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Sample records for comprehensive database including

  1. The comprehensive peptaibiotics database.

    PubMed

    Stoppacher, Norbert; Neumann, Nora K N; Burgstaller, Lukas; Zeilinger, Susanne; Degenkolb, Thomas; Brückner, Hans; Schuhmacher, Rainer

    2013-05-01

    Peptaibiotics are nonribosomally biosynthesized peptides, which - according to definition - contain the marker amino acid α-aminoisobutyric acid (Aib) and possess antibiotic properties. Being known since 1958, a constantly increasing number of peptaibiotics have been described and investigated with a particular emphasis on hypocrealean fungi. Starting from the existing online 'Peptaibol Database', first published in 1997, an exhaustive literature survey of all known peptaibiotics was carried out and resulted in a list of 1043 peptaibiotics. The gathered information was compiled and used to create the new 'The Comprehensive Peptaibiotics Database', which is presented here. The database was devised as a software tool based on Microsoft (MS) Access. It is freely available from the internet at http://peptaibiotics-database.boku.ac.at and can easily be installed and operated on any computer offering a Windows XP/7 environment. It provides useful information on characteristic properties of the peptaibiotics included such as peptide category, group name of the microheterogeneous mixture to which the peptide belongs, amino acid sequence, sequence length, producing fungus, peptide subfamily, molecular formula, and monoisotopic mass. All these characteristics can be used and combined for automated search within the database, which makes The Comprehensive Peptaibiotics Database a versatile tool for the retrieval of valuable information about peptaibiotics. Sequence data have been considered as to December 14, 2012.

  2. SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions

    PubMed Central

    Preissner, Saskia; Kroll, Katharina; Dunkel, Mathias; Senger, Christian; Goldsobel, Gady; Kuzman, Daniel; Guenther, Stefan; Winnenburg, Rainer; Schroeder, Michael; Preissner, Robert

    2010-01-01

    Much of the information on the Cytochrome P450 enzymes (CYPs) is spread across literature and the internet. Aggregating knowledge about CYPs into one database makes the search more efficient. Text mining on 57 CYPs and drugs led to a mass of papers, which were screened manually for facts about metabolism, SNPs and their effects on drug degradation. Information was put into a database, which enables the user not only to look up a particular CYP and all metabolized drugs, but also to check tolerability of drug-cocktails and to find alternative combinations, to use metabolic pathways more efficiently. The SuperCYP database contains 1170 drugs with more than 3800 interactions including references. Approximately 2000 SNPs and mutations are listed and ordered according to their effect on expression and/or activity. SuperCYP (http://bioinformatics.charite.de/supercyp) is a comprehensive resource focused on CYPs and drug metabolism. Homology-modeled structures of the CYPs can be downloaded in PDB format and related drugs are available as MOL-files. Within the resource, CYPs can be aligned with each other, drug-cocktails can be ‘mixed’, SNPs, protein point mutations, and their effects can be viewed and corresponding PubMed IDs are given. SuperCYP is meant to be a platform and a starting point for scientists and health professionals for furthering their research. PMID:19934256

  3. Comprehensive Database Service : ACE

    NASA Astrophysics Data System (ADS)

    Hiroki, Morio; Abe, Tetsuya

    The Data base, ACE commercialized by Chunichi Shimbun in Feb. 1986, aims at covering not only newspaper articles but also the other information which composes different data bases. This paper introduces newspaper articles, new material information and character information which are included in ACE. The content of ACE, how to use the online service, and future subjects are described.

  4. FPD: A comprehensive phosphorylation database in fungi.

    PubMed

    Bai, Youhuang; Chen, Bin; Li, Mingzhu; Zhou, Yincong; Ren, Silin; Xu, Qin; Chen, Ming; Wang, Shihua

    2017-10-01

    Protein phosphorylation, one of the most classic post-translational modification, plays a critical role in diverse cellular processes including cell cycle, growth, and signal transduction pathways. However, the available information about phosphorylation in fungi is limited. Here, we provided a Fungi Phosphorylation Database (FPD) that comprises high-confidence in vivo phosphosites identified by MS-based proteomics in various fungal species. This comprehensive phosphorylation database contains 62 272 non-redundant phosphorylation sites in 11 222 proteins across eight organisms, including Aspergillus flavus, Aspergillus nidulans, Fusarium graminearum, Magnaporthe oryzae, Neurospora crassa, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Cryptococcus neoformans. A fungi-specific phosphothreonine motif and several conserved phosphorylation motifs were discovered by comparatively analysing the pattern of phosphorylation sites in plants, animals, and fungi. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  5. Consistency, comprehensiveness, and compatibility of pathway databases

    PubMed Central

    2010-01-01

    Background It is necessary to analyze microarray experiments together with biological information to make better biological inferences. We investigate the adequacy of current biological databases to address this need. Description Our results show a low level of consistency, comprehensiveness and compatibility among three popular pathway databases (KEGG, Ingenuity and Wikipathways). The level of consistency for genes in similar pathways across databases ranges from 0% to 88%. The corresponding level of consistency for interacting genes pairs is 0%-61%. These three original sources can be assumed to be reliable in the sense that the interacting gene pairs reported in them are correct because they are curated. However, the lack of concordance between these databases suggests each source has missed out many genes and interacting gene pairs. Conclusions Researchers will hence find it challenging to obtain consistent pathway information out of these diverse data sources. It is therefore critical to enable them to access these sources via a consistent, comprehensive and unified pathway API. We accumulated sufficient data to create such an aggregated resource with the convenience of an API to access its information. This unified resource can be accessed at http://www.pathwayapi.com. PMID:20819233

  6. Comprehensive database of Manufactured Gas Plant tars. Part A. Database.

    PubMed

    Gallacher, Christopher; Thomas, Russell; Lord, Richard; Kalin, Robert M; Taylor, Chris

    2017-08-15

    Coal tars are a mixture of organic and inorganic compounds that were by-products from the manufactured gas and coke making industries. Different manufacturing processes have resulted in the production of distinctly different tar compositions. This study presents a comprehensive database of compounds produced using two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GCxGC/TOFMS), analysing 16 tar samples produced by five distinct production processes. Samples of coal tar were extracted using accelerated solvent extraction (ASE) and derivatised post-extraction using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS). The derivatised samples were analysed using two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GCxGC/TOFMS). A total of 16 tar samples originating from five different production processes: Low Temperature Horizontal Retorts, Horizontal Retorts, Vertical Retorts, Carbureted Water Gas and Coke Ovens, were analysed. A total of 2369 unique compounds were detected with 948 aromatic compounds, 196 aliphatic compounds, 380 sulfur-containing compounds, 209 oxygen-containing compounds, 262 nitrogen-containing compounds and 15 mixed heterocycles. Derivatisation allowed the detection of 359 unique compounds, the majority in the form of hydroxylated polycyclic aromatic hydrocarbons, many of which would not have been detected without derivatisation. Of the 2369 unique compounds detected, 173 were found to be present within all samples. A unique comprehensive database of compounds detected within 16 tar samples from five different production processes was produced. The 173 compounds identified within every sample may be of particular importance from a regulatory standpoint. This initial study indicates that different production processes produce tars with different chemical signatures and it can be further expanded upon by in-depth analysis of the different compound

  7. Comprehensive BRL-CAD Primitive Database

    DTIC Science & Technology

    2015-03-01

    such a database would be useful for training purposes , its most important use would be for regression testing. For example, with a single database ......BRL–CAD Primitive Database Mitchell Roberts Survivability/Lethality Analysis Directorate, ARL

