or data associated with these mutants. Instead, researchers relied on several independent and non-integrated databases. FgMutantDb was designed as a simple spreadsheet that is accessible globally on the web that will function as a centralized source of information on F. graminearum mutants. FgMutantDb aids in the maintenance and sharing of mutants within a research community. It will serve also as a platform for disseminating prepublication results as well as negative results that often go unreported. Additionally, the highly curated information on mutants in FgMutantDb will be shared with other databases (FungiDB, Ensembl, PhytoPath, and PHI-base) through updating reports. Here we describe the creation and potential usefulness of FgMutantDb to the F. graminearum research community, and provide a tutorial on its use. This type of database could be easily emulated for other fungal species. Published by Elsevier Inc.

Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures

PubMed Central

Kinjo, Akira R.; Bekker, Gert-Jan; Suzuki, Hirofumi; Tsuchiya, Yuko; Kawabata, Takeshi; Ikegawa, Yasuyo; Nakamura, Haruki

2017-01-01

The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described. PMID:27789697

Numerical model updating technique for structures using firefly algorithm

NASA Astrophysics Data System (ADS)

Sai Kubair, K.; Mohan, S. C.

2018-03-01

Numerical model updating is a technique used for updating the existing experimental models for any structures related to civil, mechanical, automobiles, marine, aerospace engineering, etc. The basic concept behind this technique is updating the numerical models to closely match with experimental data obtained from real or prototype test structures. The present work involves the development of numerical model using MATLAB as a computational tool and with mathematical equations that define the experimental model. Firefly algorithm is used as an optimization tool in this study. In this updating process a response parameter of the structure has to be chosen, which helps to correlate the numerical model developed with the experimental results obtained. The variables for the updating can be either material or geometrical properties of the model or both. In this study, to verify the proposed technique, a cantilever beam is analyzed for its tip deflection and a space frame has been analyzed for its natural frequencies. Both the models are updated with their respective response values obtained from experimental results. The numerical results after updating show that there is a close relationship that can be brought between the experimental and the numerical models.

Network control processor for a TDMA system

NASA Astrophysics Data System (ADS)

Suryadevara, Omkarmurthy; Debettencourt, Thomas J.; Shulman, R. B.

Two unique aspects of designing a network control processor (NCP) to monitor and control a demand-assigned, time-division multiple-access (TDMA) network are described. The first involves the implementation of redundancy by synchronizing the databases of two geographically remote NCPs. The two sets of databases are kept in synchronization by collecting data on both systems, transferring databases, sending incremental updates, and the parallel updating of databases. A periodic audit compares the checksums of the databases to ensure synchronization. The second aspect involves the use of a tracking algorithm to dynamically reallocate TDMA frame space. This algorithm detects and tracks current and long-term load changes in the network. When some portions of the network are overloaded while others have excess capacity, the algorithm automatically calculates and implements a new burst time plan.

Recent Efforts in Data Compilations for Nuclear Astrophysics

NASA Astrophysics Data System (ADS)

Dillmann, Iris

2008-05-01

Some recent efforts in compiling data for astrophysical purposes are introduced, which were discussed during a JINA-CARINA Collaboration meeting on ``Nuclear Physics Data Compilation for Nucleosynthesis Modeling'' held at the ECT* in Trento/Italy from May 29th-June 3rd, 2007. The main goal of this collaboration is to develop an updated and unified nuclear reaction database for modeling a wide variety of stellar nucleosynthesis scenarios. Presently a large number of different reaction libraries (REACLIB) are used by the astrophysics community. The ``JINA Reaclib Database'' on http://www.nscl.msu.edu/~nero/db/ aims to merge and fit the latest experimental stellar cross sections and reaction rate data of various compilations, e.g. NACRE and its extension for Big Bang nucleosynthesis, Caughlan and Fowler, Iliadis et al., and KADoNiS. The KADoNiS (Karlsruhe Astrophysical Database of Nucleosynthesis in Stars, http://nuclear-astrophysics.fzk.de/kadonis) project is an online database for neutron capture cross sections relevant to the s process. The present version v0.2 is already included in a REACLIB file from Basel university (http://download.nucastro.org/astro/reaclib). The present status of experimental stellar (n,γ) cross sections in KADoNiS is shown. It contains recommended cross sections for 355 isotopes between 1H and 210Bi, over 80% of them deduced from experimental data. A ``high priority list'' for measurements and evaluations for light charged-particle reactions set up by the JINA-CARINA collaboration is presented. The central web access point to submit and evaluate new data is provided by the Oak Ridge group via the http://www.nucastrodata.org homepage. ``Workflow tools'' aim to make the evaluation process transparent and allow users to follow the progress.

Berkeley Lab - Materials Sciences Division

Science.gov Websites

Postdoc Forum Research Highlights Awards Publications Database Events Calendar Newsletter Archive People Database Events Calendar Newsletter Archive Send us your research highlights. Reserch Highlight Template (powerpoint) Publications Database The MSD publications database has been updated to include all FY2014

Patent Databases. . .A Survey of What Is Available from DIALOG, Questel, SDC, Pergamon and INPADOC.

ERIC Educational Resources Information Center

Kulp, Carol S.

1984-01-01

Presents survey of two groups of databases covering patent literature: patent literature only and general literature that includes patents relevant to subject area of database. Description of databases and comparison tables for patent and general databases (cost, country coverage, years covered, update frequency, file size, and searchable data…

Orientation Modeling for Amateur Cameras by Matching Image Line Features and Building Vector Data

NASA Astrophysics Data System (ADS)

Hung, C. H.; Chang, W. C.; Chen, L. C.

2016-06-01

With the popularity of geospatial applications, database updating is getting important due to the environmental changes over time. Imagery provides a lower cost and efficient way to update the database. Three dimensional objects can be measured by space intersection using conjugate image points and orientation parameters of cameras. However, precise orientation parameters of light amateur cameras are not always available due to their costliness and heaviness of precision GPS and IMU. To automatize data updating, the correspondence of object vector data and image may be built to improve the accuracy of direct georeferencing. This study contains four major parts, (1) back-projection of object vector data, (2) extraction of image feature lines, (3) object-image feature line matching, and (4) line-based orientation modeling. In order to construct the correspondence of features between an image and a building model, the building vector features were back-projected onto the image using the initial camera orientation from GPS and IMU. Image line features were extracted from the imagery. Afterwards, the matching procedure was done by assessing the similarity between the extracted image features and the back-projected ones. Then, the fourth part utilized line features in orientation modeling. The line-based orientation modeling was performed by the integration of line parametric equations into collinearity condition equations. The experiment data included images with 0.06 m resolution acquired by Canon EOS Mark 5D II camera on a Microdrones MD4-1000 UAV. Experimental results indicate that 2.1 pixel accuracy may be reached, which is equivalent to 0.12 m in the object space.

T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System.

PubMed

Tay, Daniel Ming Ming; Govindarajan, Kunde Ramamoorthy; Khan, Asif M; Ong, Terenze Yao Rui; Samad, Hanif M; Soh, Wei Wei; Tong, Minyan; Zhang, Fan; Tan, Tin Wee

2010-10-15

Effectors of Type III Secretion System (T3SS) play a pivotal role in establishing and maintaining pathogenicity in the host and therefore the identification of these effectors is important in understanding virulence. However, the effectors display high level of sequence diversity, therefore making the identification a difficult process. There is a need to collate and annotate existing effector sequences in public databases to enable systematic analyses of these sequences for development of models for screening and selection of putative novel effectors from bacterial genomes that can be validated by a smaller number of key experiments. Herein, we present T3SEdb http://effectors.bic.nus.edu.sg/T3SEdb, a specialized database of annotated T3SS effector (T3SE) sequences containing 1089 records from 46 bacterial species compiled from the literature and public protein databases. Procedures have been defined for i) comprehensive annotation of experimental status of effectors, ii) submission and curation review of records by users of the database, and iii) the regular update of T3SEdb existing and new records. Keyword fielded and sequence searches (BLAST, regular expression) are supported for both experimentally verified and hypothetical T3SEs. More than 171 clusters of T3SEs were detected based on sequence identity comparisons (intra-cluster difference up to ~60%). Owing to this high level of sequence diversity of T3SEs, the T3SEdb provides a large number of experimentally known effector sequences with wide species representation for creation of effector predictors. We created a reliable effector prediction tool, integrated into the database, to demonstrate the application of the database for such endeavours. T3SEdb is the first specialised database reported for T3SS effectors, enriched with manual annotations that facilitated systematic construction of a reliable prediction model for identification of novel effectors. The T3SEdb represents a platform for inclusion of additional annotations of metadata for future developments of sophisticated effector prediction models for screening and selection of putative novel effectors from bacterial genomes/proteomes that can be validated by a small number of key experiments.

Development of a database for Louisiana highway bridge scour data : technical summary.

DOT National Transportation Integrated Search

1999-10-01

The objectives of the project included: 1) developed a database with manipulation capabilities such as data retrieval, visualization, and update; 2) Input the existing scour data from DOTD files into the database.

EcoGene 3.0

PubMed Central

Zhou, Jindan; Rudd, Kenneth E.

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection. PMID:23197660

IRIS TOXICOLOGICAL REVIEW AND SUMMARY ...

EPA Pesticide Factsheets

EPA's assessment of the noncancer health effects and carcinogenic potential of 1,2,3-trichloropropane (TCP) was added to the IRIS database in 1990. The IRIS program is updating the IRIS assessment for TCP. This update will incorporate health effects information published since the last assessment was prepared as well as new risk assessment methods. The IRIS assessment for TCP will consist of a Toxicological Review and IRIS Summary. The Toxicological Review is a critical review of the physicochemical and toxicokinetic properties of the chemical and its toxicity in humans and experimental systems. The assessment will present reference values for noncancer effects of TCP (RfD and RfC) and a cancer assessment. The Toxicological Review and IRIS Summary will be subject to internal peer consultation, Agency review, and external scientific peer review. The final products will constitute the Agency's opinion on the toxicity of TCP. EPA is undertaking an Integrated Risk Information System (IRIS) health assessment for 1,2,3-trichloropropane. IRIS is an EPA database containing the Agency's consensus scientific positions on potential adverse human effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information in support of two steps of the risk assessment process, i.e., hazard identification and dose-response evaluation. IRIS assessments are used in

EcoGene 3.0.

PubMed

Zhou, Jindan; Rudd, Kenneth E

2013-01-01

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection.

Methanol test

MedlinePlus

... Safety and Health. Emergency Response Safety and Health Database. Methanol: systemic agent. Updated May 28, 2015. www. ... ADAM Health Solutions. About MedlinePlus Site Map FAQs Customer Support Get email updates Subscribe to RSS Follow ...

Smart Location Database - Service

EPA Pesticide Factsheets

The Smart Location Database (SLD) summarizes over 80 demographic, built environment, transit service, and destination accessibility attributes for every census block group in the United States. Future updates to the SLD will include additional attributes which summarize the relative location efficiency of a block group when compared to other block groups within the same metropolitan region. EPA also plans to periodically update attributes and add new attributes to reflect latest available data. A log of SLD updates is included in the SLD User Guide. See the user guide for a full description of data sources, data currency, and known limitations: https://edg.epa.gov/data/Public/OP/SLD/SLD_userguide.pdf

Smart Location Database - Download

EPA Pesticide Factsheets

The Smart Location Database (SLD) summarizes over 80 demographic, built environment, transit service, and destination accessibility attributes for every census block group in the United States. Future updates to the SLD will include additional attributes which summarize the relative location efficiency of a block group when compared to other block groups within the same metropolitan region. EPA also plans to periodically update attributes and add new attributes to reflect latest available data. A log of SLD updates is included in the SLD User Guide. See the user guide for a full description of data sources, data currency, and known limitations: https://edg.epa.gov/data/Public/OP/SLD/SLD_userguide.pdf

HITRAN2016: Part I. Line lists for H_2O, CO_2, O_3, N_2O, CO, CH_4, and O_2

NASA Astrophysics Data System (ADS)

Gordon, Iouli E.; Rothman, Laurence S.; Tan, Yan; Kochanov, Roman V.; Hill, Christian

2017-06-01

The HITRAN2016 database is now officially released. Plethora of experimental and theoretical molecular spectroscopic data were collected, evaluated and vetted before compiling the new edition of the database. The database is now distributed through the dynamic user interface HITRANonline (available at www.hitran.org) which offers many flexible options for browsing and downloading the data. In addition HITRAN Application Programming Interface (HAPI) offers modern ways to download the HITRAN data and use it to carry out sophisticated calculations. The line-by-line lists for almost all of the 47 HITRAN molecules were updated in comparison with the previous compilation (HITRAN2012. Some of the most important updates for major atmospheric absorbers, such as H_2O, CO_2, O_3, N_2O, CO, CH_4, and O_2, will be presented in this talk, while the trace gases will be presented in the next talk by Y. Tan. The HITRAN2016 database now provides alternative line-shape representations for a number of molecules, as well as broadening by gases dominant in planetary atmospheres. In addition, substantial extension and improvement of cross-section data is featured, which will be described in a dedicated talk by R. V. Kochanov. The new edition of the database is a substantial step forward to improve retrievals of the planetary atmospheric constituents in comparison with previous editions, while offering new ways of working with the data. The HITRAN database is supported by the NASA AURA and PDART program grants NNX14AI55G and NNX16AG51G. I. E. Gordon, L. S. Rothman, C. Hill, R. V. Kochanov, Y. Tan, et al. The HITRAN2016 Molecular Spectroscopic Database. JQSRT 2017;submitted. Many spectroscopists and atmospheric scientists worldwide have contributed data to the database or provided invaluable validations. C. Hill, I. E. Gordon, R. V. Kochanov, L. Barrett, J.S. Wilzewski, L.S. Rothman, JQSRT. 177 (2016) 4-14 R.V. Kochanov, I. E. Gordon, L. S. Rothman, P. Wcislo, C. Hill, J. S. Wilzewski, JQSRT. 177 (2016) 15-30. L. S. Rothman, I. E. Gordon et al. The HITRAN2012 Molecular Spectroscopic Database. JQSRT, 113 (2013) 4-50.

Mars Science Laboratory Frame Manager for Centralized Frame Tree Database and Target Pointing

NASA Technical Reports Server (NTRS)

Kim, Won S.; Leger, Chris; Peters, Stephen; Carsten, Joseph; Diaz-Calderon, Antonio

2013-01-01

The FM (Frame Manager) flight software module is responsible for maintaining the frame tree database containing coordinate transforms between frames. The frame tree is a proper tree structure of directed links, consisting of surface and rover subtrees. Actual frame transforms are updated by their owner. FM updates site and saved frames for the surface tree. As the rover drives to a new area, a new site frame with an incremented site index can be created. Several clients including ARM and RSM (Remote Sensing Mast) update their related rover frames that they own. Through the onboard centralized FM frame tree database, client modules can query transforms between any two frames. Important applications include target image pointing for RSM-mounted cameras and frame-referenced arm moves. The use of frame tree eliminates cumbersome, error-prone calculations of coordinate entries for commands and thus simplifies flight operations significantly.

UCbase 2.0: ultraconserved sequences database (2014 update)

PubMed Central

Lomonaco, Vincenzo; Martoglia, Riccardo; Mandreoli, Federica; Anderlucci, Laura; Emmett, Warren; Bicciato, Silvio; Taccioli, Cristian

2014-01-01

UCbase 2.0 (http://ucbase.unimore.it) is an update, extension and evolution of UCbase, a Web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase 2.0 is a platform-independent Web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for Single Nucleotide Polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase 2.0 now includes a graph visualization interface directly linked to UCSC genome browser. Database URL: http://ucbase.unimore.it PMID:24951797

A decade of Web Server updates at the Bioinformatics Links Directory: 2003-2012.

PubMed

Brazas, Michelle D; Yim, David; Yeung, Winston; Ouellette, B F Francis

2012-07-01

The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

Development and Operation of a Database Machine for Online Access and Update of a Large Database.

ERIC Educational Resources Information Center

Rush, James E.

1980-01-01

Reviews the development of a fault tolerant database processor system which replaced OCLC's conventional file system. A general introduction to database management systems and the operating environment is followed by a description of the hardware selection, software processes, and system characteristics. (SW)

CycADS: an annotation database system to ease the development and update of BioCyc databases

PubMed Central

Vellozo, Augusto F.; Véron, Amélie S.; Baa-Puyoulet, Patrice; Huerta-Cepas, Jaime; Cottret, Ludovic; Febvay, Gérard; Calevro, Federica; Rahbé, Yvan; Douglas, Angela E.; Gabaldón, Toni; Sagot, Marie-France; Charles, Hubert; Colella, Stefano

2011-01-01

In recent years, genomes from an increasing number of organisms have been sequenced, but their annotation remains a time-consuming process. The BioCyc databases offer a framework for the integrated analysis of metabolic networks. The Pathway tool software suite allows the automated construction of a database starting from an annotated genome, but it requires prior integration of all annotations into a specific summary file or into a GenBank file. To allow the easy creation and update of a BioCyc database starting from the multiple genome annotation resources available over time, we have developed an ad hoc data management system that we called Cyc Annotation Database System (CycADS). CycADS is centred on a specific database model and on a set of Java programs to import, filter and export relevant information. Data from GenBank and other annotation sources (including for example: KAAS, PRIAM, Blast2GO and PhylomeDB) are collected into a database to be subsequently filtered and extracted to generate a complete annotation file. This file is then used to build an enriched BioCyc database using the PathoLogic program of Pathway Tools. The CycADS pipeline for annotation management was used to build the AcypiCyc database for the pea aphid (Acyrthosiphon pisum) whose genome was recently sequenced. The AcypiCyc database webpage includes also, for comparative analyses, two other metabolic reconstruction BioCyc databases generated using CycADS: TricaCyc for Tribolium castaneum and DromeCyc for Drosophila melanogaster. Linked to its flexible design, CycADS offers a powerful software tool for the generation and regular updating of enriched BioCyc databases. The CycADS system is particularly suited for metabolic gene annotation and network reconstruction in newly sequenced genomes. Because of the uniform annotation used for metabolic network reconstruction, CycADS is particularly useful for comparative analysis of the metabolism of different organisms. Database URL: http://www.cycadsys.org PMID:21474551

UniPROBE, update 2011: expanded content and search tools in the online database of protein-binding microarray data on protein-DNA interactions.

PubMed

Robasky, Kimberly; Bulyk, Martha L

2011-01-01

The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray (PBM) technology. Each entry for a protein (or protein complex) in UniPROBE provides the quantitative preferences for all possible nucleotide sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In this update, we describe >130% expansion of the database content, incorporation of a protein BLAST (blastp) tool for finding protein sequence matches in UniPROBE, the introduction of UniPROBE accession numbers and additional database enhancements. The UniPROBE database is available at http://uniprobe.org.

The Arabidopsis Information Resource: Making and Mining the ‘Gold Standard’ Annotated Reference Plant Genome

PubMed Central

Berardini, Tanya Z.; Reiser, Leonore; Li, Donghui; Mezheritsky, Yarik; Muller, Robert; Strait, Emily; Huala, Eva

2015-01-01

The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 Arabidopsis genes. TAIR’s biocurators systematically extract, organize, and interconnect experimental data from the literature along with computational predictions, community submissions, and high throughput datasets to present a high quality and comprehensive picture of Arabidopsis gene function. TAIR provides tools for data visualization and analysis, and enables ordering of seed and DNA stocks, protein chips and other experimental resources. TAIR actively engages with its users who contribute expertise and data that augments the work of the curatorial staff. TAIR’s focus in an extensive and evolving ecosystem of online resources for plant biology is on the critically important role of extracting experimentally-based research findings from the literature and making that information computationally accessible. In response to the loss of government grant funding, the TAIR team founded a nonprofit entity, Phoenix Bioinformatics, with the aim of developing sustainable funding models for biological databases, using TAIR as a test case. Phoenix has successfully transitioned TAIR to subscription-based funding while still keeping its data relatively open and accessible. PMID:26201819

Citation Discovery Tools for Conducting Adaptive Meta-analyses to Update Systematic Reviews.

PubMed

Bae, Jong-Myon; Kim, Eun Hee

2016-03-01

The systematic review (SR) is a research methodology that aims to synthesize related evidence. Updating previously conducted SRs is necessary when new evidence has been produced, but no consensus has yet emerged on the appropriate update methodology. The authors have developed a new SR update method called 'adaptive meta-analysis' (AMA) using the 'cited by', 'similar articles', and 'related articles' citation discovery tools in the PubMed and Scopus databases. This study evaluates the usefulness of these citation discovery tools for updating SRs. Lists were constructed by applying the citation discovery tools in the two databases to the articles analyzed by a published SR. The degree of overlap between the lists and distribution of excluded results were evaluated. The articles ultimately selected for the SR update meta-analysis were found in the lists obtained from the 'cited by' and 'similar' tools in PubMed. Most of the selected articles appeared in both the 'cited by' lists in Scopus and PubMed. The Scopus 'related' tool did not identify the appropriate articles. The AMA, which involves using both citation discovery tools in PubMed, and optionally, the 'related' tool in Scopus, was found to be useful for updating an SR.

Updating National Topographic Data Base Using Change Detection Methods

NASA Astrophysics Data System (ADS)

Keinan, E.; Felus, Y. A.; Tal, Y.; Zilberstien, O.; Elihai, Y.

2016-06-01

The traditional method for updating a topographic database on a national scale is a complex process that requires human resources, time and the development of specialized procedures. In many National Mapping and Cadaster Agencies (NMCA), the updating cycle takes a few years. Today, the reality is dynamic and the changes occur every day, therefore, the users expect that the existing database will portray the current reality. Global mapping projects which are based on community volunteers, such as OSM, update their database every day based on crowdsourcing. In order to fulfil user's requirements for rapid updating, a new methodology that maps major interest areas while preserving associated decoding information, should be developed. Until recently, automated processes did not yield satisfactory results, and a typically process included comparing images from different periods. The success rates in identifying the objects were low, and most were accompanied by a high percentage of false alarms. As a result, the automatic process required significant editorial work that made it uneconomical. In the recent years, the development of technologies in mapping, advancement in image processing algorithms and computer vision, together with the development of digital aerial cameras with NIR band and Very High Resolution satellites, allow the implementation of a cost effective automated process. The automatic process is based on high-resolution Digital Surface Model analysis, Multi Spectral (MS) classification, MS segmentation, object analysis and shape forming algorithms. This article reviews the results of a novel change detection methodology as a first step for updating NTDB in the Survey of Israel.

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

Segev, A.; Fang, W.

In currency-based updates, processing a query to a materialized view has to satisfy a currency constraint which specifies the maximum time lag of the view data with respect to a transaction database. Currency-based update policies are more general than periodical, deferred, and immediate updates; they provide additional opportunities for optimization and allow updating a materialized view from other materialized views. In this paper, we present algorithms to determine the source and timing of view updates and validate the resulting cost savings through simulation results. 20 refs.

The COMET Initiative database: progress and activities update (2015).

PubMed

Gargon, E; Williamson, P R; Altman, D G; Blazeby, J M; Tunis, S; Clarke, M

2017-02-03

This letter describes the substantial activity on the Core Outcome Measure in Effectiveness Trials (COMET) website in 2015, updating our earlier progress reports for the period from the launch of the COMET website and database in August 2011 to December 2014. As in previous years, 2015 saw further increases in the annual number of visits to the website, the number of pages viewed and the number of searches undertaken. The sustained growth in use of the website and database suggests that COMET is continuing to gain interest and prominence, and that the resources are useful to people interested in the development of core outcome sets.

Geographical Distribution of Woody Biomass Carbon in Tropical Africa: An Updated Database for 2000 (NDP-055.2007, NDP-055b))

DOE Data Explorer

Gibbs, Holly K. [Center for Sustainability and the Global Environment (SAGE), University of Wisconsin, Madison, WI (USA); Brown, Sandra [Winrock International, Arlington, VA (USA); Olsen, L. M. [Carbon Dioxide Information Analysis Center (CDIAC), Oak Ridge National Laboratory, Oak Ridge, TN (USA); Boden, Thomas A. [Carbon Dioxide Information Analysis Center (CDIAC), Oak Ridge National Laboratory, Oak Ridge, TN (USA)

2007-09-01

Maps of biomass density are critical inputs for estimating carbon emissions from deforestation and degradation of tropical forests. Brown and Gatson (1996) pioneered methods to use GIS analysis to map forest biomass based on forest inventory data (ndp055). This database is an update of ndp055 (which represent conditions in circa 1980) and accounts for land cover changes occurring up to the year 2000.

CNA’s Integrated Ship Database, Fourth Quarter 2011 Update

DTIC Science & Technology

2012-09-01

CNA’s Integrated Ship Database Fourth Quarter 2011 Update Gregory N. Suess, Lynette A . McClain, and Rhea Stone CNA Interactive Software DIS-2012-U...194) during a replenishment at sea (RAS).” Navy.mil Official Website of the United States Navy, last accessed May 24, 2012, at http://www.navy.mil...that notwithstanding any other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if

MultitaskProtDB-II: an update of a database of multitasking/moonlighting proteins

PubMed Central

Franco-Serrano, Luís; Hernández, Sergio; Calvo, Alejandra; Severi, María A; Ferragut, Gabriela; Pérez-Pons, JosepAntoni; Piñol, Jaume; Pich, Òscar; Mozo-Villarias, Ángel; Amela, Isaac

2018-01-01

Abstract Multitasking, or moonlighting, is the capability of some proteins to execute two or more biological functions. MultitaskProtDB-II is a database of multifunctional proteins that has been updated. In the previous version, the information contained was: NCBI and UniProt accession numbers, canonical and additional biological functions, organism, monomeric/oligomeric states, PDB codes and bibliographic references. In the present update, the number of entries has been increased from 288 to 694 moonlighting proteins. MultitaskProtDB-II is continually being curated and updated. The new database also contains the following information: GO descriptors for the canonical and moonlighting functions, three-dimensional structure (for those proteins lacking PDB structure, a model was made using Itasser and Phyre), the involvement of the proteins in human diseases (78% of human moonlighting proteins) and whether the protein is a target of a current drug (48% of human moonlighting proteins). These numbers highlight the importance of these proteins for the analysis and explanation of human diseases and target-directed drug design. Moreover, 25% of the proteins of the database are involved in virulence of pathogenic microorganisms, largely in the mechanism of adhesion to the host. This highlights their importance for the mechanism of microorganism infection and vaccine design. MultitaskProtDB-II is available at http://wallace.uab.es/multitaskII. PMID:29136215

The HITRAN2016 molecular spectroscopic database

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

Gordon, I. E.; Rothman, L. S.; Hill, C.

This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is comprised of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additionalmore » absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 200 additional significant molecules have been added to the database.« less

23 CFR 970.204 - Management systems requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... the management systems and their associated databases; and (5) A process for data collection, processing, analysis and updating for each management system. (d) All management systems will use databases with a geographical reference system that can be used to geolocate all database information. (e...

23 CFR 970.204 - Management systems requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... the management systems and their associated databases; and (5) A process for data collection, processing, analysis and updating for each management system. (d) All management systems will use databases with a geographical reference system that can be used to geolocate all database information. (e...

23 CFR 970.204 - Management systems requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... the management systems and their associated databases; and (5) A process for data collection, processing, analysis and updating for each management system. (d) All management systems will use databases with a geographical reference system that can be used to geolocate all database information. (e...

23 CFR 970.204 - Management systems requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

... the management systems and their associated databases; and (5) A process for data collection, processing, analysis and updating for each management system. (d) All management systems will use databases with a geographical reference system that can be used to geolocate all database information. (e...

PrionScan: an online database of predicted prion domains in complete proteomes.

PubMed

Espinosa Angarica, Vladimir; Angulo, Alfonso; Giner, Arturo; Losilla, Guillermo; Ventura, Salvador; Sancho, Javier

2014-02-05

Prions are a particular type of amyloids related to a large variety of important processes in cells, but also responsible for serious diseases in mammals and humans. The number of experimentally characterized prions is still low and corresponds to a handful of examples in microorganisms and mammals. Prion aggregation is mediated by specific protein domains with a remarkable compositional bias towards glutamine/asparagine and against charged residues and prolines. These compositional features have been used to predict new prion proteins in the genomes of different organisms. Despite these efforts, there are only a few available data sources containing prion predictions at a genomic scale. Here we present PrionScan, a new database of predicted prion-like domains in complete proteomes. We have previously developed a predictive methodology to identify and score prionogenic stretches in protein sequences. In the present work, we exploit this approach to scan all the protein sequences in public databases and compile a repository containing relevant information of proteins bearing prion-like domains. The database is updated regularly alongside UniprotKB and in its present version contains approximately 28000 predictions in proteins from different functional categories in more than 3200 organisms from all the taxonomic subdivisions. PrionScan can be used in two different ways: database query and analysis of protein sequences submitted by the users. In the first mode, simple queries allow to retrieve a detailed description of the properties of a defined protein. Queries can also be combined to generate more complex and specific searching patterns. In the second mode, users can submit and analyze their own sequences. It is expected that this database would provide relevant insights on prion functions and regulation from a genome-wide perspective, allowing researches performing cross-species prion biology studies. Our database might also be useful for guiding experimentalists in the identification of new candidates for further experimental characterization.

LIPS database with LIPService: a microscopic image database of intracellular structures in Arabidopsis guard cells.

PubMed

Higaki, Takumi; Kutsuna, Natsumaro; Hasezawa, Seiichiro

2013-05-16

Intracellular configuration is an important feature of cell status. Recent advances in microscopic imaging techniques allow us to easily obtain a large number of microscopic images of intracellular structures. In this circumstance, automated microscopic image recognition techniques are of extreme importance to future phenomics/visible screening approaches. However, there was no benchmark microscopic image dataset for intracellular organelles in a specified plant cell type. We previously established the Live Images of Plant Stomata (LIPS) database, a publicly available collection of optical-section images of various intracellular structures of plant guard cells, as a model system of environmental signal perception and transduction. Here we report recent updates to the LIPS database and the establishment of a database table, LIPService. We updated the LIPS dataset and established a new interface named LIPService to promote efficient inspection of intracellular structure configurations. Cell nuclei, microtubules, actin microfilaments, mitochondria, chloroplasts, endoplasmic reticulum, peroxisomes, endosomes, Golgi bodies, and vacuoles can be filtered using probe names or morphometric parameters such as stomatal aperture. In addition to the serial optical sectional images of the original LIPS database, new volume-rendering data for easy web browsing of three-dimensional intracellular structures have been released to allow easy inspection of their configurations or relationships with cell status/morphology. We also demonstrated the utility of the new LIPS image database for automated organelle recognition of images from another plant cell image database with image clustering analyses. The updated LIPS database provides a benchmark image dataset for representative intracellular structures in Arabidopsis guard cells. The newly released LIPService allows users to inspect the relationship between organellar three-dimensional configurations and morphometrical parameters.

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

PubMed

Bhaduri, Anirban; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

2004-04-02

The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2) database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of the family members. The search engine has been improved for simpler browsing of the database. The database resolves alignments among the structural domains consisting of evolutionarily diverged set of sequences. Availability of reliable sequence alignments of distantly related proteins despite poor sequence identity and single-member superfamilies permit better sampling of structures in libraries for fold recognition of new sequences and for the understanding of protein structure-function relationships of individual superfamilies. PASS2 is accessible at http://www.ncbs.res.in/~faculty/mini/campass/pass2.html

IRIS Toxicological Review and Summary Documents for N ...

EPA Pesticide Factsheets

EPA's assessment of the noncancer health effects and carcinogenic potential of n-hexane was last prepared and added to the IRIS data base in 1990. The IRIS program is updating the IRIS assessment for n-hexane; this update will incorporate health effects information published since the last assessment was prepared as well as new risk assessment methods. The IRIS assessment for n-hexane will consist of a Toxicological Review and IRIS Summary. The Toxicological Review is a critical review of the physicochemical and toxicokinetic properties of the chemical and its toxicity in humans and experimental systems. The assessment will present reference values for noncancer effects of n-hexane (RfD and RfC) and a cancer assessment, where supported by available data. The Toxicological Review and IRIS Summary will be subject to internal peer consultation, Agency review, and external scientific peer review. EPA is undertaking an update of the Integrated Risk Information System (IRIS) health assessment for n-hexane. The outcome of this project is an updated Toxicological Review and IRIS Summary for n-Hexane that will be entered into the IRIS database. IRIS is an EPA data base containing Agency scientific positions on potential adverse human health effects that may result from chronic (or lifetime) exposure to chemicals in the environment. IRIS contains chemical-specific summaries of qualitative and quantitative health information in support of two steps of the risk assessment

23 CFR 971.204 - Management systems requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... maintain the management systems and their associated databases; and (5) A process for data collection, processing, analysis, and updating for each management system. (c) All management systems will use databases with a common or coordinated reference system, that can be used to geolocate all database information...

23 CFR 971.204 - Management systems requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... maintain the management systems and their associated databases; and (5) A process for data collection, processing, analysis, and updating for each management system. (c) All management systems will use databases with a common or coordinated reference system, that can be used to geolocate all database information...

23 CFR 971.204 - Management systems requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... maintain the management systems and their associated databases; and (5) A process for data collection, processing, analysis, and updating for each management system. (c) All management systems will use databases with a common or coordinated reference system, that can be used to geolocate all database information...

23 CFR 971.204 - Management systems requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

... maintain the management systems and their associated databases; and (5) A process for data collection, processing, analysis, and updating for each management system. (c) All management systems will use databases with a common or coordinated reference system, that can be used to geolocate all database information...

Using Third Party Data to Update a Reference Dataset in a Quality Evaluation Service

NASA Astrophysics Data System (ADS)

Xavier, E. M. A.; Ariza-López, F. J.; Ureña-Cámara, M. A.

2016-06-01

Nowadays it is easy to find many data sources for various regions around the globe. In this 'data overload' scenario there are few, if any, information available about the quality of these data sources. In order to easily provide these data quality information we presented the architecture of a web service for the automation of quality control of spatial datasets running over a Web Processing Service (WPS). For quality procedures that require an external reference dataset, like positional accuracy or completeness, the architecture permits using a reference dataset. However, this reference dataset is not ageless, since it suffers the natural time degradation inherent to geospatial features. In order to mitigate this problem we propose the Time Degradation & Updating Module which intends to apply assessed data as a tool to maintain the reference database updated. The main idea is to utilize datasets sent to the quality evaluation service as a source of 'candidate data elements' for the updating of the reference database. After the evaluation, if some elements of a candidate dataset reach a determined quality level, they can be used as input data to improve the current reference database. In this work we present the first design of the Time Degradation & Updating Module. We believe that the outcomes can be applied in the search of a full-automatic on-line quality evaluation platform.

Update of the androgen receptor gene mutations database.

PubMed

Gottlieb, B; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

1999-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 309 to 374 during the past year. We have expanded the database by adding information on AR-interacting proteins; and we have improved the database by identifying those mutation entries that have been updated. Mutations of unknown significance have now been reported in both the 5' and 3' untranslated regions of the AR gene, and in individuals who are somatic mosaics constitutionally. In addition, single nucleotide polymorphisms, including silent mutations, have been discovered in normal individuals and in individuals with male infertility. A mutation hotspot associated with prostatic cancer has been identified in exon 5. The database is available on the internet (http://www.mcgill.ca/androgendb/), from EMBL-European Bioinformatics Institute (ftp.ebi.ac.uk/pub/databases/androgen), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca). Copyright 1999 Wiley-Liss, Inc.

A Toolkit for Active Object-Oriented Databases with Application to Interoperability

NASA Technical Reports Server (NTRS)

King, Roger

1996-01-01

In our original proposal we stated that our research would 'develop a novel technology that provides a foundation for collaborative information processing.' The essential ingredient of this technology is the notion of 'deltas,' which are first-class values representing collections of proposed updates to a database. The Heraclitus framework provides a variety of algebraic operators for building up, combining, inspecting, and comparing deltas. Deltas can be directly applied to the database to yield a new state, or used 'hypothetically' in queries against the state that would arise if the delta were applied. The central point here is that the step of elevating deltas to 'first-class' citizens in database programming languages will yield tremendous leverage on the problem of supporting updates in collaborative information processing. In short, our original intention was to develop the theoretical and practical foundation for a technology based on deltas in an object-oriented database context, develop a toolkit for active object-oriented databases, and apply this toward collaborative information processing.

A Toolkit for Active Object-Oriented Databases with Application to Interoperability

NASA Technical Reports Server (NTRS)

King, Roger

1996-01-01

In our original proposal we stated that our research would 'develop a novel technology that provides a foundation for collaborative information processing.' The essential ingredient of this technology is the notion of 'deltas,' which are first-class values representing collections of proposed updates to a database. The Heraclitus framework provides a variety of algebraic operators for building up, combining, inspecting, and comparing deltas. Deltas can be directly applied to the database to yield a new state, or used 'hypothetically' in queries against the state that would arise if the delta were applied. The central point here is that the step of elevating deltas to 'first-class' citizens in database programming languages will yield tremendous leverage on the problem of supporting updates in collaborative information processing. In short, our original intention was to develop the theoretical and practical foundation for a technology based on deltas in an object- oriented database context, develop a toolkit for active object-oriented databases, and apply this toward collaborative information processing.

Updates of ARI Databases for Tracking Army and College Fund (ACF), Montgomery GI Bill (MGIB) Usage for 2012-2013, and Post-9/11 GI Bill Benefit Usage for 2015

DTIC Science & Technology

2017-01-02

Research Note 2017-03 Updates of ARI Databases for Tracking Army and College Fund (ACF), Montgomery GI Bill (MGIB) Usage for 2012-2013...and Post-9/11 GI Bill Benefit Usage for 2015 Winnie Young Human Resources Research Organization Personnel...Assessment Research Unit Tonia Heffner, Chief January 2017 United States Army Research Institute for the Behavioral and Social Sciences

IRIS Toxicological Review of Hexahydro-1,3,5-Trinitro-1,3,5 ...

EPA Pesticide Factsheets

EPA is developing an Integrated Risk Information System (IRIS) assessment of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) and has released the draft assessment for public comment. When final, the assessment will appear on the IRIS database. EPA is undertaking an update of the Integrated Risk Information System (IRIS) health assessment for RDX. The outcome of this project is an updated Toxicological Review and IRIS Summary for RDX that will be entered into the IRIS database.

IRIS Toxicological Review of Benzo[a]pyrene (Public ...

EPA Pesticide Factsheets

EPA is developing an Integrated Risk Information System (IRIS) assessment of benzo[a]pyrene and has released the draft assessment for public comment and external peer review. When final, the assessment will appear on the IRIS database. EPA is undertaking an update of the Integrated Risk Information System (IRIS) health assessment for benzo[a]pyrene (BaP). The outcome of this project is an updated Toxicological Review and IRIS Summary for BaP that will be entered into the IRIS database.

The Zebrafish Model Organism Database: new support for human disease models, mutation details, gene expression phenotypes and searching

PubMed Central

Howe, Douglas G.; Bradford, Yvonne M.; Eagle, Anne; Fashena, David; Frazer, Ken; Kalita, Patrick; Mani, Prita; Martin, Ryan; Moxon, Sierra Taylor; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruzicka, Leyla; Schaper, Kevin; Shao, Xiang; Singer, Amy; Toro, Sabrina; Van Slyke, Ceri; Westerfield, Monte

2017-01-01

The Zebrafish Model Organism Database (ZFIN; http://zfin.org) is the central resource for zebrafish (Danio rerio) genetic, genomic, phenotypic and developmental data. ZFIN curators provide expert manual curation and integration of comprehensive data involving zebrafish genes, mutants, transgenic constructs and lines, phenotypes, genotypes, gene expressions, morpholinos, TALENs, CRISPRs, antibodies, anatomical structures, models of human disease and publications. We integrate curated, directly submitted, and collaboratively generated data, making these available to zebrafish research community. Among the vertebrate model organisms, zebrafish are superbly suited for rapid generation of sequence-targeted mutant lines, characterization of phenotypes including gene expression patterns, and generation of human disease models. The recent rapid adoption of zebrafish as human disease models is making management of these data particularly important to both the research and clinical communities. Here, we describe recent enhancements to ZFIN including use of the zebrafish experimental conditions ontology, ‘Fish’ records in the ZFIN database, support for gene expression phenotypes, models of human disease, mutation details at the DNA, RNA and protein levels, and updates to the ZFIN single box search. PMID:27899582

The thyrotropin receptor mutation database: update 2003.

PubMed

Führer, Dagmar; Lachmund, Peter; Nebel, Istvan-Tibor; Paschke, Ralf

2003-12-01

In 1999 we have created a TSHR mutation database compiling TSHR mutations with their basic characteristics and associated clinical conditions (www.uni-leipzig.de/innere/tshr). Since then, more than 2887 users from 36 countries have logged into the TSHR mutation database and have contributed several valuable suggestions for further improvement of the database. We now present an updated and extended version of the TSHR database to which several novel features have been introduced: 1. detailed functional characteristics on all 65 mutations (43 activating and 22 inactivating mutations) reported to date, 2. 40 pedigrees with detailed information on molecular aspects, clinical courses and treatment options in patients with gain-of-function and loss-of-function germline TSHR mutations, 3. a first compilation of site-directed mutagenesis studies, 4. references with Medline links, 5. a user friendly search tool for specific database searches, user-specific database output and 6. an administrator tool for the submission of novel TSHR mutations. The TSHR mutation database is installed as one of the locus specific HUGO mutation databases. It is listed under index TSHR 603372 (http://ariel.ucs.unimelb.edu.au/~cotton/glsdbq.htm) and can be accessed via www.uni-leipzig.de/innere/tshr.