  8. Generation of Comprehensive Thoracic Oncology Database - Tool for Translational Research

    PubMed Central

    Surati, Mosmi; Robinson, Matthew; Nandi, Suvobroto; Faoro, Leonardo; Demchuk, Carley; Kanteti, Rajani; Ferguson, Benjamin; Gangadhar, Tara; Hensing, Thomas; Hasina, Rifat; Husain, Aliya; Ferguson, Mark; Karrison, Theodore; Salgia, Ravi

    2011-01-01

    The Thoracic Oncology Program Database Project was created to serve as a comprehensive, verified, and accessible repository for well-annotated cancer specimens and clinical data to be available to researchers within the Thoracic Oncology Research Program. This database also captures a large volume of genomic and proteomic data obtained from various tumor tissue studies. A team of clinical and basic science researchers, a biostatistician, and a bioinformatics expert was convened to design the database. Variables of interest were clearly defined and their descriptions were written within a standard operating manual to ensure consistency of data annotation. Using a protocol for prospective tissue banking and another protocol for retrospective banking, tumor and normal tissue samples from patients consented to these protocols were collected. Clinical information such as demographics, cancer characterization, and treatment plans for these patients were abstracted and entered into an Access database. Proteomic and genomic data have been included in the database and have been linked to clinical information for patients described within the database. The data from each table were linked using the relationships function in Microsoft Access to allow the database manager to connect clinical and laboratory information during a query. The queried data can then be exported for statistical analysis and hypothesis generation. PMID:21304468

  9. 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

  10. 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.

  11. 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.

  12. Comprehension of drug toxicity: software and databases.

    PubMed

    Toropov, Andrey A; Toropova, Alla P; Raska, Ivan; Leszczynska, Danuta; Leszczynski, Jerzy

    2014-02-01

    Quantitative structure-property/activity relationships (QSPRs/QSARs) are a tool (in silico) to rapidly predict various endpoints in general, and drug toxicity in particular. However, this dynamic evolution of experimental data (expansion of existing experimental data on drugs toxicity) leads to the problem of critical estimation of the data. The carcinogenicity, mutagenicity, liver effects and cardiac toxicity should be evaluated as the most important aspects of the drug toxicity. The toxicity is a multidimensional phenomenon. It is apparent that the main reasons for the increase in applications of in silico prediction of toxicity include the following: (i) the need to reduce animal testing; (ii) computational models provide reliable toxicity prediction; (iii) development of legislation that is related to use of new substances; (iv) filling data gaps; (v) reduction of cost and time; (vi) designing of new compounds; (vii) advancement of understanding of biology and chemistry. This mini-review provides analysis of existing databases and software which are necessary for use of robust computational assessments and robust prediction of potential drug toxicities by means of in silico methods. © 2013 Published by Elsevier Ltd.

  13. A comprehensive database of Martian landslides

    NASA Astrophysics Data System (ADS)

    Battista Crosta, Giovanni; Vittorio De Blasio, Fabio; Frattini, Paolo; Valbuzzi, Elena

    2016-04-01

    During a long-term project, we have identified and classified a large number (> 3000) of Martian landslides especially but not exclusively from Valles Marineris. This database provides a more complete basis for a statistical study of landslides on Mars and its relationship with geographical and environmental conditions. Landslides have been mapped according to standard geomorphological criteria, delineating both the landslide scar and accumulation limits, associating each scarp to a deposit, and using the program ArcGis for generation of a complete digital dataset. Multiple accumulations from the same source area or from different sources have been differentiated, where possible, to obtain a more complete dataset and to allow more refined analyses. Each landslide has been classified according to a set of criteria including: type, degree of confinement, possible trigger, elevation with respect to datum, geomorphological features, degree of multiplicity, and so on. The runout, fall height, and volume have been measured for each deposit. In fact, the database is revealing a series of trends that may assist at understanding landform processes on Mars and its past climatic conditions. One of the most interesting aspects of our dataset is the presence of a population of landslides whose particularly long mobility deviates from average behavior. While some landslides have travelled unimpeded on a usually flat area, others have travelled against obstacles or mounds. Therefore, landslides are also studied in relation to i) morphologies created by the landslide itself, ii) presence of mounds, barriers or elevations than have affected the movement of the landslide mass. In some extreme cases, the landslide was capable of travelling for several tens of km along the whole valley and upon reaching the opposite side it travelled upslope for several hundreds of meters, which is indication of high travelling speed. In other cases, the high speed is revealed by dynamic deformations

  14. Dynameomics: A comprehensive database of protein dynamics

    PubMed Central

    van der Kamp, Marc W.; Schaeffer, Richard D.; Jonsson, Amanda L.; Scouras, Alexander D.; Simms, Andrew; Toofanny, Rudesh D.; Benson, Noah C.; Anderson, Peter C.; Merkley, Eric D.; Rysavy, Steve; Bromley, Denny; Beck, David A. C.; Daggett, Valerie

    2010-01-01

    Summary The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 1000 proteins, representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through www.dynameomics.org. PMID:20399180

  15. The peptaibiotics database--a comprehensive online resource.

    PubMed

    Neumann, Nora K N; Stoppacher, Norbert; Zeilinger, Susanne; Degenkolb, Thomas; Brückner, Hans; Schuhmacher, Rainer

    2015-05-01

    In this work, we present the 'Peptaibiotics Database' (PDB), a comprehensive online resource, which intends to cover all Aib-containing non-ribosomal fungal peptides currently described in scientific literature. This database shall extend and update the recently published 'Comprehensive Peptaibiotics Database' and currently consists of 1,297 peptaibiotic sequences. In a literature survey, a total of 235 peptaibiotic sequences published between January 2013 and June 2014 have been compiled, and added to the list of 1,062 peptides in the recently published 'Comprehensive Peptaibiotics Database'. The presented database is intended as a public resource freely accessible to the scientific community at peptaibiotics-database.boku.ac.at. The search options of the previously published repository and the presentation of sequence motif searches have been extended significantly. All of the available search options can be combined to create complex database queries. As a public repository, the presented database enables the easy upload of new peptaibiotic sequences or the correction of existing informations. In addition, an administrative interface for maintenance of the content of the database has been implemented, and the design of the database can be easily extended to store additional information to accommodate future needs of the 'peptaibiomics community'.

  16. Computerized comprehensive data analysis of Lung Imaging Database Consortium (LIDC)

    PubMed Central

    Tan, Jun; Pu, Jiantao; Zheng, Bin; Wang, Xingwei; Leader, Joseph K.

    2010-01-01

    Purpose: Lung Image Database Consortium (LIDC) is the largest public CT image database of lung nodules. In this study, the authors present a comprehensive and the most updated analysis of this dynamically growing database under the help of a computerized tool, aiming to assist researchers to optimally use this database for lung cancer related investigations. Methods: The authors developed a computer scheme to automatically match the nodule outlines marked manually by radiologists on CT images. A large variety of characteristics regarding the annotated nodules in the database including volume, spiculation level, elongation, interobserver variability, as well as the intersection of delineated nodule voxels and overlapping ratio between the same nodules marked by different radiologists are automatically calculated and summarized. The scheme was applied to analyze all 157 examinations with complete annotation data currently available in LIDC dataset. Results: The scheme summarizes the statistical distributions of the abovementioned geometric and diagnosis features. Among the 391 nodules, (1) 365 (93.35%) have principal axis length ≤20 mm; (2) 120, 75, 76, and 120 were marked by one, two, three, and four radiologists, respectively; and (3) 122 (32.48%) have the maximum volume overlapping ratios ≥80% for the delineations of two radiologists, while 198 (50.64%) have the maximum volume overlapping ratios <60%. The results also showed that 72.89% of the nodules were assessed with malignancy score between 2 and 4, and only 7.93% of these nodules were considered as severely malignant (malignancy ≥4). Conclusions: This study demonstrates that LIDC contains examinations covering a diverse distribution of nodule characteristics and it can be a useful resource to assess the performance of the nodule detection and∕or segmentation schemes. PMID:20831088

  17. iRootHair: a comprehensive root hair genomics database.