Human Ageing Genomic Resources: new and updated databases

PubMed Central

Tacutu, Robi; Thornton, Daniel; Johnson, Emily; Budovsky, Arie; Barardo, Diogo; Craig, Thomas; Diana, Eugene; Lehmann, Gilad; Toren, Dmitri; Wang, Jingwei; Fraifeld, Vadim E

2018-01-01

Abstract In spite of a growing body of research and data, human ageing remains a poorly understood process. Over 10 years ago we developed the Human Ageing Genomic Resources (HAGR), a collection of databases and tools for studying the biology and genetics of ageing. Here, we present HAGR’s main functionalities, highlighting new additions and improvements. HAGR consists of six core databases: (i) the GenAge database of ageing-related genes, in turn composed of a dataset of >300 human ageing-related genes and a dataset with >2000 genes associated with ageing or longevity in model organisms; (ii) the AnAge database of animal ageing and longevity, featuring >4000 species; (iii) the GenDR database with >200 genes associated with the life-extending effects of dietary restriction; (iv) the LongevityMap database of human genetic association studies of longevity with >500 entries; (v) the DrugAge database with >400 ageing or longevity-associated drugs or compounds; (vi) the CellAge database with >200 genes associated with cell senescence. All our databases are manually curated by experts and regularly updated to ensure a high quality data. Cross-links across our databases and to external resources help researchers locate and integrate relevant information. HAGR is freely available online (http://genomics.senescence.info/). PMID:29121237

Androgen-responsive gene database: integrated knowledge on androgen-responsive genes.

PubMed

Jiang, Mei; Ma, Yunsheng; Chen, Congcong; Fu, Xuping; Yang, Shu; Li, Xia; Yu, Guohua; Mao, Yumin; Xie, Yi; Li, Yao

2009-11-01

Androgen signaling plays an important role in many biological processes. Androgen Responsive Gene Database (ARGDB) is devoted to providing integrated knowledge on androgen-controlled genes. Gene records were collected on the basis of PubMed literature collections. More than 6000 abstracts and 950 original publications were manually screened, leading to 1785 human genes, 993 mouse genes, and 583 rat genes finally included in the database. All the collected genes were experimentally proved to be regulated by androgen at the expression level or to contain androgen-responsive regions. For each gene important details of the androgen regulation experiments were collected from references, such as expression change, androgen-responsive sequence, response time, tissue/cell type, experimental method, ligand identity, and androgen amount, which will facilitate further evaluation by researchers. Furthermore, the database was integrated with multiple annotation resources, including National Center for Biotechnology Information, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway, to reveal the biological characteristics and significance of androgen-regulated genes. The ARGDB web site is mainly composed of the Browse, Search, Element Scan, and Submission modules. It is user friendly and freely accessible at http://argdb.fudan.edu.cn. Preliminary analysis of the collected data was performed. Many disease pathways, such as prostate carcinogenesis, were found to be enriched in androgen-regulated genes. The discovered androgen-response motifs were similar to those in previous reports. The analysis results are displayed in the web site. In conclusion, ARGDB provides a unified gateway to storage, retrieval, and update of information on androgen-regulated genes.

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions

PubMed Central

Hao, Yajing; Wu, Wei; Li, Hui; Yuan, Jiao; Luo, Jianjun; Zhao, Yi; Chen, Runsheng

2016-01-01

Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. To enable researchers to have a better understanding of ncRNAs’ functions, we updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding tRNAs and rRNAs), especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs). In NPInter v3.0, interactions pertaining to ncRNAs are not only manually curated from scientific literature but also curated from high-throughput technologies. In addition, we also curated lncRNA–miRNA interactions from in silico predictions supported by AGO CLIP-seq data. When compared with NPInter v2.0, the interactions are more informative (with additional information on tissues or cell lines, binding sites, conservation, co-expression values and other features) and more organized (with divisions on data sets by data sources, tissues or cell lines, experiments and other criteria). NPInter v3.0 expands the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies. NPInter v3.0 also improves the user interface and adds new web services, including a local UCSC Genome Browser to visualize binding sites. Additionally, NPInter v3.0 defined a high-confidence set of interactions and predicted the functions of lncRNAs in human and mouse based on the interactions curated in the database. NPInter v3.0 is available at http://www.bioinfo.org/NPInter/. Database URL: http://www.bioinfo.org/NPInter/ PMID:27087310

77 FR 12234 - Changes in Hydric Soils Database Selection Criteria

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-29

... Conservation Service [Docket No. NRCS-2011-0026] Changes in Hydric Soils Database Selection Criteria AGENCY... Changes to the National Soil Information System (NASIS) Database Selection Criteria for Hydric Soils of the United States. SUMMARY: The National Technical Committee for Hydric Soils (NTCHS) has updated the...

Contingency Contractor Optimization Phase 3 Sustainment Database Design Document - Contingency Contractor Optimization Tool - Prototype

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

Frazier, Christopher Rawls; Durfee, Justin David; Bandlow, Alisa

The Contingency Contractor Optimization Tool – Prototype (CCOT-P) database is used to store input and output data for the linear program model described in [1]. The database allows queries to retrieve this data and updating and inserting new input data.

Universal empirical fit to L-shell X-ray production cross sections in ionization by protons

NASA Astrophysics Data System (ADS)

Lapicki, G.; Miranda, J.

2018-01-01

A compilation published in 2014, with a recent 2017 update, contains 5730 experimental total L-shell X-ray production cross sections (XRPCS). The database covers an energy range from 10 keV to 1 GeV, and targets from 18Ar to 95Am. With only two adjustable parameters, universal fit to these data normalized to XRPCS calculated at proton velocity v1 equal to the electron velocity in the L-shell v2L, is obtained in terms of a single ratio of v1/v2L. This fit reproduces 97% of the compiled XRPCS to within a factor of 2.

The World Database for Pediatric and Congenital Heart Surgery: Update.

PubMed

Louis, James St; Kirklin, James

2018-05-01

Following several years of planning and design, the World Database for Pediatric and Congenital Heart Surgery (WDPCHS) went live on January 1, 2017. The first operational year of this valuable database has proven very successful. As of February 28, 2018, more than 4,500 patients have been submitted from 39 centers; participation currently spans 19 countries over 6 continents, with 120 more centers in the enrollment pipeline. This update, the first in a series, is intended to provide World Society for Pediatric and Congenital Heart Surgery members and others who care for children with congenital heart disease with a broad overview of current progress and ongoing activities surrounding the WDPCHS.

UCbase 2.0: ultraconserved sequences database (2014 update).

PubMed

Lomonaco, Vincenzo; Martoglia, Riccardo; Mandreoli, Federica; Anderlucci, Laura; Emmett, Warren; Bicciato, Silvio; Taccioli, Cristian

2014-01-01

UCbase 2.0 (http://ucbase.unimore.it) is an update, extension and evolution of UCbase, a Web tool dedicated to the analysis of ultraconserved sequences (UCRs). UCRs are 481 sequences >200 bases sharing 100% identity among human, mouse and rat genomes. They are frequently located in genomic regions known to be involved in cancer or differentially expressed in human leukemias and carcinomas. UCbase 2.0 is a platform-independent Web resource that includes the updated version of the human genome annotation (hg19), information linking disorders to chromosomal coordinates based on the Systematized Nomenclature of Medicine classification, a query tool to search for Single Nucleotide Polymorphisms (SNPs) and a new text box to directly interrogate the database using a MySQL interface. To facilitate the interactive visual interpretation of UCR chromosomal positioning, UCbase 2.0 now includes a graph visualization interface directly linked to UCSC genome browser. Database URL: http://ucbase.unimore.it. © The Author(s) 2014. Published by Oxford University Press.

A Mathematics Software Database Update.

ERIC Educational Resources Information Center

Cunningham, R. S.; Smith, David A.

1987-01-01

Contains an update of an earlier listing of software for mathematics instruction at the college level. Topics are: advanced mathematics, algebra, calculus, differential equations, discrete mathematics, equation solving, general mathematics, geometry, linear and matrix algebra, logic, statistics and probability, and trigonometry. (PK)

Experimental Validation of Model Updating and Damage Detection via Eigenvalue Sensitivity Methods with Artificial Boundary Conditions

DTIC Science & Technology

2017-09-01

VALIDATION OF MODEL UPDATING AND DAMAGE DETECTION VIA EIGENVALUE SENSITIVITY METHODS WITH ARTIFICIAL BOUNDARY CONDITIONS by Matthew D. Bouwense...VALIDATION OF MODEL UPDATING AND DAMAGE DETECTION VIA EIGENVALUE SENSITIVITY METHODS WITH ARTIFICIAL BOUNDARY CONDITIONS 5. FUNDING NUMBERS 6. AUTHOR...unlimited. EXPERIMENTAL VALIDATION OF MODEL UPDATING AND DAMAGE DETECTION VIA EIGENVALUE SENSITIVITY METHODS WITH ARTIFICIAL BOUNDARY

Non-confidential 2002 IUR Company/Chemical Records

EPA Pesticide Factsheets

This file contains information reported to EPA under the 2002 Inventory Update Rule (IUR). The deadline for companies to report was December 31, 2002. This database includes all information received by EPA that did not have problems associated with the submission, including requests from companies to update or correct their earlier filings. Future updates to this information will be made available on this website.

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein-DNA interactions.

PubMed

Hume, Maxwell A; Barrera, Luis A; Gisselbrecht, Stephen S; Bulyk, Martha L

2015-01-01

The Universal PBM Resource for Oligonucleotide Binding Evaluation (UniPROBE) serves as a convenient source of information on published data generated using universal protein-binding microarray (PBM) technology, which provides in vitro data about the relative DNA-binding preferences of transcription factors for all possible sequence variants of a length k ('k-mers'). The database displays important information about the proteins and displays their DNA-binding specificity data in terms of k-mers, position weight matrices and graphical sequence logos. This update to the database documents the growth of UniPROBE since the last update 4 years ago, and introduces a variety of new features and tools, including a new streamlined pipeline that facilitates data deposition by universal PBM data generators in the research community, a tool that generates putative nonbinding (i.e. negative control) DNA sequences for one or more proteins and novel motifs obtained by analyzing the PBM data using the BEEML-PBM algorithm for motif inference. The UniPROBE database is available at http://uniprobe.org. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes

PubMed Central

An, Omer; Pendino, Vera; D’Antonio, Matteo; Ratti, Emanuele; Gentilini, Marco; Ciccarelli, Francesca D.

2014-01-01

NCG 4.0 is the latest update of the Network of Cancer Genes, a web-based repository of systems-level properties of cancer genes. In its current version, the database collects information on 537 known (i.e. experimentally supported) and 1463 candidate (i.e. inferred using statistical methods) cancer genes. Candidate cancer genes derive from the manual revision of 67 original publications describing the mutational screening of 3460 human exomes and genomes in 23 different cancer types. For all 2000 cancer genes, duplicability, evolutionary origin, expression, functional annotation, interaction network with other human proteins and with microRNAs are reported. In addition to providing a substantial update of cancer-related information, NCG 4.0 also introduces two new features. The first is the annotation of possible false-positive cancer drivers, defined as candidate cancer genes inferred from large-scale screenings whose association with cancer is likely to be spurious. The second is the description of the systems-level properties of 64 human microRNAs that are causally involved in cancer progression (oncomiRs). Owing to the manual revision of all information, NCG 4.0 constitutes a complete and reliable resource on human coding and non-coding genes whose deregulation drives cancer onset and/or progression. NCG 4.0 can also be downloaded as a free application for Android smart phones. Database URL: http://bio.ieo.eu/ncg/ PMID:24608173

RBOOST: RIEMANNIAN DISTANCE BASED REGULARIZED BOOSTING

PubMed Central

Liu, Meizhu; Vemuri, Baba C.

2011-01-01

Boosting is a versatile machine learning technique that has numerous applications including but not limited to image processing, computer vision, data mining etc. It is based on the premise that the classification performance of a set of weak learners can be boosted by some weighted combination of them. There have been a number of boosting methods proposed in the literature, such as the AdaBoost, LPBoost, SoftBoost and their variations. However, the learning update strategies used in these methods usually lead to overfitting and instabilities in the classification accuracy. Improved boosting methods via regularization can overcome such difficulties. In this paper, we propose a Riemannian distance regularized LPBoost, dubbed RBoost. RBoost uses Riemannian distance between two square-root densities (in closed form) – used to represent the distribution over the training data and the classification error respectively – to regularize the error distribution in an iterative update formula. Since this distance is in closed form, RBoost requires much less computational cost compared to other regularized Boosting algorithms. We present several experimental results depicting the performance of our algorithm in comparison to recently published methods, LP-Boost and CAVIAR, on a variety of datasets including the publicly available OASIS database, a home grown Epilepsy database and the well known UCI repository. Results depict that the RBoost algorithm performs better than the competing methods in terms of accuracy and efficiency. PMID:21927643

The UCL low-density lipoprotein receptor gene variant database: pathogenicity update

PubMed Central

Futema, Marta; Whittall, Ros; Taylor-Beadling, Alison; Williams, Maggie; den Dunnen, Johan T; Humphries, Steve E

2017-01-01

Background Familial hypercholesterolaemia (OMIM 143890) is most frequently caused by variations in the low-density lipoprotein receptor (LDLR) gene. Predicting whether novel variants are pathogenic may not be straightforward, especially for missense and synonymous variants. In 2013, the Association of Clinical Genetic Scientists published guidelines for the classification of variants, with categories 1 and 2 representing clearly not or unlikely pathogenic, respectively, 3 representing variants of unknown significance (VUS), and 4 and 5 representing likely to be or clearly pathogenic, respectively. Here, we update the University College London (UCL) LDLR variant database according to these guidelines. Methods PubMed searches and alerts were used to identify novel LDLR variants for inclusion in the database. Standard in silico tools were used to predict potential pathogenicity. Variants were designated as class 4/5 only when the predictions from the different programs were concordant and as class 3 when predictions were discordant. Results The updated database (http://www.lovd.nl/LDLR) now includes 2925 curated variants, representing 1707 independent events. All 129 nonsense variants, 337 small frame-shifting and 117/118 large rearrangements were classified as 4 or 5. Of the 795 missense variants, 115 were in classes 1 and 2, 605 in class 4 and 75 in class 3. 111/181 intronic variants, 4/34 synonymous variants and 14/37 promoter variants were assigned to classes 4 or 5. Overall, 112 (7%) of reported variants were class 3. Conclusions This study updates the LDLR variant database and identifies a number of reported VUS where additional family and in vitro studies will be required to confirm or refute their pathogenicity. PMID:27821657

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

PubMed

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.

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

PubMed Central

2018-01-01

Abstract 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. PMID:29140525

PubChem BioAssay: 2017 update

PubMed Central

Wang, Yanli; Bryant, Stephen H.; Cheng, Tiejun; Wang, Jiyao; Gindulyte, Asta; Shoemaker, Benjamin A.; Thiessen, Paul A.; He, Siqian; Zhang, Jian

2017-01-01

PubChem's BioAssay database (https://pubchem.ncbi.nlm.nih.gov) has served as a public repository for small-molecule and RNAi screening data since 2004 providing open access of its data content to the community. PubChem accepts data submission from worldwide researchers at academia, industry and government agencies. PubChem also collaborates with other chemical biology database stakeholders with data exchange. With over a decade's development effort, it becomes an important information resource supporting drug discovery and chemical biology research. To facilitate data discovery, PubChem is integrated with all other databases at NCBI. In this work, we provide an update for the PubChem BioAssay database describing several recent development including added sources of research data, redesigned BioAssay record page, new BioAssay classification browser and new features in the Upload system facilitating data sharing. PMID:27899599

The International Space Station Comparative Maintenance Analysis(CMAM)

DTIC Science & Technology

2004-09-01

External Component • Entire ORU Database 2. Database Connectivity The CMAM ORU database consists of three tables: an ORU master parts list , an ISS...Flight table, and an ISS Subsystem table. The ORU master parts list and the ISS Flight table can be updated or modified from the CMAM user interface

77 FR 34211 - Modification of Multiple Compulsory Reporting Points; Continental United States, Alaska and Hawaii

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-11

... previously updated in the FAA aeronautical database without accompanying regulatory action being taken. The... to ensure it matches the information contained in the FAA's aeronautical database and to ensure the... position information contained in the FAA's aeronautical database for the reporting points. When these...

47 CFR 51.217 - Nondiscriminatory access: Telephone numbers, operator services, directory assistance services...

Code of Federal Regulations, 2011 CFR

2011-10-01

... to have access to its directory assistance services, including directory assistance databases, so... provider, including transfer of the LECs' directory assistance databases in readily accessible magnetic.... Updates to the directory assistance database shall be made in the same format as the initial transfer...

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

PubMed Central

Kumar Mishra, Subodh; Kumar, Amit

2016-01-01

Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php PMID:26896846

Fast fingerprint database maintenance for indoor positioning based on UGV SLAM.

PubMed

Tang, Jian; Chen, Yuwei; Chen, Liang; Liu, Jingbin; Hyyppä, Juha; Kukko, Antero; Kaartinen, Harri; Hyyppä, Hannu; Chen, Ruizhi

2015-03-04

Indoor positioning technology has become more and more important in the last two decades. Utilizing Received Signal Strength Indicator (RSSI) fingerprints of Signals of OPportunity (SOP) is a promising alternative navigation solution. However, as the RSSIs vary during operation due to their physical nature and are easily affected by the environmental change, one challenge of the indoor fingerprinting method is maintaining the RSSI fingerprint database in a timely and effective manner. In this paper, a solution for rapidly updating the fingerprint database is presented, based on a self-developed Unmanned Ground Vehicles (UGV) platform NAVIS. Several SOP sensors were installed on NAVIS for collecting indoor fingerprint information, including a digital compass collecting magnetic field intensity, a light sensor collecting light intensity, and a smartphone which collects the access point number and RSSIs of the pre-installed WiFi network. The NAVIS platform generates a map of the indoor environment and collects the SOPs during processing of the mapping, and then the SOP fingerprint database is interpolated and updated in real time. Field tests were carried out to evaluate the effectiveness and efficiency of the proposed method. The results showed that the fingerprint databases can be quickly created and updated with a higher sampling frequency (5Hz) and denser reference points compared with traditional methods, and the indoor map can be generated without prior information. Moreover, environmental changes could also be detected quickly for fingerprint indoor positioning.

Geothopica and the interactive analysis and visualization of the updated Italian National Geothermal Database

NASA Astrophysics Data System (ADS)

Trumpy, Eugenio; Manzella, Adele

2017-02-01

The Italian National Geothermal Database (BDNG), is the largest collection of Italian Geothermal data and was set up in the 1980s. It has since been updated both in terms of content and management tools: information on deep wells and thermal springs (with temperature > 30 °C) are currently organized and stored in a PostgreSQL relational database management system, which guarantees high performance, data security and easy access through different client applications. The BDNG is the core of the Geothopica web site, whose webGIS tool allows different types of user to access geothermal data, to visualize multiple types of datasets, and to perform integrated analyses. The webGIS tool has been recently improved by two specially designed, programmed and implemented visualization tools to display data on well lithology and underground temperatures. This paper describes the contents of the database and its software and data update, as well as the webGIS tool including the new tools for data lithology and temperature visualization. The geoinformation organized in the database and accessible through Geothopica is of use not only for geothermal purposes, but also for any kind of georesource and CO2 storage project requiring the organization of, and access to, deep underground data. Geothopica also supports project developers, researchers, and decision makers in the assessment, management and sustainable deployment of georesources.

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

PubMed Central

Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M.; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P.; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M.; Latorre, Amparo; Moya, Andres

2011-01-01

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org. PMID:21036865

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.

PubMed

Llorens, Carlos; Futami, Ricardo; Covelli, Laura; Domínguez-Escribá, Laura; Viu, Jose M; Tamarit, Daniel; Aguilar-Rodríguez, Jose; Vicente-Ripolles, Miguel; Fuster, Gonzalo; Bernet, Guillermo P; Maumus, Florian; Munoz-Pomer, Alfonso; Sempere, Jose M; Latorre, Amparo; Moya, Andres

2011-01-01

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.

X-38 Experimental Aeroheating at Mach 10

NASA Technical Reports Server (NTRS)

Berry, Scott A.; Horvath, Thomas J.; Weilmuenster, K. James; Alter, Stephan J.; Merski, N. Ronald

2001-01-01

This report provides an update of the hypersonic aerothermodynamic wind tunnel test program conducted at the NASA Langley Research Center in support of the X-38 program. Global surface heat transfer distributions were measured on 0.0177 and 0.0236 scale models of the proposed X-38 configuration at Mach 10 in air. The parametrics that were investigated primarily include freestream unit Reynolds numbers of 0.6 to 2.2 million per foot and body flap deflections of 15, 20, and 25 deg for an angle-of-attack of 40 deg. The model-scale variance was tested to obtain laminar, transitional, and turbulent heating levels on the defected bodyflaps. In addition, a limited investigation of forced boundary layer transition through the use of discrete roughness elements was performed. Comparisons of the present experimental results to computational predictions and previous experimental data were conducted Laminar, transitional, and turbulent heating levels were observed on the deflected body flap, which compared favorably to the computational results and to the predicted heating based on the flight aerothermodynamic database.

Glossary – dCHPP (CHP Policies and incentives database)

EPA Pesticide Factsheets

This glossary provides descriptions of the policy and incentive types included in the CHP Partnership's CHP Policies and incentives database (dCHPP), as well as the frequency with which the EPA updates each type.

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

Gragg, Evan James; Middleton, Richard Stephen

This report describes the benefits of the BECCUS screening tools. The goals of this project are to utilize NATCARB database for site screening; enhance NATCARB database; run CO 2-EOR simulations and economic models using updated reservoir data sets (SCO 2T-EOR).

An Update on Electronic Information Sources.

ERIC Educational Resources Information Center

Ackerman, Katherine

1987-01-01

This review of new developments and products in online services discusses trends in travel related services; full text databases; statistical source databases; an emphasis on regional and international business news; and user friendly systems. (Author/CLB)

IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model

PubMed Central

Xia, Kai; Dong, Dong; Han, Jing-Dong J

2006-01-01

Background Although protein-protein interaction (PPI) networks have been explored by various experimental methods, the maps so built are still limited in coverage and accuracy. To further expand the PPI network and to extract more accurate information from existing maps, studies have been carried out to integrate various types of functional relationship data. A frequently updated database of computationally analyzed potential PPIs to provide biological researchers with rapid and easy access to analyze original data as a biological network is still lacking. Results By applying a probabilistic model, we integrated 27 heterogeneous genomic, proteomic and functional annotation datasets to predict PPI networks in human. In addition to previously studied data types, we show that phenotypic distances and genetic interactions can also be integrated to predict PPIs. We further built an easy-to-use, updatable integrated PPI database, the Integrated Network Database (IntNetDB) online, to provide automatic prediction and visualization of PPI network among genes of interest. The networks can be visualized in SVG (Scalable Vector Graphics) format for zooming in or out. IntNetDB also provides a tool to extract topologically highly connected network neighborhoods from a specific network for further exploration and research. Using the MCODE (Molecular Complex Detections) algorithm, 190 such neighborhoods were detected among all the predicted interactions. The predicted PPIs can also be mapped to worm, fly and mouse interologs. Conclusion IntNetDB includes 180,010 predicted protein-protein interactions among 9,901 human proteins and represents a useful resource for the research community. Our study has increased prediction coverage by five-fold. IntNetDB also provides easy-to-use network visualization and analysis tools that allow biological researchers unfamiliar with computational biology to access and analyze data over the internet. The web interface of IntNetDB is freely accessible at . Visualization requires Mozilla version 1.8 (or higher) or Internet Explorer with installation of SVGviewer. PMID:17112386

Updated Trends in Materials' Outgassing Technology

NASA Technical Reports Server (NTRS)

Rosecrans, Glenn; Mlucciacciaro, Anthony

2010-01-01

This slide presentation reviews the trends in materials' outgassing. The work utilized a database of reports to identify common outgassing chemical species from flight hardware, spacecraft, and ground support equipment (GSE). This work updates an earlier work that reported on chemical analysis from 1970-1978.

Olson's Major World Ecosystem Complexes Ranked by Carbon in Live Vegetation: An Updated Database Using the GLC2000 Land Cover Product (NDP-017b, a 2006 update of the original 1985 and 2001 data file))

DOE Data Explorer

Gibbs, Holly K. [Center for Sustainability and the Global Environment, University of Wisconsin, Madison, WI (United States)

2006-01-01

In the 1980s, Olson et al. developed a data base and corresponding map following more than 20 years of field investigations, consultations, and analyses of published literature. The original data characterize the use and vegetative cover of the Earth's land surface with a 0.5° by 0.5° grid. The purpose of these world-ecosystem-complex data and the accompanying map were to provide a current reference base for interpreting the role of vegetation in the global cycling of CO2 and other gases and a basis for improved estimates of vegetation and soil carbon, of natural exchanges of CO2, and of net historic shifts of carbon between the biosphere and the atmosphere. These data were widely used and cited in carbon cycle research. This updated database extends the methodology of Olson et al. to more contemporary land cover conditions of the Global Land Cover Database (GLC2000). The GLC2000 data were developed using remotely sensed imagery acquired in 2000. The updated data are presented in a GIS format and include estimates of mean and maximum carbon density values.

Updating the 2001 National Land Cover Database Impervious Surface Products to 2006 using Landsat imagery change detection methods

USGS Publications Warehouse

Xian, George; Homer, Collin G.

2010-01-01

A prototype method was developed to update the U.S. Geological Survey (USGS) National Land Cover Database (NLCD) 2001 to a nominal date of 2006. NLCD 2001 is widely used as a baseline for national land cover and impervious cover conditions. To enable the updating of this database in an optimal manner, methods are designed to be accomplished by individual Landsat scene. Using conservative change thresholds based on land cover classes, areas of change and no-change were segregated from change vectors calculated from normalized Landsat scenes from 2001 and 2006. By sampling from NLCD 2001 impervious surface in unchanged areas, impervious surface predictions were estimated for changed areas within an urban extent defined by a companion land cover classification. Methods were developed and tested for national application across six study sites containing a variety of urban impervious surface. Results show the vast majority of impervious surface change associated with urban development was captured, with overall RMSE from 6.86 to 13.12% for these areas. Changes of urban development density were also evaluated by characterizing the categories of change by percentile for impervious surface. This prototype method provides a relatively low cost, flexible approach to generate updated impervious surface using NLCD 2001 as the baseline.

Gramene database in 2010: updates and extensions.

PubMed

Youens-Clark, Ken; Buckler, Ed; Casstevens, Terry; Chen, Charles; Declerck, Genevieve; Derwent, Paul; Dharmawardhana, Palitha; Jaiswal, Pankaj; Kersey, Paul; Karthikeyan, A S; Lu, Jerry; McCouch, Susan R; Ren, Liya; Spooner, William; Stein, Joshua C; Thomason, Jim; Wei, Sharon; Ware, Doreen

2011-01-01

Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with the addition of an Ensembl genome browser and has expanded in the last decade to become a robust resource for plant genomics hosting a wide array of data sets including quantitative trait loci (QTL), metabolic pathways, genetic diversity, genes, proteins, germplasm, literature, ontologies and a fully-structured markers and sequences database integrated with genome browsers and maps from various published studies (genetic, physical, bin, etc.). In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data.

Spectr-W3 Online Database On Atomic Properties Of Atoms And Ions

NASA Astrophysics Data System (ADS)

Faenov, A. Ya.; Magunov, A. I.; Pikuz, T. A.; Skobelev, I. Yu.; Loboda, P. A.; Bakshayev, N. N.; Gagarin, S. V.; Komosko, V. V.; Kuznetsov, K. S.; Markelenkov, S. A.

2002-10-01

Recent progress in the novel information technologies based on the World-Wide Web (WWW) gives a new possibility for a worldwide exchange of atomic spectral and collisional data. This facilitates joint efforts of the international scientific community in basic and applied research, promising technological developments, and university education programs. Special-purpose atomic databases (ADBs) are needed for an effective employment of large-scale datasets. The ADB SPECTR developed at MISDC of VNIIFTRI has been used during the last decade in several laboratories in the world, including RFNC-VNIITF. The DB SPECTR accumulates a considerable amount of atomic data (about 500,000 records). These data were extracted from publications on experimental and theoretical studies in atomic physics, astrophysics, and plasma spectroscopy during the last few decades. The information for atoms and ions comprises the ionization potentials, the energy levels, the wavelengths and transition probabilities, and, to a lesser extent, -- also the autoionization rates, and the electron-ion collision cross-sections and rates. The data are supplied with source references and comments elucidating the details of computations or measurements. Our goal is to create an interactive WWW information resource based on the extended and updated Web-oriented database version SPECTR-W3 and its further integration into the family of specialized atomic databases on the Internet. The version will incorporate novel experimental and theoretical data. An appropriate revision of the previously accumulated data will be performed from the viewpoint of their consistency to the current state-of-the-art. We are particularly interested in cooperation for storing the atomic collision data. Presently, a software shell with the up-to-date Web-interface is being developed to work with the SPECTR-W3 database. The shell would include the subsystems of information retrieval, input, update, and output in/from the database and present the users a handful of capabilities to formulate the queries with various modes of the search prescriptions, to present the information in tabular, graphic, and alphanumeric form using the formats of the text and HTML documents. The SPECTR-W3 Website is being arranged now and is supposed to be freely accessible round-the-clock on a dedicated Web server at RFNC VNIITF. The Website is being created with the employment of the advanced Internet technologies and database development techniques by using the up-to-date software of the world leading software manufacturers. The SPECTR-W3 ADB FrontPage would also include a feedback channel for the user comments and proposals as well as the hyperlinks to the Websites of the other ADBs and research centers in Europe, the USA, the Middle and Far East, running the investigations in atomic physics, plasma spectroscopy, astrophysics, and in adjacent areas. The effort is being supported by the International Science and Technology Center under the project sharp/mesh/hash1785-01.

NASA Interactive Forms Type Interface - NIFTI

NASA Technical Reports Server (NTRS)

Jain, Bobby; Morris, Bill

2005-01-01

A flexible database query, update, modify, and delete tool was developed that provides an easy interface to Oracle forms. This tool - the NASA interactive forms type interface, or NIFTI - features on-the- fly forms creation, forms sharing among users, the capability to query the database from user-entered criteria on forms, traversal of query results, an ability to generate tab-delimited reports, viewing and downloading of reports to the user s workstation, and a hypertext-based help system. NIFTI is a very powerful ad hoc query tool that was developed using C++, X-Windows by a Motif application framework. A unique tool, NIFTI s capabilities appear in no other known commercial-off-the- shelf (COTS) tool, because NIFTI, which can be launched from the user s desktop, is a simple yet very powerful tool with a highly intuitive, easy-to-use graphical user interface (GUI) that will expedite the creation of database query/update forms. NIFTI, therefore, can be used in NASA s International Space Station (ISS) as well as within government and industry - indeed by all users of the widely disseminated Oracle base. And it will provide significant cost savings in the areas of user training and scalability while advancing the art over current COTS browsers. No COTS browser performs all the functions NIFTI does, and NIFTI is easier to use. NIFTI s cost savings are very significant considering the very large database with which it is used and the large user community with varying data requirements it will support. Its ease of use means that personnel unfamiliar with databases (e.g., managers, supervisors, clerks, and others) can develop their own personal reports. For NASA, a tool such as NIFTI was needed to query, update, modify, and make deletions within the ISS vehicle master database (VMDB), a repository of engineering data that includes an indentured parts list and associated resource data (power, thermal, volume, weight, and the like). Since the VMDB is used both as a collection point for data and as a common repository for engineering, integration, and operations teams, a tool such as NIFTI had to be designed that could expedite the creation of database query/update forms which could then be shared among users.

Comprehensive T-Matrix Reference Database: A 2012 - 2013 Update

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Videen, Gorden; Khlebtsov, Nikolai G.; Wriedt, Thomas

2013-01-01

The T-matrix method is one of the most versatile, efficient, and accurate theoretical techniques widely used for numerically exact computer calculations of electromagnetic scattering by single and composite particles, discrete random media, and particles imbedded in complex environments. This paper presents the fifth update to the comprehensive database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2012. It also lists several earlier publications not incorporated in the original database, including Peter Waterman's reports from the 1960s illustrating the history of the T-matrix approach and demonstrating that John Fikioris and Peter Waterman were the true pioneers of the multi-sphere method otherwise known as the generalized Lorenz - Mie theory.

Update on Geothermal Direct-Use Installations in the United States

DOE Data Explorer

Beckers, Koenraad F.; Snyder, Diana M.; Young, Katherine R.

2017-03-02

An updated database of geothermal direct-use systems in the U.S. has been compiled and analyzed, building upon the Oregon Institute of Technology (OIT) Geo-Heat Center direct-use database. Types of direct-use applications examined include hot springs resorts and pools, aquaculture farms, greenhouses, and district heating systems, among others; power-generating facilities and ground-source heat pumps were excluded. Where possible, the current operation status, open and close dates, well data, and other technical data were obtained for each entry. The database contains 545 installations, of which 407 are open, 108 are closed, and 30 have an unknown status. A report is also included which details and analyzes current geothermal direct-use installations and barriers to further implementation.

48 CFR 52.232-33 - Payment by Electronic Funds Transfer-System for Award Management.

Code of Federal Regulations, 2013 CFR

2013-10-01

... contained in the System for Award Management (SAM) database. In the event that the EFT information changes, the Contractor shall be responsible for providing the updated information to the SAM database. (c... 210. (d) Suspension of payment. If the Contractor's EFT information in the SAM database is incorrect...

48 CFR 52.232-33 - Payment by Electronic Funds Transfer-System for Award Management.

Code of Federal Regulations, 2014 CFR

2014-10-01

... contained in the System for Award Management (SAM) database. In the event that the EFT information changes, the Contractor shall be responsible for providing the updated information to the SAM database. (c... 210. (d) Suspension of payment. If the Contractor's EFT information in the SAM database is incorrect...

48 CFR 52.232-33 - Payment by Electronic Funds Transfer-Central Contractor Registration.

Code of Federal Regulations, 2010 CFR

2010-10-01

... contained in the Central Contractor Registration (CCR) database. In the event that the EFT information changes, the Contractor shall be responsible for providing the updated information to the CCR database. (c... 210. (d) Suspension of payment. If the Contractor's EFT information in the CCR database is incorrect...

Relative Impact of Print and Database Products on Database Producer Expenses and Income--A Follow-Up.

ERIC Educational Resources Information Center

Williams, Martha E.

1982-01-01

Provides update to 13-year analysis of finances of major database producer noting actions taken to improve finances (decrease expenses, increase efficiency, develop new products, market strategies and services, change pricing scheme, omit print products, increase prices) and consequences of actions (revenue increase, connect hour increase). Five…

Expanded national database collection and data coverage in the FINDbase worldwide database for clinically relevant genomic variation allele frequencies

PubMed Central

Viennas, Emmanouil; Komianou, Angeliki; Mizzi, Clint; Stojiljkovic, Maja; Mitropoulou, Christina; Muilu, Juha; Vihinen, Mauno; Grypioti, Panagiota; Papadaki, Styliani; Pavlidis, Cristiana; Zukic, Branka; Katsila, Theodora; van der Spek, Peter J.; Pavlovic, Sonja; Tzimas, Giannis; Patrinos, George P.

2017-01-01

FINDbase (http://www.findbase.org) is a comprehensive data repository that records the prevalence of clinically relevant genomic variants in various populations worldwide, such as pathogenic variants leading mostly to monogenic disorders and pharmacogenomics biomarkers. The database also records the incidence of rare genetic diseases in various populations, all in well-distinct data modules. Here, we report extensive data content updates in all data modules, with direct implications to clinical pharmacogenomics. Also, we report significant new developments in FINDbase, namely (i) the release of a new version of the ETHNOS software that catalyzes development curation of national/ethnic genetic databases, (ii) the migration of all FINDbase data content into 90 distinct national/ethnic mutation databases, all built around Microsoft's PivotViewer (http://www.getpivot.com) software (iii) new data visualization tools and (iv) the interrelation of FINDbase with DruGeVar database with direct implications in clinical pharmacogenomics. The abovementioned updates further enhance the impact of FINDbase, as a key resource for Genomic Medicine applications. PMID:27924022

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

PubMed Central

Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad; Noguchi, Shuei; Kondo, Atsushi; Severin, Jessica; Mungall, Chris; Arenillas, David; Mathelier, Anthony; Medvedeva, Yulia A.; Lennartsson, Andreas; Drabløs, Finn; Ramilowski, Jordan A.; Rackham, Owen; Gough, Julian; Andersson, Robin; Sandelin, Albin; Ienasescu, Hans; Ono, Hiromasa; Bono, Hidemasa; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R.R.; Kasukawa, Takeya; Kawaji, Hideya

2017-01-01

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives. PMID:27794045

GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms

PubMed Central

David, Fabrice P.A.; Rougemont, Jacques; Deplancke, Bart

2017-01-01

GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing gene- and transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification of one or several splice variants of most known genes. To ease selection, primers have also been ranked according to defined criteria such as genome-wide specificity (with BLAST), amplicon size, and isoform coverage. Here, we report a major upgrade (2.0) of the database: eight new species (yeast, chicken, macaque, chimpanzee, rat, platypus, pufferfish, and Anolis carolinensis) now complement the five already included in the previous version (human, mouse, zebrafish, fly, and worm). Furthermore, the genomic reference has been updated to Ensembl v81 (while keeping earlier versions for backward compatibility) as a result of re-designing the back-end database and automating the import of relevant sections of the Ensembl database in species-independent fashion. This also allowed us to map known polymorphisms to the primers (on average three per primer for human), with the aim of reducing experimental error when targeting specific strains or individuals. Another consequence is that the inclusion of future Ensembl releases and other species has now become a relatively straightforward task. PMID:28053161

LANDFIRE 2010—Updates to the national dataset to support improved fire and natural resource management

USGS Publications Warehouse

Nelson, Kurtis J.; Long, Donald G.; Connot, Joel A.

2016-02-29

The Landscape Fire and Resource Management Planning Tools (LANDFIRE) 2010 data release provides updated and enhanced vegetation, fuel, and fire regime layers consistently across the United States. The data represent landscape conditions from approximately 2010 and are the latest release in a series of planned updates to maintain currency of LANDFIRE data products. Enhancements to the data products included refinement of urban areas by incorporating the National Land Cover Database 2006 land cover product, refinement of agricultural lands by integrating the National Agriculture Statistics Service 2011 cropland data layer, and improved wetlands delineations using the National Land Cover Database 2006 land cover and the U.S. Fish and Wildlife Service National Wetlands Inventory data. Disturbance layers were generated for years 2008 through 2010 using remotely sensed imagery, polygons representing disturbance events submitted by local organizations, and fire mapping program data such as the Monitoring Trends in Burn Severity perimeters produced by the U.S. Geological Survey and the U.S. Forest Service. Existing vegetation data were updated to account for transitions in disturbed areas and to account for vegetation growth and succession in undisturbed areas. Surface and canopy fuel data were computed from the updated vegetation type, cover, and height and occasionally from potential vegetation. Historical fire frequency and succession classes were also updated. Revised topographic layers were created based on updated elevation data from the National Elevation Dataset. The LANDFIRE program also released a new Web site offering updated content, enhanced usability, and more efficient navigation.

Interstitial lung disease induced by fluoxetine: Systematic review of literature and analysis of Vigiaccess, Eudravigilance and a national pharmacovigilance database.

PubMed

Deidda, Arianna; Pisanu, Claudia; Micheletto, Laura; Bocchetta, Alberto; Del Zompo, Maria; Stochino, Maria Erminia

2017-06-01

We investigated a pulmonary adverse drug reaction possibly induced by fluoxetine, the Interstitial Lung Disease, by performing a systematic review of published case reports on this subject, a review of the World Health Organization VigiAccess database, of the European EudraVigilance database and of a national Pharmacovigilance database (Italian Pharmacovigilance Network). The research found a total of seven cases linking fluoxetine to Interstitial Lung Disease in the literature. 36 cases of interstitial lung disease related to fluoxetine were retrieved from the VigiAccess database (updated to July 2016), and 36 reports were found in EudraVigilance database (updated to June 2016). In the Italian Pharmacovigilance database (updated to August 2016), we found only one case of Interstitial Lung Disease, codified as "pulmonary disease". Our investigation shows that fluoxetine might be considered as a possible cause of Interstitial Lung Disease. In particular, although here we do not discuss the assessment of benefits and harms of fluoxetine, since this antidepressant is widely used, our review suggests that fluoxetine-induced Interstitial Lung Disease should be considered in patients with dyspnea, associated or not with dry cough, who are treated with this drug. An early withdrawn of fluoxetine could be useful to obtain a complete remission of this adverse drug reaction and special attention should be particularly devoted to long-term therapy, and to female and elderly patients. Although the spontaneous reporting system is affected by important limitations, drug post- marketing surveillance represents an important tool to evaluate the real world effectiveness and safety of drugs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Development of the Orion Crew Module Static Aerodynamic Database. Part 1; Hypersonic

NASA Technical Reports Server (NTRS)

Bibb, Karen L.; Walker, Eric L.; Robinson, Philip E.