    PubMed

    Kwasniewski, Miroslaw; Nowakowska, Urszula; Szumera, Jakub; Chwialkowska, Karolina; Szarejko, Iwona

    2013-01-01

    The specialized root epidermis cells of higher plants produce long, tubular outgrowths called root hairs. Root hairs play an important role in nutrient and water uptake, and they serve as a valuable model in studies of plant cell morphogenesis. More than 1,300 articles that describe the biological processes of these unique cells have been published to date. As new fields of root hair research are emerging, the number of new papers published each year and the volumes of new relevant data are continuously increasing. Therefore, there is a general need to facilitate studies on root hair biology by collecting, presenting, and sharing the available information in a systematic, curated manner. Consequently, in this paper, we present a comprehensive database of root hair genomics, iRootHair, which is accessible as a Web-based service. The current version of the database includes information about 153 root hair-related genes that have been identified to date in dicots and monocots along with their putative orthologs in higher plants with sequenced genomes. In order to facilitate the use of the iRootHair database, it is subdivided into interrelated, searchable sections that describe genes, processes of root hair formation, root hair mutants, and available references. The database integrates bioinformatics tools with a focus on sequence identification and annotation. iRootHair is a unique resource for root hair research that integrates the large volume of data related to root hair genomics in a single, curated, and expandable database that is freely available at www.iroothair.org.

  18. Computerized comprehensive data analysis of Lung Imaging Database Consortium (LIDC)

    SciTech Connect

    Tan Jun; Pu Jiantao; Zheng Bin; Wang Xingwei; Leader, Joseph K.

    2010-07-15

    Purpose: Lung Image Database Consortium (LIDC) is the largest public CT image database of lung nodules. In this study, the authors present a comprehensive and the most updated analysis of this dynamically growing database under the help of a computerized tool, aiming to assist researchers to optimally use this database for lung cancer related investigations. Methods: The authors developed a computer scheme to automatically match the nodule outlines marked manually by radiologists on CT images. A large variety of characteristics regarding the annotated nodules in the database including volume, spiculation level, elongation, interobserver variability, as well as the intersection of delineated nodule voxels and overlapping ratio between the same nodules marked by different radiologists are automatically calculated and summarized. The scheme was applied to analyze all 157 examinations with complete annotation data currently available in LIDC dataset. Results: The scheme summarizes the statistical distributions of the abovementioned geometric and diagnosis features. Among the 391 nodules, (1) 365 (93.35%) have principal axis length {<=}20 mm; (2) 120, 75, 76, and 120 were marked by one, two, three, and four radiologists, respectively; and (3) 122 (32.48%) have the maximum volume overlapping ratios {>=}80% for the delineations of two radiologists, while 198 (50.64%) have the maximum volume overlapping ratios <60%. The results also showed that 72.89% of the nodules were assessed with malignancy score between 2 and 4, and only 7.93% of these nodules were considered as severely malignant (malignancy {>=}4). Conclusions: This study demonstrates that LIDC contains examinations covering a diverse distribution of nodule characteristics and it can be a useful resource to assess the performance of the nodule detection and/or segmentation schemes.

  19. RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers

    PubMed Central

    Thodima, Venkata; Pirooznia, Mehdi; Deng, Youping

    2006-01-01

    Background Catalytic RNA molecules are called ribozymes. The aptamers are DNA or RNA molecules that have been selected from vast populations of random sequences, through a combinatorial approach known as SELEX. The selected oligo-nucleotide sequences (~200 bp in length) have the ability to recognize a broad range of specific ligands by forming binding pockets. These novel aptamer sequences can bind to nucleic acids, proteins or small organic and inorganic chemical compounds and have many potential uses in medicine and technology. Results The comprehensive sequence information on aptamers and ribozymes that have been generated by in vitro selection methods are included in this RiboaptDB database. Such types of unnatural data generated by in vitro methods are not available in the public 'natural' sequence databases such as GenBank and EMBL. The amount of sequence data generated by in vitro selection experiments has been accumulating exponentially. There are 370 artificial ribozyme sequences and 3842 aptamer sequences in the total 4212 sequences from 423 citations in this RiboaptDB. We included general search feature, and individual feature wise search, user submission form for new data through online and also local BLAST search. Conclusion This database, besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility in medicine, provides valuable information for computational and theoretical biologists. The RiboaptDB is extremely useful for garnering information about in vitro selection experiments as a whole and for better understanding the distribution of functional nucleic acids in sequence space. The database is updated regularly and is publicly available at . PMID:17118149

  20. Development of a Comprehensive Database System for Safety Analyst

    PubMed Central

    Paz, Alexander; Veeramisti, Naveen; Khanal, Indira; Baker, Justin; de la Fuente-Mella, Hanns

    2015-01-01

    This study addressed barriers associated with the use of Safety Analyst, a state-of-the-art tool that has been developed to assist during the entire Traffic Safety Management process but that is not widely used due to a number of challenges as described in this paper. As part of this study, a comprehensive database system and tools to provide data to multiple traffic safety applications, with a focus on Safety Analyst, were developed. A number of data management tools were developed to extract, collect, transform, integrate, and load the data. The system includes consistency-checking capabilities to ensure the adequate insertion and update of data into the database. This system focused on data from roadways, ramps, intersections, and traffic characteristics for Safety Analyst. To test the proposed system and tools, data from Clark County, which is the largest county in Nevada and includes the cities of Las Vegas, Henderson, Boulder City, and North Las Vegas, was used. The database and Safety Analyst together help identify the sites with the potential for safety improvements. Specifically, this study examined the results from two case studies. The first case study, which identified sites having a potential for safety improvements with respect to fatal and all injury crashes, included all roadway elements and used default and calibrated Safety Performance Functions (SPFs). The second case study identified sites having a potential for safety improvements with respect to fatal and all injury crashes, specifically regarding intersections; it used default and calibrated SPFs as well. Conclusions were developed for the calibration of safety performance functions and the classification of site subtypes. Guidelines were provided about the selection of a particular network screening type or performance measure for network screening. PMID:26167531

  1. Development of a Comprehensive Database System for Safety Analyst.

    PubMed

    Paz, Alexander; Veeramisti, Naveen; Khanal, Indira; Baker, Justin; de la Fuente-Mella, Hanns

    2015-01-01

    This study addressed barriers associated with the use of Safety Analyst, a state-of-the-art tool that has been developed to assist during the entire Traffic Safety Management process but that is not widely used due to a number of challenges as described in this paper. As part of this study, a comprehensive database system and tools to provide data to multiple traffic safety applications, with a focus on Safety Analyst, were developed. A number of data management tools were developed to extract, collect, transform, integrate, and load the data. The system includes consistency-checking capabilities to ensure the adequate insertion and update of data into the database. This system focused on data from roadways, ramps, intersections, and traffic characteristics for Safety Analyst. To test the proposed system and tools, data from Clark County, which is the largest county in Nevada and includes the cities of Las Vegas, Henderson, Boulder City, and North Las Vegas, was used. The database and Safety Analyst together help identify the sites with the potential for safety improvements. Specifically, this study examined the results from two case studies. The first case study, which identified sites having a potential for safety improvements with respect to fatal and all injury crashes, included all roadway elements and used default and calibrated Safety Performance Functions (SPFs). The second case study identified sites having a potential for safety improvements with respect to fatal and all injury crashes, specifically regarding intersections; it used default and calibrated SPFs as well. Conclusions were developed for the calibration of safety performance functions and the classification of site subtypes. Guidelines were provided about the selection of a particular network screening type or performance measure for network screening.

  2. A new comprehensive database of global volcanic gas analyses

    NASA Astrophysics Data System (ADS)

    Clor, L. E.; Fischer, T. P.; Lehnert, K. A.; McCormick, B.; Hauri, E. H.

    2013-12-01

    Volcanic volatiles are the driving force behind eruptions, powerful indicators of magma provenance, present localized hazards, and have implications for climate. Studies of volcanic emissions are necessary for understanding volatile cycling from the mantle to the atmosphere. Gas compositions vary with volcanic activity, making it important to track their chemical variability over time. As studies become increasingly interdisciplinary, it is critical to have a mechanism to integrate decades of gas studies across disciplines. Despite the value of this research to a variety of fields, there is currently no integrated network to house all volcanic and hydrothermal gas data, making spatial, temporal, and interdisciplinary comparison studies time-consuming. To remedy this, we are working to establish a comprehensive database of volcanic gas emissions and compositions worldwide, as part of the Deep Carbon Observatory's DECADE (Deep Carbon Degassing) initiative. Volcanic gas data have been divided into two broad categories: 1) chemical analyses from samples collected directly at the volcanic source, and 2) measurements of gas concentrations and fluxes, such as remotely by mini-DOAS or satellite, or in-plume such as by multiGAS. The gas flux database effort is realized by the Global Volcanism Program of the Smithsonian Institution (abstract by Brendan McCormick, this meeting). The direct-sampling data is the subject of this presentation. Data from direct techniques include samples of gases collected at the volcanic source from fumaroles and springs, tephras analyzed for gas contents, filter pack samples of gases collected in a plume, and any other data types that involve collection of a sample. Data are incorporated into the existing framework of the Petrological Database, PetDB. Association with PetDB is advantageous as it will allow volcanic gas data to be linked to chemical data from lava or tephra samples, forming more complete ties between the eruptive products and the

  3. 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.

  4. Database trial impact on graduate nursing comprehensive exams.

    PubMed

    Pionke, Katharine; Huckstadt, Alicia

    2015-10-01

    While the authors were doing a test period of databases, the question of whether or not databases affect outcomes of graduate nursing comprehensive examinations came up. This study explored that question through using citation analysis of exams that were taken during a database trial and exams that were not. The findings showed no difference in examination pass/fail rates. While the pass/fail rates did not change, a great deal was learned in terms of citation accuracy and types of materials that students used, leading to discussions about changing how citation and plagiarism awareness were taught.

  5. THE NATIONAL EXPOSURE RESEARCH LABORATORY'S COMPREHENSIVE HUMAN ACTIVITY DATABASE

    EPA Science Inventory

    EPA's National Exposure Research Laboratory (NERL) has combined data from nine U.S. studies related to human activities into one comprehensive data system that can be accessed via the world-wide web. The data system is called CHAD-Consolidated Human Activity Database-and it is ...

  6. THE NATIONAL EXPOSURE RESEARCH LABORATORY'S COMPREHENSIVE HUMAN ACTIVITY DATABASE

    EPA Science Inventory

    EPA's National Exposure Research Laboratory (NERL) has combined data from nine U.S. studies related to human activities into one comprehensive data system that can be accessed via the world-wide web. The data system is called CHAD-Consolidated Human Activity Database-and it is ...

  7. Bolbase: a comprehensive genomics database for Brassica oleracea.

    PubMed

    Yu, Jingyin; Zhao, Meixia; Wang, Xiaowu; Tong, Chaobo; Huang, Shunmou; Tehrim, Sadia; Liu, Yumei; Hua, Wei; Liu, Shengyi

    2013-09-30

    Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, Brussels sprouts. This diversity along with its phylogenetic membership in a group of three diploid and three tetraploid species, and the recent availability of genome sequences within Brassica provide an unprecedented opportunity to study intra- and inter-species divergence and evolution in this species and its close relatives. We have developed a comprehensive database, Bolbase, which provides access to the B. oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 predicted genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomics information is available, including syntenic regions among B. oleracea, Brassica rapa and Arabidopsis thaliana, synonymous (Ks) and non-synonymous (Ka) substitution rates between orthologous gene pairs, gene families or clusters, and differences in quantity, category, and distribution of transposable elements on chromosomes. Bolbase provides useful search and data mining tools, including a keyword search, a local BLAST server, and a customized GBrowse tool, which can be used to extract annotations of genome components, identify similar sequences and visualize syntenic regions among species. Users can download all genomic data and explore comparative genomics in a highly visual setting. Bolbase is the first resource platform for the B. oleracea genome and for genomic comparisons with its relatives, and thus it will help the research community to better study the function and evolution of Brassica genomes as well as enhance molecular breeding research. This database will be updated regularly with new features, improvements to genome annotation, and new genomic sequences as they

  8. Bolbase: a comprehensive genomics database for Brassica oleracea

    PubMed Central

    2013-01-01

    Background Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, Brussels sprouts. This diversity along with its phylogenetic membership in a group of three diploid and three tetraploid species, and the recent availability of genome sequences within Brassica provide an unprecedented opportunity to study intra- and inter-species divergence and evolution in this species and its close relatives. Description We have developed a comprehensive database, Bolbase, which provides access to the B. oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 predicted genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomics information is available, including syntenic regions among B. oleracea, Brassica rapa and Arabidopsis thaliana, synonymous (Ks) and non-synonymous (Ka) substitution rates between orthologous gene pairs, gene families or clusters, and differences in quantity, category, and distribution of transposable elements on chromosomes. Bolbase provides useful search and data mining tools, including a keyword search, a local BLAST server, and a customized GBrowse tool, which can be used to extract annotations of genome components, identify similar sequences and visualize syntenic regions among species. Users can download all genomic data and explore comparative genomics in a highly visual setting. Conclusions Bolbase is the first resource platform for the B. oleracea genome and for genomic comparisons with its relatives, and thus it will help the research community to better study the function and evolution of Brassica genomes as well as enhance molecular breeding research. This database will be updated regularly with new features, improvements to genome annotation

  9. A comprehensive global genotype-phenotype database for rare diseases.

    PubMed

    Trujillano, Daniel; Oprea, Gabriela-Elena; Schmitz, Yvonne; Bertoli-Avella, Aida M; Abou Jamra, Rami; Rolfs, Arndt

    2017-01-01

    The ability to discover genetic variants in a patient runs far ahead of the ability to interpret them. Databases with accurate descriptions of the causal relationship between the variants and the phenotype are valuable since these are critical tools in clinical genetic diagnostics. Here, we introduce a comprehensive and global genotype-phenotype database focusing on rare diseases. This database (CentoMD (®)) is a browser-based tool that enables access to a comprehensive, independently curated system utilizing stringent high-quality criteria and a quickly growing repository of genetic and human phenotype ontology (HPO)-based clinical information. Its main goals are to aid the evaluation of genetic variants, to enhance the validity of the genetic analytical workflow, to increase the quality of genetic diagnoses, and to improve evaluation of treatment options for patients with hereditary diseases. The database software correlates clinical information from consented patients and probands of different geographical backgrounds with a large dataset of genetic variants and, when available, biomarker information. An automated follow-up tool is incorporated that informs all users whenever a variant classification has changed. These unique features fully embedded in a CLIA/CAP-accredited quality management system allow appropriate data quality and enhanced patient safety. More than 100,000 genetically screened individuals are documented in the database, resulting in more than 470 million variant detections. Approximately, 57% of the clinically relevant and uncertain variants in the database are novel. Notably, 3% of the genetic variants identified and previously reported in the literature as being associated with a particular rare disease were reclassified, based on internal evidence, as clinically irrelevant. The database offers a comprehensive summary of the clinical validity and causality of detected gene variants with their associated phenotypes, and is a valuable tool

  10. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis

    PubMed Central

    Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

    2009-01-01

    Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed. PMID:19015126

  11. Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis.