2011-01-01

The Orion aerodynamic database provides force and moment coefficients given the velocity, attitude, configuration, etc. of the Crew Exploration Vehicle (CEV). The database is developed and maintained by the NASA CEV Aerosciences Project team from computational and experimental aerodynamic simulations. The database is used primarily by the Guidance, Navigation, and Control (GNC) team to design vehicle trajectories and assess flight performance. The initial hypersonic re-entry portion of the Crew Module (CM) database was developed in 2006. Updates incorporating additional data and improvements to the database formulation and uncertainty methodologies have been made since then. This paper details the process used to develop the CM database, including nominal values and uncertainties, for Mach numbers greater than 8 and angles of attack between 140deg and 180deg. The primary available data are more than 1000 viscous, reacting gas chemistry computational simulations using both the Laura and Dplr codes, over a range of Mach numbers from 2 to 37 and a range of angles of attack from 147deg to 172deg. Uncertainties were based on grid convergence, laminar-turbulent solution variations, combined altitude and code-to-code variations, and expected heatshield asymmetry. A radial basis function response surface tool, NEAR-RS, was used to fit the coefficient data smoothly in a velocity-angle-of-attack space. The resulting database is presented and includes some data comparisons and a discussion of the predicted variation of trim angle of attack and lift-to-drag ratio. The database provides a variation in trim angle of attack on the order of +/-2deg, and a range in lift-to-drag ratio of +/-0.035 for typical vehicle flight conditions.

Useful Life | Energy Analysis | NREL

Science.gov Websites

Useful Life Useful Life Transparent Cost Database Button The table below gives ranges on useful seeking utility-scale technology cost and performance estimates, please visit the Transparent Cost Cost (February 2016 Update) Operations & Maintenance (February 2016 Update) Utility-Scale Capacity

IRIS TOXICOLOGICAL REVIEW AND SUMMARY DOCUMENTS FOR BERYLLIUM AND COMPOUNDS

EPA Science Inventory

EPA's assessment of the noncancer health effects and carcinogenic potential of Beryllium was added to the IRIS database in 1998. The IRIS program is updating the IRIS assessment for Beryllium. This update will incorporate health effects information published since the last assess...

76 FR 73564 - Federal Acquisition Regulation; Updates to Contract Reporting and Central Contractor Registration

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-29

... Federal Acquisition Regulation; Updates to Contract Reporting and Central Contractor Registration AGENCIES... Procurement Data System (FPDS). Additionally, changes are proposed for the clauses requiring contractor registration in the Central Contractor Registration (CCR) database and DUNS number reporting. DATES: Interested...

How Documentalists Update SIMBAD

NASA Astrophysics Data System (ADS)

Buga, M.; Bot, C.; Brouty, M.; Bruneau, C.; Brunet, C.; Cambresy, L.; Eisele, A.; Genova, F.; Lesteven, S.; Loup, C.; Neuville, M.; Oberto, A.; Ochsenbein, F.; Perret, E.; Siebert, A.; Son, E.; Vannier, P.; Vollmer, B.; Vonflie, P.; Wenger, M.; Woelfel, F.

2015-04-01

The Strasbourg astronomical Data Center (CDS) was created in 1972 and has had a major role in astronomy for more than forty years. CDS develops a service called SIMBAD that provides basic data, cross-identifications, bibliography, and measurements for astronomical objects outside the solar system. It brings to the scientific community an added value to content which is updated daily by a team of documentalists working together in close collaboration with astronomers and IT specialists. We explain how the CDS staff updates SIMBAD with object citations in the main astronomical journals, as well as with astronomical data and measurements. We also explain how the identification is made between the objects found in the literature and those already existing in SIMBAD. We show the steps followed by the documentalist team to update the database using different tools developed at CDS, like the sky visualizer Aladin, and the large catalogues and survey database VizieR. As a direct result of this teamwork, SIMBAD integrates almost 10.000 bibliographic references per year. The service receives more than 400.000 queries per day.

The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes

PubMed Central

Rigden, Daniel J

2017-01-01

Abstract This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR. As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein–protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as ‘breakthrough’ contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the ‘golden set’ of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/. PMID:28053160

Integration, warehousing, and analysis strategies of Omics data.

PubMed

Gedela, Srinubabu

2011-01-01

"-Omics" is a current suffix for numerous types of large-scale biological data generation procedures, which naturally demand the development of novel algorithms for data storage and analysis. With next generation genome sequencing burgeoning, it is pivotal to decipher a coding site on the genome, a gene's function, and information on transcripts next to the pure availability of sequence information. To explore a genome and downstream molecular processes, we need umpteen results at the various levels of cellular organization by utilizing different experimental designs, data analysis strategies and methodologies. Here comes the need for controlled vocabularies and data integration to annotate, store, and update the flow of experimental data. This chapter explores key methodologies to merge Omics data by semantic data carriers, discusses controlled vocabularies as eXtensible Markup Languages (XML), and provides practical guidance, databases, and software links supporting the integration of Omics data.

VKCDB: voltage-gated K+ channel database updated and upgraded.

PubMed

Gallin, Warren J; Boutet, Patrick A

2011-01-01

The Voltage-gated K(+) Channel DataBase (VKCDB) (http://vkcdb.biology.ualberta.ca) makes a comprehensive set of sequence data readily available for phylogenetic and comparative analysis. The current update contains 2063 entries for full-length or nearly full-length unique channel sequences from Bacteria (477), Archaea (18) and Eukaryotes (1568), an increase from 346 solely eukaryotic entries in the original release. In addition to protein sequences for channels, corresponding nucleotide sequences of the open reading frames corresponding to the amino acid sequences are now available and can be extracted in parallel with sets of protein sequences. Channels are categorized into subfamilies by phylogenetic analysis and by using hidden Markov model analyses. Although the raw database contains a number of fragmentary, duplicated, obsolete and non-channel sequences that were collected in early steps of data collection, the web interface will only return entries that have been validated as likely K(+) channels. The retrieval function of the web interface allows retrieval of entries that contain a substantial fraction of the core structural elements of VKCs, fragmentary entries, or both. The full database can be downloaded as either a MySQL dump or as an XML dump from the web site. We have now implemented automated updates at quarterly intervals.

Designing a User Manual to Support an In-House Database.

ERIC Educational Resources Information Center

Kraft, Melissa A.; Pugh, W. Jean

1988-01-01

Describes the steps involved in designing a user manual for an in-house database. Topics covered include goal definition, target audience identification, production scheduling, design and production choices, testing and review, and updating of the manual. (CLB)

Storage and utilization of HLA genomic data--new approaches to HLA typing.

PubMed

Helmberg, W

2000-01-01

Currently available DNA-based HLA typing assays can provide detailed information about sequence motifs of a tested sample. It is still a common practice, however, for information acquired by high-resolution sequence specific oligonucleotide probe (SSOP) typing or sequence specific priming (SSP) to be presented in a low-resolution serological format. Unfortunately, this representation can lead to significant loss of useful data in many cases. An alternative to assigning allele equivalents to suchDNA typing results is simply to store the observed typing pattern and utilize the information with the help of Virtual DNA Analysis (VDA). Interpretation of the stored typing patterns can then be updated based on newly defined alleles, assuming the sequence motifs detected by the typing reagents are known. Rather than updating reagent specificities in individual laboratories, such updates should be performed in a central, publicly available sequence database. By referring to this database, HLA genomic data can then be stored and transferred between laboratories without loss of information. The 13th International Histocompatibility Workshop offers an ideal opportunity to begin building this common database for the entire human MHC.

IRIS Toxicological Review of 1,4-Dioxane (with Inhalation Update) (External Review Draft)

EPA Science Inventory

EPA is conducting a peer review and public comment of the scientific basis supporting the human health hazard and dose-response assessment of 1,4-Dioxane (with inhalation update) that when finalized will appear on the Integrated Risk Information System (IRIS) database.

IRIS TOXICOLOGICAL REVIEW AND SUMMARY DOCUMENTS FOR 1,2,3-TRICHLOROPROPANE

EPA Science Inventory

EPA's assessment of the noncancer health effects and carcinogenic potential of 1,2,3-trichloropropane (TCP) was added to the IRIS database in 1990. The IRIS program is updating the IRIS assessment for TCP. This update will incorporate health effects information published since t...

Rutgers/NJDOT Pavement Resource Program (NJDOT Statewide GPR Project Network GPR Data Collection and Analysis Update of HPMA GPR Database)

DOT National Transportation Integrated Search

2008-05-01

Center for Advanced Transportation Infrastructure (CAIT) of Rutgers University is mandated to conduct Ground Penetrating Radar (GPR) surveys to update the NJDOT's pavement management system with GPR measured pavement layer thicknesses. Based on the r...

7 CFR 400.55 - Qualification for actual production history coverage program.

Code of Federal Regulations, 2013 CFR

2013-01-01

... APH yield is calculated from a database containing a minimum of four yields and will be updated each subsequent crop year. The database may contain a maximum of the 10 most recent crop years and may include... only occur in the database when there are less than four years of actual and/or assigned yields. (b...

7 CFR 400.55 - Qualification for actual production history coverage program.

Code of Federal Regulations, 2011 CFR

2011-01-01

... APH yield is calculated from a database containing a minimum of four yields and will be updated each subsequent crop year. The database may contain a maximum of the 10 most recent crop years and may include... only occur in the database when there are less than four years of actual and/or assigned yields. (b...

7 CFR 400.55 - Qualification for actual production history coverage program.

Code of Federal Regulations, 2010 CFR

2010-01-01

... APH yield is calculated from a database containing a minimum of four yields and will be updated each subsequent crop year. The database may contain a maximum of the 10 most recent crop years and may include... only occur in the database when there are less than four years of actual and/or assigned yields. (b...

7 CFR 400.55 - Qualification for actual production history coverage program.

Code of Federal Regulations, 2012 CFR

2012-01-01

... APH yield is calculated from a database containing a minimum of four yields and will be updated each subsequent crop year. The database may contain a maximum of the 10 most recent crop years and may include... only occur in the database when there are less than four years of actual and/or assigned yields. (b...

NGA-West2 Flatfiles and GMPE Reports Now Available! | PEER News

Science.gov Websites

equations (GMPEs) and other research studies supporting GMPE development, along with the NGA-West2 Database NGA-West2 database "flatfiles" used in various research components of NGA-West2 have also database for download have been incorporated into an updated version of the online user-friendly PEER

MaizeGDB update: New tools, data, and interface for the maize model organism database

USDA-ARS?s Scientific Manuscript database

MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp. mays. Although some form of the maize community database has existed over the last 25 years, there have only been two major releases. In 1991, ...

78 FR 19985 - Modification of VOR Federal Airways V-68, V-76, V-194, and V-548 in the Vicinity of Houston, TX

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-03

... FAA's aeronautical database and depicted on the associated aeronautical charts. DATES: Effective date... changed and was updated in the FAA aeronautical database. However, the associated rulemaking action to... contained in the FAA's aeronautical database or the charted depiction of the airways on the aeronautical...

Fast Fingerprint Database Maintenance for Indoor Positioning Based on UGV SLAM

PubMed Central

Tang, Jian; Chen, Yuwei; Chen, Liang; Liu, Jingbin; Hyyppä, Juha; Kukko, Antero; Kaartinen, Harri; Hyyppä, Hannu; Chen, Ruizhi

2015-01-01

Indoor positioning technology has become more and more important in the last two decades. Utilizing Received Signal Strength Indicator (RSSI) fingerprints of Signals of OPportunity (SOP) is a promising alternative navigation solution. However, as the RSSIs vary during operation due to their physical nature and are easily affected by the environmental change, one challenge of the indoor fingerprinting method is maintaining the RSSI fingerprint database in a timely and effective manner. In this paper, a solution for rapidly updating the fingerprint database is presented, based on a self-developed Unmanned Ground Vehicles (UGV) platform NAVIS. Several SOP sensors were installed on NAVIS for collecting indoor fingerprint information, including a digital compass collecting magnetic field intensity, a light sensor collecting light intensity, and a smartphone which collects the access point number and RSSIs of the pre-installed WiFi network. The NAVIS platform generates a map of the indoor environment and collects the SOPs during processing of the mapping, and then the SOP fingerprint database is interpolated and updated in real time. Field tests were carried out to evaluate the effectiveness and efficiency of the proposed method. The results showed that the fingerprint databases can be quickly created and updated with a higher sampling frequency (5Hz) and denser reference points compared with traditional methods, and the indoor map can be generated without prior information. Moreover, environmental changes could also be detected quickly for fingerprint indoor positioning. PMID:25746096

23 CFR 971.204 - Management systems requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION FEDERAL LANDS HIGHWAYS FOREST SERVICE... maintain the management systems and their associated databases; and (5) A process for data collection, processing, analysis, and updating for each management system. (c) All management systems will use databases...

23 CFR 970.204 - Management systems requirements.

Code of Federal Regulations, 2014 CFR

2014-04-01

... Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION FEDERAL LANDS HIGHWAYS NATIONAL PARK... the management systems and their associated databases; and (5) A process for data collection, processing, analysis and updating for each management system. (d) All management systems will use databases...

Development and operations of the astrophysics data system

NASA Technical Reports Server (NTRS)

Murray, Stephen S.; Oliversen, Ronald (Technical Monitor)

2005-01-01

Abstract service - Continued regular updates of abstracts in the databases, both at SA0 and at all mirror sites. - Modified loading scripts to accommodate changes in data format (PhyS) - Discussed data deliveries with providers to clear up problems with format or other errors (EGU) - Continued inclusion of large numbers of historical literature volumes and physics conference volumes xeroxed from the library. - Performed systematic fixes on some data sets in the database to account for changes in article numbering (AGU journals) - Implemented linking of ADS bibliographic records with multimedia files - Debugged and fixed obscure connection problems with the ADS Korean mirror site which were preventing successful updates of the data holdings. - Wrote procedure to parse citation data and characterize an ADS record based on its citation ratios within each database.

NONCODE v2.0: decoding the non-coding.

PubMed

He, Shunmin; Liu, Changning; Skogerbø, Geir; Zhao, Haitao; Wang, Jie; Liu, Tao; Bai, Baoyan; Zhao, Yi; Chen, Runsheng

2008-01-01

The NONCODE database is an integrated knowledge database designed for the analysis of non-coding RNAs (ncRNAs). Since NONCODE was first released 3 years ago, the number of known ncRNAs has grown rapidly, and there is growing recognition that ncRNAs play important regulatory roles in most organisms. In the updated version of NONCODE (NONCODE v2.0), the number of collected ncRNAs has reached 206 226, including a wide range of microRNAs, Piwi-interacting RNAs and mRNA-like ncRNAs. The improvements brought to the database include not only new and updated ncRNA data sets, but also an incorporation of BLAST alignment search service and access through our custom UCSC Genome Browser. NONCODE can be found under http://www.noncode.org or http://noncode.bioinfo.org.cn.

CNA’s Integrated Ship Database: Third Quarter CY 2012 Update

DTIC Science & Technology

2013-11-01

rogram!- -;OJ"’T’-" A "’K"C~¥-go"Shi"~P:----------------t---’~;;1~ ® T- AKR Veh icle-Car o 9 S T- ADT Tran rt 0i1er 1 9 Mitita.y Sealift Command (MSC). in...CNA’s Integrated Ship Database Third Quarter CY 2012 Update Gregory N. Suess • Lynette A . McClain • Linette O. Neal CNA Interactive Software DIS...law, no person shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB

Comprehensive Thematic T-Matrix Reference Database: A 2014-2015 Update

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Zakharova, Nadezhda; Khlebtsov, Nikolai G.; Videen, Gorden; Wriedt, Thomas

2015-01-01

The T-matrix method is one of the most versatile and efficient direct computer solvers of the macroscopic Maxwell equations and is widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, and particles in the vicinity of an interface separating two half-spaces with different refractive indices. This paper is the seventh update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated by us in 2004 and includes relevant publications that have appeared since 2013. It also lists a number of earlier publications overlooked previously.

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals.

PubMed

Lizio, Marina; Harshbarger, Jayson; Abugessaisa, Imad; Noguchi, Shuei; Kondo, Atsushi; Severin, Jessica; Mungall, Chris; Arenillas, David; Mathelier, Anthony; Medvedeva, Yulia A; Lennartsson, Andreas; Drabløs, Finn; Ramilowski, Jordan A; Rackham, Owen; Gough, Julian; Andersson, Robin; Sandelin, Albin; Ienasescu, Hans; Ono, Hiromasa; Bono, Hidemasa; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Kasukawa, Takeya; Kawaji, Hideya

2017-01-04

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Time and Space Efficient Algorithms for Two-Party Authenticated Data Structures

NASA Astrophysics Data System (ADS)

Papamanthou, Charalampos; Tamassia, Roberto

Authentication is increasingly relevant to data management. Data is being outsourced to untrusted servers and clients want to securely update and query their data. For example, in database outsourcing, a client's database is stored and maintained by an untrusted server. Also, in simple storage systems, clients can store very large amounts of data but at the same time, they want to assure their integrity when they retrieve them. In this paper, we present a model and protocol for two-party authentication of data structures. Namely, a client outsources its data structure and verifies that the answers to the queries have not been tampered with. We provide efficient algorithms to securely outsource a skip list with logarithmic time overhead at the server and client and logarithmic communication cost, thus providing an efficient authentication primitive for outsourced data, both structured (e.g., relational databases) and semi-structured (e.g., XML documents). In our technique, the client stores only a constant amount of space, which is optimal. Our two-party authentication framework can be deployed on top of existing storage applications, thus providing an efficient authentication service. Finally, we present experimental results that demonstrate the practical efficiency and scalability of our scheme.

Transterm: a database to aid the analysis of regulatory sequences in mRNAs

PubMed Central

Jacobs, Grant H.; Chen, Augustine; Stevens, Stewart G.; Stockwell, Peter A.; Black, Michael A.; Tate, Warren P.; Brown, Chris M.

2009-01-01

Messenger RNAs, in addition to coding for proteins, may contain regulatory elements that affect how the protein is translated. These include protein and microRNA-binding sites. Transterm (http://mRNA.otago.ac.nz/Transterm.html) is a database of regions and elements that affect translation with two major unique components. The first is integrated results of analysis of general features that affect translation (initiation, elongation, termination) for species or strains in Genbank, processed through a standard pipeline. The second is curated descriptions of experimentally determined regulatory elements that function as translational control elements in mRNAs. Transterm focuses on protein binding sites, particularly those in 3′-untranslated regions (3′-UTR). For this release the interface has been extensively updated based on user feedback. The data is now accessible by strain rather than species, for example there are 10 Escherichia coli strains (genomes) analysed separately. In addition to providing a repository of data, the database also provides tools for users to query their own mRNA sequences. Users can search sequences for Transterm or user defined regulatory elements, including protein or miRNA targets. Transterm also provides a central core of links to related resources for complementary analyses. PMID:18984623

ProtaBank: A repository for protein design and engineering data.

PubMed

Wang, Connie Y; Chang, Paul M; Ary, Marie L; Allen, Benjamin D; Chica, Roberto A; Mayo, Stephen L; Olafson, Barry D

2018-03-25

We present ProtaBank, a repository for storing, querying, analyzing, and sharing protein design and engineering data in an actively maintained and updated database. ProtaBank provides a format to describe and compare all types of protein mutational data, spanning a wide range of properties and techniques. It features a user-friendly web interface and programming layer that streamlines data deposition and allows for batch input and queries. The database schema design incorporates a standard format for reporting protein sequences and experimental data that facilitates comparison of results across different data sets. A suite of analysis and visualization tools are provided to facilitate discovery, to guide future designs, and to benchmark and train new predictive tools and algorithms. ProtaBank will provide a valuable resource to the protein engineering community by storing and safeguarding newly generated data, allowing for fast searching and identification of relevant data from the existing literature, and exploring correlations between disparate data sets. ProtaBank invites researchers to contribute data to the database to make it accessible for search and analysis. ProtaBank is available at https://protabank.org. © 2018 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

SmedGD 2.0: The Schmidtea mediterranea genome database

PubMed Central

Robb, Sofia M.C.; Gotting, Kirsten; Ross, Eric; Sánchez Alvarado, Alejandro

2016-01-01

Planarians have emerged as excellent models for the study of key biological processes such as stem cell function and regulation, axial polarity specification, regeneration, and tissue homeostasis among others. The most widely used organism for these studies is the free-living flatworm Schmidtea mediterranea. In 2007, the Schmidtea mediterranea Genome Database (SmedGD) was first released to provide a much needed resource for the small, but growing planarian community. SmedGD 1.0 has been a depository for genome sequence, a draft assembly, and related experimental data (e.g., RNAi phenotypes, in situ hybridization images, and differential gene expression results). We report here a comprehensive update to SmedGD (SmedGD 2.0) that aims to expand its role as an interactive community resource. The new database includes more recent, and up-to-date transcription data, provides tools that enhance interconnectivity between different genome assemblies and transcriptomes, including next generation assemblies for both the sexual and asexual biotypes of S. mediterranea. SmedGD 2.0 (http://smedgd.stowers.org) not only provides significantly improved gene annotations, but also tools for data sharing, attributes that will help both the planarian and biomedical communities to more efficiently mine the genomics and transcriptomics of S. mediterranea. PMID:26138588

dbDSM: a manually curated database for deleterious synonymous mutations.

PubMed

Wen, Pengbo; Xiao, Peng; Xia, Junfeng

2016-06-15

Synonymous mutations (SMs), which changed the sequence of a gene without directly altering the amino acid sequence of the encoded protein, were thought to have no functional consequences for a long time. They are often assumed to be neutral in models of mutation and selection and were completely ignored in many studies. However, accumulating experimental evidence has demonstrated that these mutations exert their impact on gene functions via splicing accuracy, mRNA stability, translation fidelity, protein folding and expression, and some of these mutations are implicated in human diseases. To the best of our knowledge, there is still no database specially focusing on disease-related SMs. We have developed a new database called dbDSM (database of Deleterious Synonymous Mutation), a continually updated database that collects, curates and manages available human disease-related SM data obtained from published literature. In the current release, dbDSM collects 1936 SM-disease association entries, including 1289 SMs and 443 human diseases from ClinVar, GRASP, GWAS Catalog, GWASdb, PolymiRTS database, PubMed database and Web of Knowledge. Additionally, we provided users a link to download all the data in the dbDSM and a link to submit novel data into the database. We hope dbDSM will be a useful resource for investigating the roles of SMs in human disease. dbDSM is freely available online at http://bioinfo.ahu.edu.cn:8080/dbDSM/index.jsp with all major browser supported. jfxia@ahu.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Aptamer Database

PubMed Central

Lee, Jennifer F.; Hesselberth, Jay R.; Meyers, Lauren Ancel; Ellington, Andrew D.

2004-01-01

The aptamer database is designed to contain comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods. Such data are not normally collected in ‘natural’ sequence databases, such as GenBank. Besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility, the database serves as a valuable resource for theoretical biologists who describe and explore fitness landscapes. The database is updated monthly and is publicly available at http://aptamer.icmb.utexas.edu/. PMID:14681367

Recent Updates on the Phytochemistry, Pharmacological, and Toxicological Activities of Zingiber zerumbet (L.) Roscoe ex Sm.

PubMed

Haque, Md Areeful; Jantan, Ibrahim

2017-01-01

Zingiber zerumbet (L.) Roscoe ex Sm. (family, Zingiberaceae) is a potent medicinal herb widely known as shampoo ginger and its rhizome is used in numerous ethnomedicinal applications including antipyretic, anti-inflammatory, antibacterial, anti-diarrheal, antidiabetics, carminative, and diuretic. The aim of this review was to bring together all the scientific updates on the phytochemistry and pharmacological activities of this herb, including their toxicological studies, and critically analyzed the outcomes to provide directions for future research on the herb as potential source of bioactive metabolites for pharmaceutical and nutraceutical applications. A structured electronic search on worldwide accepted scientific databases (Web of Science, PubMed, Google Scholar, Science Direct, SciFinder, Wiley Online Library) was carried out to compile the relevant information. Some information was obtained from books and database on medicinal plants used in various countries. About 60 metabolites, mainly polyphenols, and terpenoids have been isolated and identified. However, most of the reported pharmacological studies were based on crude extracts, and only a few of those isolated metabolites, particularly zerumbone have been investigated for biological and pharmacological activities. Many of the mechanistic studies to understand the pharmacological effects of the plant are limited by many considerations with regard to design, experimentation and interpretation. The bioactive metabolites should be further investigated on their safety and more elaborate preclinical studies before clinical trials can be undertaken. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Completion of the 2011 National Land Cover Database for the Conterminous United States – Representing a Decade of Land Cover Change Information

EPA Science Inventory

The National Land Cover Database (NLCD) provides nationwide data on land cover and land cover change at the native 30-m spatial resolution of the Landsat Thematic Mapper (TM). The database is designed to provide five-year cyclical updating of United States land cover and associat...

NIST/ASME Steam Properties Database

National Institute of Standards and Technology Data Gateway

SRD 10 NIST/ASME Steam Properties Database (PC database for purchase)   Based upon the International Association for the Properties of Water and Steam (IAPWS) 1995 formulation for the thermodynamic properties of water and the most recent IAPWS formulations for transport and other properties, this updated version provides water properties over a wide range of conditions according to the accepted international standards.

GANESH: software for customized annotation of genome regions.

PubMed

Huntley, Derek; Hummerich, Holger; Smedley, Damian; Kittivoravitkul, Sasivimol; McCarthy, Mark; Little, Peter; Sergot, Marek

2003-09-01

GANESH is a software package designed to support the genetic analysis of regions of human and other genomes. It provides a set of components that may be assembled to construct a self-updating database of DNA sequence, mapping data, and annotations of possible genome features. Once one or more remote sources of data for the target region have been identified, all sequences for that region are downloaded, assimilated, and subjected to a (configurable) set of standard database-searching and genome-analysis packages. The results are stored in compressed form in a relational database, and are updated automatically on a regular schedule so that they are always immediately available in their most up-to-date versions. A Java front-end, executed as a stand alone application or web applet, provides a graphical interface for navigating the database and for viewing the annotations. There are facilities for importing and exporting data in the format of the Distributed Annotation System (DAS), enabling a GANESH database to be used as a component of a DAS configuration. The system has been used to construct databases for about a dozen regions of human chromosomes and for three regions of mouse chromosomes.

Recent and Upcoming Changes to NOAA Marine Forecasts

Science.gov Websites

tropical cyclone forecast products effective on or about June 1, 2018 Updated: Continuing experimental around May 15, 2018 Updated: Continuing experimental status in offshore and high seas gridded forecasts been disestablished Discontinuing experimental text products used in the creation of the Tampa Bay

MNDR v2.0: an updated resource of ncRNA–disease associations in mammals

PubMed Central

Cui, Tianyu; Zhang, Lin; Huang, Yan; Yi, Ying; Tan, Puwen; Zhao, Yue; Hu, Yongfei

2018-01-01

Abstract Accumulating evidence suggests that diverse non-coding RNAs (ncRNAs) are involved in the progression of a wide variety of diseases. In recent years, abundant ncRNA–disease associations have been found and predicted according to experiments and prediction algorithms. Diverse ncRNA–disease associations are scattered over many resources and mammals, whereas a global view of diverse ncRNA–disease associations is not available for any mammals. Hence, we have updated the MNDR v2.0 database (www.rna-society.org/mndr/) by integrating experimental and prediction associations from manual literature curation and other resources under one common framework. The new developments in MNDR v2.0 include (i) an over 220-fold increase in ncRNA–disease associations enhancement compared with the previous version (including lncRNA, miRNA, piRNA, snoRNA and more than 1400 diseases); (ii) integrating experimental and prediction evidence from 14 resources and prediction algorithms for each ncRNA–disease association; (iii) mapping disease names to the Disease Ontology and Medical Subject Headings (MeSH); (iv) providing a confidence score for each ncRNA–disease association and (v) an increase of species coverage to six mammals. Finally, MNDR v2.0 intends to provide the scientific community with a resource for efficient browsing and extraction of the associations between diverse ncRNAs and diseases, including >260 000 ncRNA–disease associations. PMID:29106639

California Fault Parameters for the National Seismic Hazard Maps and Working Group on California Earthquake Probabilities 2007

USGS Publications Warehouse

Wills, Chris J.; Weldon, Ray J.; Bryant, W.A.

2008-01-01

This report describes development of fault parameters for the 2007 update of the National Seismic Hazard Maps and the Working Group on California Earthquake Probabilities (WGCEP, 2007). These reference parameters are contained within a database intended to be a source of values for use by scientists interested in producing either seismic hazard or deformation models to better understand the current seismic hazards in California. These parameters include descriptions of the geometry and rates of movements of faults throughout the state. These values are intended to provide a starting point for development of more sophisticated deformation models which include known rates of movement on faults as well as geodetic measurements of crustal movement and the rates of movements of the tectonic plates. The values will be used in developing the next generation of the time-independent National Seismic Hazard Maps, and the time-dependant seismic hazard calculations being developed for the WGCEP. Due to the multiple uses of this information, development of these parameters has been coordinated between USGS, CGS and SCEC. SCEC provided the database development and editing tools, in consultation with USGS, Golden. This database has been implemented in Oracle and supports electronic access (e.g., for on-the-fly access). A GUI-based application has also been developed to aid in populating the database. Both the continually updated 'living' version of this database, as well as any locked-down official releases (e.g., used in a published model for calculating earthquake probabilities or seismic shaking hazards) are part of the USGS Quaternary Fault and Fold Database http://earthquake.usgs.gov/regional/qfaults/ . CGS has been primarily responsible for updating and editing of the fault parameters, with extensive input from USGS and SCEC scientists.

The Dutch Hospital Standardised Mortality Ratio (HSMR) method and cardiac surgery: benchmarking in a national cohort using hospital administration data versus a clinical database

PubMed Central

Siregar, S; Pouw, M E; Moons, K G M; Versteegh, M I M; Bots, M L; van der Graaf, Y; Kalkman, C J; van Herwerden, L A; Groenwold, R H H

2014-01-01

Objective To compare the accuracy of data from hospital administration databases and a national clinical cardiac surgery database and to compare the performance of the Dutch hospital standardised mortality ratio (HSMR) method and the logistic European System for Cardiac Operative Risk Evaluation, for the purpose of benchmarking of mortality across hospitals. Methods Information on all patients undergoing cardiac surgery between 1 January 2007 and 31 December 2010 in 10 centres was extracted from The Netherlands Association for Cardio-Thoracic Surgery database and the Hospital Discharge Registry. The number of cardiac surgery interventions was compared between both databases. The European System for Cardiac Operative Risk Evaluation and hospital standardised mortality ratio models were updated in the study population and compared using the C-statistic, calibration plots and the Brier-score. Results The number of cardiac surgery interventions performed could not be assessed using the administrative database as the intervention code was incorrect in 1.4–26.3%, depending on the type of intervention. In 7.3% no intervention code was registered. The updated administrative model was inferior to the updated clinical model with respect to discrimination (c-statistic of 0.77 vs 0.85, p<0.001) and calibration (Brier Score of 2.8% vs 2.6%, p<0.001, maximum score 3.0%). Two average performing hospitals according to the clinical model became outliers when benchmarking was performed using the administrative model. Conclusions In cardiac surgery, administrative data are less suitable than clinical data for the purpose of benchmarking. The use of either administrative or clinical risk-adjustment models can affect the outlier status of hospitals. Risk-adjustment models including procedure-specific clinical risk factors are recommended. PMID:24334377

Comparison of two optimization algorithms for fuzzy finite element model updating for damage detection in a wind turbine blade

NASA Astrophysics Data System (ADS)

Turnbull, Heather; Omenzetter, Piotr

2018-03-01

vDifficulties associated with current health monitoring and inspection practices combined with harsh, often remote, operational environments of wind turbines highlight the requirement for a non-destructive evaluation system capable of remotely monitoring the current structural state of turbine blades. This research adopted a physics based structural health monitoring methodology through calibration of a finite element model using inverse techniques. A 2.36m blade from a 5kW turbine was used as an experimental specimen, with operational modal analysis techniques utilised to realize the modal properties of the system. Modelling the experimental responses as fuzzy numbers using the sub-level technique, uncertainty in the response parameters was propagated back through the model and into the updating parameters. Initially, experimental responses of the blade were obtained, with a numerical model of the blade created and updated. Deterministic updating was carried out through formulation and minimisation of a deterministic objective function using both firefly algorithm and virus optimisation algorithm. Uncertainty in experimental responses were modelled using triangular membership functions, allowing membership functions of updating parameters (Young's modulus and shear modulus) to be obtained. Firefly algorithm and virus optimisation algorithm were again utilised, however, this time in the solution of fuzzy objective functions. This enabled uncertainty associated with updating parameters to be quantified. Varying damage location and severity was simulated experimentally through addition of small masses to the structure intended to cause a structural alteration. A damaged model was created, modelling four variable magnitude nonstructural masses at predefined points and updated to provide a deterministic damage prediction and information in relation to the parameters uncertainty via fuzzy updating.

ThermoFit: A Set of Software Tools, Protocols and Schema for the Organization of Thermodynamic Data and for the Development, Maintenance, and Distribution of Internally Consistent Thermodynamic Data/Model Collections

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2013-12-01

Internally consistent thermodynamic databases are critical resources that facilitate the calculation of heterogeneous phase equilibria and thereby support geochemical, petrological, and geodynamical modeling. These 'databases' are actually derived data/model systems that depend on a diverse suite of physical property measurements, calorimetric data, and experimental phase equilibrium brackets. In addition, such databases are calibrated with the adoption of various models for extrapolation of heat capacities and volumetric equations of state to elevated temperature and pressure conditions. Finally, these databases require specification of thermochemical models for the mixing properties of solid, liquid, and fluid solutions, which are often rooted in physical theory and, in turn, depend on additional experimental observations. The process of 'calibrating' a thermochemical database involves considerable effort and an extensive computational infrastructure. Because of these complexities, the community tends to rely on a small number of thermochemical databases, generated by a few researchers; these databases often have limited longevity and are universally difficult to maintain. ThermoFit is a software framework and user interface whose aim is to provide a modeling environment that facilitates creation, maintenance and distribution of thermodynamic data/model collections. Underlying ThermoFit are data archives of fundamental physical property, calorimetric, crystallographic, and phase equilibrium constraints that provide the essential experimental information from which thermodynamic databases are traditionally calibrated. ThermoFit standardizes schema for accessing these data archives and provides web services for data mining these collections. Beyond simple data management and interoperability, ThermoFit provides a collection of visualization and software modeling tools that streamline the model/database generation process. Most notably, ThermoFit facilitates the rapid visualization of predicted model outcomes and permits the user to modify these outcomes using tactile- or mouse-based GUI interaction, permitting real-time updates that reflect users choices, preferences, and priorities involving derived model results. This ability permits some resolution of the problem of correlated model parameters in the common situation where thermodynamic models must be calibrated from inadequate data resources. The ability also allows modeling constraints to be imposed using natural data and observations (i.e. petrologic or geochemical intuition). Once formulated, ThermoFit facilitates deployment of data/model collections by automated creation of web services. Users consume these services via web-, excel-, or desktop-clients. ThermoFit is currently under active development and not yet generally available; a limited capability prototype system has been coded for Macintosh computers and utilized to construct thermochemical models for H2O-CO2 mixed fluid saturation in silicate liquids. The longer term goal is to release ThermoFit as a web portal application client with server-based cloud computations supporting the modeling environment.

Monitoring urban land cover change by updating the national land cover database impervious surface products

USGS Publications Warehouse

Xian, George Z.; Homer, Collin G.

2009-01-01

The U.S. Geological Survey (USGS) National Land Cover Database (NLCD) 2001 is widely used as a baseline for national land cover and impervious conditions. To ensure timely and relevant data, it is important to update this base to a more recent time period. A prototype method was developed to update the land cover and impervious surface by individual Landsat path and row. This method updates NLCD 2001 to a nominal date of 2006 by using both Landsat imagery and data from NLCD 2001 as the baseline. Pairs of Landsat scenes in the same season from both 2001 and 2006 were acquired according to satellite paths and rows and normalized to allow calculation of change vectors between the two dates. Conservative thresholds based on Anderson Level I land cover classes were used to segregate the change vectors and determine areas of change and no-change. Once change areas had been identified, impervious surface was estimated for areas of change by sampling from NLCD 2001 in unchanged areas. Methods were developed and tested across five Landsat path/row study sites that contain a variety of metropolitan areas. Results from the five study areas show that the vast majority of impervious surface changes associated with urban developments were accurately captured and updated. The approach optimizes mapping efficiency and can provide users a flexible method to generate updated impervious surface at national and regional scales.

Model updating in flexible-link multibody systems

NASA Astrophysics Data System (ADS)

Belotti, R.; Caneva, G.; Palomba, I.; Richiedei, D.; Trevisani, A.

2016-09-01

The dynamic response of flexible-link multibody systems (FLMSs) can be predicted through nonlinear models based on finite elements, to describe the coupling between rigid- body and elastic behaviour. Their accuracy should be as high as possible to synthesize controllers and observers. Model updating based on experimental measurements is hence necessary. By taking advantage of the experimental modal analysis, this work proposes a model updating procedure for FLMSs and applies it experimentally to a planar robot. Indeed, several peculiarities of the model of FLMS should be carefully tackled. On the one hand, nonlinear models of a FLMS should be linearized about static equilibrium configurations. On the other, the experimental mode shapes should be corrected to be consistent with the elastic displacements represented in the model, which are defined with respect to a fictitious moving reference (the equivalent rigid link system). Then, since rotational degrees of freedom are also represented in the model, interpolation of the experimental data should be performed to match the model displacement vector. Model updating has been finally cast as an optimization problem in the presence of bounds on the feasible values, by also adopting methods to improve the numerical conditioning and to compute meaningful updated inertial and elastic parameters.

15 CFR 995.4 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... database resulting from the transformation of the ENC by ECDIS for appropriate use, updates to the ENC by... of the 1974 SOLAS Convention. Electronic Navigational Chart (ENC) means a database, standardized as to content, structure, and format, issued for use with ECDIS on the authority of government...

SysML model of exoplanet archive functionality and activities

NASA Astrophysics Data System (ADS)

Ramirez, Solange

2016-08-01

The NASA Exoplanet Archive is an online service that serves data and information on exoplanets and their host stars to help astronomical research related to search for and characterization of extra-solar planetary systems. In order to provide the most up to date data sets to the users, the exoplanet archive performs weekly updates that include additions into the database and updates to the services as needed. These weekly updates are complex due to interfaces within the archive. I will be presenting a SysML model that helps us perform these update activities in a weekly basis.

Glucose-6-phosphate dehydrogenase (G6PD) mutations database: review of the "old" and update of the new mutations.

PubMed

Minucci, Angelo; Moradkhani, Kamran; Hwang, Ming Jing; Zuppi, Cecilia; Giardina, Bruno; Capoluongo, Ettore

2012-03-15

In the present paper we have updated the G6PD mutations database, including all the last discovered G6PD genetic variants. We underline that the last database has been published by Vulliamy et al. [1] who analytically reported 140 G6PD mutations: along with Vulliamy's database, there are two main sites, such as http://202.120.189.88/mutdb/ and www.LOVD.nl/MR, where almost all G6PD mutations can be found. Compared to the previous mutation reports, in our paper we have included for each mutation some additional information, such as: the secondary structure and the enzyme 3D position involving by mutation, the creation or abolition of a restriction site (with the enzyme involved) and the conservation score associated with each amino acid position. The mutations reported in the present tab have been divided according to the gene's region involved (coding and non-coding) and mutations affecting the coding region in: single, multiple (at least with two bases involved) and deletion. We underline that for the listed mutations, reported in italic, literature doesn't provide all the biochemical or bio-molecular information or the research data. Finally, for the "old" mutations, we tried to verify features previously reported and, when subsequently modified, we updated the specific information using the latest literature data. Copyright © 2012 Elsevier Inc. All rights reserved.

2016 update of the PRIDE database and its related tools

PubMed Central

Vizcaíno, Juan Antonio; Csordas, Attila; del-Toro, Noemi; Dianes, José A.; Griss, Johannes; Lavidas, Ilias; Mayer, Gerhard; Perez-Riverol, Yasset; Reisinger, Florian; Ternent, Tobias; Xu, Qing-Wei; Wang, Rui; Hermjakob, Henning

2016-01-01

The PRoteomics IDEntifications (PRIDE) database is one of the world-leading data repositories of mass spectrometry (MS)-based proteomics data. Since the beginning of 2014, PRIDE Archive (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system, replacing the original PRIDE database. Here we summarize the developments in PRIDE resources and related tools since the previous update manuscript in the Database Issue in 2013. PRIDE Archive constitutes a complete redevelopment of the original PRIDE, comprising a new storage backend, data submission system and web interface, among other components. PRIDE Archive supports the most-widely used PSI (Proteomics Standards Initiative) data standard formats (mzML and mzIdentML) and implements the data requirements and guidelines of the ProteomeXchange Consortium. The wide adoption of ProteomeXchange within the community has triggered an unprecedented increase in the number of submitted data sets (around 150 data sets per month). We outline some statistics on the current PRIDE Archive data contents. We also report on the status of the PRIDE related stand-alone tools: PRIDE Inspector, PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we will give a brief update on the resources under development ‘PRIDE Cluster’ and ‘PRIDE Proteomes’, which provide a complementary view and quality-scored information of the peptide and protein identification data available in PRIDE Archive. PMID:26527722

eBASIS (Bioactive Substances in Food Information Systems) and Bioactive Intakes: Major Updates of the Bioactive Compound Composition and Beneficial Bioeffects Database and the Development of a Probabilistic Model to Assess Intakes in Europe.