    PubMed

    Peng, Zhi-yu; Zhou, Xin; Li, Linchuan; Yu, Xiangchun; Li, Hongjiang; Jiang, Zhiqiang; Cao, Guangyu; Bai, Mingyi; Wang, Xingchun; Jiang, Caifu; Lu, Haibin; Hou, Xianhui; Qu, Lijia; Wang, Zhiyong; Zuo, Jianru; Fu, Xiangdong; Su, Zhen; Li, Songgang; Guo, Hongwei

    2009-01-01

    Plant hormones are small organic molecules that influence almost every aspect of plant growth and development. Genetic and molecular studies have revealed a large number of genes that are involved in responses to numerous plant hormones, including auxin, gibberellin, cytokinin, abscisic acid, ethylene, jasmonic acid, salicylic acid, and brassinosteroid. Here, we develop an Arabidopsis hormone database, which aims to provide a systematic and comprehensive view of genes participating in plant hormonal regulation, as well as morphological phenotypes controlled by plant hormones. Based on data from mutant studies, transgenic analysis and gene ontology (GO) annotation, we have identified a total of 1026 genes in the Arabidopsis genome that participate in plant hormone functions. Meanwhile, a phenotype ontology is developed to precisely describe myriad hormone-regulated morphological processes with standardized vocabularies. A web interface (http://ahd.cbi.pku.edu.cn) would allow users to quickly get access to information about these hormone-related genes, including sequences, functional category, mutant information, phenotypic description, microarray data and linked publications. Several applications of this database in studying plant hormonal regulation and hormone cross-talk will be presented and discussed.

  12. RiboDB Database: A Comprehensive Resource for Prokaryotic Systematics.

    PubMed

    Jauffrit, Frédéric; Penel, Simon; Delmotte, Stéphane; Rey, Carine; de Vienne, Damien M; Gouy, Manolo; Charrier, Jean-Philippe; Flandrois, Jean-Pierre; Brochier-Armanet, Céline

    2016-08-01

    Ribosomal proteins (r-proteins) are increasingly used as an alternative to ribosomal rRNA for prokaryotic systematics. However, their routine use is difficult because r-proteins are often not or wrongly annotated in complete genome sequences, and there is currently no dedicated exhaustive database of r-proteins. RiboDB aims at fulfilling this gap. This weekly updated comprehensive database allows the fast and easy retrieval of r-protein sequences from publicly available complete prokaryotic genome sequences. The current version of RiboDB contains 90 r-proteins from 3,750 prokaryotic complete genomes encompassing 38 phyla/major classes and 1,759 different species. RiboDB is accessible at http://ribodb.univ-lyon1.fr and through ACNUC interfaces. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. ClassLess: A Comprehensive Database of Young Stellar Objects

    NASA Astrophysics Data System (ADS)

    Hillenbrand, Lynne; Baliber, Nairn

    2015-01-01

    We have designed and constructed a database housing published measurements of Young Stellar Objects (YSOs) within ~1 kpc of the Sun. ClassLess, so called because it includes YSOs in all stages of evolution, is a relational database in which user interaction is conducted via HTML web browsers, queries are performed in scientific language, and all data are linked to the sources of publication. Each star is associated with a cluster (or clusters), and both spatially resolved and unresolved measurements are stored, allowing proper use of data from multiple star systems. With this fully searchable tool, myriad ground- and space-based instruments and surveys across wavelength regimes can be exploited. In addition to primary measurements, the database self consistently calculates and serves higher level data products such as extinction, luminosity, and mass. As a result, searches for young stars with specific physical characteristics can be completed with just a few mouse clicks.

  14. 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.

  15. 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.

  16. Flybrain neuron database: a comprehensive database system of the Drosophila brain neurons.

    PubMed

    Shinomiya, Kazunori; Matsuda, Keiji; Oishi, Takao; Otsuna, Hideo; Ito, Kei

    2011-04-01

    The long history of neuroscience has accumulated information about numerous types of neurons in the brain of various organisms. Because such neurons have been reported in diverse publications without controlled format, it is not easy to keep track of all the known neurons in a particular nervous system. To address this issue we constructed an online database called Flybrain Neuron Database (Flybrain NDB), which serves as a platform to collect and provide information about all the types of neurons published so far in the brain of Drosophila melanogaster. Projection patterns of the identified neurons in diverse areas of the brain were recorded in a unified format, with text-based descriptions as well as images and movies wherever possible. In some cases projection sites and the distribution of the post- and presynaptic sites were determined with greater detail than described in the original publication. Information about the labeling patterns of various antibodies and expression driver strains to visualize identified neurons are provided as a separate sub-database. We also implemented a novel visualization tool with which users can interactively examine three-dimensional reconstruction of the confocal serial section images with desired viewing angles and cross sections. Comprehensive collection and versatile search function of the anatomical information reported in diverse publications make it possible to analyze possible connectivity between different brain regions. We analyzed the preferential connectivity among optic lobe layers and the plausible olfactory sensory map in the lateral horn to show the usefulness of such a database.

  17. ClassLess: A Comprehensive Database of Young Stellar Objects

    NASA Astrophysics Data System (ADS)

    Hillenbrand, Lynne A.; baliber, nairn

    2015-08-01

    We have designed and constructed a database intended to house catalog and literature-published measurements of Young Stellar Objects (YSOs) within ~1 kpc of the Sun. ClassLess, so called because it includes YSOs in all stages of evolution, is a relational database in which user interaction is conducted via HTML web browsers, queries are performed in scientific language, and all data are linked to the sources of publication. Each star is associated with a cluster (or clusters), and both spatially resolved and unresolved measurements are stored, allowing proper use of data from multiple star systems. With this fully searchable tool, myriad ground- and space-based instruments and surveys across wavelength regimes can be exploited. In addition to primary measurements, the database self consistently calculates and serves higher level data products such as extinction, luminosity, and mass. As a result, searches for young stars with specific physical characteristics can be completed with just a few mouse clicks. We are in the database population phase now, and are eager to engage with interested experts worldwide on local galactic star formation and young stellar populations.

  18. MIPS: curated databases and comprehensive secondary data resources in 2010.

    PubMed

    Mewes, H Werner; Ruepp, Andreas; Theis, Fabian; Rattei, Thomas; Walter, Mathias; Frishman, Dmitrij; Suhre, Karsten; Spannagl, Manuel; Mayer, Klaus F X; Stümpflen, Volker; Antonov, Alexey

    2011-01-01

    The Munich Information Center for Protein Sequences (MIPS at the Helmholtz Center for Environmental Health, Neuherberg, Germany) has many years of experience in providing annotated collections of biological data. Selected data sets of high relevance, such as model genomes, are subjected to careful manual curation, while the bulk of high-throughput data is annotated by automatic means. High-quality reference resources developed in the past and still actively maintained include Saccharomyces cerevisiae, Neurospora crassa and Arabidopsis thaliana genome databases as well as several protein interaction data sets (MPACT, MPPI and CORUM). More recent projects are PhenomiR, the database on microRNA-related phenotypes, and MIPS PlantsDB for integrative and comparative plant genome research. The interlinked resources SIMAP and PEDANT provide homology relationships as well as up-to-date and consistent annotation for 38,000,000 protein sequences. PPLIPS and CCancer are versatile tools for proteomics and functional genomics interfacing to a database of compilations from gene lists extracted from literature. A novel literature-mining tool, EXCERBT, gives access to structured information on classified relations between genes, proteins, phenotypes and diseases extracted from Medline abstracts by semantic analysis. All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de).

  19. dbPPT: a comprehensive database of protein phosphorylation in plants.

    PubMed

    Cheng, Han; Deng, Wankun; Wang, Yongbo; Ren, Jian; Liu, Zexian; Xue, Yu

    2014-01-01

    As one of the most important protein post-translational modifications, the reversible phosphorylation is critical for plants in regulating a variety of biological processes such as cellular metabolism, signal transduction and responses to environmental stress. Numerous efforts especially large-scale phosphoproteome profiling studies have been contributed to dissect the phosphorylation signaling in various plants, while a large number of phosphorylation events were identified. To provide an integrated data resource for further investigations, here we present a comprehensive database of dbPPT (database of Phosphorylation site in PlanTs, at http://dbppt.biocuckoo.org), which contains experimentally identified phosphorylation sites in proteins from plants. The phosphorylation sites in dbPPT were manually curated from the literatures, whereas datasets in other public databases were also integrated. In total, there were 82,175 phosphorylation sites in 31,012 proteins from 20 plant organisms in dbPPT, presenting a larger quantity of phosphorylation sites and a higher coverage of plant species in comparison with other databases. The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively. All the phosphoproteins and phosphorylation sites in the database were critically annotated. Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community. Database URL: http://dbppt.biocuckoo.or © The Author(s) 2014. Published by Oxford University Press.

  20. dbPPT: a comprehensive database of protein phosphorylation in plants

    PubMed Central

    Cheng, Han; Deng, Wankun; Wang, Yongbo; Ren, Jian; Liu, Zexian; Xue, Yu

    2014-01-01

    As one of the most important protein post-translational modifications, the reversible phosphorylation is critical for plants in regulating a variety of biological processes such as cellular metabolism, signal transduction and responses to environmental stress. Numerous efforts especially large-scale phosphoproteome profiling studies have been contributed to dissect the phosphorylation signaling in various plants, while a large number of phosphorylation events were identified. To provide an integrated data resource for further investigations, here we present a comprehensive database of dbPPT (database of Phosphorylation site in PlanTs, at http://dbppt.biocuckoo.org), which contains experimentally identified phosphorylation sites in proteins from plants. The phosphorylation sites in dbPPT were manually curated from the literatures, whereas datasets in other public databases were also integrated. In total, there were 82 175 phosphorylation sites in 31 012 proteins from 20 plant organisms in dbPPT, presenting a larger quantity of phosphorylation sites and a higher coverage of plant species in comparison with other databases. The proportions of residue types including serine, threonine and tyrosine were 77.99, 17.81 and 4.20%, respectively. All the phosphoproteins and phosphorylation sites in the database were critically annotated. Since the phosphorylation signaling in plants attracted great attention recently, such a comprehensive resource of plant protein phosphorylation can be useful for the research community. Database URL: http://dbppt.biocuckoo.org PMID:25534750

  1. Generation of comprehensive thoracic oncology database--tool for translational research.

    PubMed

    Surati, Mosmi; Robinson, Matthew; Nandi, Suvobroto; Faoro, Leonardo; Demchuk, Carley; Kanteti, Rajani; Ferguson, Benjamin; Gangadhar, Tara; Hensing, Thomas; Hasina, Rifat; Husain, Aliya; Ferguson, Mark; Karrison, Theodore; Salgia, Ravi

    2011-01-22

    The Thoracic Oncology Program Database Project was created to serve as a comprehensive, verified, and accessible repository for well-annotated cancer specimens and clinical data to be available to researchers within the Thoracic Oncology Research Program. This database also captures a large volume of genomic and proteomic data obtained from various tumor tissue studies. A team of clinical and basic science researchers, a biostatistician, and a bioinformatics expert was convened to design the database. Variables of interest were clearly defined and their descriptions were written within a standard operating manual to ensure consistency of data annotation. Using a protocol for prospective tissue banking and another protocol for retrospective banking, tumor and normal tissue samples from patients consented to these protocols were collected. Clinical information such as demographics, cancer characterization, and treatment plans for these patients were abstracted and entered into an Access database. Proteomic and genomic data have been included in the database and have been linked to clinical information for patients described within the database. The data from each table were linked using the relationships function in Microsoft Access to allow the database manager to connect clinical and laboratory information during a query. The queried data can then be exported for statistical analysis and hypothesis generation.

  2. LmTDRM database: a comprehensive database on thiol metabolic gene/gene products in Listeria monocytogenes EGDe.

    PubMed

    Srinivas, Vanishree; Gopal, Shubha

    2014-09-17

    There are a number of databases on the Listeria species and about their genome. However, these databases do not specifically address a set of network that is important in defence mechanism of the bacteria. Listeria monocytogenes EGDe is a well-established intracellular model organism to study host pathogenicity because of its versatility in the host environment. Here, we have focused on thiol disulphide redox metabolic network proteins, specifically in L. monocytogenes EGDe. The thiol redox metabolism is involved in oxidative stress mechanism and is found in all living cells. It functions to maintain the thiol disulphide balance required for protein folding by providing reducing power. Nevertheless, they are involved in the reversible oxidation of thiol groups in biomolecules by creating disulphide bonds; therefore, the term thiol disulphide redox metabolism (TDRM). TDRM network genes play an important role in oxidative stress mechanism and during host–pathogen interaction. Therefore, it is essential to have detailed information on these proteins with regard to other bacteria and its genome analysis to understand the presence of tRNA, transposons, and insertion elements for horizontal gene transfer. LmTDRM database is a new comprehensive web-based database on thiol proteins and their functions. It includes: Description, Search, TDRM analysis, and genome viewer. The quality of these data has been evaluated before they were aggregated to produce a final representation. The web interface allows for various queries to understand the protein function and their annotation with respect to their relationship with other bacteria. LmTDRM is a major step towards the development of databases on thiol disulphide redox proteins; it would definitely help researchers to understand the mechanism of these proteins and their interaction. Database URL: www.lmtdrm.com.

  3. Tomato functional genomics database (TFGD): a comprehensive collection and analysis package for tomato functional genomics

    USDA-ARS?s Scientific Manuscript database

    Tomato Functional Genomics Database (TFGD; http://ted.bti.cornell.edu) provides a comprehensive systems biology resource to store, mine, analyze, visualize and integrate large-scale tomato functional genomics datasets. The database is expanded from the previously described Tomato Expression Database...

  4. Comprehensive T-matrix reference database: A 2012-2013 update

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

    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.

  5. A comprehensive and scalable database search system for metaproteomics.

    PubMed

    Chatterjee, Sandip; Stupp, Gregory S; Park, Sung Kyu Robin; Ducom, Jean-Christophe; Yates, John R; Su, Andrew I; Wolan, Dennis W

    2016-08-16

    Mass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations. Our approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed "Blazmass") to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy and allowing for a more in-depth characterization of the functional landscape of the samples. The combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomic search engine, and the proteomic data files for

  6. circRNADb: A comprehensive database for human circular RNAs with protein-coding annotations

    PubMed Central

    Chen, Xiaoping; Han, Ping; Zhou, Tao; Guo, Xuejiang; Song, Xiaofeng; Li, Yan

    2016-01-01

    It has been known that circular RNAs are widely expressed in human tissues and cells, and play important regulatory roles in physiological or pathological processes. However, there is lack of comprehensively annotated human circular RNAs database. In this study we established a circRNA database, named as circRNADb, containing 32,914 human exonic circRNAs carefully selected from diversified sources. The detailed information of the circRNA, including genomic information, exon splicing, genome sequence, internal ribosome entry site (IRES), open reading frame (ORF) and references were provided in circRNADb. In addition, circRNAs were found to be able to encode proteins, which have not been reported in any species. 16328 circRNAs were annotated to have ORF longer than 100 amino acids, of which 7170 have IRES elements. 46 circRNAs from 37 genes were found to have their corresponding proteins expressed according mass spectrometry. The database provides the function of data search, browse, download, submit and feedback for the user to study particular circular RNA of interest and update the database continually. circRNADb will be built to be a biological information platform for circRNA molecules and related biological functions in the future. The database can be freely available through the web server at http://reprod.njmu.edu.cn/circrnadb. PMID:27725737