PubMed

Plumb, Jenny; Pigat, Sandrine; Bompola, Foteini; Cushen, Maeve; Pinchen, Hannah; Nørby, Eric; Astley, Siân; Lyons, Jacqueline; Kiely, Mairead; Finglas, Paul

2017-03-23

eBASIS (Bioactive Substances in Food Information Systems), a web-based database that contains compositional and biological effects data for bioactive compounds of plant origin, has been updated with new data on fruits and vegetables, wheat and, due to some evidence of potential beneficial effects, extended to include meat bioactives. eBASIS remains one of only a handful of comprehensive and searchable databases, with up-to-date coherent and validated scientific information on the composition of food bioactives and their putative health benefits. The database has a user-friendly, efficient, and flexible interface facilitating use by both the scientific community and food industry. Overall, eBASIS contains data for 267 foods, covering the composition of 794 bioactive compounds, from 1147 quality-evaluated peer-reviewed publications, together with information from 567 publications describing beneficial bioeffect studies carried out in humans. This paper highlights recent updates and expansion of eBASIS and the newly-developed link to a probabilistic intake model, allowing exposure assessment of dietary bioactive compounds to be estimated and modelled in human populations when used in conjunction with national food consumption data. This new tool could assist small- and medium-sized enterprises (SMEs) in the development of food product health claim dossiers for submission to the European Food Safety Authority (EFSA).

Paracetamol (acetaminophen) poisoning.

PubMed

Park, B Kevin; Dear, James W; Antoine, Daniel J

2015-10-19

Paracetamol directly causes around 150 deaths per year in UK. We conducted a systematic overview, aiming to answer the following clinical question: What are the effects of treatments for acute paracetamol poisoning? We searched: Medline, Embase, The Cochrane Library, and other important databases up to October 2014 (Clinical Evidence overviews are updated periodically; please check our website for the most up-to-date version of this overview). At this update, searching of electronic databases retrieved 127 studies. After deduplication and removal of conference abstracts, 64 records were screened for inclusion in the overview. Appraisal of titles and abstracts led to the exclusion of 46 studies and the further review of 18 full publications. Of the 18 full articles evaluated, one systematic review was updated and one RCT was added at this update. In addition, two systematic reviews and three RCTs not meeting our inclusion criteria were added to the Comment sections. We performed a GRADE evaluation for three PICO combinations. In this systematic overview we categorised the efficacy for six interventions, based on information about the effectiveness and safety of activated charcoal (single or multiple dose), gastric lavage, haemodialysis, liver transplant, methionine, and acetylcysteine.

Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain

PubMed Central

Matthes, Michaela; Preusse, Martin; Zhang, Jingzhong; Schechter, Julia; Mayer, Daniela; Lentes, Bernd; Theis, Fabian; Prakash, Nilima; Wurst, Wolfgang; Trümbach, Dietrich

2014-01-01

The study of developmental processes in the mouse and other vertebrates includes the understanding of patterning along the anterior–posterior, dorsal–ventral and medial– lateral axis. Specifically, neural development is also of great clinical relevance because several human neuropsychiatric disorders such as schizophrenia, autism disorders or drug addiction and also brain malformations are thought to have neurodevelopmental origins, i.e. pathogenesis initiates during childhood and adolescence. Impacts during early neurodevelopment might also predispose to late-onset neurodegenerative disorders, such as Parkinson’s disease. The neural tube develops from its precursor tissue, the neural plate, in a patterning process that is determined by compartmentalization into morphogenetic units, the action of local signaling centers and a well-defined and locally restricted expression of genes and their interactions. While public databases provide gene expression data with spatio-temporal resolution, they usually neglect the genetic interactions that govern neural development. Here, we introduce Mouse IDGenes, a reference database for genetic interactions in the developing mouse brain. The database is highly curated and offers detailed information about gene expressions and the genetic interactions at the developing mid-/hindbrain boundary. To showcase the predictive power of interaction data, we infer new Wnt/β-catenin target genes by machine learning and validate one of them experimentally. The database is updated regularly. Moreover, it can easily be extended by the research community. Mouse IDGenes will contribute as an important resource to the research on mouse brain development, not exclusively by offering data retrieval, but also by allowing data input. Database URL: http://mouseidgenes.helmholtz-muenchen.de. PMID:25145340

Genetically optimizing weather predictions

NASA Astrophysics Data System (ADS)

Potter, S. B.; Staats, Kai; Romero-Colmenero, Encarni

2016-07-01

humidity, air pressure, wind speed and wind direction) into a database. Built upon this database, we have developed a remarkably simple approach to derive a functional weather predictor. The aim is provide up to the minute local weather predictions in order to e.g. prepare dome environment conditions ready for night time operations or plan, prioritize and update weather dependent observing queues. In order to predict the weather for the next 24 hours, we take the current live weather readings and search the entire archive for similar conditions. Predictions are made against an averaged, subsequent 24 hours of the closest matches for the current readings. We use an Evolutionary Algorithm to optimize our formula through weighted parameters. The accuracy of the predictor is routinely tested and tuned against the full, updated archive to account for seasonal trends and total, climate shifts. The live (updated every 5 minutes) SALT weather predictor can be viewed here: http://www.saao.ac.za/ sbp/suthweather_predict.html

Water-level database update for the Death Valley regional groundwater flow system, Nevada and California, 1907-2007

USGS Publications Warehouse

Pavelko, Michael T.

2010-01-01

The water-level database for the Death Valley regional groundwater flow system in Nevada and California was updated. The database includes more than 54,000 water levels collected from 1907 to 2007, from more than 1,800 wells. Water levels were assigned a primary flag and multiple secondary flags that describe hydrologic conditions and trends at the time of the measurement and identify pertinent information about the well or water-level measurement. The flags provide a subjective measure of the relative accuracy of the measurements and are used to identify which water levels are appropriate for calculating head observations in a regional transient groundwater flow model. Included in the report appendix are all water-level data and their flags, selected well data, and an interactive spreadsheet for viewing hydrographs and well locations.

LARCRIM user's guide, version 1.0

NASA Technical Reports Server (NTRS)

Davis, John S.; Heaphy, William J.

1993-01-01

LARCRIM is a relational database management system (RDBMS) which performs the conventional duties of an RDBMS with the added feature that it can store attributes which consist of arrays or matrices. This makes it particularly valuable for scientific data management. It is accessible as a stand-alone system and through an application program interface. The stand-alone system may be executed in two modes: menu or command. The menu mode prompts the user for the input required to create, update, and/or query the database. The command mode requires the direct input of LARCRIM commands. Although LARCRIM is an update of an old database family, its performance on modern computers is quite satisfactory. LARCRIM is written in FORTRAN 77 and runs under the UNIX operating system. Versions have been released for the following computers: SUN (3 & 4), Convex, IRIS, Hewlett-Packard, CRAY 2 & Y-MP.

Data for Regional Heat flow Studies in and around Japan and its relationship to seismogenic layer

NASA Astrophysics Data System (ADS)

Tanaka, A.

2017-12-01

Heat flow is a fundamental parameter to constrain the thermal structure of the lithosphere. It also provides a constraint to lithospheric rheology, which is sensitive to temperature. General features of the heat flow distribution in and around Japan had been revealed by the early 1970's, and heat flow data have been continuously updated by further data compilation from mainly published data and investigations. These include additional data, which were not published individually, but were included in site-specific reports. Also, thermal conductivity measurements were conducted on cores from boreholes using a line-source device with a half-space type box probe and an optical scanning device, and previously unpublished thermal conductivities were compiled. It has been more than 10 years since the last published compilation and analysis of heat flow data of Tanaka et al. (2004), which published all of the heat flow data in the northwestern Pacific area (from 0 to 60oN and from 120 to 160oE) and geothermal gradient data in and around Japan. Because these added data and information are drawn from various sources, the updated database is compiled in each datasets: heat flow, geothermal gradient, and thermal conductivity. The updated and improved database represents considerable improvement to past updates and presents an opportunity to revisit the thermal state of the lithosphere along with other geophysical/geochemical constraints on heat flow extrapolation. The spatial distribution of the cut-off depth of shallow seismicity of Japan using relocated hypocentres during the last decade (Omuralieva et al., 2012) and this updated database are used to quantify the concept of temperature as a fundamental parameter for determining the seismogenic thickness.

An Update of the Bodeker Scientific Vertically Resolved, Global, Gap-Free Ozone Database

NASA Astrophysics Data System (ADS)

Kremser, S.; Bodeker, G. E.; Lewis, J.; Hassler, B.

2016-12-01

High vertical resolution ozone measurements from multiple satellite-based instruments have been merged with measurements from the global ozonesonde network to calculate monthly mean ozone values in 5º latitude zones. Ozone number densities and ozone mixing ratios are provided on 70 altitude levels (1 to 70 km) and on 70 pressure levels spaced approximately 1 km apart (878.4 hPa to 0.046 hPa). These data are sparse and do not cover the entire globe or altitude range. To provide a gap-free database, a least squares regression model is fitted to these data and then evaluated globally. By applying a single fit at each level, and using the approach of allowing the regression fits to change only slightly from one level to the next, the regression is less sensitive to measurement anomalies at individual stations or to individual satellite-based instruments. Particular attention is paid to ensuring that the low ozone abundances in the polar regions are captured. This presentation reports on updates to an earlier version of the vertically resolved ozone database, including the incorporation of new ozone measurements and new techniques for combining the data. Compared to previous versions of the database, particular attention is paid to avoiding spatial and temporal sampling biases and tracing uncertainties through to the final product. This updated database, developed within the New Zealand Deep South National Science Challenge, is suitable for assessing ozone fields from chemistry-climate model simulations or for providing the ozone boundary conditions for global climate model simulations that do not treat stratospheric chemistry interactively.

Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses.

PubMed

Falagas, Matthew E; Pitsouni, Eleni I; Malietzis, George A; Pappas, Georgios

2008-02-01

The evolution of the electronic age has led to the development of numerous medical databases on the World Wide Web, offering search facilities on a particular subject and the ability to perform citation analysis. We compared the content coverage and practical utility of PubMed, Scopus, Web of Science, and Google Scholar. The official Web pages of the databases were used to extract information on the range of journals covered, search facilities and restrictions, and update frequency. We used the example of a keyword search to evaluate the usefulness of these databases in biomedical information retrieval and a specific published article to evaluate their utility in performing citation analysis. All databases were practical in use and offered numerous search facilities. PubMed and Google Scholar are accessed for free. The keyword search with PubMed offers optimal update frequency and includes online early articles; other databases can rate articles by number of citations, as an index of importance. For citation analysis, Scopus offers about 20% more coverage than Web of Science, whereas Google Scholar offers results of inconsistent accuracy. PubMed remains an optimal tool in biomedical electronic research. Scopus covers a wider journal range, of help both in keyword searching and citation analysis, but it is currently limited to recent articles (published after 1995) compared with Web of Science. Google Scholar, as for the Web in general, can help in the retrieval of even the most obscure information but its use is marred by inadequate, less often updated, citation information.

Security in the CernVM File System and the Frontier Distributed Database Caching System

NASA Astrophysics Data System (ADS)

Dykstra, D.; Blomer, J.

2014-06-01

Both the CernVM File System (CVMFS) and the Frontier Distributed Database Caching System (Frontier) distribute centrally updated data worldwide for LHC experiments using http proxy caches. Neither system provides privacy or access control on reading the data, but both control access to updates of the data and can guarantee the authenticity and integrity of the data transferred to clients over the internet. CVMFS has since its early days required digital signatures and secure hashes on all distributed data, and recently Frontier has added X.509-based authenticity and integrity checking. In this paper we detail and compare the security models of CVMFS and Frontier.

CNA’s Integrated Ship Database, Fourth Quarter 2011 Update

DTIC Science & Technology

2012-09-01

AKR300 G T-AKR301 G T-AKR302 8 T-AKR303 A 8 T-AKR304 G T-AKR305 G T-AKR30S 8 T- AKR 31l R - G T- AKR 312 G T- AKR 313 8 T- AKR 314 G T- AKR 315...CNA’s Integrated Ship Database Fourth Quarter 2011 Update Gregory N. Suess, Lynette A . McClain, and Rhea Stone CNA Interactive Software DIS-2012-U...no person shall be subject to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control

Comprehensive Thematic T-Matrix Reference Database: A 2015-2017 Update

NASA Technical Reports Server (NTRS)

Mishchenko, Michael I.; Zakharova, Nadezhda; Khlebtsov, Nikolai G.; Videen, Gorden; Wriedt, Thomas

2017-01-01

The T-matrix method pioneered by Peter C. Waterman is one of the most versatile and efficient numerically exact computer solvers of the time-harmonic macroscopic Maxwell equations. It is widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, periodic structures (including metamaterials), and particles in the vicinity of plane or rough interfaces separating media with different refractive indices. This paper is the eighth update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated in 2004 and lists relevant publications that have appeared since 2015. It also references a small number of earlier publications overlooked previously.

Comprehensive thematic T-matrix reference database: A 2015-2017 update

NASA Astrophysics Data System (ADS)

Mishchenko, Michael I.; Zakharova, Nadezhda T.; Khlebtsov, Nikolai G.; Videen, Gorden; Wriedt, Thomas

2017-11-01

The T-matrix method pioneered by Peter C. Waterman is one of the most versatile and efficient numerically exact computer solvers of the time-harmonic macroscopic Maxwell equations. It is widely used for the computation of electromagnetic scattering by single and composite particles, discrete random media, periodic structures (including metamaterials), and particles in the vicinity of plane or rough interfaces separating media with different refractive indices. This paper is the eighth update to the comprehensive thematic database of peer-reviewed T-matrix publications initiated in 2004 and lists relevant publications that have appeared since 2015. It also references a small number of earlier publications overlooked previously.

Literature classification for semi-automated updating of biological knowledgebases

PubMed Central

2013-01-01

Background As the output of biological assays increase in resolution and volume, the body of specialized biological data, such as functional annotations of gene and protein sequences, enables extraction of higher-level knowledge needed for practical application in bioinformatics. Whereas common types of biological data, such as sequence data, are extensively stored in biological databases, functional annotations, such as immunological epitopes, are found primarily in semi-structured formats or free text embedded in primary scientific literature. Results We defined and applied a machine learning approach for literature classification to support updating of TANTIGEN, a knowledgebase of tumor T-cell antigens. Abstracts from PubMed were downloaded and classified as either "relevant" or "irrelevant" for database update. Training and five-fold cross-validation of a k-NN classifier on 310 abstracts yielded classification accuracy of 0.95, thus showing significant value in support of data extraction from the literature. Conclusion We here propose a conceptual framework for semi-automated extraction of epitope data embedded in scientific literature using principles from text mining and machine learning. The addition of such data will aid in the transition of biological databases to knowledgebases. PMID:24564403

GETPrime 2.0: gene- and transcript-specific qPCR primers for 13 species including polymorphisms.

PubMed

David, Fabrice P A; Rougemont, Jacques; Deplancke, Bart

2017-01-04

GETPrime (http://bbcftools.epfl.ch/getprime) is a database with a web frontend providing gene- and transcript-specific, pre-computed qPCR primer pairs. The primers have been optimized for genome-wide specificity and for allowing the selective amplification of one or several splice variants of most known genes. To ease selection, primers have also been ranked according to defined criteria such as genome-wide specificity (with BLAST), amplicon size, and isoform coverage. Here, we report a major upgrade (2.0) of the database: eight new species (yeast, chicken, macaque, chimpanzee, rat, platypus, pufferfish, and Anolis carolinensis) now complement the five already included in the previous version (human, mouse, zebrafish, fly, and worm). Furthermore, the genomic reference has been updated to Ensembl v81 (while keeping earlier versions for backward compatibility) as a result of re-designing the back-end database and automating the import of relevant sections of the Ensembl database in species-independent fashion. This also allowed us to map known polymorphisms to the primers (on average three per primer for human), with the aim of reducing experimental error when targeting specific strains or individuals. Another consequence is that the inclusion of future Ensembl releases and other species has now become a relatively straightforward task. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases. To appear in an article of Journal of Database Management.

Update on NASA Space Shuttle Earth Observations Photography on the laser videodisc for rapid image access

NASA Technical Reports Server (NTRS)

Lulla, Kamlesh

1994-01-01

There have been many significant improvements in the public access to the Space Shuttle Earth Observations Photography Database. New information is provided for the user community on the recently released videodisc of this database. Topics covered included the following: earlier attempts; our first laser videodisc in 1992; the new laser videodisc in 1994; and electronic database access.

GenoBase: comprehensive resource database of Escherichia coli K-12

PubMed Central

Otsuka, Yuta; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Koichiro; Yamamoto, Natsuko; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Suharnan, Sivasundaram; Nomura, Wataru; Nakayashiki, Toru; Aref, Walid G.; Bochner, Barry R.; Conway, Tyrrell; Gribskov, Michael; Kihara, Daisuke; Rudd, Kenneth E.; Tohsato, Yukako; Wanner, Barry L.; Mori, Hirotada

2015-01-01

Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources. PMID:25399415

75 FR 41140 - Agency Information Collection Activities: Proposed Collection; Comment Request-Child Nutrition...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-15

... DEPARTMENT OF AGRICULTURE Food and Nutrition Service Agency Information Collection Activities: Proposed Collection; Comment Request--Child Nutrition Database AGENCY: Food and Nutrition Service, USDA... nutrient data from the food service industry to update and expand the Child Nutrition Database in support...

Publications | Hydrogen and Fuel Cells | NREL

Science.gov Websites

, and demonstration activities in hydrogen and fuel cells. NREL Publications Database Access the full library of our publications. Search the database View all NREL publications about hydrogen and fuel cell research. Transportation and Hydrogen Newsletter Get semi-monthly updates on NREL's research, development

75 FR 45093 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-02

...; student tracker database updates, 16 hours. Burden Hours: 11,328. Needs and Uses: Under the authority of... application, by academic professors/advisors. NOAA OEd student scholar alumni are also requested to provide... tracker database with the required student information. In addition, the collected student data supports...

The Hidden Dimensions of Databases.

ERIC Educational Resources Information Center

Jacso, Peter

1994-01-01

Discusses methods of evaluating commercial online databases and provides examples that illustrate their hidden dimensions. Topics addressed include size, including the number of records or the number of titles; the number of years covered; and the frequency of updates. Comparisons of Readers' Guide Abstracts and Magazine Article Summaries are…

Planned and ongoing projects (pop) database: development and results.

PubMed

Wild, Claudia; Erdös, Judit; Warmuth, Marisa; Hinterreiter, Gerda; Krämer, Peter; Chalon, Patrice

2014-11-01

The aim of this study was to present the development, structure and results of a database on planned and ongoing health technology assessment (HTA) projects (POP Database) in Europe. The POP Database (POP DB) was set up in an iterative process from a basic Excel sheet to a multifunctional electronic online database. The functionalities, such as the search terminology, the procedures to fill and update the database, the access rules to enter the database, as well as the maintenance roles, were defined in a multistep participatory feedback loop with EUnetHTA Partners. The POP Database has become an online database that hosts not only the titles and MeSH categorizations, but also some basic information on status and contact details about the listed projects of EUnetHTA Partners. Currently, it stores more than 1,200 planned, ongoing or recently published projects of forty-three EUnetHTA Partners from twenty-four countries. Because the POP Database aims to facilitate collaboration, it also provides a matching system to assist in identifying similar projects. Overall, more than 10 percent of the projects in the database are identical both in terms of pathology (indication or disease) and technology (drug, medical device, intervention). In addition, approximately 30 percent of the projects are similar, meaning that they have at least some overlap in content. Although the POP DB is successful concerning regular updates of most national HTA agencies within EUnetHTA, little is known about its actual effects on collaborations in Europe. Moreover, many non-nationally nominated HTA producing agencies neither have access to the POP DB nor can share their projects.

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid.

PubMed

Kumar Mishra, Subodh; Kumar, Amit

2016-01-01

Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php. © The Author(s) 2016. Published by Oxford University Press.

Aging in Biometrics: An Experimental Analysis on On-Line Signature

PubMed Central

Galbally, Javier; Martinez-Diaz, Marcos; Fierrez, Julian

2013-01-01

The first consistent and reproducible evaluation of the effect of aging on dynamic signature is reported. Experiments are carried out on a database generated from two previous datasets which were acquired, under very similar conditions, in 6 sessions distributed in a 15-month time span. Three different systems, representing the current most popular approaches in signature recognition, are used in the experiments, proving the degradation suffered by this trait with the passing of time. Several template update strategies are also studied as possible measures to reduce the impact of aging on the system’s performance. Different results regarding the way in which signatures tend to change with time, and their most and least stable features, are also given. PMID:23894557

An editor for pathway drawing and data visualization in the Biopathways Workbench.

PubMed

Byrnes, Robert W; Cotter, Dawn; Maer, Andreia; Li, Joshua; Nadeau, David; Subramaniam, Shankar

2009-10-02

Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server http://www.lipidmaps.org. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system. Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.

An Investigation Into the Effects of Frequency Response Function Estimators on Model Updating

NASA Astrophysics Data System (ADS)

Ratcliffe, M. J.; Lieven, N. A. J.

1999-03-01

Model updating is a very active research field, in which significant effort has been invested in recent years. Model updating methodologies are invariably successful when used on noise-free simulated data, but tend to be unpredictable when presented with real experimental data that are—unavoidably—corrupted with uncorrelated noise content. In the development and validation of model-updating strategies, a random zero-mean Gaussian variable is added to simulated test data to tax the updating routines more fully. This paper proposes a more sophisticated model for experimental measurement noise, and this is used in conjunction with several different frequency response function estimators, from the classical H1and H2to more refined estimators that purport to be unbiased. Finite-element model case studies, in conjunction with a genuine experimental test, suggest that the proposed noise model is a more realistic representation of experimental noise phenomena. The choice of estimator is shown to have a significant influence on the viability of the FRF sensitivity method. These test cases find that the use of the H2estimator for model updating purposes is contraindicated, and that there is no advantage to be gained by using the sophisticated estimators over the classical H1estimator.

ISASS Policy 2016 Update – Minimally Invasive Sacroiliac Joint Fusion

PubMed Central

Lorio, Morgan P.

2016-01-01

Rationale The index 2014 ISASS Policy Statement - Minimally Invasive Sacroiliac Joint Fusion was generated out of necessity to provide an ICD9-based background and emphasize tools to ensure correct diagnosis. A timely ICD10-based 2016 Update provides a granular threshold selection with improved level of evidence and a more robust, relevant database. PMID:27652197

Administrative Information Systems: The 1980 Profile. CAUSE Monograph Series.

ERIC Educational Resources Information Center

Thomas, Charles R.

The first summaries of the CAUSE National Database, which was established in 1980, are presented. The database is updated annually to provide members with baseline reference information on the status of administrative information systems in colleges and universities. Information is based on responses from 350 CAUSE member campuses, which are…

PIECE 2.0: an update for the plant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparision and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in ...

Expansion of the MANAGE database with forest and drainage studies

USDA-ARS?s Scientific Manuscript database

The “Measured Annual Nutrient loads from AGricultural Environments” (MANAGE) database was published in 2006 to expand an early 1980’s compilation of nutrient export (load) data from agricultural land uses at the field or farm spatial scale. Then in 2008, MANAGE was updated with 15 additional studie...

Discontinued Codes in The USDA Food and Nutrient Database for Dietary Studies

USDA-ARS?s Scientific Manuscript database

For each new version of the Food and Nutrient Database for Dietary Studies (FNDDS), foods and beverages, portions, and nutrient values are reviewed and updated. New food and beverage codes are added based on changes in consumption and the marketplace; additionally, codes are discontinued. To date,...

78 FR 48417 - Proposed Information Collection; Comment Request; Educational Partnership Program (EPP), Ernest F...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-08

... support of the scholarship application by academic professors/advisors. NOAA OEd student scholar alumni... are required to update the student tracker database with the required student information. In addition... System database form, 17 hours; undergraduate application form, 8 hours; reference forms, 1 hour; alumni...

78 FR 27188 - Proposed Information Collection-Renewal; Comment Request; Educational Partnership Program (EPP...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-09

... form in support of the scholarship application by academic professors/advisors. NOAA OEd student... grantees are required to update the student tracker database with the required student information. In... Tracking System database form, 17 hours; undergraduate application form, 8 hours; reference forms, 1 hour...

75 FR 20981 - Proposed Information Collection; Comment Request; Educational Partnership Program (EPP) and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-22

... completion of a NOAA student scholar reference form in support of the scholarship application by academic... internal tracking purposes. NOAA OEd grantees are required to update the student tracker database with the... tracker database form, 16 hours; graduate application form, 8 hours; undergraduate application form, 8...

SLIMMER--A UNIX System-Based Information Retrieval System.

ERIC Educational Resources Information Center

Waldstein, Robert K.

1988-01-01

Describes an information retrieval system developed at Bell Laboratories to create and maintain a variety of different but interrelated databases, and to provide controlled access to these databases. The components discussed include the interfaces, indexing rules, display languages, response time, and updating procedures of the system. (6 notes…

Estimation of beam material random field properties via sensitivity-based model updating using experimental frequency response functions

NASA Astrophysics Data System (ADS)

Machado, M. R.; Adhikari, S.; Dos Santos, J. M. C.; Arruda, J. R. F.

2018-03-01

Structural parameter estimation is affected not only by measurement noise but also by unknown uncertainties which are present in the system. Deterministic structural model updating methods minimise the difference between experimentally measured data and computational prediction. Sensitivity-based methods are very efficient in solving structural model updating problems. Material and geometrical parameters of the structure such as Poisson's ratio, Young's modulus, mass density, modal damping, etc. are usually considered deterministic and homogeneous. In this paper, the distributed and non-homogeneous characteristics of these parameters are considered in the model updating. The parameters are taken as spatially correlated random fields and are expanded in a spectral Karhunen-Loève (KL) decomposition. Using the KL expansion, the spectral dynamic stiffness matrix of the beam is expanded as a series in terms of discretized parameters, which can be estimated using sensitivity-based model updating techniques. Numerical and experimental tests involving a beam with distributed bending rigidity and mass density are used to verify the proposed method. This extension of standard model updating procedures can enhance the dynamic description of structural dynamic models.

The GEM Global Active Faults Database: The growth and synthesis of a worldwide database of active structures for PSHA, research, and education

NASA Astrophysics Data System (ADS)

Styron, R. H.; Garcia, J.; Pagani, M.

2017-12-01

A global catalog of active faults is a resource of value to a wide swath of the geoscience, earthquake engineering, and hazards risk communities. Though construction of such a dataset has been attempted now and again through the past few decades, success has been elusive. The Global Earthquake Model (GEM) Foundation has been working on this problem, as a fundamental step in its goal of making a global seismic hazard model. Progress on the assembly of the database is rapid, with the concatenation of many national—, orogen—, and continental—scale datasets produced by different research groups throughout the years. However, substantial data gaps exist throughout much of the deforming world, requiring new mapping based on existing publications as well as consideration of seismicity, geodesy and remote sensing data. Thus far, new fault datasets have been created for the Caribbean and Central America, North Africa, and northeastern Asia, with Madagascar, Canada and a few other regions in the queue. The second major task, as formidable as the initial data concatenation, is the 'harmonization' of data. This entails the removal or recombination of duplicated structures, reconciliation of contrastinginterpretations in areas of overlap, and the synthesis of many different types of attributes or metadata into a consistent whole. In a project of this scale, the methods used in the database construction are as critical to project success as the data themselves. After some experimentation, we have settled on an iterative methodology that involves rapid accumulation of data followed by successive episodes of data revision, and a computer-scripted data assembly using GIS file formats that is flexible, reproducible, and as able as possible to cope with updates to the constituent datasets. We find that this approach of initially maximizing coverage and then increasing resolution is the most robust to regional data problems and the most amenable to continued updates and refinement. Combined with the public, open-source nature of this project, GEM is producing a resource that can continue to evolve with the changing knowledge and needs of the community.

Stereo Reconstruction Study

DTIC Science & Technology

1983-06-01

be registered on the agenda. At each step or analysis, the action with the highest score is executed and the database is changed. The agenda controls...activation of production rules according to changes in the database . The agenda is updated whenever the database is changed. Each time, the number of...views of an object. Total prediction has combinatorial complexity. For a polyhedron with n distinct faces, there are 2" views. Instead, ACRONYM predicts

The Plant Organelles Database 3 (PODB3) update 2014: integrating electron micrographs and new options for plant organelle research.

PubMed

Mano, Shoji; Nakamura, Takanori; Kondo, Maki; Miwa, Tomoki; Nishikawa, Shuh-ichi; Mimura, Tetsuro; Nagatani, Akira; Nishimura, Mikio

2014-01-01

The Plant Organelles Database 2 (PODB2), which was first launched in 2006 as PODB, provides static image and movie data of plant organelles, protocols for plant organelle research and external links to relevant websites. PODB2 has facilitated plant organellar research and the understanding of plant organelle dynamics. To provide comprehensive information on plant organelles in more detail, PODB2 was updated to PODB3 (http://podb.nibb.ac.jp/Organellome/). PODB3 contains two additional components: the electron micrograph database and the perceptive organelles database. Through the electron micrograph database, users can examine the subcellular and/or suborganellar structures in various organs of wild-type and mutant plants. The perceptive organelles database provides information on organelle dynamics in response to external stimuli. In addition to the extra components, the user interface for access has been enhanced in PODB3. The data in PODB3 are directly submitted by plant researchers and can be freely downloaded for use in further analysis. PODB3 contains all the information included in PODB2, and the volume of data and protocols deposited in PODB3 continue to grow steadily. We welcome contributions of data from all plant researchers to enhance the utility and comprehensiveness of PODB3.

CEBS: a comprehensive annotated database of toxicological data

PubMed Central

Lea, Isabel A.; Gong, Hui; Paleja, Anand; Rashid, Asif; Fostel, Jennifer

2017-01-01

The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in recent years and currently contains over 11 000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies. Study data provided to CEBS are manually curated, accessioned and subject to quality assurance review prior to release to ensure high quality. The CEBS database has two main components: data collection and data delivery. To accommodate the breadth of data produced by NTP, the CEBS data collection component is an integrated relational design that allows the flexibility to capture any type of electronic data (to date). The data delivery component of the database comprises a series of dedicated user interface tables containing pre-processed data that support each component of the user interface. The user interface has been updated to include a series of nine Guided Search tools that allow access to NTP summary and conclusion data and larger non-NTP datasets. The CEBS database can be accessed online at http://www.niehs.nih.gov/research/resources/databases/cebs/. PMID:27899660

Assembly: a resource for assembled genomes at NCBI

PubMed Central

Kitts, Paul A.; Church, Deanna M.; Thibaud-Nissen, Françoise; Choi, Jinna; Hem, Vichet; Sapojnikov, Victor; Smith, Robert G.; Tatusova, Tatiana; Xiang, Charlie; Zherikov, Andrey; DiCuccio, Michael; Murphy, Terence D.; Pruitt, Kim D.; Kimchi, Avi

2016-01-01

The NCBI Assembly database (www.ncbi.nlm.nih.gov/assembly/) provides stable accessioning and data tracking for genome assembly data. The model underlying the database can accommodate a range of assembly structures, including sets of unordered contig or scaffold sequences, bacterial genomes consisting of a single complete chromosome, or complex structures such as a human genome with modeled allelic variation. The database provides an assembly accession and version to unambiguously identify the set of sequences that make up a particular version of an assembly, and tracks changes to updated genome assemblies. The Assembly database reports metadata such as assembly names, simple statistical reports of the assembly (number of contigs and scaffolds, contiguity metrics such as contig N50, total sequence length and total gap length) as well as the assembly update history. The Assembly database also tracks the relationship between an assembly submitted to the International Nucleotide Sequence Database Consortium (INSDC) and the assembly represented in the NCBI RefSeq project. Users can find assemblies of interest by querying the Assembly Resource directly or by browsing available assemblies for a particular organism. Links in the Assembly Resource allow users to easily download sequence and annotations for current versions of genome assemblies from the NCBI genomes FTP site. PMID:26578580

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

Sassani, David; Price, Laura L.; Rechard, Robert P.

This report provides an update to Sassani et al. (2016) and includes: (1) an updated set of inputs (Sections 2.3) on various additional waste forms (WF) covering both DOE-managed spent nuclear fuel (SNF) and DOE-managed (as) high-level waste (HLW) for use in the inventory represented in the geologic disposal safety analyses (GDSA); (2) summaries of evaluations initiated to refine specific characteristics of particular WF for future use (Section 2.4); (3) updated development status of the Online Waste Library (OWL) database (Section 3.1.2) and an updated user guide to OWL (Section 3.1.3); and (4) status updates (Section 3.2) for the OWLmore » inventory content, data entry checking process, and external OWL BETA testing initiated in fiscal year 2017.« less

Improvements on a privacy-protection algorithm for DNA sequences with generalization lattices.

PubMed

Li, Guang; Wang, Yadong; Su, Xiaohong

2012-10-01

When developing personal DNA databases, there must be an appropriate guarantee of anonymity, which means that the data cannot be related back to individuals. DNA lattice anonymization (DNALA) is a successful method for making personal DNA sequences anonymous. However, it uses time-consuming multiple sequence alignment and a low-accuracy greedy clustering algorithm. Furthermore, DNALA is not an online algorithm, and so it cannot quickly return results when the database is updated. This study improves the DNALA method. Specifically, we replaced the multiple sequence alignment in DNALA with global pairwise sequence alignment to save time, and we designed a hybrid clustering algorithm comprised of a maximum weight matching (MWM)-based algorithm and an online algorithm. The MWM-based algorithm is more accurate than the greedy algorithm in DNALA and has the same time complexity. The online algorithm can process data quickly when the database is updated. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update

PubMed Central

Hu, Yanhui; Comjean, Aram; Roesel, Charles; Vinayagam, Arunachalam; Flockhart, Ian; Zirin, Jonathan; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E.

2017-01-01

The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website (http://fgr.hms.harvard.edu) serve as a reagent production tracking system, screen data repository, and portal to the community. Through this portal, we make available protocols, online tools, and other resources useful to researchers at all stages of high-throughput functional genomics screening, from assay design and reagent identification to data analysis and interpretation. In this update, we describe recent changes and additions to our website, database and suite of online tools. Recent changes reflect a shift in our focus from a single technology (RNAi) and model species (Drosophila) to the application of additional technologies (e.g. CRISPR) and support of integrated, cross-species approaches to uncovering gene function using functional genomics and other approaches. PMID:27924039

The BioGRID interaction database: 2017 update

PubMed Central

Chatr-aryamontri, Andrew; Oughtred, Rose; Boucher, Lorrie; Rust, Jennifer; Chang, Christie; Kolas, Nadine K.; O'Donnell, Lara; Oster, Sara; Theesfeld, Chandra; Sellam, Adnane; Stark, Chris; Breitkreutz, Bobby-Joe; Dolinski, Kara; Tyers, Mike

2017-01-01

The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions for all major model organism species and humans. As of September 2016 (build 3.4.140), the BioGRID contains 1 072 173 genetic and protein interactions, and 38 559 post-translational modifications, as manually annotated from 48 114 publications. This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update. BioGRID curates the biomedical literature for major model organism species, including humans, with a recent emphasis on central biological processes and specific human diseases. To facilitate network-based approaches to drug discovery, BioGRID now incorporates 27 501 chemical–protein interactions for human drug targets, as drawn from the DrugBank database. A new dynamic interaction network viewer allows the easy navigation and filtering of all genetic and protein interaction data, as well as for bioactive compounds and their established targets. BioGRID data are directly downloadable without restriction in a variety of standardized formats and are freely distributed through partner model organism databases and meta-databases. PMID:27980099

eBASIS (Bioactive Substances in Food Information Systems) and Bioactive Intakes: Major Updates of the Bioactive Compound Composition and Beneficial Bioeffects Database and the Development of a Probabilistic Model to Assess Intakes in Europe

PubMed Central

Plumb, Jenny; Pigat, Sandrine; Bompola, Foteini; Cushen, Maeve; Pinchen, Hannah; Nørby, Eric; Astley, Siân; Lyons, Jacqueline; Kiely, Mairead; Finglas, Paul

2017-01-01

eBASIS (Bioactive Substances in Food Information Systems), a web-based database that contains compositional and biological effects data for bioactive compounds of plant origin, has been updated with new data on fruits and vegetables, wheat and, due to some evidence of potential beneficial effects, extended to include meat bioactives. eBASIS remains one of only a handful of comprehensive and searchable databases, with up-to-date coherent and validated scientific information on the composition of food bioactives and their putative health benefits. The database has a user-friendly, efficient, and flexible interface facilitating use by both the scientific community and food industry. Overall, eBASIS contains data for 267 foods, covering the composition of 794 bioactive compounds, from 1147 quality-evaluated peer-reviewed publications, together with information from 567 publications describing beneficial bioeffect studies carried out in humans. This paper highlights recent updates and expansion of eBASIS and the newly-developed link to a probabilistic intake model, allowing exposure assessment of dietary bioactive compounds to be estimated and modelled in human populations when used in conjunction with national food consumption data. This new tool could assist small- and medium-sized enterprises (SMEs) in the development of food product health claim dossiers for submission to the European Food Safety Authority (EFSA). PMID:28333085

AtomDB: Expanding an Accessible and Accurate Atomic Database for X-ray Astronomy

NASA Astrophysics Data System (ADS)

Smith, Randall

Since its inception in 2001, the AtomDB has become the standard repository of accurate and accessible atomic data for the X-ray astrophysics community, including laboratory astrophysicists, observers, and modelers. Modern calculations of collisional excitation rates now exist - and are in AtomDB - for all abundant ions in a hot plasma. AtomDB has expanded beyond providing just a collisional model, and now also contains photoionization data from XSTAR as well as a charge exchange model, amongst others. However, building and maintaining an accurate and complete database that can fully exploit the diagnostic potential of high-resolution X-ray spectra requires further work. The Hitomi results, sadly limited as they were, demonstrated the urgent need for the best possible wavelength and rate data, not merely for the strongest lines but for the diagnostic features that may have 1% or less of the flux of the strong lines. In particular, incorporation of weak but powerfully diagnostic satellite lines will be crucial to understanding the spectra expected from upcoming deep observations with Chandra and XMM-Newton, as well as the XARM and Athena satellites. Beyond incorporating this new data, a number of groups, both experimental and theoretical, have begun to produce data with errors and/or sensitivity estimates. We plan to use this to create statistically meaningful spectral errors on collisional plasmas, providing practical uncertainties together with model spectra. We propose to continue to (1) engage the X-ray astrophysics community regarding their issues and needs, notably by a critical comparison with other related databases and tools, (2) enhance AtomDB to incorporate a large number of satellite lines as well as updated wavelengths with error estimates, (3) continue to update the AtomDB with the latest calculations and laboratory measurements, in particular velocity-dependent charge exchange rates, and (4) enhance existing tools, and create new ones as needed to increase the functionality of, and access to, AtomDB.

Proposal of Network-Based Multilingual Space Dictionary Database System

NASA Astrophysics Data System (ADS)

Yoshimitsu, T.; Hashimoto, T.; Ninomiya, K.

2002-01-01

The International Academy of Astronautics (IAA) is now constructing a multilingual dictionary database system of space-friendly terms. The database consists of a lexicon and dictionaries of multiple languages. The lexicon is a table which relates corresponding terminology in different languages. Each language has a dictionary which contains terms and their definitions. The database assumes the use on the internet. Updating and searching the terms and definitions are conducted via the network. Maintaining the database is conducted by the international cooperation. A new word arises day by day, thus to easily input new words and their definitions to the database is required for the longstanding success of the system. The main key of the database is an English term which is approved at the table held once or twice with the working group members. Each language has at lease one working group member who is responsible of assigning the corresponding term and the definition of the term of his/her native language. Inputting and updating terms and their definitions can be conducted via the internet from the office of each member which may be located at his/her native country. The system is constructed by freely distributed database server program working on the Linux operating system, which will be installed at the head office of IAA. Once it is installed, it will be open to all IAA members who can search the terms via the internet. Currently the authors are constructing the prototype system which is described in this paper.

Data update in a land information network

NASA Astrophysics Data System (ADS)

Mullin, Robin C.

1988-01-01

The on-going update of data exchanged in a land information network is examined. In the past, major developments have been undertaken to enable the exchange of data between land information systems. A model of a land information network and the data update process have been developed. Based on these, a functional description of the database and software to perform data updating is presented. A prototype of the data update process was implemented using the ARC/INFO geographic information system. This was used to test four approaches to data updating, i.e., bulk, block, incremental, and alert updates. A bulk update is performed by replacing a complete file with an updated file. A block update requires that the data set be partitioned into blocks. When an update occurs, only the blocks which are affected need to be transferred. An incremental update approach records each feature which is added or deleted and transmits only the features needed to update the copy of the file. An alert is a marker indicating that an update has occurred. It can be placed in a file to warn a user that if he is active in an area containing markers, updated data is available. The four approaches have been tested using a cadastral data set.

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

PubMed

Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

2017-01-04

Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

DAMIT: a database of asteroid models

NASA Astrophysics Data System (ADS)

Durech, J.; Sidorin, V.; Kaasalainen, M.

2010-04-01

Context. Apart from a few targets that were directly imaged by spacecraft, remote sensing techniques are the main source of information about the basic physical properties of asteroids, such as the size, the spin state, or the spectral type. The most widely used observing technique - time-resolved photometry - provides us with data that can be used for deriving asteroid shapes and spin states. In the past decade, inversion of asteroid lightcurves has led to more than a hundred asteroid models. In the next decade, when data from all-sky surveys are available, the number of asteroid models will increase. Combining photometry with, e.g., adaptive optics data produces more detailed models. Aims: We created the Database of Asteroid Models from Inversion Techniques (DAMIT) with the aim of providing the astronomical community access to reliable and up-to-date physical models of asteroids - i.e., their shapes, rotation periods, and spin axis directions. Models from DAMIT can be used for further detailed studies of individual objects, as well as for statistical studies of the whole set. Methods: Most DAMIT models were derived from photometric data by the lightcurve inversion method. Some of them have been further refined or scaled using adaptive optics images, infrared observations, or occultation data. A substantial number of the models were derived also using sparse photometric data from astrometric databases. Results: At present, the database contains models of more than one hundred asteroids. For each asteroid, DAMIT provides the polyhedral shape model, the sidereal rotation period, the spin axis direction, and the photometric data used for the inversion. The database is updated when new models are available or when already published models are updated or refined. We have also released the C source code for the lightcurve inversion and for the direct problem (updates and extensions will follow).

Verification and Updating of the Database of Topographic Objects with Geometric Information About Buildings by Means of Airborne Laser Scanning Data

NASA Astrophysics Data System (ADS)

Mendela-Anzlik, Małgorzata; Borkowski, Andrzej

2017-06-01

Airborne laser scanning data (ALS) are used mainly for creation of precise digital elevation models. However, it appears that the informative potential stored in ALS data can be also used for updating spatial databases, including the Database of Topographic Objects (BDOT10k). Typically, geometric representations of buildings in the BDOT10k are equal to their entities in the Land and Property Register (EGiB). In this study ALS is considered as supporting data source. The thresholding method of original ALS data with the use of the alpha shape algorithm, proposed in this paper, allows for extraction of points that represent horizontal cross section of building walls, leading to creation of vector, geometric models of buildings that can be then used for updating the BDOT10k. This method gives also the possibility of an easy verification of up-to-dateness of both the BDOT10k and the district EGiB databases within geometric information about buildings. For verification of the proposed methodology there have been used the classified ALS data acquired with a density of 4 points/m2. The accuracy assessment of the identified building outlines has been carried out by their comparison to the corresponding EGiB objects. The RMSE values for 78 buildings are from a few to tens of centimeters and the average value is about 0,5 m. At the same time for several objects there have been revealed huge geometric discrepancies. Further analyses have shown that these discrepancies could be resulted from incorrect representations of buildings in the EGiB database.

Identifying relevant data for a biological database: handcrafted rules versus machine learning.

PubMed

Sehgal, Aditya Kumar; Das, Sanmay; Noto, Keith; Saier, Milton H; Elkan, Charles

2011-01-01

With well over 1,000 specialized biological databases in use today, the task of automatically identifying novel, relevant data for such databases is increasingly important. In this paper, we describe practical machine learning approaches for identifying MEDLINE documents and Swiss-Prot/TrEMBL protein records, for incorporation into a specialized biological database of transport proteins named TCDB. We show that both learning approaches outperform rules created by hand by a human expert. As one of the first case studies involving two different approaches to updating a deployed database, both the methods compared and the results will be of interest to curators of many specialized databases.

HITRAN2016 Database Part II: Overview of the Spectroscopic Parameters of the Trace Gases

NASA Astrophysics Data System (ADS)

Tan, Yan; Gordon, Iouli E.; Rothman, Laurence S.; Kochanov, Roman V.; Hill, Christian

2017-06-01

The 2016 edition of HITRAN database is available now. This new edition of the database takes advantage of the new structure and can be accessed through HITRANonline (www.hitran.org). The line-by-line lists for almost all of the trace atmospheric species were updated in comparison with the previous edition HITRAN2012. These extended update covers not only updating few transitions of the certain molecules, but also complete replacements of the whole line lists, and as well as introduction of new spectroscopic parameters for non-Voigt line shape. The new line lists for NH_3, HNO_3, OCS, HCN, CH_3Cl, C_2H_2, C_2H_6, PH_3, C_2H_4, CH_3CN, CF_4, C_4H_2, and SO_3 feature substantial expansion of the spectral and dynamic ranges in addition of the improved accuracy of the parameters for already existing lines. A semi-empirical procedure was developed to update the air-broadening and self-broadening coefficients of N_2O, SO_2, NH_3, CH_3Cl, H_2S, and HO_2. We draw particular attention to flaws in the commonly used expression n_{air}=0.79n_{N_2}+0.21n_{O_2} to determine the air-broadening temperature dependence exponent in the power law from those for nitrogen and oxygen broadening. A more meaningful approach will be presented. The semi-empirical line width, pressure shifts and temperature-dependence exponents of CO, NH_3, HF, HCl, OCS, C_2H_2, SO_2 perturbed by H_2, He, and CO_2 have been added to the database based on the algorithm described in Wilzewski et al.. The new spectroscopic parameters for HT profile were implemented into the database for hydrogen molecule. The HITRAN database is supported by the NASA AURA program grant NNX14AI55G and NASA PDART grant NNX16AG51G. I. E. Gordon, L. S. Rothman, et al., J Quant Spectrosc Radiat Transf 2017; submitted. Hill C, et al., J Quant Spectrosc Radiat Transf 2013;130:51-61. Wilzewski JS,et al., J Quant Spectrosc Radiat Transf 2016;168:193-206. Wcislo P, et al., J Quant Spectrosc Radiat Transf 2016;177:75-91.

Does Posting Facebook Status Updates Increase or Decrease Loneliness? An Online Social Networking Experiment

PubMed Central

Deters, Fenne große; Mehl, Matthias R.

2013-01-01

Online social networking is a pervasive but empirically understudied phenomenon. Strong public opinions on its consequences exist but are backed up by little empirical evidence and almost no causally-conclusive, experimental research. The current study tested the psychological effects of posting status updates on Facebook using an experimental design. For one week, participants in the experimental condition were asked to post more than they usually do, whereas participants in the control condition received no instructions. Participants added a lab “Research Profile” as a Facebook friend allowing for the objective documentation of protocol compliance, participants’ status updates, and friends’ responses. Results revealed (1) that the experimentally-induced increase in status updating activity reduced loneliness, (2) that the decrease in loneliness was due to participants feeling more connected to their friends on a daily basis and (3) that the effect of posting on loneliness was independent of direct social feedback (i.e. responses) by friends. PMID:24224070

Integrated Functional and Executional Modelling of Software Using Web-Based Databases

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

NASA's software subsystems undergo extensive modification and updates over the operational lifetimes. It is imperative that modified software should satisfy safety goals. This report discusses the difficulties encountered in doing so and discusses a solution based on integrated modelling of software, use of automatic information extraction tools, web technology and databases.

Piece2.0: an update for the pant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in pl...

A meta-analysis of bacterial diversity in the feces of cattle

USDA-ARS?s Scientific Manuscript database

In this study, we conducted a meta-analysis on 16S rRNA gene sequences of bovine fecal origin that are publicly available in the RDP database. A total of 13663 sequences including 603 isolate sequences were identified in the RDP database (Release 11, Update 1), where 13447 sequences were assigned t...

Fluorescence- and capillary electrophoresis (CE)-based SSR DNA fingerprinting and a molecular identity database for the Louisiana sugarcane industry

USDA-ARS?s Scientific Manuscript database

A database of Louisiana sugarcane molecular identity has been constructed and is being updated annually using FAM or HEX or NED fluorescence- and capillary electrophoresis (CE)-based microsatellite (SSR) fingerprinting information. The fingerprints are PCR-amplified from leaf DNA samples of current ...

Update on terrestrial ecological classification in the highlands of West Virginia

Treesearch

James P. Vanderhorst

2010-01-01

The West Virginia Natural Heritage Program (WVNHP) maintains databases on the biological diversity of the state, including species and natural communities, to help focus conservation efforts by agencies and organizations. Information on terrestrial communities (also called vegetation, or habitat, depending on user or audience focus) is maintained in two databases. The...

An Overview of the Object Protocol Model (OPM) and the OPM Data Management Tools.

ERIC Educational Resources Information Center

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

1995-01-01

Discussion of database management tools for scientific information focuses on the Object Protocol Model (OPM) and data management tools based on OPM. Topics include the need for new constructs for modeling scientific experiments, modeling object structures and experiments in OPM, queries and updates, and developing scientific database applications…

45 CFR 30.13 - Debt reporting and use of credit reporting agencies.

Code of Federal Regulations, 2013 CFR

2013-10-01

... agencies. 30.13 Section 30.13 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION... over $100 to credit bureaus or other automated databases. Debts arising under the Social Security Act..., any subsequent reporting to or updating of a credit bureau or other automated database may be handled...

45 CFR 30.13 - Debt reporting and use of credit reporting agencies.

Code of Federal Regulations, 2011 CFR

2011-10-01

... agencies. 30.13 Section 30.13 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION... over $100 to credit bureaus or other automated databases. Debts arising under the Social Security Act..., any subsequent reporting to or updating of a credit bureau or other automated database may be handled...

45 CFR 30.13 - Debt reporting and use of credit reporting agencies.

Code of Federal Regulations, 2012 CFR

2012-10-01

... agencies. 30.13 Section 30.13 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION... over $100 to credit bureaus or other automated databases. Debts arising under the Social Security Act..., any subsequent reporting to or updating of a credit bureau or other automated database may be handled...

45 CFR 30.13 - Debt reporting and use of credit reporting agencies.

Code of Federal Regulations, 2014 CFR

2014-10-01

... agencies. 30.13 Section 30.13 Public Welfare Department of Health and Human Services GENERAL ADMINISTRATION... over $100 to credit bureaus or other automated databases. Debts arising under the Social Security Act..., any subsequent reporting to or updating of a credit bureau or other automated database may be handled...

RTECS database (on the internet). Online data

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

NONE

The Registry of Toxic Effects of Chemical Substances (RTECS (trademark)) is a database of toxicological information compiled, maintained, and updated by the National Institute for Occupational Safety and Health. The program is mandated by the Occupational Safety and Health Act of 1970. The original edition, known as the `Toxic Substances List,` was published on June 28, 1971, and included toxicologic data for approximately 5,000 chemicals. Since that time, the list has continuously grown and been updated, and its name changed to the current title, `Registry of Toxic Effects of Chemical Substances.` RTECS (trademark) now contains over 133,000 chemicals as NIOSHmore » strives to fulfill the mandate to list `all known toxic substances...and the concentrations at which...toxicity is known to occur.` This database is now available for searching through the Gov. Research-Center (GRC) service. GRC is a single online web-based search service to well known Government databases. Featuring powerful search and retrieval software, GRC is an important research tool. The GRC web site is at http://grc.ntis.gov.« less

The Fossil Calibration Database-A New Resource for Divergence Dating.

PubMed

Ksepka, Daniel T; Parham, James F; Allman, James F; Benton, Michael J; Carrano, Matthew T; Cranston, Karen A; Donoghue, Philip C J; Head, Jason J; Hermsen, Elizabeth J; Irmis, Randall B; Joyce, Walter G; Kohli, Manpreet; Lamm, Kristin D; Leehr, Dan; Patané, Josés L; Polly, P David; Phillips, Matthew J; Smith, N Adam; Smith, Nathan D; Van Tuinen, Marcel; Ware, Jessica L; Warnock, Rachel C M

2015-09-01

Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important-often least appreciated-step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as a key pipeline for peer-reviewed calibrations to enter the database. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Open-access evidence database of controlled trials and systematic reviews in youth mental health.

PubMed

De Silva, Stefanie; Bailey, Alan P; Parker, Alexandra G; Montague, Alice E; Hetrick, Sarah E

2018-06-01

To present an update to an evidence-mapping project that consolidates the evidence base of interventions in youth mental health. To promote dissemination of this resource, the evidence map has been translated into a free online database (https://orygen.org.au/Campus/Expert-Network/Evidence-Finder or https://headspace.org.au/research-database/). Included studies are extensively indexed to facilitate searching. A systematic search for prevention and treatment studies in young people (mean age 6-25 years) is conducted annually using Embase, MEDLINE, PsycINFO and the Cochrane Library. Included studies are restricted to controlled trials and systematic reviews published since 1980. To date, 221 866 publications have been screened, of which 2680 have been included in the database. Updates are conducted annually. This shared resource can be utilized to substantially reduce the amount of time involved with conducting literature searches. It is designed to promote the uptake of evidence-based practice and facilitate research to address gaps in youth mental health. © 2017 John Wiley & Sons Australia, Ltd.

A practical approach to screen for authorised and unauthorised genetically modified plants.

PubMed

Waiblinger, Hans-Ulrich; Grohmann, Lutz; Mankertz, Joachim; Engelbert, Dirk; Pietsch, Klaus

2010-03-01

In routine analysis, screening methods based on real-time PCR are most commonly used for the detection of genetically modified (GM) plant material in food and feed. In this paper, it is shown that the combination of five DNA target sequences can be used as a universal screening approach for at least 81 GM plant events authorised or unauthorised for placing on the market and described in publicly available databases. Except for maize event LY038, soybean events DP-305423 and BPS-CV127-9 and cotton event 281-24-236 x 3006-210-23, at least one of the five genetic elements has been inserted in these GM plants and is targeted by this screening approach. For the detection of these sequences, fully validated real-time PCR methods have been selected. A screening table is presented that describes the presence or absence of the target sequences for most of the listed GM plants. These data have been verified either theoretically according to available databases or experimentally using available reference materials. The screening table will be updated regularly by a network of German enforcement laboratories.

Robust Pedestrian Tracking and Recognition from FLIR Video: A Unified Approach via Sparse Coding

PubMed Central

Li, Xin; Guo, Rui; Chen, Chao

2014-01-01

Sparse coding is an emerging method that has been successfully applied to both robust object tracking and recognition in the vision literature. In this paper, we propose to explore a sparse coding-based approach toward joint object tracking-and-recognition and explore its potential in the analysis of forward-looking infrared (FLIR) video to support nighttime machine vision systems. A key technical contribution of this work is to unify existing sparse coding-based approaches toward tracking and recognition under the same framework, so that they can benefit from each other in a closed-loop. On the one hand, tracking the same object through temporal frames allows us to achieve improved recognition performance through dynamical updating of template/dictionary and combining multiple recognition results; on the other hand, the recognition of individual objects facilitates the tracking of multiple objects (i.e., walking pedestrians), especially in the presence of occlusion within a crowded environment. We report experimental results on both the CASIAPedestrian Database and our own collected FLIR video database to demonstrate the effectiveness of the proposed joint tracking-and-recognition approach. PMID:24961216

WebBee: A Platform for Secure Coordination and Communication in Crisis Scenarios

DTIC Science & Technology

2008-04-16

implemented through database triggers. The Webbee Database Server contains an Information Server, which is a Postgres database with PostGIS [5] extension...sends it to the target user. The heavy lifting for this mechanism is done through an extension of Postgres triggers (Figures 6.1 and 6.2), resulting...in fewer queries and better performance. Trigger support in Postgres is table-based and comparatively primitive: with n table triggers, an update

Automated Simulation Updates based on Flight Data

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.; Ward, David G.

2007-01-01

A statistically-based method for using flight data to update aerodynamic data tables used in flight simulators is explained and demonstrated. A simplified wind-tunnel aerodynamic database for the F/A-18 aircraft is used as a starting point. Flight data from the NASA F-18 High Alpha Research Vehicle (HARV) is then used to update the data tables so that the resulting aerodynamic model characterizes the aerodynamics of the F-18 HARV. Prediction cases are used to show the effectiveness of the automated method, which requires no ad hoc adjustments by the analyst.

Apollo Lunar Sample Photograph Digitization Project Update

NASA Technical Reports Server (NTRS)

Todd, N. S.; Lofgren, G. E.

2012-01-01

This is an update of the progress of a 4-year data restoration project effort funded by the LASER program to digitize photographs of the Apollo lunar rock samples and create high resolution digital images and undertaken by the Astromaterials Acquisition and Curation Office at JSC [1]. The project is currently in its last year of funding. We also provide an update on the derived products that make use of the digitized photos including the Lunar Sample Catalog and Photo Database[2], Apollo Sample data files for GoogleMoon[3].

Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain.

PubMed

Matthes, Michaela; Preusse, Martin; Zhang, Jingzhong; Schechter, Julia; Mayer, Daniela; Lentes, Bernd; Theis, Fabian; Prakash, Nilima; Wurst, Wolfgang; Trümbach, Dietrich

2014-01-01

The study of developmental processes in the mouse and other vertebrates includes the understanding of patterning along the anterior-posterior, dorsal-ventral and medial- lateral axis. Specifically, neural development is also of great clinical relevance because several human neuropsychiatric disorders such as schizophrenia, autism disorders or drug addiction and also brain malformations are thought to have neurodevelopmental origins, i.e. pathogenesis initiates during childhood and adolescence. Impacts during early neurodevelopment might also predispose to late-onset neurodegenerative disorders, such as Parkinson's disease. The neural tube develops from its precursor tissue, the neural plate, in a patterning process that is determined by compartmentalization into morphogenetic units, the action of local signaling centers and a well-defined and locally restricted expression of genes and their interactions. While public databases provide gene expression data with spatio-temporal resolution, they usually neglect the genetic interactions that govern neural development. Here, we introduce Mouse IDGenes, a reference database for genetic interactions in the developing mouse brain. The database is highly curated and offers detailed information about gene expressions and the genetic interactions at the developing mid-/hindbrain boundary. To showcase the predictive power of interaction data, we infer new Wnt/β-catenin target genes by machine learning and validate one of them experimentally. The database is updated regularly. Moreover, it can easily be extended by the research community. Mouse IDGenes will contribute as an important resource to the research on mouse brain development, not exclusively by offering data retrieval, but also by allowing data input. http://mouseidgenes.helmholtz-muenchen.de. © The Author(s) 2014. Published by Oxford University Press.

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

PubMed Central

Chèneby, Jeanne; Gheorghe, Marius; Artufel, Marie

2018-01-01

Abstract With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions. Specifically, we have collected, analyzed and retained after quality control a total of 2829 ChIP-seq datasets available from public sources, covering a total of 485 TRs with a catalog of 80M peaks. Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public track hubs. Finally, full access to this catalog is available online together with a TR binding enrichment analysis tool. ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human. PMID:29126285

A Brief Review of RNA–Protein Interaction Database Resources

PubMed Central

Yi, Ying; Zhao, Yue; Huang, Yan; Wang, Dong

2017-01-01

RNA–Protein interactions play critical roles in various biological processes. By collecting and analyzing the RNA–Protein interactions and binding sites from experiments and predictions, RNA–Protein interaction databases have become an essential resource for the exploration of the transcriptional and post-transcriptional regulatory network. Here, we briefly review several widely used RNA–Protein interaction database resources developed in recent years to provide a guide of these databases. The content and major functions in databases are presented. The brief description of database helps users to quickly choose the database containing information they interested. In short, these RNA–Protein interaction database resources are continually updated, but the current state shows the efforts to identify and analyze the large amount of RNA–Protein interactions. PMID:29657278

Group updates Gravity Database for central Andes

NASA Astrophysics Data System (ADS)

MIGRA Group; Götze, H.-J.

Between 1993 and 1995 a group of scientists from Chile, Argentina, and Germany incorporated some 2000 new gravity observations into a database that covers a remote region of the Central Andes in northern Chile and northwestern Argentina (between 64°-71°W and 20°-29°S). The database can be used to study the structure and evolution of the Andes. About 14,000 gravity values are included in the database, including older, reprocessed data. Researchers at universities or governmental agencies are welcome to use the data for noncommercial purposes.

High throughput profile-profile based fold recognition for the entire human proteome.

PubMed

McGuffin, Liam J; Smith, Richard T; Bryson, Kevin; Sørensen, Søren-Aksel; Jones, David T

2006-06-07

In order to maintain the most comprehensive structural annotation databases we must carry out regular updates for each proteome using the latest profile-profile fold recognition methods. The ability to carry out these updates on demand is necessary to keep pace with the regular updates of sequence and structure databases. Providing the highest quality structural models requires the most intensive profile-profile fold recognition methods running with the very latest available sequence databases and fold libraries. However, running these methods on such a regular basis for every sequenced proteome requires large amounts of processing power. In this paper we describe and benchmark the JYDE (Job Yield Distribution Environment) system, which is a meta-scheduler designed to work above cluster schedulers, such as Sun Grid Engine (SGE) or Condor. We demonstrate the ability of JYDE to distribute the load of genomic-scale fold recognition across multiple independent Grid domains. We use the most recent profile-profile version of our mGenTHREADER software in order to annotate the latest version of the Human proteome against the latest sequence and structure databases in as short a time as possible. We show that our JYDE system is able to scale to large numbers of intensive fold recognition jobs running across several independent computer clusters. Using our JYDE system we have been able to annotate 99.9% of the protein sequences within the Human proteome in less than 24 hours, by harnessing over 500 CPUs from 3 independent Grid domains. This study clearly demonstrates the feasibility of carrying out on demand high quality structural annotations for the proteomes of major eukaryotic organisms. Specifically, we have shown that it is now possible to provide complete regular updates of profile-profile based fold recognition models for entire eukaryotic proteomes, through the use of Grid middleware such as JYDE.

The Updated IAU MDC Catalogue of Photographic Meteor Orbits

NASA Technical Reports Server (NTRS)

Porubcan, V.; Svoren, J.; Neslusan, L.; Schunova, E.

2011-01-01

The database of photographic meteor orbits of the IAU Meteor Data Center at the Astronomical Institute SAS has gradually been updated. To the 2003 version of 4581 photographic orbits compiled from 17 different stations and obtained in the period 1936-1996, additional new 211 orbits compiled from 7 sources have been added. Thus, the updated version of the catalogue contains 4792 photographic orbits (equinox J2000.0) available either in two separate orbital and geophysical data files or a file with the merged data. All the updated files with relevant documentation are available at the web of the IAU Meteor Data Center. Keywords astronomical databases photographic meteor orbits 1 Introduction Meteoroid orbits are a basic tool for investigation of distribution and spatial structure of the meteoroid population in the close surroundings of the Earth s orbit. However, information about them is usually widely scattered in literature and often in publications with limited circulation. Therefore, the IAU Comm. 22 during the 1976 IAU General Assembly proposed to establish a meteor data center for collection of meteor orbits recorded by photographic and radio techniques. The decision was confirmed by the next IAU GA in 1982 and the data center was established (Lindblad, 1987). The purpose of the data center was to acquire, format, check and disseminate information on precise meteoroid orbits obtained by multi-station techniques and the database gradually extended as documented in previous reports on the activity of the Meteor Data Center by Lindblad (1987, 1995, 1999 and 2001) or Lindblad and Steel (1993). Up to present, the database consists of 4581 photographic meteor orbits (Lindblad et al., 2005), 63.330 radar determined orbit: Harvard Meteor Project (1961-1965, 1968-1969), Adelaide (1960-1961, 1968-1969), Kharkov (1975), Obninsk (1967-1968), Mogadish (1969-1970) and 1425 video-recordings (Lindblad, 1999) to which additional 817 video meteors orbits published by Koten el al. (2003) were

Knowledge structure representation and automated updates in intelligent information management systems

NASA Technical Reports Server (NTRS)

Corey, Stephen; Carnahan, Richard S., Jr.

1990-01-01

A continuing effort to apply rapid prototyping and Artificial Intelligence techniques to problems associated with projected Space Station-era information management systems is examined. In particular, timely updating of the various databases and knowledge structures within the proposed intelligent information management system (IIMS) is critical to support decision making processes. Because of the significantly large amounts of data entering the IIMS on a daily basis, information updates will need to be automatically performed with some systems requiring that data be incorporated and made available to users within a few hours. Meeting these demands depends first, on the design and implementation of information structures that are easily modified and expanded, and second, on the incorporation of intelligent automated update techniques that will allow meaningful information relationships to be established. Potential techniques are studied for developing such an automated update capability and IIMS update requirements are examined in light of results obtained from the IIMS prototyping effort.

White Paper on Nuclear Data Needs and Capabilities for Basic Science

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

Batchelder, J.; Kawano, T.; Kelley, J.

Reliable nuclear structure and reaction data represent the fundamental building blocks of nuclear physics and astrophysics research, and are also of importance in many applications. There is a continuous demand for high-quality updates of the main nuclear physics databases via the prompt compilation and evaluation of the latest experimental and theoretical results. The nuclear physics research community benefits greatly from comprehensive, systematic and up-to-date reviews of the experimentally determined nuclear properties and observables, as well as from the ability to rapidly access these data in user-friendly forms. Such credible databases also act as a bridge between science, technology, and societymore » by making the results of basic nuclear physics research available to a broad audience of users, and hence expand the societal utilization of nuclear science. Compilation and evaluation of nuclear data has deep roots in the history of nuclear science research, as outlined in Appendix 1. They have an enormous impact on many areas of science and applications, as illustrated in Figure 2 for the Evaluated Nuclear Structure Data File (ENSDF) database. The present workshop concentrated on the needs of the basic nuclear science community for data and capabilities. The main role of this community is to generate and use data in order to understand the basic nuclear forces and interactions that are responsible for the existence and the properties of all nuclides and, as a consequence, to gain knowledge about the origins, evolution and structure of the universe. Thus, the experiments designed to measure a wealth of nuclear properties towards these fundamental scientific goals are typically performed from within this community.« less

Options as information: rational reversals of evaluation and preference.

PubMed

Sher, Shlomi; McKenzie, Craig R M

2014-06-01

This article develops a rational analysis of an important class of apparent preference reversals-joint-separate reversals traditionally explained by the evaluability hypothesis. The "options-as-information" model considers a hypothetical rational actor with limited knowledge about the market distribution of a stimulus attribute. The actor's evaluations are formed via a 2-stage process-an inferential stage in which beliefs are updated on the basis of the sample of options received, followed by an assessment stage in which options are evaluated in light of these updated beliefs. This process generates joint-separate reversals in standard experimental designs. The normative model explains why the evaluability hypothesis works when it does, identifies boundary conditions for the hypothesis, and clarifies some common misconceptions about these effects. In particular, it implies that joint-separate reversals are not irrational; in fact, they are not preference reversals. However, in expanded designs where more than 2 options are jointly evaluated, the model predicts that genuine (and rational) preference reversals will sometimes emerge. Results of 3 experiments suggest an excellent fit between the rational actor model and the judgments of human actors in joint-separate experiments. PsycINFO Database Record (c) 2014 APA, all rights reserved.

DebriSat Project Update and Planning

NASA Technical Reports Server (NTRS)

Sorge, M.; Krisko, P. H.

2016-01-01

DebriSat Reporting Topics: DebriSat Fragment Analysis Calendar; Near-term Fragment Extraction Strategy; Fragment Characterization and Database; HVI (High-Velocity Impact) Considerations; Requirements Document.

Revenues: Where Does the Money Come from? A Delta Data Update, 2000-2010

ERIC Educational Resources Information Center

Kirshstein, Rita J.; Hurlburt, Steven

2012-01-01

This is one in a series of data briefs developed by the Delta Cost Project at AIR using data from the "IPEDS Analytics: Delta Cost Project Database 1987-2010," which was released on August 14, 2012, by the U.S. Department of Education, National Center for Education Statistics. The intent of these briefs is to update key tables and figures from…

Spending: Where Does the Money Go? A Delta Data Update, 2000-2010

ERIC Educational Resources Information Center

Hurlburt, Steven; Kirshstein, Rita J.

2012-01-01

This is one in a series of data briefs developed by the Delta Cost Project at AIR using data from the "IPEDS Analytics: Delta Cost Project Database 1987-2010," which was released on August 14, 2012, by the U.S. Department of Education, National Center for Education Statistics. The intent of these briefs is to update key tables and figures from…

Semantic Segmentation and Difference Extraction via Time Series Aerial Video Camera and its Application

NASA Astrophysics Data System (ADS)

Amit, S. N. K.; Saito, S.; Sasaki, S.; Kiyoki, Y.; Aoki, Y.

2015-04-01

Google earth with high-resolution imagery basically takes months to process new images before online updates. It is a time consuming and slow process especially for post-disaster application. The objective of this research is to develop a fast and effective method of updating maps by detecting local differences occurred over different time series; where only region with differences will be updated. In our system, aerial images from Massachusetts's road and building open datasets, Saitama district datasets are used as input images. Semantic segmentation is then applied to input images. Semantic segmentation is a pixel-wise classification of images by implementing deep neural network technique. Deep neural network technique is implemented due to being not only efficient in learning highly discriminative image features such as road, buildings etc., but also partially robust to incomplete and poorly registered target maps. Then, aerial images which contain semantic information are stored as database in 5D world map is set as ground truth images. This system is developed to visualise multimedia data in 5 dimensions; 3 dimensions as spatial dimensions, 1 dimension as temporal dimension, and 1 dimension as degenerated dimensions of semantic and colour combination dimension. Next, ground truth images chosen from database in 5D world map and a new aerial image with same spatial information but different time series are compared via difference extraction method. The map will only update where local changes had occurred. Hence, map updating will be cheaper, faster and more effective especially post-disaster application, by leaving unchanged region and only update changed region.

A Recommender System in the Cyber Defense Domain

DTIC Science & Technology

2014-03-27

monitoring software is a java based program sending updates to the database on the sensor machine. The host monitoring program gathers information about...3.2.2 Database. A MySQL database located on the sensor machine acts as the storage for the sensors on the network. Snort, Nmap, vulnerability scores, and...machine with the IDS and the recommender is labeled “sensor”. The recommender system code is written in java and compiled using java version 1.6.024

A Unified Approach to Joint Regional/Teleseismic Calibration and Event Location with a 3D Earth Model

DTIC Science & Technology

2010-09-01

raytracing and travel-time calculation in 3D Earth models, such as the finite-difference eikonal method (e.g., Podvin and Lecomte, 1991), fast...by Reiter and Rodi (2009) in constructing JWM. Two teleseismic data sets were considered, both extracted from the EHB database (Engdahl et al...extracted from the updated EHB database distributed by the International Seismological Centre (http://www.isc.ac.uk/EHB/index.html). The new database

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation

PubMed Central

Kristensen, David M.; Wolf, Yuri I.; Koonin, Eugene V.

2017-01-01

The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is useful for macroevolutionary studies. The ATGC database includes many forms of pre-computed data, in particular ATGC-COGs (Clusters of Orthologous Genes), multiple sequence alignments, a set of ‘index’ orthologs representing the most well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc. Although the ATGC database contains several million proteins from thousands of genomes organized into hundreds of clusters (roughly a 4-fold increase since the last version of the ATGC database), it is now built with completely automated methods and will be regularly updated following new releases of the NCBI RefSeq database. The ATGC database is hosted jointly at the University of Iowa at dmk-brain.ecn.uiowa.edu/ATGC/ and the NCBI at ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html. PMID:28053163

Updates to the Cool Season Food Legume Genome Database: Resources for pea, lentil, faba bean and chickpea genetics, genomics and breeding

USDA-ARS?s Scientific Manuscript database

The Cool Season Food Legume Genome database (CSFL, www.coolseasonfoodlegume.org) is an online resource for genomics, genetics, and breeding research for chickpea, lentil,pea, and faba bean. The user-friendly and curated website allows for all publicly available map,marker,trait, gene,transcript, ger...

The Changing Face of Scientific Discourse: Analysis of Genomic and Proteomic Database Usage and Acceptance.

ERIC Educational Resources Information Center

Brown, Cecelia

2003-01-01

Discusses the growth in use and acceptance of Web-based genomic and proteomic databases (GPD) in scholarly communication. Confirms the role of GPD in the scientific literature cycle, suggests GPD are a storage and retrieval mechanism for molecular biology information, and recommends that existing models of scientific communication be updated to…

Worldwide Ocean Optics Database (WOOD)

DTIC Science & Technology

2001-09-30

user can obtain values computed from empirical algorithms (e.g., beam attenuation estimated from diffuse attenuation and backscatter data). Error ...from empirical algorithms (e.g., beam attenuation estimated from diffuse attenuation and backscatter data). Error estimates will also be provided for...properties, including diffuse attenuation, beam attenuation, and scattering. The database shall be easy to use, Internet accessible, and frequently updated

Transition to a Unified System: Using Perl To Drive Library Databases and Enhance Web Site Functionality.

ERIC Educational Resources Information Center

Fagan, Judy Condit

2001-01-01

Discusses the need for libraries to routinely redesign their Web sites, and presents a case study that describes how a Perl-driven database at Southern Illinois University's library improved Web site organization and patron access, simplified revisions, and allowed staff unfamiliar with HTML to update content. (Contains 56 references.) (Author/LRW)

Advancement of a soil parameters geodatabase for the modeling assessment of conservation practice outcomes in the United States

USDA-ARS?s Scientific Manuscript database

US-ModSoilParms-TEMPLE is a database composed of a set of geographic databases functionally storing soil-spatial units and soil hydraulic, physical, and chemical parameters for three agriculture management simulation models, SWAT, APEX, and ALMANAC. This paper introduces the updated US-ModSoilParms-...

Nutrient database improvement project: Separable components and proximate composition of retail cuts from the beef loin and round

USDA-ARS?s Scientific Manuscript database

Beef nutrition research has become increasingly important domestically and internationally for the beef industry and its consumers. The objective of this study was to analyze the nutrient composition of ten beef loin and round cuts to update the nutrient data in the USDA National Nutrient Database f...

DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems.

PubMed

Memišević, Vesna; Kumar, Kamal; Zavaljevski, Nela; DeShazer, David; Wallqvist, Anders; Reifman, Jaques

2016-09-20

Burkholderia mallei and B. pseudomallei are the causative agents of glanders and melioidosis, respectively, diseases with high morbidity and mortality rates. B. mallei and B. pseudomallei are closely related genetically; B. mallei evolved from an ancestral strain of B. pseudomallei by genome reduction and adaptation to an obligate intracellular lifestyle. Although these two bacteria cause different diseases, they share multiple virulence factors, including bacterial secretion systems, which represent key components of bacterial pathogenicity. Despite recent progress, the secretion system proteins for B. mallei and B. pseudomallei, their pathogenic mechanisms of action, and host factors are not well characterized. We previously developed a manually curated database, DBSecSys, of bacterial secretion system proteins for B. mallei. Here, we report an expansion of the database with corresponding information about B. pseudomallei. DBSecSys 2.0 contains comprehensive literature-based and computationally derived information about B. mallei ATCC 23344 and literature-based and computationally derived information about B. pseudomallei K96243. The database contains updated information for 163 B. mallei proteins from the previous database and 61 additional B. mallei proteins, and new information for 281 B. pseudomallei proteins associated with 5 secretion systems, their 1,633 human- and murine-interacting targets, and 2,400 host-B. mallei interactions and 2,286 host-B. pseudomallei interactions. The database also includes information about 13 pathogenic mechanisms of action for B. mallei and B. pseudomallei secretion system proteins inferred from the available literature or computationally. Additionally, DBSecSys 2.0 provides details about 82 virulence attenuation experiments for 52 B. mallei secretion system proteins and 98 virulence attenuation experiments for 61 B. pseudomallei secretion system proteins. We updated the Web interface and data access layer to speed-up users' search of detailed information for orthologous proteins related to secretion systems of the two pathogens. The updates of DBSecSys 2.0 provide unique capabilities to access comprehensive information about secretion systems of B. mallei and B. pseudomallei. They enable studies and comparisons of corresponding proteins of these two closely related pathogens and their host-interacting partners. The database is available at http://dbsecsys.bhsai.org .

Integrating Radar Image Data with Google Maps

NASA Technical Reports Server (NTRS)

Chapman, Bruce D.; Gibas, Sarah

2010-01-01

A public Web site has been developed as a method for displaying the multitude of radar imagery collected by NASA s Airborne Synthetic Aperture Radar (AIRSAR) instrument during its 16-year mission. Utilizing NASA s internal AIRSAR site, the new Web site features more sophisticated visualization tools that enable the general public to have access to these images. The site was originally maintained at NASA on six computers: one that held the Oracle database, two that took care of the software for the interactive map, and three that were for the Web site itself. Several tasks were involved in moving this complicated setup to just one computer. First, the AIRSAR database was migrated from Oracle to MySQL. Then the back-end of the AIRSAR Web site was updated in order to access the MySQL database. To do this, a few of the scripts needed to be modified; specifically three Perl scripts that query that database. The database connections were then updated from Oracle to MySQL, numerous syntax errors were corrected, and a query was implemented that replaced one of the stored Oracle procedures. Lastly, the interactive map was designed, implemented, and tested so that users could easily browse and access the radar imagery through the Google Maps interface.

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

PubMed

Ahmadi, Farshid Farnood; Ebadi, Hamid

2009-01-01

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

Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes.

PubMed

Winsor, Geoffrey L; Van Rossum, Thea; Lo, Raymond; Khaira, Bhavjinder; Whiteside, Matthew D; Hancock, Robert E W; Brinkman, Fiona S L

2009-01-01

Pseudomonas aeruginosa is a well-studied opportunistic pathogen that is particularly known for its intrinsic antimicrobial resistance, diverse metabolic capacity, and its ability to cause life threatening infections in cystic fibrosis patients. The Pseudomonas Genome Database (http://www.pseudomonas.com) was originally developed as a resource for peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome. In order to facilitate cross-strain and cross-species genome comparisons with other Pseudomonas species of importance, we have now expanded the database capabilities to include all Pseudomonas species, and have developed or incorporated methods to facilitate high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. A choice of simple and more flexible user-friendly Boolean search features allows researchers to search and compare annotations or sequences within or between genomes. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. This database aims to continue to provide a high quality, annotated genome resource for the research community and is available under an open source license.

Scalable Indoor Localization via Mobile Crowdsourcing and Gaussian Process

PubMed Central

Chang, Qiang; Li, Qun; Shi, Zesen; Chen, Wei; Wang, Weiping

2016-01-01

Indoor localization using Received Signal Strength Indication (RSSI) fingerprinting has been extensively studied for decades. The positioning accuracy is highly dependent on the density of the signal database. In areas without calibration data, however, this algorithm breaks down. Building and updating a dense signal database is labor intensive, expensive, and even impossible in some areas. Researchers are continually searching for better algorithms to create and update dense databases more efficiently. In this paper, we propose a scalable indoor positioning algorithm that works both in surveyed and unsurveyed areas. We first propose Minimum Inverse Distance (MID) algorithm to build a virtual database with uniformly distributed virtual Reference Points (RP). The area covered by the virtual RPs can be larger than the surveyed area. A Local Gaussian Process (LGP) is then applied to estimate the virtual RPs’ RSSI values based on the crowdsourced training data. Finally, we improve the Bayesian algorithm to estimate the user’s location using the virtual database. All the parameters are optimized by simulations, and the new algorithm is tested on real-case scenarios. The results show that the new algorithm improves the accuracy by 25.5% in the surveyed area, with an average positioning error below 2.2 m for 80% of the cases. Moreover, the proposed algorithm can localize the users in the neighboring unsurveyed area. PMID:26999139

GenoBase: comprehensive resource database of Escherichia coli K-12.

PubMed

Otsuka, Yuta; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Koichiro; Yamamoto, Natsuko; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Suharnan, Sivasundaram; Nomura, Wataru; Nakayashiki, Toru; Aref, Walid G; Bochner, Barry R; Conway, Tyrrell; Gribskov, Michael; Kihara, Daisuke; Rudd, Kenneth E; Tohsato, Yukako; Wanner, Barry L; Mori, Hirotada

2015-01-01

Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dietary Supplement Ingredient Database

MedlinePlus

... ARS Site Map | ARS Policies and Links | Plain Writing | FOIA | Accessibility Statement | Privacy Policy | Nondiscrimination Statement | Information Quality | USA.gov | White House | Technical Support Last updated: 8/14/2017

Pressure Scalings and Influence Region Research

DTIC Science & Technology

2018-01-01

the results are briefly discussed. Additionally, updated experimental results are presented along with discussion of collaborative research efforts...with upstream and downstream influence, where the influence lengths are defined in terms of a-priori quantities (freestream conditions and...governing equations and the result is briefly discussed. Additionally, updated experimental results are presented along with discussion of

Experimental validation of a new heterogeneous mechanical test design

NASA Astrophysics Data System (ADS)

Aquino, J.; Campos, A. Andrade; Souto, N.; Thuillier, S.