  7. LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes.

    PubMed

    Wang, Dapeng; Zhang, Yubin; Fan, Zhonghua; Liu, Guiming; Yu, Jun

    2012-01-01

    Animal genes of different lineages, such as vertebrates and arthropods, are well-organized and blended into dynamic chromosomal structures that represent a primary regulatory mechanism for body development and cellular differentiation. The majority of genes in a genome are actually clustered, which are evolutionarily stable to different extents and biologically meaningful when evaluated among genomes within and across lineages. Until now, many questions concerning gene organization, such as what is the minimal number of genes in a cluster and what is the driving force leading to gene co-regulation, remain to be addressed. Here, we provide a user-friendly database-LCGbase (a comprehensive database for lineage-based co-regulated genes)-hosting information on evolutionary dynamics of gene clustering and ordering within animal kingdoms in two different lineages: vertebrates and arthropods. The database is constructed on a web-based Linux-Apache-MySQL-PHP framework and effective interactive user-inquiry service. Compared to other gene annotation databases with similar purposes, our database has three comprehensible advantages. First, our database is inclusive, including all high-quality genome assemblies of vertebrates and representative arthropod species. Second, it is human-centric since we map all gene clusters from other genomes in an order of lineage-ranks (such as primates, mammals, warm-blooded, and reptiles) onto human genome and start the database from well-defined gene pairs (a minimal cluster where the two adjacent genes are oriented as co-directional, convergent, and divergent pairs) to large gene clusters. Furthermore, users can search for any adjacent genes and their detailed annotations. Third, the database provides flexible parameter definitions, such as the distance of transcription start sites between two adjacent genes, which is extendable to genes that flanking the cluster across species. We also provide useful tools for sequence alignment, gene

  8. Milk bioactive peptide database: A comprehensive database of milk protein-derived bioactive peptides and novel visualization.

    PubMed

    Nielsen, Søren Drud; Beverly, Robert L; Qu, Yunyao; Dallas, David C

    2017-10-01

    During processing and digestion, milk proteins are disassembled into peptides with an array of biological functions, including antimicrobial, angiotensin-converting enzyme inhibition, antioxidant, opioid, and immunomodulation. These functions are summarized in numerous reviews, yet information on which peptides have which functions remains scattered across hundreds of research articles. We systematically searched the literature for all instances of bioactive peptides derived from milk proteins from any mammalian source. The data were compiled into a comprehensive database, which can be used to search for specific functions, peptides, or proteins (http://mbpdb.nws.oregonstate.edu). To review this large dataset, the bioactive peptides reported in the literature were visually mapped on the parent protein sequences, providing information on sites with highest abundance of bioactive peptides. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. 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.

  10. 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.

  11. MIDAS (Material Implementation, Database, and Analysis Source): A comprehensive resource of material properties

    SciTech Connect

    Tang, M; Norquist, P; Barton, N; Durrenberger, K; Florando, J; Attia, A

    2010-12-13

    MIDAS is aimed to be an easy-to-use and comprehensive common source for material properties including both experimental data and models and their parameters. At LLNL, we will develop MIDAS to be the central repository for material strength related data and models with the long-term goal to encompass other material properties. MIDAS will allow the users to upload experimental data and updated models, to view and read materials data and references, to manipulate models and their parameters, and to serve as the central location for the application codes to access the continuously growing model source codes. MIDAS contains a suite of interoperable tools and utilizes components already existing at LLNL: MSD (material strength database), MatProp (database of materials properties files), and MSlib (library of material model source codes). MIDAS requires significant development of the computer science framework for the interfaces between different components. We present the current status of MIDAS and its future development in this paper.

  12. Comprehensive Health Education Standards (Including Physical Activity Standards). Comprehensive Health Rationale.

    ERIC Educational Resources Information Center

    Arizona State Dept. of Education, Phoenix.

    Arizona's comprehensive health education standards begins with a health rationale for each standard, then details the seven standards: (1) students comprehend concepts related to health promotion and disease prevention; (2) students demonstrate the ability to access accurate health information; (3) students demonstrate the ability to practice…

  13. SuperToxic: a comprehensive database of toxic compounds

    PubMed Central

    Schmidt, Ulrike; Struck, Swantje; Gruening, Bjoern; Hossbach, Julia; Jaeger, Ines S.; Parol, Roza; Lindequist, Ulrike; Teuscher, Eberhard; Preissner, Robert

    2009-01-01

    Within our everyday life, we are confronted with a variety of toxic substances of natural or artificial origin. Toxins are already used, e.g. in medicine, but there is still an increasing number of toxic compounds, representing a tremendous potential to extract new substances. Since predictive toxicology gains in importance, the careful and extensive investigation of known toxins is the basis to assess the properties of unknown substances. In order to achieve this aim, we have collected toxic compounds from literature and web sources in the database SuperToxic. The current version of this database compiles about 60 000 compounds and their structures. These molecules are classified according to their toxicity, based on more than 2 million measurements. The SuperToxic database provides a variety of search options like name, CASRN, molecular weight and measured values of toxicity. With the aid of implemented similarity searches, information about possible biological interactions can be gained. Furthermore, connections to the Protein Data Bank, UniProt and the KEGG database are available, to allow the identification of targets and those pathways, the searched compounds are involved in. This database is available online at: http://bioinformatics.charite.de/supertoxic. PMID:19004875

  14. Characterizing Scattering of PSD-Integrated Aggregate Ensembles using a Comprehensive Particle Scattering Database

    NASA Astrophysics Data System (ADS)

    Kuo, Kwo-Sen; Skofronick-Jackson, Gail; Olson, William; Tanelli, Simone; Haddad, Ziad; van Aartsen, Bruce

    2013-04-01

    We have constructed ~10,000 realistic snow particles, including both pristine and aggregate types, with maximum diameter spanning ~100 micron to 15 mm. The scattering property for each of these particles has subsequently been obtained using the open source discrete-dipole-approximation (DDA) code, DDSCAT, at thirteen (13) microwave frequencies ranging from 10 to 190 GHz. A scattering property database has thus been constructed to support precipitation remote sensing involving ice particles in the GPM era. Preliminary trial retrievals, utilizing radar and radiometer measurements from a field campaign and the GPM radar-radiometer combined algorithm currently under development, demonstrates that much better consistency between radar and radiometer is achieved when using scattering properties from this database rather than the ones derived with simplified assumptions. Although this scattering database, using more realistic particles and being more comprehensive in scope, represents a considerable stride forward in the advancement of solid-precipitation remote sensing, there are still important tasks to be accomplished in order to effectively use this database for practical retrievals. One of such tasks is to find parameters, preferably a very small number of them, that can adequately characterize the single-scattering properties for realistic ensembles of these particles, i.e. with realistic particle size distributions, of these particles. This study reports an approach that holds great promise in reducing the seemingly insurmountable complexity in the plethora of particle shapes into a few parameters.

  15. Comprehensive Network Map of ADME-Tox Databases.

    PubMed

    Canault, Baptiste; Bourg, Stéphane; Vayer, Philippe; Bonnet, Pascal

    2017-06-29

    In the last decade, many statistical-based approaches have been developed to improve poor pharmacokinetics (PK) and to reduce toxicity of lead compounds, which are one of the main causes of high failure rate in drug development. Predictive QSAR models are not always very efficient due to the low number of available biological data and the differences in the experimental protocols. Fortunately, the number of available databases continues to grow every year. However, it remains a challenge to determine the source and the quality of the original data. The main goal is to identify the relevant databases required to generate the most robust predictive models. In this study, an interactive network of databases was proposed to easily find online data sources related to ADME-Tox parameters data. In this map, relevant information regarding scope of application, data availability and data redundancy can be obtained for each data source. To illustrate the usage of data mining from the network, a dataset on plasma protein binding is selected based on various sources such as DrugBank, PubChem and ChEMBL databases. A total of 2,606 unique molecules with experimental values of PPB were extracted and can constitute a consistent dataset for QSAR modeling. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. MOAtox: A comprehensive mode of action and acute aquatic toxicity database for predictive model development.