2018-05-01

Standard material parameters identification strategies generally use an extensive number of classical tests for collecting the required experimental data. However, a great effort has been made recently by the scientific and industrial communities to support this experimental database on heterogeneous tests. These tests can provide richer information on the material behavior allowing the identification of a more complete set of material parameters. This is a result of the recent development of full-field measurements techniques, like digital image correlation (DIC), that can capture the heterogeneous deformation fields on the specimen surface during the test. Recently, new specimen geometries were designed to enhance the richness of the strain field and capture supplementary strain states. The butterfly specimen is an example of these new geometries, designed through a numerical optimization procedure where an indicator capable of evaluating the heterogeneity and the richness of strain information. However, no experimental validation was yet performed. The aim of this work is to experimentally validate the heterogeneous butterfly mechanical test in the parameter identification framework. For this aim, DIC technique and a Finite Element Model Up-date inverse strategy are used together for the parameter identification of a DC04 steel, as well as the calculation of the indicator. The experimental tests are carried out in a universal testing machine with the ARAMIS measuring system to provide the strain states on the specimen surface. The identification strategy is accomplished with the data obtained from the experimental tests and the results are compared to a reference numerical solution.

US Gateway to SIMBAD Astronomical Database

NASA Technical Reports Server (NTRS)

Eichhorn, G.

1998-01-01

During the last year the US SIMBAD Gateway Project continued to provide services like user registration to the US users of the SIMBAD database in France. User registration is required by the SIMBAD project in France. Currently, there are almost 3000 US users registered. We also provide user support by answering questions from users and handling requests for lost passwords. We have worked with the CDS SIMBAD project to provide access to the SIMBAD database to US users on an Internet address basis. This will allow most US users to access SIMBAD without having to enter passwords. This new system was installed in August, 1998. The SIMBAD mirror database at SAO is fully operational. We worked with the CDS to adapt it to our computer system. We implemented automatic updating procedures that update the database and password files daily. This mirror database provides much better access to the US astronomical community. We also supported a demonstration of the SIMBAD database at the meeting of the American Astronomical Society in January. We shipped computer equipment to the meeting and provided support for the demonstration activities at the SIMBAD booth. We continued to improve the cross-linking between the SIMBAD project and the Astro- physics Data System. This cross-linking between these systems is very much appreciated by the users of both the SIMBAD database and the ADS Abstract Service. The mirror of the SIMBAD database at SAO makes this connection faster for the US astronomers. The close cooperation between the CDS in Strasbourg and SAO, facilitated by this project, is an important part of the astronomy-wide digital library initiative called Urania. It has proven to be a model in how different data centers can collaborate and enhance the value of their products by linking with other data centers.

Improved Differentiation of Streptococcus pneumoniae and Other S. mitis Group Streptococci by MALDI Biotyper Using an Improved MALDI Biotyper Database Content and a Novel Result Interpretation Algorithm.

PubMed

Harju, Inka; Lange, Christoph; Kostrzewa, Markus; Maier, Thomas; Rantakokko-Jalava, Kaisu; Haanperä, Marjo

2017-03-01

Reliable distinction of Streptococcus pneumoniae and viridans group streptococci is important because of the different pathogenic properties of these organisms. Differentiation between S. pneumoniae and closely related Sreptococcus mitis species group streptococci has always been challenging, even when using such modern methods as 16S rRNA gene sequencing or matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. In this study, a novel algorithm combined with an enhanced database was evaluated for differentiation between S. pneumoniae and S. mitis species group streptococci. One hundred one clinical S. mitis species group streptococcal strains and 188 clinical S. pneumoniae strains were identified by both the standard MALDI Biotyper database alone and that combined with a novel algorithm. The database update from 4,613 strains to 5,627 strains drastically improved the differentiation of S. pneumoniae and S. mitis species group streptococci: when the new database version containing 5,627 strains was used, only one of the 101 S. mitis species group isolates was misidentified as S. pneumoniae , whereas 66 of them were misidentified as S. pneumoniae when the earlier 4,613-strain MALDI Biotyper database version was used. The updated MALDI Biotyper database combined with the novel algorithm showed even better performance, producing no misidentifications of the S. mitis species group strains as S. pneumoniae All S. pneumoniae strains were correctly identified as S. pneumoniae with both the standard MALDI Biotyper database and the standard MALDI Biotyper database combined with the novel algorithm. This new algorithm thus enables reliable differentiation between pneumococci and other S. mitis species group streptococci with the MALDI Biotyper. Copyright © 2017 American Society for Microbiology.

The Papillomavirus Episteme: a major update to the papillomavirus sequence database.

PubMed

Van Doorslaer, Koenraad; Li, Zhiwen; Xirasagar, Sandhya; Maes, Piet; Kaminsky, David; Liou, David; Sun, Qiang; Kaur, Ramandeep; Huyen, Yentram; McBride, Alison A

2017-01-04

The Papillomavirus Episteme (PaVE) is a database of curated papillomavirus genomic sequences, accompanied by web-based sequence analysis tools. This update describes the addition of major new features. The papillomavirus genomes within PaVE have been further annotated, and now includes the major spliced mRNA transcripts. Viral genes and transcripts can be visualized on both linear and circular genome browsers. Evolutionary relationships among PaVE reference protein sequences can be analysed using multiple sequence alignments and phylogenetic trees. To assist in viral discovery, PaVE offers a typing tool; a simplified algorithm to determine whether a newly sequenced virus is novel. PaVE also now contains an image library containing gross clinical and histopathological images of papillomavirus infected lesions. Database URL: https://pave.niaid.nih.gov/. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Validation of the European Prototype for Integrated Care at Municipal Level in Savona: Updating and Maintenance

DTIC Science & Technology

2001-10-25

within one of the programmes sponsored by the European Commission.The system mainly consists of a shared care database in which each groups of...care database in which each community facility, or group of facilities, is supported by a local area network (LAN). Each of these LANs is connected over...functions. The software is layered, so that the client application is not affected by how the servers are implemented or which database system they use

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

Humphrey, Walter R.

CMS is a Windows application for tracking chemical inventories. Partners will use this application to record chemicals that are stored on their site and to perform periodic inventories of those chemicals. The application records information about stored chemicals from user input via the keyboard and barcode readers and stores that information into a single-file database (SQLite). A simple user login mechanism is used to control access to functions in the application. A user interface is provided that allows users to search the database and update data in the database.

Radioactivity and Environmental Security in the Oceans: New Research and Policy Priorities in the Arctic and North Atlantic

DTIC Science & Technology

1993-06-09

within the framework of an update for the computer database "DiaNIK" which has been developed at the Vernadsky Institute of Geochemistry and Analytical...chemical thermodynamic data for minerals and mineral-forming substances. The structure of thermodynamic database "DiaNIK" is based on the principles...in the database . A substantial portion of the thermodynamic values recommended by "DiaNIK" experts for the substances in User Version 3.1 resulted from

Context and Content Aware Routing of Managed Information Objects

DTIC Science & Technology

2014-05-01

datatype . Siena, however, does not support incremental updates (i.e., subscription posting and deletion) and so updates must be done in batch mode...Although the present implementation of PUBSUB does not support the string datatype , its architecture is sufficiently versatile to accommodate this... datatype with the inclusion of additional data structures as de- scribed in Section 3. 3. PUBSUB Section 3.1 describes how PUBSUB organizes its database of

77 FR 67831 - Announcement of National Geospatial Advisory Committee Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-14

... from governmental, private sector, non-profit, and academic organizations, has been established to... Dialogue --National Address Database --Geospatial Priorities --NGAC Subcommittee Activities --FGDC Update...

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

PubMed Central

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.

2016-01-01

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. PMID:26531826

Documentation for the U.S. Geological Survey Public-Supply Database (PSDB): A database of permitted public-supply wells, surface-water intakes, and systems in the United States

USGS Publications Warehouse

Price, Curtis V.; Maupin, Molly A.

2014-01-01

The purpose of this report is to document the PSDB and explain the methods used to populate and update the data from the SDWIS, State datasets, and map and geospatial imagery. This report describes 3 data tables and 11 domain tables, including field contents, data sources, and relations between tables. Although the PSDB database is not available to the general public, this information should be useful for others who are developing other database systems to store and analyze public-supply system and facility data.

Choosing Important Health Outcomes for Comparative Effectiveness Research: An Updated Review and Identification of Gaps.

PubMed

Gorst, Sarah L; Gargon, Elizabeth; Clarke, Mike; Smith, Valerie; Williamson, Paula R

2016-01-01

The COMET (Core Outcome Measures in Effectiveness Trials) Initiative promotes the development and application of core outcome sets (COS), including relevant studies in an online database. In order to keep the database current, an annual search of the literature is undertaken. This study aimed to update a previous systematic review, in order to identify any further studies where a COS has been developed. Furthermore, no prioritization for COS development has previously been undertaken, therefore this study also aimed to identify COS relevant to the world's most prevalent health conditions. The methods used in this updated review followed the same approach used in the original review and the previous update. A survey was also sent to the corresponding authors of COS identified for inclusion in this review, to ascertain what lessons they had learnt from developing their COS. Additionally, the COMET database was searched to identify COS that might be relevant to the conditions with the highest global prevalence. Twenty-five reports relating to 22 new studies were eligible for inclusion in the review. Further improvements were identified in relation to the description of the scope of the COS, use of the Delphi technique, and the inclusion of patient participants within the development process. Additionally, 33 published and ongoing COS were identified for 13 of the world's most prevalent conditions. The development of a reporting guideline and minimum standards should contribute towards future improvements in development and reporting of COS. This study has also described a first approach to identifying gaps in existing COS, and to priority setting in this area. Important gaps have been identified, on the basis of global burden of disease, and the development and application of COS in these areas should be considered a priority.

A Probabilistic Approach to Model Update

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Reaves, Mercedes C.; Voracek, David F.

2001-01-01

Finite element models are often developed for load validation, structural certification, response predictions, and to study alternate design concepts. In rare occasions, models developed with a nominal set of parameters agree with experimental data without the need to update parameter values. Today, model updating is generally heuristic and often performed by a skilled analyst with in-depth understanding of the model assumptions. Parameter uncertainties play a key role in understanding the model update problem and therefore probabilistic analysis tools, developed for reliability and risk analysis, may be used to incorporate uncertainty in the analysis. In this work, probability analysis (PA) tools are used to aid the parameter update task using experimental data and some basic knowledge of potential error sources. Discussed here is the first application of PA tools to update parameters of a finite element model for a composite wing structure. Static deflection data at six locations are used to update five parameters. It is shown that while prediction of individual response values may not be matched identically, the system response is significantly improved with moderate changes in parameter values.

Global Ground Motion Prediction Equations Program | Just another WordPress

Science.gov Websites

Motion Task 2: Compile and Critically Review GMPEs Task 3: Select or Derive a Global Set of GMPEs Task 6 : Design the Specifications to Compile a Global Database of Soil Classification Task 5: Build a Database of Update on PEER's Global GMPEs Project from recent workshop in Turkey Posted on June 11, 2012 During May

An Updated Site Index Equation for Naturally Regenerated Longleaf Pine Stands

Treesearch

Jyoti N. Rayamajhi; John S. Kush; Ralph S. Meldahl

1999-01-01

From 1964 to 1967. the U.S. Forest Service established the Regional Longleaf Growth Study (RLGS) in the Gulf States with the objective of obtaining a database for the development of prediction systems for naturally regenerated, even-aged. longleaf pine stands. The database has been used for numerous quantitative studies. One of these efforts was a site index equation...

Nutrient database improvement project: Separable components and proximate composition of raw and cooked retail cuts from the beef rib and plate

USDA-ARS?s Scientific Manuscript database

Beef nutrition is very important to the worldwide beef industry and its consumers. The objective of this study was to analyze nutrient composition of eight beef rib and plate cuts to update the nutrient data in the USDA National Nutrient Database for Standard Reference (SR). Seventy-two carcasses ...

Mapping PDB chains to UniProtKB entries.

PubMed

Martin, Andrew C R

2005-12-01

UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file. We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping. The resource may be queried interactively or downloaded from http://www.bioinf.org.uk/pdbsws/.

The ASTRAL Compendium in 2004

DOE R&D Accomplishments Database

Chandonia, John-Marc; Hon, Gary; Walker, Nigel S.; Lo Conte, Loredana; Koehl, Patrice; Levitt, Michael; Brenner, Steven E.

2003-09-15

The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. Partially derived from the SCOP database of protein structure domains, it includes sequences for each domain and other resources useful for studying these sequences and domain structures. The current release of ASTRAL contains 54,745 domains, more than three times as many as the initial release four years ago. ASTRAL has undergone major transformations in the past two years. In addition to several complete updates each year, ASTRAL is now updated on a weekly basis with preliminary classifications of domains from newly released PDB structures. These classifications are available as a stand-alone database, as well as available integrated into other ASTRAL databases such as representative subsets. To enhance the utility of ASTRAL to structural biologists, all SCOP domains are now made available as PDB-style coordinate files as well as sequences. In addition to sequences and representative subsets based on SCOP domains, sequences and subsets based on PDB chains are newly included in ASTRAL. Several search tools have been added to ASTRAL to facilitate retrieval of data by individual users and automated methods.

probeBase—an online resource for rRNA-targeted oligonucleotide probes and primers: new features 2016

PubMed Central

Greuter, Daniel; Loy, Alexander; Horn, Matthias; Rattei, Thomas

2016-01-01

probeBase http://www.probebase.net is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence databases are provided for each oligonucleotide entry, which makes probeBase an important and frequently used resource for microbiology research and diagnostics. Here we present a major update of probeBase, which was last featured in the NAR Database Issue 2007. This update describes a complete remodeling of the database architecture and environment to accommodate computationally efficient access. Improved search functions, sequence match tools and data output now extend the opportunities for finding suitable hierarchical probe sets that target an organism or taxon at different taxonomic levels. To facilitate the identification of complementary probe sets for organisms represented by short rRNA sequence reads generated by amplicon sequencing or metagenomic analysis with next generation sequencing technologies such as Illumina and IonTorrent, we introduce a novel tool that recovers surrogate near full-length rRNA sequences for short query sequences and finds matching oligonucleotides in probeBase. PMID:26586809

Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources

PubMed Central

Mochida, Keiichi; Uehara-Yamaguchi, Yukiko; Takahashi, Fuminori; Yoshida, Takuhiro; Sakurai, Tetsuya; Shinozaki, Kazuo

2013-01-01

A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the −3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops. PMID:24130698

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments.

PubMed

Chèneby, Jeanne; Gheorghe, Marius; Artufel, Marie; Mathelier, Anthony; Ballester, Benoit

2018-01-04

With this latest release of ReMap (http://remap.cisreg.eu), we present a unique collection of regulatory regions in human, as a result of a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. In 2015, we introduced the ReMap database to capture the genome regulatory space by integrating public ChIP-seq datasets, covering 237 TRs across 13 million (M) peaks. In this release, we have extended this catalog to constitute a unique collection of regulatory regions. Specifically, we have collected, analyzed and retained after quality control a total of 2829 ChIP-seq datasets available from public sources, covering a total of 485 TRs with a catalog of 80M peaks. Additionally, the updated database includes new search features for TR names as well as aliases, including cell line names and the ability to navigate the data directly within genome browsers via public track hubs. Finally, full access to this catalog is available online together with a TR binding enrichment analysis tool. ReMap 2018 provides a significant update of the ReMap database, providing an in depth view of the complexity of the regulatory landscape in human. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance

PubMed Central

Heavner, Benjamin D.; Smallbone, Kieran; Price, Nathan D.; Walker, Larry P.

2013-01-01

Updates to maintain a state-of-the art reconstruction of the yeast metabolic network are essential to reflect our understanding of yeast metabolism and functional organization, to eliminate any inaccuracies identified in earlier iterations, to improve predictive accuracy and to continue to expand into novel subsystems to extend the comprehensiveness of the model. Here, we present version 6 of the consensus yeast metabolic network (Yeast 6) as an update to the community effort to computationally reconstruct the genome-scale metabolic network of Saccharomyces cerevisiae S288c. Yeast 6 comprises 1458 metabolites participating in 1888 reactions, which are annotated with 900 yeast genes encoding the catalyzing enzymes. Compared with Yeast 5, Yeast 6 demonstrates improved sensitivity, specificity and positive and negative predictive values for predicting gene essentiality in glucose-limited aerobic conditions when analyzed with flux balance analysis. Additionally, Yeast 6 improves the accuracy of predicting the likelihood that a mutation will cause auxotrophy. The network reconstruction is available as a Systems Biology Markup Language (SBML) file enriched with Minimium Information Requested in the Annotation of Biochemical Models (MIRIAM)-compliant annotations. Small- and macromolecules in the network are referenced to authoritative databases such as Uniprot or ChEBI. Molecules and reactions are also annotated with appropriate publications that contain supporting evidence. Yeast 6 is freely available at http://yeast.sf.net/ as three separate SBML files: a model using the SBML level 3 Flux Balance Constraint package, a model compatible with the MATLAB® COBRA Toolbox for backward compatibility and a reconstruction containing only reactions for which there is experimental evidence (without the non-biological reactions necessary for simulating growth). Database URL: http://yeast.sf.net/ PMID:23935056

MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

PubMed Central

Trevarton, Alexander J.; Mann, Michael B.; Knapp, Christoph; Araki, Hiromitsu; Wren, Jonathan D.; Stones-Havas, Steven; Black, Michael A.; Print, Cristin G.

2013-01-01

Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g., mutations) in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability, and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html. A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research. The MelanomaDB database illustrates dysregulation of specific signaling pathways across 310 exome-sequenced melanomas and in individual tumors and identifies the distribution of somatic variants in melanoma. We suggest that MelanomaDB can provide a context in which to interpret the tumor molecular profiles of individual melanoma patients relative to biological information and available drug therapies. PMID:23875173

An environmental database for Venice and tidal zones

NASA Astrophysics Data System (ADS)

Macaluso, L.; Fant, S.; Marani, A.; Scalvini, G.; Zane, O.

2003-04-01

The natural environment is a complex, highly variable and physically non reproducible system (not in laboratory, nor in a confined territory). Environmental experimental studies are thus necessarily based on field measurements distributed in time and space. Only extensive data collections can provide the representative samples of the system behavior which are essential for scientific advancement. The assimilation of large data collections into accessible archives must necessarily be implemented in electronic databases. In the case of tidal environments in general, and of the Venice lagoon in particular, it is useful to establish a database, freely accessible to the scientific community, documenting the dynamics of such systems and their response to anthropic pressures and climatic variability. At the Istituto Veneto di Scienze, Lettere ed Arti in Venice (Italy) two internet environmental databases has been developed: one collects information regarding in detail the Venice lagoon; the other co-ordinate the research consortium of the "TIDE" EU RTD project, that attends to three different tidal areas: Venice Lagoon (Italy), Morecambe Bay (England), and Forth Estuary (Scotland). The archives may be accessed through the URL: www.istitutoveneto.it. The first one is freely available and applies to anyone is interested. It is continuously updated and has been structured in order to promote documentation concerning Venetian environment and disseminate this information for educational purposes (see "Dissemination" section). The second one is supplied by scientists and engineers working on this tidal system for various purposes (scientific, management, conservation purposes, etc.); it applies to interested researchers and grows with their own contributions. Both intend to promote scientific communication, to contribute to the realization of a distributed information system collecting homogeneous themes, and to initiate the interconnection among databases regarding different kinds of environment.

Databases for multilevel biophysiology research available at Physiome.jp.

PubMed

Asai, Yoshiyuki; Abe, Takeshi; Li, Li; Oka, Hideki; Nomura, Taishin; Kitano, Hiroaki

2015-01-01

Physiome.jp (http://physiome.jp) is a portal site inaugurated in 2007 to support model-based research in physiome and systems biology. At Physiome.jp, several tools and databases are available to support construction of physiological, multi-hierarchical, large-scale models. There are three databases in Physiome.jp, housing mathematical models, morphological data, and time-series data. In late 2013, the site was fully renovated, and in May 2015, new functions were implemented to provide information infrastructure to support collaborative activities for developing models and performing simulations within the database framework. This article describes updates to the databases implemented since 2013, including cooperation among the three databases, interactive model browsing, user management, version management of models, management of parameter sets, and interoperability with applications.

Updating the 2001 National Land Cover Database land cover classification to 2006 by using Landsat imagery change detection methods

USGS Publications Warehouse

Xian, George; Homer, Collin G.; Fry, Joyce

2009-01-01

The recent release of the U.S. Geological Survey (USGS) National Land Cover Database (NLCD) 2001, which represents the nation's land cover status based on a nominal date of 2001, is widely used as a baseline for national land cover conditions. To enable the updating of this land cover information in a consistent and continuous manner, a prototype method was developed to update land cover by an individual Landsat path and row. This method updates NLCD 2001 to a nominal date of 2006 by using both Landsat imagery and data from NLCD 2001 as the baseline. Pairs of Landsat scenes in the same season in 2001 and 2006 were acquired according to satellite paths and rows and normalized to allow calculation of change vectors between the two dates. Conservative thresholds based on Anderson Level I land cover classes were used to segregate the change vectors and determine areas of change and no-change. Once change areas had been identified, land cover classifications at the full NLCD resolution for 2006 areas of change were completed by sampling from NLCD 2001 in unchanged areas. Methods were developed and tested across five Landsat path/row study sites that contain several metropolitan areas including Seattle, Washington; San Diego, California; Sioux Falls, South Dakota; Jackson, Mississippi; and Manchester, New Hampshire. Results from the five study areas show that the vast majority of land cover change was captured and updated with overall land cover classification accuracies of 78.32%, 87.5%, 88.57%, 78.36%, and 83.33% for these areas. The method optimizes mapping efficiency and has the potential to provide users a flexible method to generate updated land cover at national and regional scales by using NLCD 2001 as the baseline.

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

PubMed Central

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 strategy will significantly advance the curation status of all organism-specific databases in SolCyc resulting in the improvement on database accuracy, data analysis and visualization of biochemical networks in those species. Database URL https://solgenomics.net/tools/solcyc/ PMID:29762652

A Database of Historical Information on Landslides and Floods in Italy

NASA Astrophysics Data System (ADS)

Guzzetti, F.; Tonelli, G.

2003-04-01

For the past 12 years we have maintained and updated a database of historical information on landslides and floods in Italy, known as the National Research Council's AVI (Damaged Urban Areas) Project archive. The database was originally designed to respond to a specific request of the Minister of Civil Protection, and was aimed at helping the regional assessment of landslide and flood risk in Italy. The database was first constructed in 1991-92 to cover the period 1917 to 1990. Information of damaging landslide and flood event was collected by searching archives, by screening thousands of newspaper issues, by reviewing the existing technical and scientific literature on landslides and floods in Italy, and by interviewing landslide and flood experts. The database was then updated chiefly through the analysis of hundreds of newspaper articles, and it now covers systematically the period 1900 to 1998, and non-systematically the periods 1900 to 1916 and 1999 to 2002. Non systematic information on landslide and flood events older than 20th century is also present in the database. The database currently contains information on more than 32,000 landslide events occurred at more than 25,700 sites, and on more than 28,800 flood events occurred at more than 15,600 sites. After a brief outline of the history and evolution of the AVI Project archive, we present and discuss: (a) the present structure of the database, including the hardware and software solutions adopted to maintain, manage, use and disseminate the information stored in the database, (b) the type and amount of information stored in the database, including an estimate of its completeness, and (c) examples of recent applications of the database, including a web-based GIS systems to show the location of sites historically affected by landslides and floods, and an estimate of geo-hydrological (i.e., landslide and flood) risk in Italy based on the available historical information.

VizieR Online Data Catalog: AAVSO International Variable Star Index VSX (Watson+, 2006-2014)

NASA Astrophysics Data System (ADS)

Watson, C.; Henden, A. A.; Price, A.

2017-05-01

This file contains Galactic stars known or suspected to be variable. It lists all stars that have an entry in the AAVSO International Variable Star Index (VSX; http://www.aavso.org/vsx). The database consisted initially of the General Catalogue of Variable Stars (GCVS) and the New Catalogue of Suspected Variables (NSV) and was then supplemented with a large number of variable star catalogues, as well as individual variable star discoveries or variables found in the literature. Effort has also been invested to update the entries with the latest information regarding position, type and period and to remove duplicates. The VSX database is being continually updated and maintained. For historical reasons some objects outside of the Galaxy have been included. (3 data files).

SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund)

EPA Pesticide Factsheets

The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access Database contains a selected set of non-enforcement confidential information and is updated by the regions every 90 days. The data describes what has happened at Superfund sites prior to this quarter (updated quarterly). This database includes lists of involved parties (other Federal Agencies, states, and tribes), Human Exposure and Ground Water Migration, and Site Wide Ready for Reuse, Construction Completion, and Final Assessment Decision (GPRA-like measures) for fund lead sites. Other information that is included has been included only as a service to allow public evaluations utilizing this data. EPA does not have specific Data Quality Objectives for use of the data. Independent Quality Assessments may be made of this data by reviewing the Quality Assurance Action Plan (QAPP).

VizieR Online Data Catalog: AAVSO International Variable Star Index VSX (Watson+, 2006-2014)

NASA Astrophysics Data System (ADS)

Watson, C.; Henden, A. A.; Price, A.

2018-05-01

This file contains Galactic stars known or suspected to be variable. It lists all stars that have an entry in the AAVSO International Variable Star Index (VSX; http://www.aavso.org/vsx). The database consisted initially of the General Catalogue of Variable Stars (GCVS) and the New Catalogue of Suspected Variables (NSV) and was then supplemented with a large number of variable star catalogues, as well as individual variable star discoveries or variables found in the literature. Effort has also been invested to update the entries with the latest information regarding position, type and period and to remove duplicates. The VSX database is being continually updated and maintained. For historical reasons some objects outside of the Galaxy have been included. (3 data files).

Specialized microbial databases for inductive exploration of microbial genome sequences

PubMed Central

Fang, Gang; Ho, Christine; Qiu, Yaowu; Cubas, Virginie; Yu, Zhou; Cabau, Cédric; Cheung, Frankie; Moszer, Ivan; Danchin, Antoine

2005-01-01

Background The enormous amount of genome sequence data asks for user-oriented databases to manage sequences and annotations. Queries must include search tools permitting function identification through exploration of related objects. Methods The GenoList package for collecting and mining microbial genome databases has been rewritten using MySQL as the database management system. Functions that were not available in MySQL, such as nested subquery, have been implemented. Results Inductive reasoning in the study of genomes starts from "islands of knowledge", centered around genes with some known background. With this concept of "neighborhood" in mind, a modified version of the GenoList structure has been used for organizing sequence data from prokaryotic genomes of particular interest in China. GenoChore , a set of 17 specialized end-user-oriented microbial databases (including one instance of Microsporidia, Encephalitozoon cuniculi, a member of Eukarya) has been made publicly available. These databases allow the user to browse genome sequence and annotation data using standard queries. In addition they provide a weekly update of searches against the world-wide protein sequences data libraries, allowing one to monitor annotation updates on genes of interest. Finally, they allow users to search for patterns in DNA or protein sequences, taking into account a clustering of genes into formal operons, as well as providing extra facilities to query sequences using predefined sequence patterns. Conclusion This growing set of specialized microbial databases organize data created by the first Chinese bacterial genome programs (ThermaList, Thermoanaerobacter tencongensis, LeptoList, with two different genomes of Leptospira interrogans and SepiList, Staphylococcus epidermidis) associated to related organisms for comparison. PMID:15698474

Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.

PubMed

Sakai, Hiroaki; Lee, Sung Shin; Tanaka, Tsuyoshi; Numa, Hisataka; Kim, Jungsok; Kawahara, Yoshihiro; Wakimoto, Hironobu; Yang, Ching-chia; Iwamoto, Masao; Abe, Takashi; Yamada, Yuko; Muto, Akira; Inokuchi, Hachiro; Ikemura, Toshimichi; Matsumoto, Takashi; Sasaki, Takuji; Itoh, Takeshi

2013-02-01

The Rice Annotation Project Database (RAP-DB, http://rapdb.dna.affrc.go.jp/) has been providing a comprehensive set of gene annotations for the genome sequence of rice, Oryza sativa (japonica group) cv. Nipponbare. Since the first release in 2005, RAP-DB has been updated several times along with the genome assembly updates. Here, we present our newest RAP-DB based on the latest genome assembly, Os-Nipponbare-Reference-IRGSP-1.0 (IRGSP-1.0), which was released in 2011. We detected 37,869 loci by mapping transcript and protein sequences of 150 monocot species. To provide plant researchers with highly reliable and up to date rice gene annotations, we have been incorporating literature-based manually curated data, and 1,626 loci currently incorporate literature-based annotation data, including commonly used gene names or gene symbols. Transcriptional activities are shown at the nucleotide level by mapping RNA-Seq reads derived from 27 samples. We also mapped the Illumina reads of a Japanese leading japonica cultivar, Koshihikari, and a Chinese indica cultivar, Guangluai-4, to the genome and show alignments together with the single nucleotide polymorphisms (SNPs) and gene functional annotations through a newly developed browser, Short-Read Assembly Browser (S-RAB). We have developed two satellite databases, Plant Gene Family Database (PGFD) and Integrative Database of Cereal Gene Phylogeny (IDCGP), which display gene family and homologous gene relationships among diverse plant species. RAP-DB and the satellite databases offer simple and user-friendly web interfaces, enabling plant and genome researchers to access the data easily and facilitating a broad range of plant research topics.

Helicobacter pylori eradication: gastric cancer prevention.

PubMed

Leontiadis, Grigorios I; Ford, Alexander Charles

2015-12-01

The principal effect of Helicobacter pylori infection is lifelong chronic gastritis, affecting up to 20% of younger adults but 50% to 80% of adults born in resource-rich countries before 1950. We conducted a systematic overview, aiming to answer the following clinical question: What are the effects of H pylori eradication treatment on the risk of developing gastric cancer? We searched: Medline, Embase, The Cochrane Library, and other important databases up to July 2014 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). At this update, searching of electronic databases retrieved 208 studies. After deduplication and removal of conference abstracts, 166 records were screened for inclusion in the overview. Appraisal of titles and abstracts led to the exclusion of 124 studies and the further review of 42 full publications. Of the 42 full articles evaluated, one systematic review was added at this update. We performed a GRADE evaluation for two PICO combinations. In this systematic overview, we categorised the efficacy for one intervention based on information about the effectiveness and safety of H pylori eradication treatment for the prevention of gastric cancer.

Burning mouth syndrome

PubMed Central

2016-01-01

Introduction Burning mouth syndrome mainly affects women, particularly after the menopause, when its prevalence may be 18% to 33%. Methods and outcomes We conducted a systematic overview, aiming to answer the following clinical question: What are the effects of selected treatments for burning mouth syndrome? We searched: Medline, Embase, The Cochrane Library, and other important databases up to January 2015 (BMJ Clinical Evidence overviews are updated periodically; please check our website for the most up-to-date version of this overview). Results At this update, searching of electronic databases retrieved 70 studies. After deduplication and removal of conference abstracts, 45 records were screened for inclusion in the overview. Appraisal of titles and abstracts led to the exclusion of 25 studies and the further review of 20 full publications. Of the 20 full articles evaluated, one systematic review and nine RCTs were added at this update. We performed a GRADE evaluation for five PICO combinations. Conclusions In this systematic overview, we categorised the efficacy for six interventions based on information about the effectiveness and safety of alphalipoic acid, benzodiazepines, benzydamine hydrochloride, cognitive behavioural therapy (CBT), selective serotonin re-uptake inhibitors (SSRIs), and tricyclic antidepressants. PMID:26745781

The MeSH translation maintenance system: structure, interface design, and implementation.

PubMed

Nelson, Stuart J; Schopen, Michael; Savage, Allan G; Schulman, Jacque-Lynne; Arluk, Natalie

2004-01-01

The National Library of Medicine (NLM) produces annual editions of the Medical Subject Headings (MeSH). Translations of MeSH are often done to make the vocabulary useful for non-English users. However, MeSH translators have encountered difficulties with entry vocabulary as they maintain and update their translation. Tracking MeSH changes and updating their translations in a reasonable time frame is cumbersome. NLM has developed and implemented a concept-centered vocabulary maintenance system for MeSH. This system has been extended to create an interlingual database of translations, the MeSH Translation Maintenance System (MTMS). This database allows continual updating of the translations, as well as facilitating tracking of the changes within MeSH from one year to another. The MTMS interface uses a Web-based design with multiple colors and fonts to indicate concepts needing translation or review. Concepts for which there is no exact English equivalent can be added. The system software encourages compliance with the Unicode standard in order to ensure that character sets with native alphabets and full orthography are used consistently.

ChEBI in 2016: Improved services and an expanding collection of metabolites

PubMed Central

Hastings, Janna; Owen, Gareth; Dekker, Adriano; Ennis, Marcus; Kale, Namrata; Muthukrishnan, Venkatesh; Turner, Steve; Swainston, Neil; Mendes, Pedro; Steinbeck, Christoph

2016-01-01

ChEBI is a database and ontology containing information about chemical entities of biological interest. It currently includes over 46 000 entries, each of which is classified within the ontology and assigned multiple annotations including (where relevant) a chemical structure, database cross-references, synonyms and literature citations. All content is freely available and can be accessed online at http://www.ebi.ac.uk/chebi. In this update paper, we describe recent improvements and additions to the ChEBI offering. We have substantially extended our collection of endogenous metabolites for several organisms including human, mouse, Escherichia coli and yeast. Our front-end has also been reworked and updated, improving the user experience, removing our dependency on Java applets in favour of embedded JavaScript components and moving from a monthly release update to a ‘live’ website. Programmatic access has been improved by the introduction of a library, libChEBI, in Java, Python and Matlab. Furthermore, we have added two new tools, namely an analysis tool, BiNChE, and a query tool for the ontology, OntoQuery. PMID:26467479

Interactive Exploration for Continuously Expanding Neuron Databases.

PubMed

Li, Zhongyu; Metaxas, Dimitris N; Lu, Aidong; Zhang, Shaoting

2017-02-15

This paper proposes a novel framework to help biologists explore and analyze neurons based on retrieval of data from neuron morphological databases. In recent years, the continuously expanding neuron databases provide a rich source of information to associate neuronal morphologies with their functional properties. We design a coarse-to-fine framework for efficient and effective data retrieval from large-scale neuron databases. In the coarse-level, for efficiency in large-scale, we employ a binary coding method to compress morphological features into binary codes of tens of bits. Short binary codes allow for real-time similarity searching in Hamming space. Because the neuron databases are continuously expanding, it is inefficient to re-train the binary coding model from scratch when adding new neurons. To solve this problem, we extend binary coding with online updating schemes, which only considers the newly added neurons and update the model on-the-fly, without accessing the whole neuron databases. In the fine-grained level, we introduce domain experts/users in the framework, which can give relevance feedback for the binary coding based retrieval results. This interactive strategy can improve the retrieval performance through re-ranking the above coarse results, where we design a new similarity measure and take the feedback into account. Our framework is validated on more than 17,000 neuron cells, showing promising retrieval accuracy and efficiency. Moreover, we demonstrate its use case in assisting biologists to identify and explore unknown neurons. Copyright © 2017 Elsevier Inc. All rights reserved.

LymPHOS 2.0: an update of a phosphosite database of primary human T cells

PubMed Central

Nguyen, Tien Dung; Vidal-Cortes, Oriol; Gallardo, Oscar; Abian, Joaquin; Carrascal, Montserrat

2015-01-01

LymPHOS is a web-oriented database containing peptide and protein sequences and spectrometric information on the phosphoproteome of primary human T-Lymphocytes. Current release 2.0 contains 15 566 phosphorylation sites from 8273 unique phosphopeptides and 4937 proteins, which correspond to a 45-fold increase over the original database description. It now includes quantitative data on phosphorylation changes after time-dependent treatment with activators of the TCR-mediated signal transduction pathway. Sequence data quality has also been improved with the use of multiple search engines for database searching. LymPHOS can be publicly accessed at http://www.lymphos.org. Database URL: http://www.lymphos.org. PMID:26708986

Hawaii bibliographic database

USGS Publications Warehouse

Wright, T.L.; Takahashi, T.J.

1998-01-01

The Hawaii bibliographic database has been created to contain all of the literature, from 1779 to the present, pertinent to the volcanological history of the Hawaiian-Emperor volcanic chain. References are entered in a PC- and Macintosh-compatible EndNote Plus bibliographic database with keywords and abstracts or (if no abstract) with annotations as to content. Keywords emphasize location, discipline, process, identification of new chemical data or age determinations, and type of publication. The database is updated approximately three times a year and is available to upload from an ftp site. The bibliography contained 8460 references at the time this paper was submitted for publication. Use of the database greatly enhances the power and completeness of library searches for anyone interested in Hawaiian volcanism.

Nuclear Science References Database

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

Pritychenko, B., E-mail: pritychenko@bnl.gov; Běták, E.; Singh, B.

2014-06-15

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

OGEE v2: an update of the online gene essentiality database with special focus on differentially essential genes in human cancer cell lines.

PubMed

Chen, Wei-Hua; Lu, Guanting; Chen, Xiao; Zhao, Xing-Ming; Bork, Peer

2017-01-04

OGEE is an Online GEne Essentiality database. To enhance our understanding of the essentiality of genes, in OGEE we collected experimentally tested essential and non-essential genes, as well as associated gene properties known to contribute to gene essentiality. We focus on large-scale experiments, and complement our data with text-mining results. We organized tested genes into data sets according to their sources, and tagged those with variable essentiality statuses across data sets as conditionally essential genes, intending to highlight the complex interplay between gene functions and environments/experimental perturbations. Developments since the last public release include increased numbers of species and gene essentiality data sets, inclusion of non-coding essential sequences and genes with intermediate essentiality statuses. In addition, we included 16 essentiality data sets from cancer cell lines, corresponding to 9 human cancers; with OGEE, users can easily explore the shared and differentially essential genes within and between cancer types. These genes, especially those derived from cell lines that are similar to tumor samples, could reveal the oncogenic drivers, paralogous gene expression pattern and chromosomal structure of the corresponding cancer types, and can be further screened to identify targets for cancer therapy and/or new drug development. OGEE is freely available at http://ogee.medgenius.info. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The 2006 Cape Canaveral Air Force Station Range Reference Atmosphere Model Validation Study and Sensitivity Analysis to the National Aeronautics and Space Administration's Space Shuttle

NASA Technical Reports Server (NTRS)

Burns, Lee; Merry, Carl; Decker, Ryan; Harrington, Brian

2008-01-01

The 2006 Cape Canaveral Air Force Station (CCAFS) Range Reference Atmosphere (RRA) is a statistical model summarizing the wind and thermodynamic atmospheric variability from surface to 70 kin. Launches of the National Aeronautics and Space Administration's (NASA) Space Shuttle from Kennedy Space Center utilize CCAFS RRA data to evaluate environmental constraints on various aspects of the vehicle during ascent. An update to the CCAFS RRA was recently completed. As part of the update, a validation study on the 2006 version was conducted as well as a comparison analysis of the 2006 version to the existing CCAFS RRA database version 1983. Assessments to the Space Shuttle vehicle ascent profile characteristics were performed to determine impacts of the updated model to the vehicle performance. Details on the model updates and the vehicle sensitivity analyses with the update model are presented.

Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome

PubMed Central

Kim, Woonsu; Park, Hyesun; Seo, Seongwon

2016-01-01

The sequence of cattle genome provided a valuable opportunity to systematically link genetic and metabolic traits of cattle. The objectives of this study were 1) to reconstruct genome-scale cattle-specific metabolic pathways based on the most recent and updated cattle genome build and 2) to identify duplicated metabolic genes in the cattle genome for better understanding of metabolic adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating genomic annotations from multiple sources was updated. Using this, an amalgamated cattle genome database based on UMD_3.1, was created. The amalgamated cattle genome database is composed of a total of 33,292 genes: 19,123 consensus genes between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic reconstruction of the cattle genome and cattle pathway genome database (PGDB) was also developed using Pathway Tools, followed by an intensive manual curation. The manual curation filled or revised 68 pathway holes, deleted 36 metabolic pathways, and added 23 metabolic pathways. Consequently, the curated cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371 enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight duplicated genes in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these duplicated genes are related with specific hormone biosynthesis and detoxifications. The updated genome-scale metabolic reconstruction is a useful tool for understanding biology and metabolic characteristics in cattle. There has been significant improvements in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle genome compared to human and mouse implies evolutionary changes in the cattle genome and provides a useful information for further research on understanding metabolic adaptations of cattle. PMID:26992093

Space transfer concepts and analysis for exploration missions

NASA Technical Reports Server (NTRS)

1990-01-01

The progress and results are summarized for mission/system requirements database; mission analysis; GN and C (Guidance, Navigation, and Control), aeroheating, Mars landing; radiation protection; aerobrake mass analysis; Shuttle-Z, TMIS (Trans-Mars Injection Stage); Long Duration Habitat Trade Study; evolutionary lunar and Mars options; NTR (Nuclear Thermal Rocket); NEP (Nuclear Electric Propulsion) update; SEP (Solar Electric Propulsion) update; orbital and space-based requirements; technology; piloted rover; programmatic task; and evolutionary and innovative architecture.

Signal reception and transmission.

PubMed

Gough, Nancy R

2006-12-05

From plants to yeast to animals, new pathways and updates to the Database of Cell Signaling highlight how signals received at the surface are transmitted into the cell to mediate complex cellular responses.

AIDSinfo Drug Database

MedlinePlus

... HIV/AIDS-related drugs for that condition. OK Filters Approval: What's this? FDA-Approved Investigational Class: What's ... Encephalitis Tuberculosis Varicella-Zoster Virus Diseases Update Loading... Filter by approval status, drug class, and condition Browse ...

DrugBank 5.0: a major update to the DrugBank database for 2018.

PubMed

Wishart, David S; Feunang, Yannick D; Guo, An C; Lo, Elvis J; Marcu, Ana; Grant, Jason R; Sajed, Tanvir; Johnson, Daniel; Li, Carin; Sayeeda, Zinat; Assempour, Nazanin; Iynkkaran, Ithayavani; Liu, Yifeng; Maciejewski, Adam; Gale, Nicola; Wilson, Alex; Chin, Lucy; Cummings, Ryan; Le, Diana; Pon, Allison; Knox, Craig; Wilson, Michael

2018-01-04

DrugBank (www.drugbank.ca) is a web-enabled database containing comprehensive molecular information about drugs, their mechanisms, their interactions and their targets. First described in 2006, DrugBank has continued to evolve over the past 12 years in response to marked improvements to web standards and changing needs for drug research and development. This year's update, DrugBank 5.0, represents the most significant upgrade to the database in more than 10 years. In many cases, existing data content has grown by 100% or more over the last update. For instance, the total number of investigational drugs in the database has grown by almost 300%, the number of drug-drug interactions has grown by nearly 600% and the number of SNP-associated drug effects has grown more than 3000%. Significant improvements have been made to the quantity, quality and consistency of drug indications, drug binding data as well as drug-drug and drug-food interactions. A great deal of brand new data have also been added to DrugBank 5.0. This includes information on the influence of hundreds of drugs on metabolite levels (pharmacometabolomics), gene expression levels (pharmacotranscriptomics) and protein expression levels (pharmacoprotoemics). New data have also been added on the status of hundreds of new drug clinical trials and existing drug repurposing trials. Many other important improvements in the content, interface and performance of the DrugBank website have been made and these should greatly enhance its ease of use, utility and potential applications in many areas of pharmacological research, pharmaceutical science and drug education. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

GeneSCF: a real-time based functional enrichment tool with support for multiple organisms.

PubMed

Subhash, Santhilal; Kanduri, Chandrasekhar

2016-09-13

High-throughput technologies such as ChIP-sequencing, RNA-sequencing, DNA sequencing and quantitative metabolomics generate a huge volume of data. Researchers often rely on functional enrichment tools to interpret the biological significance of the affected genes from these high-throughput studies. However, currently available functional enrichment tools need to be updated frequently to adapt to new entries from the functional database repositories. Hence there is a need for a simplified tool that can perform functional enrichment analysis by using updated information directly from the source databases such as KEGG, Reactome or Gene Ontology etc. In this study, we focused on designing a command-line tool called GeneSCF (Gene Set Clustering based on Functional annotations), that can predict the functionally relevant biological information for a set of genes in a real-time updated manner. It is designed to handle information from more than 4000 organisms from freely available prominent functional databases like KEGG, Reactome and Gene Ontology. We successfully employed our tool on two of published datasets to predict the biologically relevant functional information. The core features of this tool were tested on Linux machines without the need for installation of more dependencies. GeneSCF is more reliable compared to other enrichment tools because of its ability to use reference functional databases in real-time to perform enrichment analysis. It is an easy-to-integrate tool with other pipelines available for downstream analysis of high-throughput data. More importantly, GeneSCF can run multiple gene lists simultaneously on different organisms thereby saving time for the users. Since the tool is designed to be ready-to-use, there is no need for any complex compilation and installation procedures.

A technique for routinely updating the ITU-R database using radio occultation electron density profiles

NASA Astrophysics Data System (ADS)

Brunini, Claudio; Azpilicueta, Francisco; Nava, Bruno

2013-09-01

Well credited and widely used ionospheric models, such as the International Reference Ionosphere or NeQuick, describe the variation of the electron density with height by means of a piecewise profile tied to the F2-peak parameters: the electron density,, and the height, . Accurate values of these parameters are crucial for retrieving reliable electron density estimations from those models. When direct measurements of these parameters are not available, the models compute the parameters using the so-called ITU-R database, which was established in the early 1960s. This paper presents a technique aimed at routinely updating the ITU-R database using radio occultation electron density profiles derived from GPS measurements gathered from low Earth orbit satellites. Before being used, these radio occultation profiles are validated by fitting to them an electron density model. A re-weighted Least Squares algorithm is used for down-weighting unreliable measurements (occasionally, entire profiles) and to retrieve and values—together with their error estimates—from the profiles. These values are used to monthly update the database, which consists of two sets of ITU-R-like coefficients that could easily be implemented in the IRI or NeQuick models. The technique was tested with radio occultation electron density profiles that are delivered to the community by the COSMIC/FORMOSAT-3 mission team. Tests were performed for solstices and equinoxes seasons in high and low-solar activity conditions. The global mean error of the resulting maps—estimated by the Least Squares technique—is between and elec/m for the F2-peak electron density (which is equivalent to 7 % of the value of the estimated parameter) and from 2.0 to 5.6 km for the height (2 %).

Modernization of the International Volcanic Ash Website - a global resource for ashfall preparedness and impact guidance.

NASA Astrophysics Data System (ADS)

Wallace, K.; Leonard, G.; Stewart, C.; Wilson, T. M.; Randall, M.; Stovall, W. K.

2015-12-01

The internationally collaborative volcanic ash website (http://volcanoes.usgs.gov/ash/) has been an important global information resource for ashfall preparedness and impact guidance since 2004. Recent volcanic ashfalls with significant local, regional, and global impacts highlighted the need to improve the website to make it more accessible and pertinent to users worldwide. Recently, the Volcanic Ash Impacts Working Group (Cities and Volcanoes Commission of IAVCEI) redesigned and modernized the website. Improvements include 1) a database-driven back end, 2) reorganized menu navigation, 3) language translation, 4) increased downloadable content, 5) addition of ash-impact case studies, 7) expanded and updated references , 8) an image database, and 9) inclusion of cooperating organization's logos. The database-driven platform makes the website more dynamic and efficient to operate and update. New menus provide information about specific impact topics (buildings, transportation, power, health, agriculture, water and waste water, equipment and communications, clean up) and updated content has been added throughout all topics. A new "for scientists" menu includes information on ash collection and analysis. Website translation using Google translate will significantly increase user base. Printable resources (e.g. checklists, pamphlets, posters) provide information to people without Internet access. Ash impact studies are used to improve mitigation measures during future eruptions, and links to case studies will assist communities' preparation and response plans. The Case Studies menu is intended to be a living topic area, growing as new case studies are published. A database of all images from the website allows users to access larger resolution images and additional descriptive details. Logos clarify linkages among key contributors and assure users that the site is authoritative and science-based.

Review and assessment of turbulence models for hypersonic flows

NASA Astrophysics Data System (ADS)

Roy, Christopher J.; Blottner, Frederick G.

2006-10-01

Accurate aerodynamic prediction is critical for the design and optimization of hypersonic vehicles. Turbulence modeling remains a major source of uncertainty in the computational prediction of aerodynamic forces and heating for these systems. The first goal of this article is to update the previous comprehensive review of hypersonic shock/turbulent boundary-layer interaction experiments published in 1991 by Settles and Dodson (Hypersonic shock/boundary-layer interaction database. NASA CR 177577, 1991). In their review, Settles and Dodson developed a methodology for assessing experiments appropriate for turbulence model validation and critically surveyed the existing hypersonic experiments. We limit the scope of our current effort by considering only two-dimensional (2D)/axisymmetric flows in the hypersonic flow regime where calorically perfect gas models are appropriate. We extend the prior database of recommended hypersonic experiments (on four 2D and two 3D shock-interaction geometries) by adding three new geometries. The first two geometries, the flat plate/cylinder and the sharp cone, are canonical, zero-pressure gradient flows which are amenable to theory-based correlations, and these correlations are discussed in detail. The third geometry added is the 2D shock impinging on a turbulent flat plate boundary layer. The current 2D hypersonic database for shock-interaction flows thus consists of nine experiments on five different geometries. The second goal of this study is to review and assess the validation usage of various turbulence models on the existing experimental database. Here we limit the scope to one- and two-equation turbulence models where integration to the wall is used (i.e., we omit studies involving wall functions). A methodology for validating turbulence models is given, followed by an extensive evaluation of the turbulence models on the current hypersonic experimental database. A total of 18 one- and two-equation turbulence models are reviewed, and results of turbulence model assessments for the six models that have been extensively applied to the hypersonic validation database are compiled and presented in graphical form. While some of the turbulence models do provide reasonable predictions for the surface pressure, the predictions for surface heat flux are generally poor, and often in error by a factor of four or more. In the vast majority of the turbulence model validation studies we review, the authors fail to adequately address the numerical accuracy of the simulations (i.e., discretization and iterative error) and the sensitivities of the model predictions to freestream turbulence quantities or near-wall y+ mesh spacing. We recommend new hypersonic experiments be conducted which (1) measure not only surface quantities but also mean and fluctuating quantities in the interaction region and (2) provide careful estimates of both random experimental uncertainties and correlated bias errors for the measured quantities and freestream conditions. For the turbulence models, we recommend that a wide-range of turbulence models (including newer models) be re-examined on the current hypersonic experimental database, including the more recent experiments. Any future turbulence model validation efforts should carefully assess the numerical accuracy and model sensitivities. In addition, model corrections (e.g., compressibility corrections) should be carefully examined for their effects on a standard, low-speed validation database. Finally, as new experiments or direct numerical simulation data become available with information on mean and fluctuating quantities, they should be used to improve the turbulence models and thus increase their predictive capability.

X-48B Phase 1 Flight Maneuver Database and ICP Airspace Constraint Analysis

NASA Technical Reports Server (NTRS)

Fast, Peter Alan

2010-01-01

The work preformed during the Summer 2010 by Peter Fast. The main tasks assigned were to update and improve the X-48 Flight Maneuver Database and conduct an Airspace Constraint Analysis for the Remotely Operated Aircraft Area used to flight test Unmanned Arial Vehicles. The final task was to develop and demonstrate a working knowledge of flight control theory.

Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content

PubMed Central

Rothwell, Joseph A.; Perez-Jimenez, Jara; Neveu, Vanessa; Medina-Remón, Alexander; M'Hiri, Nouha; García-Lobato, Paula; Manach, Claudine; Knox, Craig; Eisner, Roman; Wishart, David S.; Scalbert, Augustin

2013-01-01

Polyphenols are a major class of bioactive phytochemicals whose consumption may play a role in the prevention of a number of chronic diseases such as cardiovascular diseases, type II diabetes and cancers. Phenol-Explorer, launched in 2009, is the only freely available web-based database on the content of polyphenols in food and their in vivo metabolism and pharmacokinetics. Here we report the third release of the database (Phenol-Explorer 3.0), which adds data on the effects of food processing on polyphenol contents in foods. Data on >100 foods, covering 161 polyphenols or groups of polyphenols before and after processing, were collected from 129 peer-reviewed publications and entered into new tables linked to the existing relational design. The effect of processing on polyphenol content is expressed in the form of retention factor coefficients, or the proportion of a given polyphenol retained after processing, adjusted for change in water content. The result is the first database on the effects of food processing on polyphenol content and, following the model initially defined for Phenol-Explorer, all data may be traced back to original sources. The new update will allow polyphenol scientists to more accurately estimate polyphenol exposure from dietary surveys. Database URL: http://www.phenol-explorer.eu PMID:24103452

Integrated sequence and immunology filovirus database at Los Alamos

PubMed Central

Yoon, Hyejin; Foley, Brian; Feng, Shihai; Macke, Jennifer; Dimitrijevic, Mira; Abfalterer, Werner; Szinger, James; Fischer, Will; Kuiken, Carla; Korber, Bette

2016-01-01

The Ebola outbreak of 2013–15 infected more than 28 000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. As this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family Filoviridae sequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy. Database URL: www.hfv.lanl.gov PMID:27103629

Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources.

PubMed

Wang, Xiaobo; Wu, Jian; Liang, Jianli; Cheng, Feng; Wang, Xiaowu

2015-01-01

The Brassica database (BRAD) was built initially to assist users apply Brassica rapa and Arabidopsis thaliana genomic data efficiently to their research. However, many Brassicaceae genomes have been sequenced and released after its construction. These genomes are rich resources for comparative genomics, gene annotation and functional evolutionary studies of Brassica crops. Therefore, we have updated BRAD to version 2.0 (V2.0). In BRAD V2.0, 11 more Brassicaceae genomes have been integrated into the database, namely those of Arabidopsis lyrata, Aethionema arabicum, Brassica oleracea, Brassica napus, Camelina sativa, Capsella rubella, Leavenworthia alabamica, Sisymbrium irio and three extremophiles Schrenkiella parvula, Thellungiella halophila and Thellungiella salsuginea. BRAD V2.0 provides plots of syntenic genomic fragments between pairs of Brassicaceae species, from the level of chromosomes to genomic blocks. The Generic Synteny Browser (GBrowse_syn), a module of the Genome Browser (GBrowse), is used to show syntenic relationships between multiple genomes. Search functions for retrieving syntenic and non-syntenic orthologs, as well as their annotation and sequences are also provided. Furthermore, genome and annotation information have been imported into GBrowse so that all functional elements can be visualized in one frame. We plan to continually update BRAD by integrating more Brassicaceae genomes into the database. Database URL: http://brassicadb.org/brad/. © The Author(s) 2015. Published by Oxford University Press.

The Atomic Mass Evaluation (AME2012): Status and Perspectives

NASA Astrophysics Data System (ADS)

Kondev, F. G.; Audi, G.; Wang, M.; Xu, X.; Wapstra, A. H.; MacCormick, M.; Pfeiffer, B.

2013-10-01

The atomic mass is a fundamental property of the nucleus that has wide applications in natural sciences and technology. The new evaluated mass table, AME2012, has been recently published as a collaborative effort between scientists from China, Europe and USA, under the leadership of G. Audi. It represents a significant update of the previous AME2003 evaluation by considering a large number of precise experimental results obtained at existing Penning Trap and Storage Ring facilities, thus expending the region of experimentally known masses towards exotic neutron- and proton-rich nuclei. Since the presence of isomers plays an important role in determining the masses of many nuclei, a complementary database, NUBASE2012, that contains the isomer-level properties for all nuclei was also developed. This presentation will briefly review recent achievements of the collaboration, present on-going activities, and reflect on ideas for future developments and challenges in the field of evaluation of atomic masses. The work at ANL was supported by the U.S. Department of Energy, Office of Nuclear Physics, under Contract No. DE-AC02-06CH11357.

A global experimental dataset for assessing grain legume production

PubMed Central

Cernay, Charles; Pelzer, Elise; Makowski, David

2016-01-01

Grain legume crops are a significant component of the human diet and animal feed and have an important role in the environment, but the global diversity of agricultural legume species is currently underexploited. Experimental assessments of grain legume performances are required, to identify potential species with high yields. Here, we introduce a dataset including results of field experiments published in 173 articles. The selected experiments were carried out over five continents on 39 grain legume species. The dataset includes measurements of grain yield, aerial biomass, crop nitrogen content, residual soil nitrogen content and water use. When available, yields for cereals and oilseeds grown after grain legumes in the crop sequence are also included. The dataset is arranged into a relational database with nine structured tables and 198 standardized attributes. Tillage, fertilization, pest and irrigation management are systematically recorded for each of the 8,581 crop*field site*growing season*treatment combinations. The dataset is freely reusable and easy to update. We anticipate that it will provide valuable information for assessing grain legume production worldwide. PMID:27676125

IRIS Toxicological Review of Benzo[a]pyrene (Final Report) ...

EPA Pesticide Factsheets

EPA has finalized the Integrated Risk Information System (IRIS) assessment of benzo[a]pyrene. This assessment addresses the potential cancer and noncancer human health effects from long-term exposure to benzo[a]pyrene. Now final, this assessment will update the toxicological information on benzo[a]pyrene posted in 1987. EPA’s program and regional offices may use this assessment to inform decisions to protect human health. EPA is undertaking an update of the Integrated Risk Information System (IRIS) health assessment for benzo[a]pyrene (BaP). The outcome of this project is an updated Toxicological Review and IRIS Summary for BaP that will be entered into the IRIS database.

HMDB 4.0: the human metabolome database for 2018

PubMed Central

Feunang, Yannick Djoumbou; Marcu, Ana; Guo, An Chi; Liang, Kevin; Vázquez-Fresno, Rosa; Sajed, Tanvir; Johnson, Daniel; Li, Carin; Karu, Naama; Sayeeda, Zinat; Lo, Elvis; Assempour, Nazanin; Berjanskii, Mark; Singhal, Sandeep; Arndt, David; Liang, Yonjie; Badran, Hasan; Grant, Jason; Serra-Cayuela, Arnau; Liu, Yifeng; Mandal, Rupa; Neveu, Vanessa; Pon, Allison; Knox, Craig; Wilson, Michael; Manach, Claudine; Scalbert, Augustin

2018-01-01

Abstract The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the HMDB is now considered the standard metabolomic resource for human metabolic studies. Over the past decade the HMDB has continued to grow and evolve in response to emerging needs for metabolomics researchers and continuing changes in web standards. This year's update, HMDB 4.0, represents the most significant upgrade to the database in its history. For instance, the number of fully annotated metabolites has increased by nearly threefold, the number of experimental spectra has grown by almost fourfold and the number of illustrated metabolic pathways has grown by a factor of almost 60. Significant improvements have also been made to the HMDB’s chemical taxonomy, chemical ontology, spectral viewing, and spectral/text searching tools. A great deal of brand new data has also been added to HMDB 4.0. This includes large quantities of predicted MS/MS and GC–MS reference spectral data as well as predicted (physiologically feasible) metabolite structures to facilitate novel metabolite identification. Additional information on metabolite-SNP interactions and the influence of drugs on metabolite levels (pharmacometabolomics) has also been added. Many other important improvements in the content, the interface, and the performance of the HMDB website have been made and these should greatly enhance its ease of use and its potential applications in nutrition, biochemistry, clinical chemistry, clinical genetics, medicine, and metabolomics science. PMID:29140435

Update Your Member Lab Compendium Data

EPA Pesticide Factsheets

The Compendium of Environmental Testing Laboratories is a limited-access online database of environmental laboratories nationwide that is available to EPA; Federal, State, and local emergency responders; laboratory personnel; and water utilities.

78 FR 76811 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-19

... support of the scholarship application by academic professors/advisors. NOAA OEd student scholar alumni... are required to update the student tracker database with the required student information. In addition...

Alternatives to relational databases in precision medicine: Comparison of NoSQL approaches for big data storage using supercomputers

NASA Astrophysics Data System (ADS)

Velazquez, Enrique Israel

Improvements in medical and genomic technologies have dramatically increased the production of electronic data over the last decade. As a result, data management is rapidly becoming a major determinant, and urgent challenge, for the development of Precision Medicine. Although successful data management is achievable using Relational Database Management Systems (RDBMS), exponential data growth is a significant contributor to failure scenarios. Growing amounts of data can also be observed in other sectors, such as economics and business, which, together with the previous facts, suggests that alternate database approaches (NoSQL) may soon be required for efficient storage and management of big databases. However, this hypothesis has been difficult to test in the Precision Medicine field since alternate database architectures are complex to assess and means to integrate heterogeneous electronic health records (EHR) with dynamic genomic data are not easily available. In this dissertation, we present a novel set of experiments for identifying NoSQL database approaches that enable effective data storage and management in Precision Medicine using patients' clinical and genomic information from the cancer genome atlas (TCGA). The first experiment draws on performance and scalability from biologically meaningful queries with differing complexity and database sizes. The second experiment measures performance and scalability in database updates without schema changes. The third experiment assesses performance and scalability in database updates with schema modifications due dynamic data. We have identified two NoSQL approach, based on Cassandra and Redis, which seems to be the ideal database management systems for our precision medicine queries in terms of performance and scalability. We present NoSQL approaches and show how they can be used to manage clinical and genomic big data. Our research is relevant to the public health since we are focusing on one of the main challenges to the development of Precision Medicine and, consequently, investigating a potential solution to the progressively increasing demands on health care.

The 2003 edition of geisa: a spectroscopic database system for the second generation vertical sounders radiance simulation

NASA Astrophysics Data System (ADS)

Jacquinet-Husson, N.; Lmd Team

The GEISA (Gestion et Etude des Informations Spectroscopiques Atmosphériques: Management and Study of Atmospheric Spectroscopic Information) computer accessible database system, in its former 1997 and 2001 versions, has been updated in 2003 (GEISA-03). It is developed by the ARA (Atmospheric Radiation Analysis) group at LMD (Laboratoire de Météorologie Dynamique, France) since 1974. This early effort implemented the so-called `` line-by-line and layer-by-layer '' approach for forward radiative transfer modelling action. The GEISA 2003 system comprises three databases with their associated management softwares: a database of spectroscopic parameters required to describe adequately the individual spectral lines belonging to 42 molecules (96 isotopic species) and located in a spectral range from the microwave to the limit of the visible. The featured molecules are of interest in studies of the terrestrial as well as the other planetary atmospheres, especially those of the Giant Planets. a database of absorption cross-sections of molecules such as chlorofluorocarbons which exhibit unresolvable spectra. a database of refractive indices of basic atmospheric aerosol components. Illustrations will be given of GEISA-03, data archiving method, contents, management softwares and Web access facilities at: http://ara.lmd.polytechnique.fr The performance of instruments like AIRS (Atmospheric Infrared Sounder; http://www-airs.jpl.nasa.gov) in the USA, and IASI (Infrared Atmospheric Sounding Interferometer; http://smsc.cnes.fr/IASI/index.htm) in Europe, which have a better vertical resolution and accuracy, compared to the presently existing satellite infrared vertical sounders, is directly related to the quality of the spectroscopic parameters of the optically active gases, since these are essential input in the forward models used to simulate recorded radiance spectra. For these upcoming atmospheric sounders, the so-called GEISA/IASI sub-database system has been elaborated, from GEISA. Its content, will be described, as well. This work is ongoing, with the purpose of assessing the IASI measurements capabilities and the spectroscopic information quality, within the ISSWG (IASI Sounding Science Working Group), in the frame of the CNES (Centre National d'Etudes Spatiales, France)/EUMETSAT (EUropean organization for the exploitation of METeorological SATellites) Polar System (EPS) project, by simulating high resolution radiances and/or using experimental data. EUMETSAT will implement GEISA/IASI into the EPS ground segment. The IASI soundings spectroscopic data archive requirements will be discussed in the context of comparisons between recorded and calculated experimental spectra, using the ARA/4A forward line-by-line radiative transfer modelling code in its latest version.

United States Air Force Summer Research Program -- 1993. Volume 4. Rome Laboratory

DTIC Science & Technology

1993-12-01

H., eds., Object-Oriented Concepts, Databases , and Applications, Addison-Wesley, Reading, MA, 1989. [Lano9l] Lano, K., "Z++, An Object-Orientated...1433 46.92 60 TCP janus.rl.af.mil mensa.rl.af.mil 1433 2611 The Target Filter Manager responds to requests for data and accesses the target database . A...2.5 2- 1.5- 28 -3 -2 -10 12 3 AZIMUTH (OE(3) Figure 12. Contour plot of antenna pattern, QC2 algorithm 5-32 UPDATING PROBABILISTIC DATABASES Michael A

NEEDS v.5.15 User Guide

EPA Pesticide Factsheets

View a user guide for the the updated National Electric Energy Data System (NEEDS), the database used to construct the model plants that represent existing and planned/committed units in EPA modeling applications.

MEPD: a Medaka gene expression pattern database

PubMed Central

Henrich, Thorsten; Ramialison, Mirana; Quiring, Rebecca; Wittbrodt, Beate; Furutani-Seiki, Makoto; Wittbrodt, Joachim; Kondoh, Hisato

2003-01-01

The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensity, category and comments and through a comprehensive, hierarchically organized dictionary of anatomical terms. Sequences of the ESTs are available and searchable through BLAST. ESTs in the database are clustered upon entry and have been blasted against public data-bases. The BLAST results are updated regularly, stored within the database and searchable. The MEPD is a project within the Medaka Genome Initiative (MGI) and entries will be interconnected to integrated genomic map databases. MEPD is accessible through the WWW at http://medaka.dsp.jst.go.jp/MEPD. PMID:12519950

DOE technology information management system database study report

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

Widing, M.A.; Blodgett, D.W.; Braun, M.D.

1994-11-01

To support the missions of the US Department of Energy (DOE) Special Technologies Program, Argonne National Laboratory is defining the requirements for an automated software system that will search electronic databases on technology. This report examines the work done and results to date. Argonne studied existing commercial and government sources of technology databases in five general areas: on-line services, patent database sources, government sources, aerospace technology sources, and general technology sources. First, it conducted a preliminary investigation of these sources to obtain information on the content, cost, frequency of updates, and other aspects of their databases. The Laboratory then performedmore » detailed examinations of at least one source in each area. On this basis, Argonne recommended which databases should be incorporated in DOE`s Technology Information Management System.« less

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

PubMed

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.

Effect of audience response system technology on learning outcomes in health students and professionals: an updated systematic review.

PubMed

Atlantis, Evan; Cheema, Birinder S

2015-03-01

: Audience response system (ARS) technology is a recent innovation that is increasingly being used by health educators to improve learning outcomes. Equivocal results from previous systematic review research provide weak support for the use of ARS for improving learning outcomes at both short and long terms. This review sought to update and critically review the body of controlled experimental evidence on the use of ARS technology on learning outcomes in health students and professionals. This review searched using all identified keywords both electronic databases (CINAHL, Embase, ERIC, Medline, Science Direct, Scopus, and Web of Science) and reference lists of retrieved articles to find relevant published studies for review, from 2010 to April 2014. A descriptive synthesis of important study characteristics and effect estimates for learning outcomes was done. Three controlled trials in 321 participants from the United States were included for review. ARS knowledge retention scores were lower than the control group in one study, higher than control group provided that immediate feedback was given about each question in one study, and equivalent between intervention and control groups in another study. There is an absence of good quality evidence on effectiveness of ARS technologies for improving learning outcomes in health students and professionals.

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

PubMed Central

Gama-Castro, Socorro; Salgado, Heladia; Santos-Zavaleta, Alberto; Ledezma-Tejeida, Daniela; Muñiz-Rascado, Luis; García-Sotelo, Jair Santiago; Alquicira-Hernández, Kevin; Martínez-Flores, Irma; Pannier, Lucia; Castro-Mondragón, Jaime Abraham; Medina-Rivera, Alejandra; Solano-Lira, Hilda; Bonavides-Martínez, César; Pérez-Rueda, Ernesto; Alquicira-Hernández, Shirley; Porrón-Sotelo, Liliana; López-Fuentes, Alejandra; Hernández-Koutoucheva, Anastasia; Moral-Chávez, Víctor Del; Rinaldi, Fabio; Collado-Vides, Julio

2016-01-01

RegulonDB (http://regulondb.ccg.unam.mx) is one of the most useful and important resources on bacterial gene regulation,as it integrates the scattered scientific knowledge of the best-characterized organism, Escherichia coli K-12, in a database that organizes large amounts of data. Its electronic format enables researchers to compare their results with the legacy of previous knowledge and supports bioinformatics tools and model building. Here, we summarize our progress with RegulonDB since our last Nucleic Acids Research publication describing RegulonDB, in 2013. In addition to maintaining curation up-to-date, we report a collection of 232 interactions with small RNAs affecting 192 genes, and the complete repertoire of 189 Elementary Genetic Sensory-Response units (GENSOR units), integrating the signal, regulatory interactions, and metabolic pathways they govern. These additions represent major progress to a higher level of understanding of regulated processes. We have updated the computationally predicted transcription factors, which total 304 (184 with experimental evidence and 120 from computational predictions); we updated our position-weight matrices and have included tools for clustering them in evolutionary families. We describe our semiautomatic strategy to accelerate curation, including datasets from high-throughput experiments, a novel coexpression distance to search for ‘neighborhood’ genes to known operons and regulons, and computational developments. PMID:26527724

Mammogram segmentation using maximal cell strength updation in cellular automata.

PubMed

Anitha, J; Peter, J Dinesh

2015-08-01

Breast cancer is the most frequently diagnosed type of cancer among women. Mammogram is one of the most effective tools for early detection of the breast cancer. Various computer-aided systems have been introduced to detect the breast cancer from mammogram images. In a computer-aided diagnosis system, detection and segmentation of breast masses from the background tissues is an important issue. In this paper, an automatic segmentation method is proposed to identify and segment the suspicious mass regions of mammogram using a modified transition rule named maximal cell strength updation in cellular automata (CA). In coarse-level segmentation, the proposed method performs an adaptive global thresholding based on the histogram peak analysis to obtain the rough region of interest. An automatic seed point selection is proposed using gray-level co-occurrence matrix-based sum average feature in the coarse segmented image. Finally, the method utilizes CA with the identified initial seed point and the modified transition rule to segment the mass region. The proposed approach is evaluated over the dataset of 70 mammograms with mass from mini-MIAS database. Experimental results show that the proposed approach yields promising results to segment the mass region in the mammograms with the sensitivity of 92.25% and accuracy of 93.48%.

Recent Developments in the NIST Atomic Databases

NASA Astrophysics Data System (ADS)

Kramida, Alexander

2011-05-01

New versions of the NIST Atomic Spectra Database (ASD, v. 4.0) and three bibliographic databases (Atomic Energy Levels and Spectra, v. 2.0, Atomic Transition Probabilities, v. 9.0, and Atomic Line Broadening and Shapes, v. 3.0) have recently been released. In this contribution I will describe the main changes in the way users get the data through the Web. The contents of ASD have been significantly extended. In particular, the data on highly ionized tungsten (W III-LXXIV) have been added from a recently published NIST compilation. The tables for Fe I and Fe II have been replaced with newer, much more extensive lists (10000 lines for Fe I). The other updated or new spectra include H, D, T, He I-II, Li I-III, Be I-IV, B I-V, C I-II, N I-II, O I-II, Na I-X, K I-XIX, and Hg I. The new version of ASD now incorporates data on isotopes of several elements. I will describe some of the issues the NIST ASD Team faces when updating the data.

Recent Developments in the NIST Atomic Databases

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

Kramida, Alexander

New versions of the NIST Atomic Spectra Database (ASD, v. 4.0) and three bibliographic databases (Atomic Energy Levels and Spectra, v. 2.0, Atomic Transition Probabilities, v. 9.0, and Atomic Line Broadening and Shapes, v. 3.0) have recently been released. In this contribution I will describe the main changes in the way users get the data through the Web. The contents of ASD have been significantly extended. In particular, the data on highly ionized tungsten (W III-LXXIV) have been added from a recently published NIST compilation. The tables for Fe I and Fe II have been replaced with newer, much moremore » extensive lists (10000 lines for Fe I). The other updated or new spectra include H, D, T, He I-II, Li I-III, Be I-IV, B I-V, C I-II, N I-II, O I-II, Na I-X, K I-XIX, and Hg I. The new version of ASD now incorporates data on isotopes of several elements. I will describe some of the issues the NIST ASD Team faces when updating the data.« less

[Plug-in Based Centralized Control System in Operating Rooms].

PubMed

Wang, Yunlong

2017-05-30

Centralized equipment controls in an operating room (OR) is crucial to an efficient workflow in the OR. To achieve centralized control, an integrative OR needs to focus on designing a control panel that can appropriately incorporate equipment from different manufactures with various connecting ports and controls. Here we propose to achieve equipment integration using plug-in modules. Each OR will be equipped with a dynamic plug-in control panel containing physically removable connecting ports. Matching outlets will be installed onto the control panels of each equipment used at any given time. This dynamic control panel will be backed with a database containing plug-in modules that can connect any two types of connecting ports common among medical equipment manufacturers. The correct connecting ports will be called using reflection dynamics. This database will be updated regularly to include new connecting ports on the market, making it easy to maintain, update, expand and remain relevant as new equipment are developed. Together, the physical panel and the database will achieve centralized equipment controls in the OR that can be easily adapted to any equipment in the OR.

Using an incentive spirometer

MedlinePlus

... postoperative pulmonary complications in upper abdominal surgery. Cochrane Database Syst Rev . 2014;(2):CD006058. PMID: 24510642 www. ... ADAM Health Solutions. About MedlinePlus Site Map FAQs Customer Support Get email updates Subscribe to RSS Follow ...

Optimization-based method for automated road network extraction

DOT National Transportation Integrated Search

2001-09-18

Automated road information extraction has significant applicability in transportation. : It provides a means for creating, maintaining, and updating transportation network databases that : are needed for purposes ranging from traffic management to au...

SPECIATE Version 4.5 Database Development Documentation

EPA Science Inventory

This product updated SPECIATE 4.4 with new emission profiles to address high priority Agency data gaps and to included new, more accurate emission profiles generated by research underway within and outside the Agency.

An integrated knowledge system for wind tunnel testing - Project Engineers' Intelligent Assistant

NASA Technical Reports Server (NTRS)

Lo, Ching F.; Shi, George Z.; Hoyt, W. A.; Steinle, Frank W., Jr.

1993-01-01

The Project Engineers' Intelligent Assistant (PEIA) is an integrated knowledge system developed using artificial intelligence technology, including hypertext, expert systems, and dynamic user interfaces. This system integrates documents, engineering codes, databases, and knowledge from domain experts into an enriched hypermedia environment and was designed to assist project engineers in planning and conducting wind tunnel tests. PEIA is a modular system which consists of an intelligent user-interface, seven modules and an integrated tool facility. Hypermedia technology is discussed and the seven PEIA modules are described. System maintenance and updating is very easy due to the modular structure and the integrated tool facility provides user access to commercial software shells for documentation, reporting, or database updating. PEIA is expected to provide project engineers with technical information, increase efficiency and productivity, and provide a realistic tool for personnel training.

The Reference Genome Sequence of Saccharomyces cerevisiae: Then and Now

PubMed Central

Engel, Stacia R.; Dietrich, Fred S.; Fisk, Dianna G.; Binkley, Gail; Balakrishnan, Rama; Costanzo, Maria C.; Dwight, Selina S.; Hitz, Benjamin C.; Karra, Kalpana; Nash, Robert S.; Weng, Shuai; Wong, Edith D.; Lloyd, Paul; Skrzypek, Marek S.; Miyasato, Stuart R.; Simison, Matt; Cherry, J. Michael

2014-01-01

The genome of the budding yeast Saccharomyces cerevisiae was the first completely sequenced from a eukaryote. It was released in 1996 as the work of a worldwide effort of hundreds of researchers. In the time since, the yeast genome has been intensively studied by geneticists, molecular biologists, and computational scientists all over the world. Maintenance and annotation of the genome sequence have long been provided by the Saccharomyces Genome Database, one of the original model organism databases. To deepen our understanding of the eukaryotic genome, the S. cerevisiae strain S288C reference genome sequence was updated recently in its first major update since 1996. The new version, called “S288C 2010,” was determined from a single yeast colony using modern sequencing technologies and serves as the anchor for further innovations in yeast genomic science. PMID:24374639

The Pfam protein families database

PubMed Central

Finn, Robert D.; Mistry, Jaina; Tate, John; Coggill, Penny; Heger, Andreas; Pollington, Joanne E.; Gavin, O. Luke; Gunasekaran, Prasad; Ceric, Goran; Forslund, Kristoffer; Holm, Liisa; Sonnhammer, Erik L. L.; Eddy, Sean R.; Bateman, Alex

2010-01-01

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is ∼100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11 912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/). PMID:19920124

Extension of the sasCIF format and its applications for data processing and deposition

DOE PAGES

Kachala, Michael; Westbrook, John; Svergun, Dmitri

2016-02-01

Recent advances in small-angle scattering (SAS) experimental facilities and data analysis methods have prompted a dramatic increase in the number of users and of projects conducted, causing an upsurge in the number of objects studied, experimental data available and structural models generated. To organize the data and models and make them accessible to the community, the Task Forces on SAS and hybrid methods for the International Union of Crystallography and the Worldwide Protein Data Bank envisage developing a federated approach to SAS data and model archiving. Within the framework of this approach, the existing databases may exchange information and providemore » independent but synchronized entries to users. At present, ways of exchanging information between the various SAS databases are not established, leading to possible duplication and incompatibility of entries, and limiting the opportunities for data-driven research for SAS users. In this work, a solution is developed to resolve these issues and provide a universal exchange format for the community, based on the use of the widely adopted crystallographic information framework (CIF). The previous version of the sasCIF format, implemented as an extension of the core CIF dictionary, has been available since 2000 to facilitate SAS data exchange between laboratories. The sasCIF format has now been extended to describe comprehensively the necessary experimental information, results and models, including relevant metadata for SAS data analysis and for deposition into a database. Processing tools for these files (sasCIFtools) have been developed, and these are available both as standalone open-source programs and integrated into the SAS Biological Data Bank, allowing the export and import of data entries as sasCIF files. Software modules to save the relevant information directly from beamline data-processing pipelines in sasCIF format are also developed. Lastly, this update of sasCIF and the relevant tools are an important step in the standardization of the way SAS data are presented and exchanged, to make the results easily accessible to users and to promote further the application of SAS in the structural biology community.« less

Spatial database for a global assessment of undiscovered copper resources: Chapter Z in Global mineral resource assessment

USGS Publications Warehouse

Dicken, Connie L.; Dunlap, Pamela; Parks, Heather L.; Hammarstrom, Jane M.; Zientek, Michael L.; Zientek, Michael L.; Hammarstrom, Jane M.; Johnson, Kathleen M.

2016-07-13

As part of the first-ever U.S. Geological Survey global assessment of undiscovered copper resources, data common to several regional spatial databases published by the U.S. Geological Survey, including one report from Finland and one from Greenland, were standardized, updated, and compiled into a global copper resource database. This integrated collection of spatial databases provides location, geologic and mineral resource data, and source references for deposits, significant prospects, and areas permissive for undiscovered deposits of both porphyry copper and sediment-hosted copper. The copper resource database allows for efficient modeling on a global scale in a geographic information system (GIS) and is provided in an Esri ArcGIS file geodatabase format.

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

PubMed

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/

Cross-checking of Large Evaluated and Experimental Nuclear Reaction Databases

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

Zeydina, O.; Koning, A.J.; Soppera, N.

2014-06-15

Automated methods are presented for the verification of large experimental and evaluated nuclear reaction databases (e.g. EXFOR, JEFF, TENDL). These methods allow an assessment of the overall consistency of the data and detect aberrant values in both evaluated and experimental databases.

Image

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

Marsh, Amber; Harsch, Tim; Pitt, Julie

2007-08-31

The computer side of the IMAGE project consists of a collection of Perl scripts that perform a variety of tasks; scripts are available to insert, update and delete data from the underlying Oracle database, download data from NCBI's Genbank and other sources, and generate data files for download by interested parties. Web scripts make up the tracking interface, and various tools available on the project web-site (image.llnl.gov) that provide a search interface to the database.

Real Time Baseball Database

NASA Astrophysics Data System (ADS)

Fukue, Yasuhiro

The author describes the system outline, features and operations of "Nikkan Sports Realtime Basaball Database" which was developed and operated by Nikkan Sports Shimbun, K. K. The system enables to input numerical data of professional baseball games as they proceed simultaneously, and execute data updating at realtime, just-in-time. Other than serving as supporting tool for prepareing newspapers it is also available for broadcasting media, general users through NTT dial Q2 and others.

Phenol-Explorer 3.0: a major update of the Phenol-Explorer database to incorporate data on the effects of food processing on polyphenol content.

PubMed

Rothwell, Joseph A; Perez-Jimenez, Jara; Neveu, Vanessa; Medina-Remón, Alexander; M'hiri, Nouha; García-Lobato, Paula; Manach, Claudine; Knox, Craig; Eisner, Roman; Wishart, David S; Scalbert, Augustin

2013-01-01

Polyphenols are a major class of bioactive phytochemicals whose consumption may play a role in the prevention of a number of chronic diseases such as cardiovascular diseases, type II diabetes and cancers. Phenol-Explorer, launched in 2009, is the only freely available web-based database on the content of polyphenols in food and their in vivo metabolism and pharmacokinetics. Here we report the third release of the database (Phenol-Explorer 3.0), which adds data on the effects of food processing on polyphenol contents in foods. Data on >100 foods, covering 161 polyphenols or groups of polyphenols before and after processing, were collected from 129 peer-reviewed publications and entered into new tables linked to the existing relational design. The effect of processing on polyphenol content is expressed in the form of retention factor coefficients, or the proportion of a given polyphenol retained after processing, adjusted for change in water content. The result is the first database on the effects of food processing on polyphenol content and, following the model initially defined for Phenol-Explorer, all data may be traced back to original sources. The new update will allow polyphenol scientists to more accurately estimate polyphenol exposure from dietary surveys.

A new version of the RDP (Ribosomal Database Project)

NASA Technical Reports Server (NTRS)

Maidak, B. L.; Cole, J. R.; Parker, C. T. Jr; Garrity, G. M.; Larsen, N.; Li, B.; Lilburn, T. G.; McCaughey, M. J.; Olsen, G. J.; Overbeek, R.;

Coordination and Hydrolysis of Plutonium Ions in Aqueous Solution using Car-Parrinello Molecular Dynamics Free Energy Simulations

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

Odoh, Samuel O.; Bylaska, Eric J.; De Jong, Wibe A.

Car-Parrinello molecular dynamics (CPMD) simulations have been used to examine the hydration structures, coordination energetics and the first hydrolysis constants of Pu3+, Pu4+, PuO2+ and PuO22+ ions in aqueous solution at 300 K. The coordination numbers and structural properties of the first shell of these ions are in good agreement with available experimental estimates. The hexavalent PuO22+ species is coordinated to 5 aquo ligands while the pentavalent PuO2+ complex is coordinated to 4 aquo ligands. The Pu3+ and Pu4+ ions are both coordinated to 8 water molecules. The first hydrolysis constants obtained for Pu3+ and PuO22+ are 6.65 and 5.70more » respectively, all within 0.3 pH units of the experimental values (6.90 and 5.50 respectively). The hydrolysis constant of Pu4+, 0.17, disagrees with the value of -0.60 in the most recent update of the Nuclear Energy Agency Thermochemical Database (NEA-TDB) but supports recent experimental findings. The hydrolysis constant of PuO2+, 9.51, supports the experimental results of Bennett et al. (Radiochim. Act. 1992, 56, 15). A correlation between the pKa of the first hydrolysis reaction and the effective charge of the plutonium center was found.« less

On the Future of Thermochemical Databases, the Development of Solution Models and the Practical Use of Computational Thermodynamics in Volcanology, Geochemistry and Petrology: Can Innovations of Modern Data Science Democratize an Oligarchy?

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2014-12-01

Computational thermodynamics (CT) has now become an essential tool of petrologic and geochemical research. CT is the basis for the construction of phase diagrams, the application of geothermometers and geobarometers, the equilibrium speciation of solutions, the construction of pseudosections, calculations of mass transfer between minerals, melts and fluids, and, it provides a means of estimating materials properties for the evaluation of constitutive relations in fluid dynamical simulations. The practical application of CT to Earth science problems requires data. Data on the thermochemical properties and the equation of state of relevant materials, and data on the relative stability and partitioning of chemical elements between phases as a function of temperature and pressure. These data must be evaluated and synthesized into a self consistent collection of theoretical models and model parameters that is colloquially known as a thermodynamic database. Quantitative outcomes derived from CT reply on the existence, maintenance and integrity of thermodynamic databases. Unfortunately, the community is reliant on too few such databases, developed by a small number of research groups, and mostly under circumstances where refinement and updates to the database lag behind or are unresponsive to need. Given the increasing level of reliance on CT calculations, what is required is a paradigm shift in the way thermodynamic databases are developed, maintained and disseminated. They must become community resources, with flexible and assessable software interfaces that permit easy modification, while at the same time maintaining theoretical integrity and fidelity to the underlying experimental observations. Advances in computational and data science give us the tools and resources to address this problem, allowing CT results to be obtained at the speed of thought, and permitting geochemical and petrological intuition to play a key role in model development and calibration.

ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation.

PubMed

Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2017-01-04

The Alignable Tight Genomic Clusters (ATGCs) database is a collection of closely related bacterial and archaeal genomes that provides several tools to aid research into evolutionary processes in the microbial world. Each ATGC is a taxonomy-independent cluster of 2 or more completely sequenced genomes that meet the objective criteria of a high degree of local gene order (synteny) and a small number of synonymous substitutions in the protein-coding genes. As such, each ATGC is suited for analysis of microevolutionary variations within a cohesive group of organisms (e.g. species), whereas the entire collection of ATGCs is useful for macroevolutionary studies. The ATGC database includes many forms of pre-computed data, in particular ATGC-COGs (Clusters of Orthologous Genes), multiple sequence alignments, a set of 'index' orthologs representing the most well-conserved members of each ATGC-COG, the phylogenetic tree of the organisms within each ATGC, etc. Although the ATGC database contains several million proteins from thousands of genomes organized into hundreds of clusters (roughly a 4-fold increase since the last version of the ATGC database), it is now built with completely automated methods and will be regularly updated following new releases of the NCBI RefSeq database. The ATGC database is hosted jointly at the University of Iowa at dmk-brain.ecn.uiowa.edu/ATGC/ and the NCBI at ftp.ncbi.nlm.nih.gov/pub/kristensen/ATGC/atgc_home.html. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

[Cystic Fibrosis Cloud database: An information system for storage and management of clinical and microbiological data of cystic fibrosis patients].

PubMed

Prieto, Claudia I; Palau, María J; Martina, Pablo; Achiary, Carlos; Achiary, Andrés; Bettiol, Marisa; Montanaro, Patricia; Cazzola, María L; Leguizamón, Mariana; Massillo, Cintia; Figoli, Cecilia; Valeiras, Brenda; Perez, Silvia; Rentería, Fernando; Diez, Graciela; Yantorno, Osvaldo M; Bosch, Alejandra

2016-01-01

The epidemiological and clinical management of cystic fibrosis (CF) patients suffering from acute pulmonary exacerbations or chronic lung infections demands continuous updating of medical and microbiological processes associated with the constant evolution of pathogens during host colonization. In order to monitor the dynamics of these processes, it is essential to have expert systems capable of storing and subsequently extracting the information generated from different studies of the patients and microorganisms isolated from them. In this work we have designed and developed an on-line database based on an information system that allows to store, manage and visualize data from clinical studies and microbiological analysis of bacteria obtained from the respiratory tract of patients suffering from cystic fibrosis. The information system, named Cystic Fibrosis Cloud database is available on the http://servoy.infocomsa.com/cfc_database site and is composed of a main database and a web-based interface, which uses Servoy's product architecture based on Java technology. Although the CFC database system can be implemented as a local program for private use in CF centers, it can also be used, updated and shared by different users who can access the stored information in a systematic, practical and safe manner. The implementation of the CFC database could have a significant impact on the monitoring of respiratory infections, the prevention of exacerbations, the detection of emerging organisms, and the adequacy of control strategies for lung infections in CF patients. Copyright © 2015 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

A MATLAB toolbox for the efficient estimation of the psychometric function using the updated maximum-likelihood adaptive procedure.

PubMed

Shen, Yi; Dai, Wei; Richards, Virginia M

2015-03-01

A MATLAB toolbox for the efficient estimation of the threshold, slope, and lapse rate of the psychometric function is described. The toolbox enables the efficient implementation of the updated maximum-likelihood (UML) procedure. The toolbox uses an object-oriented architecture for organizing the experimental variables and computational algorithms, which provides experimenters with flexibility in experimental design and data management. Descriptions of the UML procedure and the UML Toolbox are provided, followed by toolbox use examples. Finally, guidelines and recommendations of parameter configurations are given.

Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation.

PubMed

Kleinboelting, Nils; Huep, Gunnar; Weisshaar, Bernd

2017-01-01

SimpleSearch provides access to a database containing information about T-DNA insertion lines of the GABI-Kat collection of Arabidopsis thaliana mutants. These mutants are an important tool for reverse genetics, and GABI-Kat is the second largest collection of such T-DNA insertion mutants. Insertion sites were deduced from flanking sequence tags (FSTs), and the database contains information about mutant plant lines as well as insertion alleles. Here, we describe improvements within the interface (available at http://www.gabi-kat.de/db/genehits.php) and with regard to the database content that have been realized in the last five years. These improvements include the integration of the Araport11 genome sequence annotation data containing the recently updated A. thaliana structural gene descriptions, an updated visualization component that displays groups of insertions with very similar insertion positions, mapped confirmation sequences, and primers. The visualization component provides a quick way to identify insertions of interest, and access to improved data about the exact structure of confirmed insertion alleles. In addition, the database content has been extended by incorporating additional insertion alleles that were detected during the confirmation process, as well as by adding new FSTs that have been produced during continued efforts to complement gaps in FST availability. Finally, the current database content regarding predicted and confirmed insertion alleles as well as primer sequences has been made available as downloadable flat files. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

[Informatics support for risk assessment and identification of preventive measures in small and micro-enterprises: occupational hazard datasheets].

PubMed

de Merich, D; Forte, Giulia

2011-01-01

Risk assessment is the fundamental process of an enterprise's prevention system and is the principal mandatory provision contained in the Health and Safety Law (Legislative Decree 81/2008) amended by Legislative Decree 106/2009. In order to properly comply with this obligation also in small-sized enterprises, the appropriate regulatory bodies should provide the enterprises with standardized tools and methods for identifying, assessing and managing risks. To assist in particular small and micro-enterprises (SMEs) with risk assessment, by providing a flexible tool that can also be standardized in the form of a datasheet, that can be updated with more detailed information on the various work contexts in Italy. Official efforts to provide Italian SMEs with information may initially make use of the findings of research conducted by ISPESL over the past 20 years, thanks in part to cooperation with other institutions (Regions, INAIL-National Insurance Institute for Occupational Accidents and Diseases), which have led to the creation of an information system on prevention consisting of numerous databases, both statistical and documental ("National System of Surveillance on fatal and serious accidents", "National System of Surveillance on work-related diseases", "Sector hazard profiles" database, "Solutions and Best Practices" database, "Technical Guidelines" database, "Training packages for prevention professionals in enterprises" database). With regard to evaluation criteria applicable within the enterprise, the possibility of combining traditional and uniform areas of assessment (by sector or by risk factor) with assessments by job/occupation has become possible thanks to the cooperation agreement made in 2009 by ISPESL, the ILO (International Labour Organisation) of Geneva and IIOSH (Israel Institute for Occupational Health and Hygiene) regarding the creation of an international Database (HDODB) based on risk datasheets per occupation. The project sets out to assist in particular small and micro-enterprises with risk assessment, providing a flexible and standardized tool in the form of a datasheet, that can be updated with more detailed information on the various work contexts in Italy. The model proposed by ISPESL selected the ILO's "Hazard Datasheet on Occupation" as an initial information tool to steer efforts to assess and manage hazards in small and micro-enterprises. In addition to being an internationally validated tool, the occupation datasheet has a very simple structure that is very effective in communicating and updating information in relation to the local context. According to the logic based on the providing support to enterprises by means of a collaborative network among institutions, local supervisory services and social partners, standardised hazard assessment procedures should be, irrespective of any legal obligations, the preferred tools of an "updatable information system" capable of providing support for the need to improve the process of assessing and managing hazards in enterprises.

NREL Opens Large Database of Inorganic Thin-Film Materials | News | NREL

Science.gov Websites

Inorganic Thin-Film Materials April 3, 2018 An extensive experimental database of inorganic thin-film Energy Laboratory (NREL) is now publicly available. The High Throughput Experimental Materials (HTEM Schroeder / NREL) "All existing experimental databases either contain many entries or have all this

Key Contact Databases - National Site for the Regional IPM Centers

Science.gov Websites

of Agriculture - National Institute of Food and Agriculture Website managed by the Southern IPM the USDA National Institute of Food and Agriculture. Last update: May 4, 2017.

13 CFR 127.604 - How will SBA process an EDWOSB or WOSB status protest?

Code of Federal Regulations, 2012 CFR

2012-01-01

... women claiming economic disadvantage and their spouses, unless the individuals and their spouses are... officer must update the Federal Procurement Data System and other procurement reporting databases to...

Validation Studies for Diet History Questionnaire II | EGRP/DCCPS/NCI/NIH

Cancer.gov

Links to validation findings from the original Diet History Questionnaire (DHQ). These findings are unlikely to be greatly modified by minimal modifications to DHQ II food list and the updated nutrient database.

40 CFR 51.370 - Compliance with recall notices.

Code of Federal Regulations, 2013 CFR

2013-07-01

... Administrator. The State shall update its list of unresolved recalls on a quarterly basis at a minimum. (2) The... database, the quality control methods used to insure that recall repairs are properly documented and...

40 CFR 51.370 - Compliance with recall notices.

Code of Federal Regulations, 2012 CFR

2012-07-01

... Administrator. The State shall update its list of unresolved recalls on a quarterly basis at a minimum. (2) The... database, the quality control methods used to insure that recall repairs are properly documented and...

40 CFR 51.370 - Compliance with recall notices.

Code of Federal Regulations, 2014 CFR

2014-07-01

... Administrator. The State shall update its list of unresolved recalls on a quarterly basis at a minimum. (2) The... database, the quality control methods used to insure that recall repairs are properly documented and...

40 CFR 51.370 - Compliance with recall notices.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Administrator. The State shall update its list of unresolved recalls on a quarterly basis at a minimum. (2) The... database, the quality control methods used to insure that recall repairs are properly documented and...

40 CFR 51.370 - Compliance with recall notices.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Administrator. The State shall update its list of unresolved recalls on a quarterly basis at a minimum. (2) The... database, the quality control methods used to insure that recall repairs are properly documented and...

Thermodynamic characterization of tandem mismatches found in naturally occurring RNA

PubMed Central

Christiansen, Martha E.; Znosko, Brent M.

2009-01-01

Although all sequence symmetric tandem mismatches and some sequence asymmetric tandem mismatches have been thermodynamically characterized and a model has been proposed to predict the stability of previously unmeasured sequence asymmetric tandem mismatches [Christiansen,M.E. and Znosko,B.M. (2008) Biochemistry, 47, 4329–4336], experimental thermodynamic data for frequently occurring tandem mismatches is lacking. Since experimental data is preferred over a predictive model, the thermodynamic parameters for 25 frequently occurring tandem mismatches were determined. These new experimental values, on average, are 1.0 kcal/mol different from the values predicted for these mismatches using the previous model. The data for the sequence asymmetric tandem mismatches reported here were then combined with the data for 72 sequence asymmetric tandem mismatches that were published previously, and the parameters used to predict the thermodynamics of previously unmeasured sequence asymmetric tandem mismatches were updated. The average absolute difference between the measured values and the values predicted using these updated parameters is 0.5 kcal/mol. This updated model improves the prediction for tandem mismatches that were predicted rather poorly by the previous model. This new experimental data and updated predictive model allow for more accurate calculations of the free energy of RNA duplexes containing tandem mismatches, and, furthermore, should allow for improved prediction of secondary structure from sequence. PMID:19509311

A review of drug-induced liver injury databases.

PubMed

Luo, Guangwen; Shen, Yiting; Yang, Lizhu; Lu, Aiping; Xiang, Zheng

2017-09-01

Drug-induced liver injuries have been a major focus of current research in drug development, and are also one of the major reasons for the failure and withdrawal of drugs in development. Drug-induced liver injuries have been systematically recorded in many public databases, which have become valuable resources in this field. In this study, we provide an overview of these databases, including the liver injury-specific databases LiverTox, LTKB, Open TG-GATEs, LTMap and Hepatox, and the general databases, T3DB, DrugBank, DITOP, DART, CTD and HSDB. The features and limitations of these databases are summarized and discussed in detail. Apart from their powerful functions, we believe that these databases can be improved in several ways: by providing the data about the molecular targets involved in liver toxicity, by incorporating information regarding liver injuries caused by drug interactions, and by regularly updating the data.

ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

PubMed

Konc, Janez; Cesnik, Tomo; Konc, Joanna Trykowska; Penca, Matej; Janežič, Dušanka

2012-02-27

ProBiS-Database is a searchable repository of precalculated local structural alignments in proteins detected by the ProBiS algorithm in the Protein Data Bank. Identification of functionally important binding regions of the protein is facilitated by structural similarity scores mapped to the query protein structure. PDB structures that have been aligned with a query protein may be rapidly retrieved from the ProBiS-Database, which is thus able to generate hypotheses concerning the roles of uncharacterized proteins. Presented with uncharacterized protein structure, ProBiS-Database can discern relationships between such a query protein and other better known proteins in the PDB. Fast access and a user-friendly graphical interface promote easy exploration of this database of over 420 million local structural alignments. The ProBiS-Database is updated weekly and is freely available online at http://probis.cmm.ki.si/database.

IPD—the Immuno Polymorphism Database

PubMed Central

Robinson, James; Halliwell, Jason A.; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G. E.

2013-01-01

The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project. PMID:23180793

Effect of display update interval, update type, and background on perception of aircraft separation on a cockpit display on traffic information

NASA Technical Reports Server (NTRS)

Jago, S.; Baty, D.; Oconnor, S.; Palmer, E.

1981-01-01

The concept of a cockpit display of traffic information (CDTI) includes the integration of air traffic, navigation, and other pertinent information in a single electronic display in the cockpit. Concise display symbology was developed for use in later full-mission simulator evaluations of the CDTI concept. Experimental variables used included the update interval motion of the aircraft, the update type, (that is, whether the two aircraft were updated at the same update interval or not), the background (grid pattern or no background), and encounter type (straight or curved). Only the type of encounter affected performance.

Heartburn in pregnancy.

PubMed

Vazquez, Juan C

2015-09-08

Heartburn is a common complaint during pregnancy; the incidence is reported to be between 17% and 45%. We conducted a systematic overview and aimed to answer the following clinical question: What are the effects of interventions to prevent or treat heartburn in pregnancy? We searched Medline, Embase, The Cochrane Library, and other important databases up to December 2014 (Clinical Evidence reviews are updated periodically; please check our website for the most up-to-date version of this review). At this update, searching of electronic databases retrieved 80 studies. After deduplication and removal of conference abstracts, 59 records were screened for inclusion in the review. Appraisal of titles and abstracts led to the exclusion of 58 studies and the further review of one full publication. The full article evaluated did not meet our reporting criteria, and thus no new evidence was added at this update. We performed a GRADE evaluation for two PICO combinations. In this systematic overview, we categorised the efficacy for six interventions, based on information about the effectiveness and safety of acid-suppressing drugs, antacids with or without alginates, raising the head of the bed, reducing caffeine intake, reducing intake of fatty foods, and reducing the size and frequency of meals.

Relational databases: a transparent framework for encouraging biology students to think informatically.

PubMed

Rice, Michael; Gladstone, William; Weir, Michael

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills.

MRNIDX - Marine Data Index: Database Description, Operation, Retrieval, and Display

USGS Publications Warehouse

Paskevich, Valerie F.

1982-01-01

A database referencing the location and content of data stored on magnetic medium was designed to assist in the indexing of time-series and spatially dependent marine geophysical data collected or processed by the U. S. Geological Survey. The database was designed and created for input to the Geologic Retrieval and Synopsis Program (GRASP) to allow selective retrievals of information pertaining to location of data, data format, cruise, geographical bounds and collection dates of data. This information is then used to locate the stored data for administrative purposes or further processing. Database utilization is divided into three distinct operations. The first is the inventorying of the data and the updating of the database, the second is the retrieval of information from the database, and the third is the graphic display of the geographical boundaries to which the retrieved information pertains.

Relational Databases: A Transparent Framework for Encouraging Biology Students To Think Informatically

PubMed Central

2004-01-01

We discuss how relational databases constitute an ideal framework for representing and analyzing large-scale genomic data sets in biology. As a case study, we describe a Drosophila splice-site database that we recently developed at Wesleyan University for use in research and teaching. The database stores data about splice sites computed by a custom algorithm using Drosophila cDNA transcripts and genomic DNA and supports a set of procedures for analyzing splice-site sequence space. A generic Web interface permits the execution of the procedures with a variety of parameter settings and also supports custom structured query language queries. Moreover, new analytical procedures can be added by updating special metatables in the database without altering the Web interface. The database provides a powerful setting for students to develop informatic thinking skills. PMID:15592597

RADS Version 4: An Efficient Way to Analyse the Multi-Mission Altimeter Database

NASA Astrophysics Data System (ADS)

Scharroo, Remko; Leuliette, Eric; Naeije, Marc; Martin-Puig, Cristina; Pires, Nelson

2016-08-01

The Radar Altimeter Database System (RADS) has grown to become a mature altimeter database. Over the last 18 years it is continuously being developed, first at Delft University of Technology, now also at the National Oceanic and Atmospheric Administration (NOAA) and the European Organisation for the Exploitation of Meteorological Satellites (EUMETSAT).RADS now serves as a fundamental Climate Data Record for sea level. Because of the multiple users involved in vetting the data and the regular updates to the database, RADS is one of the most accurate and complete databases of satellite altimeter data around.RADS version 4 is a major change from the previous version. While the database is compatible with both software versions, the new software provides new tools, allows easier expansion, and has a better and more standardised interface.

Evaluation of Online Information Sources on Alien Species in Europe: The Need of Harmonization and Integration

NASA Astrophysics Data System (ADS)

Gatto, Francesca; Katsanevakis, Stelios; Vandekerkhove, Jochen; Zenetos, Argyro; Cardoso, Ana Cristina

2013-06-01

Europe is severely affected by alien invasions, which impact biodiversity, ecosystem services, economy, and human health. A large number of national, regional, and global online databases provide information on the distribution, pathways of introduction, and impacts of alien species. The sufficiency and efficiency of the current online information systems to assist the European policy on alien species was investigated by a comparative analysis of occurrence data across 43 online databases. Large differences among databases were found which are partially explained by variations in their taxonomical, environmental, and geographical scopes but also by the variable efforts for continuous updates and by inconsistencies on the definition of "alien" or "invasive" species. No single database covered all European environments, countries, and taxonomic groups. In many European countries national databases do not exist, which greatly affects the quality of reported information. To be operational and useful to scientists, managers, and policy makers, online information systems need to be regularly updated through continuous monitoring on a country or regional level. We propose the creation of a network of online interoperable web services through which information in distributed resources can be accessed, aggregated and then used for reporting and further analysis at different geographical and political scales, as an efficient approach to increase the accessibility of information. Harmonization, standardization, conformity on international standards for nomenclature, and agreement on common definitions of alien and invasive species are among the necessary prerequisites.

Allie: a database and a search service of abbreviations and long forms.

PubMed

Yamamoto, Yasunori; Yamaguchi, Atsuko; Bono, Hidemasa; Takagi, Toshihisa

2011-01-01

Many abbreviations are used in the literature especially in the life sciences, and polysemous abbreviations appear frequently, making it difficult to read and understand scientific papers that are outside of a reader's expertise. Thus, we have developed Allie, a database and a search service of abbreviations and their long forms (a.k.a. full forms or definitions). Allie searches for abbreviations and their corresponding long forms in a database that we have generated based on all titles and abstracts in MEDLINE. When a user query matches an abbreviation, Allie returns all potential long forms of the query along with their bibliographic data (i.e. title and publication year). In addition, for each candidate, co-occurring abbreviations and a research field in which it frequently appears in the MEDLINE data are displayed. This function helps users learn about the context in which an abbreviation appears. To deal with synonymous long forms, we use a dictionary called GENA that contains domain-specific terms such as gene, protein or disease names along with their synonymic information. Conceptually identical domain-specific terms are regarded as one term, and then conceptually identical abbreviation-long form pairs are grouped taking into account their appearance in MEDLINE. To keep up with new abbreviations that are continuously introduced, Allie has an automatic update system. In addition, the database of abbreviations and their long forms with their corresponding PubMed IDs is constructed and updated weekly. Database URL: The Allie service is available at http://allie.dbcls.jp/.

NPIDB: Nucleic acid-Protein Interaction DataBase.

PubMed

Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

2013-01-01

The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

RESIS-II: An Updated Version of the Original Reservoir Sedimentation Survey Information System (RESIS) Database

USGS Publications Warehouse

Ackerman, Katherine V.; Mixon, David M.; Sundquist, Eric T.; Stallard, Robert F.; Schwarz, Gregory E.; Stewart, David W.

2009-01-01

The Reservoir Sedimentation Survey Information System (RESIS) database, originally compiled by the Soil Conservation Service (now the Natural Resources Conservation Service) in collaboration with the Texas Agricultural Experiment Station, is the most comprehensive compilation of data from reservoir sedimentation surveys throughout the conterminous United States (U.S.). The database is a cumulative historical archive that includes data from as early as 1755 and as late as 1993. The 1,823 reservoirs included in the database range in size from farm ponds to the largest U.S. reservoirs (such as Lake Mead). Results from 6,617 bathymetric surveys are available in the database. This Data Series provides an improved version of the original RESIS database, termed RESIS-II, and a report describing RESIS-II. The RESIS-II relational database is stored in Microsoft Access and includes more precise location coordinates for most of the reservoirs than the original database but excludes information on reservoir ownership. RESIS-II is anticipated to be a template for further improvements in the database.

The 2006 Kennedy Space Center Range Reference Atmosphere Model Validation Study and Sensitivity Analysis to the Performance of the National Aeronautics and Space Administration's Space Shuttle Vehicle

NASA Technical Reports Server (NTRS)

Burns, Lee; Decker, Ryan; Harrington, Brian; Merry, Carl

2008-01-01

The Kennedy Space Center (KSC) Range Reference Atmosphere (RRA) is a statistical model that summarizes wind and thermodynamic atmospheric variability from surface to 70 km. The National Aeronautics and Space Administration's (NASA) Space Shuttle program, which launches from KSC, utilizes the KSC RRA data to evaluate environmental constraints on various aspects of the vehicle during ascent. An update to the KSC RRA was recently completed. As part of the update, the Natural Environments Branch at NASA's Marshall Space Flight Center (MSFC) conducted a validation study and a comparison analysis to the existing KSC RRA database version 1983. Assessments to the Space Shuttle vehicle ascent profile characteristics were performed by JSC/Ascent Flight Design Division to determine impacts of the updated model to the vehicle performance. Details on the model updates and the vehicle sensitivity analyses with the update model are presented.

QRFXFreeze: Queryable Compressor for RFX.

PubMed

Senthilkumar, Radha; Nandagopal, Gomathi; Ronald, Daphne

2015-01-01

The verbose nature of XML has been mulled over again and again and many compression techniques for XML data have been excogitated over the years. Some of the techniques incorporate support for querying the XML database in its compressed format while others have to be decompressed before they can be queried. XML compression in which querying is directly supported instantaneously with no compromise over time is forced to compromise over space. In this paper, we propose the compressor, QRFXFreeze, which not only reduces the space of storage but also supports efficient querying. The compressor does this without decompressing the compressed XML file. The compressor supports all kinds of XML documents along with insert, update, and delete operations. The forte of QRFXFreeze is that the textual data are semantically compressed and are indexed to reduce the querying time. Experimental results show that the proposed compressor performs much better than other well-known compressors.

Enhancing GADRAS Source Term Inputs for Creation of Synthetic Spectra.

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

Horne, Steven M.; Harding, Lee

The Gamma Detector Response and Analysis Software (GADRAS) team has enhanced the source term input for the creation of synthetic spectra. These enhancements include the following: allowing users to programmatically provide source information to GADRAS through memory, rather than through a string limited to 256 characters; allowing users to provide their own source decay database information; and updating the default GADRAS decay database to fix errors and include coincident gamma information.

5S ribosomal RNA database Y2K

PubMed Central

Szymanski, Maciej; Barciszewska, Miroslawa Z.; Barciszewski, Jan; Erdmann, Volker A.

2000-01-01

This paper presents the updated version (Y2K) of the database of ribosomal 5S ribonucleic acids (5S rRNA) and their genes (5S rDNA), http://rose.man/poznan. pl/5SData/index.html . This edition of the database contains 1985 primary structures of 5S rRNA and 5S rDNA. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms. PMID:10592212

5S ribosomal RNA database Y2K.

PubMed

Szymanski, M; Barciszewska, M Z; Barciszewski, J; Erdmann, V A

2000-01-01

This paper presents the updated version (Y2K) of the database of ribosomal 5S ribonucleic acids (5S rRNA) and their genes (5S rDNA), http://rose.man/poznan.pl/5SData/index.html. This edition of the database contains 1985primary structures of 5S rRNA and 5S rDNA. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms.

The HITRAN2016 molecular spectroscopic database

NASA Astrophysics Data System (ADS)

Gordon, I. E.; Rothman, L. S.; Hill, C.; Kochanov, R. V.; Tan, Y.; Bernath, P. F.; Birk, M.; Boudon, V.; Campargue, A.; Chance, K. V.; Drouin, B. J.; Flaud, J.-M.; Gamache, R. R.; Hodges, J. T.; Jacquemart, D.; Perevalov, V. I.; Perrin, A.; Shine, K. P.; Smith, M.-A. H.; Tennyson, J.; Toon, G. C.; Tran, H.; Tyuterev, V. G.; Barbe, A.; Császár, A. G.; Devi, V. M.; Furtenbacher, T.; Harrison, J. J.; Hartmann, J.-M.; Jolly, A.; Johnson, T. J.; Karman, T.; Kleiner, I.; Kyuberis, A. A.; Loos, J.; Lyulin, O. M.; Massie, S. T.; Mikhailenko, S. N.; Moazzen-Ahmadi, N.; Müller, H. S. P.; Naumenko, O. V.; Nikitin, A. V.; Polyansky, O. L.; Rey, M.; Rotger, M.; Sharpe, S. W.; Sung, K.; Starikova, E.; Tashkun, S. A.; Auwera, J. Vander; Wagner, G.; Wilzewski, J.; Wcisło, P.; Yu, S.; Zak, E. J.

2017-12-01

This paper describes the contents of the 2016 edition of the HITRAN molecular spectroscopic compilation. The new edition replaces the previous HITRAN edition of 2012 and its updates during the intervening years. The HITRAN molecular absorption compilation is composed of five major components: the traditional line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, infrared absorption cross-sections for molecules not yet amenable to representation in a line-by-line form, collision-induced absorption data, aerosol indices of refraction, and general tables such as partition sums that apply globally to the data. The new HITRAN is greatly extended in terms of accuracy, spectral coverage, additional absorption phenomena, added line-shape formalisms, and validity. Moreover, molecules, isotopologues, and perturbing gases have been added that address the issues of atmospheres beyond the Earth. Of considerable note, experimental IR cross-sections for almost 300 additional molecules important in different areas of atmospheric science have been added to the database. The compilation can be accessed through www.hitran.org. Most of the HITRAN data have now been cast into an underlying relational database structure that offers many advantages over the long-standing sequential text-based structure. The new structure empowers the user in many ways. It enables the incorporation of an extended set of fundamental parameters per transition, sophisticated line-shape formalisms, easy user-defined output formats, and very convenient searching, filtering, and plotting of data. A powerful application programming interface making use of structured query language (SQL) features for higher-level applications of HITRAN is also provided.

A novel association rule mining approach using TID intermediate itemset.

PubMed

Aqra, Iyad; Herawan, Tutut; Abdul Ghani, Norjihan; Akhunzada, Adnan; Ali, Akhtar; Bin Razali, Ramdan; Ilahi, Manzoor; Raymond Choo, Kim-Kwang

2018-01-01

Designing an efficient association rule mining (ARM) algorithm for multilevel knowledge-based transactional databases that is appropriate for real-world deployments is of paramount concern. However, dynamic decision making that needs to modify the threshold either to minimize or maximize the output knowledge certainly necessitates the extant state-of-the-art algorithms to rescan the entire database. Subsequently, the process incurs heavy computation cost and is not feasible for real-time applications. The paper addresses efficiently the problem of threshold dynamic updation for a given purpose. The paper contributes by presenting a novel ARM approach that creates an intermediate itemset and applies a threshold to extract categorical frequent itemsets with diverse threshold values. Thus, improving the overall efficiency as we no longer needs to scan the whole database. After the entire itemset is built, we are able to obtain real support without the need of rebuilding the itemset (e.g. Itemset list is intersected to obtain the actual support). Moreover, the algorithm supports to extract many frequent itemsets according to a pre-determined minimum support with an independent purpose. Additionally, the experimental results of our proposed approach demonstrate the capability to be deployed in any mining system in a fully parallel mode; consequently, increasing the efficiency of the real-time association rules discovery process. The proposed approach outperforms the extant state-of-the-art and shows promising results that reduce computation cost, increase accuracy, and produce all possible itemsets.

A novel association rule mining approach using TID intermediate itemset

PubMed Central

Ali, Akhtar; Bin Razali, Ramdan; Ilahi, Manzoor; Raymond Choo, Kim-Kwang

2018-01-01

Designing an efficient association rule mining (ARM) algorithm for multilevel knowledge-based transactional databases that is appropriate for real-world deployments is of paramount concern. However, dynamic decision making that needs to modify the threshold either to minimize or maximize the output knowledge certainly necessitates the extant state-of-the-art algorithms to rescan the entire database. Subsequently, the process incurs heavy computation cost and is not feasible for real-time applications. The paper addresses efficiently the problem of threshold dynamic updation for a given purpose. The paper contributes by presenting a novel ARM approach that creates an intermediate itemset and applies a threshold to extract categorical frequent itemsets with diverse threshold values. Thus, improving the overall efficiency as we no longer needs to scan the whole database. After the entire itemset is built, we are able to obtain real support without the need of rebuilding the itemset (e.g. Itemset list is intersected to obtain the actual support). Moreover, the algorithm supports to extract many frequent itemsets according to a pre-determined minimum support with an independent purpose. Additionally, the experimental results of our proposed approach demonstrate the capability to be deployed in any mining system in a fully parallel mode; consequently, increasing the efficiency of the real-time association rules discovery process. The proposed approach outperforms the extant state-of-the-art and shows promising results that reduce computation cost, increase accuracy, and produce all possible itemsets. PMID:29351287

Systematic review of interventions to improve prescribing.

PubMed

Ostini, Remo; Hegney, Desley; Jackson, Claire; Williamson, Margaret; Mackson, Judith M; Gurman, Karin; Hall, Wayne; Tett, Susan E

2009-03-01

To update 2 comprehensive reviews of systematic reviews on prescribing interventions and identify the latest evidence about the effectiveness of the interventions. Systematic searches for English-language reports of experimental and quasi-experimental research were conducted in PubMed (1951-May 2007), EMBASE (1974-March 2008), International Pharmaceutical Abstracts (1970-March 2008), and 11 other bibliographic databases of medical, social science, and business research. Following an initial title screening process and after selecting 6 specific intervention categories (identified from the previous reviews) in community settings, 2 reviewers independently assessed abstracts and then full studies for relevance and quality and extracted relevant data using formal assessment and data extraction tools. Results were then methodically incorporated into the findings of the 2 earlier reviews of systematic reviews. DATA SELECTION AND SYNTHESIS: Twenty-nine of 26,314 articles reviewed were assessed to be of relevant, high-quality research. Audit and feedback, together with educational outreach visits, were the focus of the majority of recent, high-quality research into prescribing interventions. These interventions were also the most effective in improving prescribing practice. A smaller number of studies included a patient-mediated intervention; this intervention was not consistently effective. There is insufficient recent research into manual reminders to confidently update earlier reviews and there remains insufficient evidence to draw conclusions regarding the effectiveness of local consensus processes or multidisciplinary teams. Educational outreach as well as audit and feedback continue to dominate research into prescribing interventions. These 2 prescribing interventions also most consistently show positive results. Much less research is conducted into other types of interventions and there is still very little effort to systematically test why interventions do or do not work.

IPM Databases - National Site for the Regional IPM Centers

Science.gov Websites

Pesticide Information United States Department of Agriculture - National Institute of Food and Agriculture . Regional IPM Centers are sponsored by the USDA National Institute of Food and Agriculture. Last update

Flight movement inventory : SAGE-AERO2K

DOT National Transportation Integrated Search

2004-04-28

A global air traffic emissions database is an essential tool for both policy makers and climate change : scientists. Since the last comprehensive aircraft emissions inventories were developed in 1992, an : update is necessary. This need is being addr...

Software Update.

ERIC Educational Resources Information Center

Currents, 2000

2000-01-01

A chart of 40 alumni-development database systems provides information on vendor/Web site, address, contact/phone, software name, price range, minimum suggested workstation/suggested server, standard reports/reporting tools, minimum/maximum record capacity, and number of installed sites/client type. (DB)

DynAstVO : a Europlanet database of NEA orbits

NASA Astrophysics Data System (ADS)

Desmars, J.; Thuillot, W.; Hestroffer, D.; David, P.; Le Sidaner, P.

2017-09-01

DynAstVO is a new orbital database developed within the Europlanet 2020 RI and the Virtual European Solar and Planetary Access (VESPA) frameworks. The database is dedicated to Near-Earth asteroids and provide parameters related to orbits: osculating elements, observational information, ephemeris through SPICE kernel, and in particular, orbit uncertainty and associated covariance matrix. DynAstVO is daily updated on a automatic process of orbit determination on the basis of the Minor Planet Electronic Circulars that reports new observations or the discover of a new asteroid. This database conforms to EPN-TAP environment and is accessible through VO protocols and on the VESPA portal web access (http://vespa.obspm.fr/). A comparison with other classical databases such as Astorb, MPCORB, NEODyS and JPL is also presented.

Construction of In-house Databases in a Corporation

NASA Astrophysics Data System (ADS)

Kato, Toshio

Osaka Gas Co., Ltd. constructed Osaka Gas Technical Information System (OGTIS) in 1979, which stores and retrieves the in-house technical information and provides even primary materials by unifying optical disk files, facsimile system and so on. The major information sources are technical materials, survey materials, planning documents, design materials, research reports, business tour reports which are all generated inside the Company. At the present moment it amounts to 25,000 items in total adding 1,000 items annually. The data file is updated once in a month and also outputs the abstract journal OGTIS Report monthly. In 1983 it constructed System for International Exchange of Personal Information (SIP) as a subsystem of OGTIS in order to compile SIP database which covers exchange outlines with oversea enterprises or organizations. The data size is 2,600 totally adding about 500 annually with monthly data updating.

Quality assurance for the query and distribution systems of the RCSB Protein Data Bank

PubMed Central

Bluhm, Wolfgang F.; Beran, Bojan; Bi, Chunxiao; Dimitropoulos, Dimitris; Prlić, Andreas; Quinn, Gregory B.; Rose, Peter W.; Shah, Chaitali; Young, Jasmine; Yukich, Benjamin; Berman, Helen M.; Bourne, Philip E.

2011-01-01

The RCSB Protein Data Bank (RCSB PDB, www.pdb.org) is a key online resource for structural biology and related scientific disciplines. The website is used on average by 165 000 unique visitors per month, and more than 2000 other websites link to it. The amount and complexity of PDB data as well as the expectations on its usage are growing rapidly. Therefore, ensuring the reliability and robustness of the RCSB PDB query and distribution systems are crucially important and increasingly challenging. This article describes quality assurance for the RCSB PDB website at several distinct levels, including: (i) hardware redundancy and failover, (ii) testing protocols for weekly database updates, (iii) testing and release procedures for major software updates and (iv) miscellaneous monitoring and troubleshooting tools and practices. As such it provides suggestions for how other websites might be operated. Database URL: www.pdb.org PMID:21382834

DockoMatic: automated peptide analog creation for high throughput virtual screening.

PubMed

Jacob, Reed B; Bullock, Casey W; Andersen, Tim; McDougal, Owen M

2011-10-01

The purpose of this manuscript is threefold: (1) to describe an update to DockoMatic that allows the user to generate cyclic peptide analog structure files based on protein database (pdb) files, (2) to test the accuracy of the peptide analog structure generation utility, and (3) to evaluate the high throughput capacity of DockoMatic. The DockoMatic graphical user interface interfaces with the software program Treepack to create user defined peptide analogs. To validate this approach, DockoMatic produced cyclic peptide analogs were tested for three-dimensional structure consistency and binding affinity against four experimentally determined peptide structure files available in the Research Collaboratory for Structural Bioinformatics database. The peptides used to evaluate this new functionality were alpha-conotoxins ImI, PnIA, and their published analogs. Peptide analogs were generated by DockoMatic and tested for their ability to bind to X-ray crystal structure models of the acetylcholine binding protein originating from Aplysia californica. The results, consisting of more than 300 simulations, demonstrate that DockoMatic predicts the binding energy of peptide structures to within 3.5 kcal mol(-1), and the orientation of bound ligand compares to within 1.8 Å root mean square deviation for ligand structures as compared to experimental data. Evaluation of high throughput virtual screening capacity demonstrated that Dockomatic can collect, evaluate, and summarize the output of 10,000 AutoDock jobs in less than 2 hours of computational time, while 100,000 jobs requires approximately 15 hours and 1,000,000 jobs is estimated to take up to a week. Copyright © 2011 Wiley Periodicals, Inc.

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments.

PubMed

Zhou, Bailing; Zhao, Huiying; Yu, Jiafeng; Guo, Chengang; Dou, Xianghua; Song, Feng; Hu, Guodong; Cao, Zanxia; Qu, Yuanxu; Yang, Yuedong; Zhou, Yaoqi; Wang, Jihua

2018-01-04

Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases or interactions). Thus, it is highly desirable to have a comprehensive dataset for experimentally validated lncRNAs as a central repository for all of their structures, functions and phenotypes. Here, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to 1 May 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species that is 2.9 times larger than the current largest database for experimentally validated lncRNAs. Seventy-four percent lncRNA entries are partially or completely new, comparing to all existing experimentally validated databases. The established database allows users to browse, search and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments

PubMed Central

Zhao, Huiying; Yu, Jiafeng; Guo, Chengang; Dou, Xianghua; Song, Feng; Hu, Guodong; Cao, Zanxia; Qu, Yuanxu

2018-01-01

Abstract Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases or interactions). Thus, it is highly desirable to have a comprehensive dataset for experimentally validated lncRNAs as a central repository for all of their structures, functions and phenotypes. Here, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to 1 May 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species that is 2.9 times larger than the current largest database for experimentally validated lncRNAs. Seventy-four percent lncRNA entries are partially or completely new, comparing to all existing experimentally validated databases. The established database allows users to browse, search and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs. PMID:28985416