    PubMed

    Barron, M G; Lilavois, C R; Martin, T M

    2015-04-01

    The mode of toxic action (MOA) has been recognized as a key determinant of chemical toxicity and as an alternative to chemical class-based predictive toxicity modeling. However, the development of quantitative structure activity relationship (QSAR) and other models has been limited by the availability of comprehensive high quality MOA and toxicity databases. The current study developed a dataset of MOA assignments for 1213 chemicals that included a diversity of metals, pesticides, and other organic compounds that encompassed six broad and 31 specific MOAs. MOA assignments were made using a combination of high confidence approaches that included international consensus classifications, QSAR predictions, and weight of evidence professional judgment based on an assessment of structure and literature information. A toxicity database of 674 acute values linked to chemical MOA was developed for fish and invertebrates. Additionally, species-specific measured or high confidence estimated acute values were developed for the four aquatic species with the most reported toxicity values: rainbow trout (Oncorhynchus mykiss), fathead minnow (Pimephales promelas), bluegill (Lepomis macrochirus), and the cladoceran (Daphnia magna). Measured acute toxicity values met strict standardization and quality assurance requirements. Toxicity values for chemicals with missing species-specific data were estimated using established interspecies correlation models and procedures (Web-ICE; http://epa.gov/ceampubl/fchain/webice/), with the highest confidence values selected. The resulting dataset of MOA assignments and paired toxicity values are provided in spreadsheet format as a comprehensive standardized dataset available for predictive aquatic toxicology model development.

  17. RNAcentral: a comprehensive database of non-coding RNA sequences

    PubMed Central

    2017-01-01

    RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/. PMID:27794554

  18. RNAcentral: A comprehensive database of non-coding RNA sequences

    DOE PAGES

    Williams, Kelly Porter; Lau, Britney Yan

    2016-10-28

    RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. Furthermore, the website has been subject to continuous improvements focusing on text and sequence similaritymore » searches as well as genome browsing functionality.« less

  19. RNAcentral: A comprehensive database of non-coding RNA sequences

    SciTech Connect

    Williams, Kelly Porter; Lau, Britney Yan

    2016-10-28

    RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. Furthermore, the website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality.

  20. Comprehensiveness of "Social Work Abstracts" as a Database for Researchers and Practitioners

    ERIC Educational Resources Information Center

    Shek, Daniel T. L.

    2008-01-01

    Objective: The comprehensiveness of "Social Work Abstracts (SWA)" as a database was examined. Method: The coverage of articles of "Research on Social Work Practice" and "Social Work Research" in "SWA" from 1995 to 2005 was examined. "SWA" was compared with other databases on several dimensions. A case study based on the author's publications was…

  1. MGDB: a comprehensive database of genes involved in melanoma

    PubMed Central

    Zhang, Di; Zhu, Rongrong; Zhang, Hanqian; Zheng, Chun-Hou; Xia, Junfeng

    2015-01-01

    The Melanoma Gene Database (MGDB) is a manually curated catalog of molecular genetic data relating to genes involved in melanoma. The main purpose of this database is to establish a network of melanoma related genes and to facilitate the mechanistic study of melanoma tumorigenesis. The entries describing the relationships between melanoma and genes in the current release were manually extracted from PubMed abstracts, which contains cumulative to date 527 human melanoma genes (422 protein-coding and 105 non-coding genes). Each melanoma gene was annotated in seven different aspects (General Information, Expression, Methylation, Mutation, Interaction, Pathway and Drug). In addition, manually curated literature references have also been provided to support the inclusion of the gene in MGDB and establish its association with melanoma. MGDB has a user-friendly web interface with multiple browse and search functions. We hoped MGDB will enrich our knowledge about melanoma genetics and serve as a useful complement to the existing public resources. Database URL: http://bioinfo.ahu.edu.cn:8080/Melanoma/index.jsp PMID:26424083

  2. Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders

    PubMed Central

    Chen, Chong; Jiang, Yi; Xu, Chenyang; Liu, Xinting; Hu, Lin; Xiang, Yanbao; Chen, Qingshuang; Chen, Denghui; Li, Huanzheng; Xu, Xueqin; Tang, Shaohua

    2016-01-01

    Genetic skeletal disorders (GSD) involving the skeletal system arises through disturbances in the complex processes of skeletal development, growth and homeostasis and remain a diagnostic challenge because of their clinical heterogeneity and genetic variety. Over the past decades, tremendous effort platforms have been made to explore the complex heterogeneity, and massive new genes and mutations have been identified in different GSD, but the information supplied by literature is still limited and it is hard to meet the further needs of scientists and clinicians. In this study, combined with Nosology and Classification of genetic skeletal disorders, we developed the first comprehensive and annotated genetic skeletal disorders database, named ‘SkeletonGenetics’, which contains information about all GSD-related knowledge including 8225 mutations in 357 genes, with detailed information associated with 481 clinical diseases (2260 clinical phenotype) classified in 42 groups defined by molecular, biochemical and/or radiographic criteria from 1698 publications. Further annotations were performed to each entry including Gene Ontology, pathways analysis, protein–protein interaction, mutation annotations, disease–disease clustering and gene–disease networking. Furthermore, using concise search methods, intuitive graphical displays, convenient browsing functions and constantly updatable features, ‘SkeletonGenetics’ could serve as a central and integrative database for unveiling the genetic and pathways pre-dispositions of GSD. Database URL: http://101.200.211.232/skeletongenetics/ PMID:27580923

  3. iRootHair: A Comprehensive Root Hair Genomics Database1[W

    PubMed Central

    Kwasniewski, Miroslaw; Nowakowska, Urszula; Szumera, Jakub; Chwialkowska, Karolina; Szarejko, Iwona

    2013-01-01

    The specialized root epidermis cells of higher plants produce long, tubular outgrowths called root hairs. Root hairs play an important role in nutrient and water uptake, and they serve as a valuable model in studies of plant cell morphogenesis. More than 1,300 articles that describe the biological processes of these unique cells have been published to date. As new fields of root hair research are emerging, the number of new papers published each year and the volumes of new relevant data are continuously increasing. Therefore, there is a general need to facilitate studies on root hair biology by collecting, presenting, and sharing the available information in a systematic, curated manner. Consequently, in this paper, we present a comprehensive database of root hair genomics, iRootHair, which is accessible as a Web-based service. The current version of the database includes information about 153 root hair-related genes that have been identified to date in dicots and monocots along with their putative orthologs in higher plants with sequenced genomes. In order to facilitate the use of the iRootHair database, it is subdivided into interrelated, searchable sections that describe genes, processes of root hair formation, root hair mutants, and available references. The database integrates bioinformatics tools with a focus on sequence identification and annotation. iRootHair is a unique resource for root hair research that integrates the large volume of data related to root hair genomics in a single, curated, and expandable database that is freely available at www.iroothair.org. PMID:23129204

  4. Developing a Comprehensive Active Region Database for the IRIS Observatory

    NASA Astrophysics Data System (ADS)

    Ho, A. Q. A.; Schmit, D. J.

    2016-12-01

    The fleet of space-based solar observatories provides a plethora of data to allow further analysis of the dynamics of active regions. In order to compare different solar remote sensing datasets, we determine the spatial and temporal overlap of datasets from different sources. We aim to facilitate analysis by creating an interactive visual tool that aids the comparison of observations of active regions from numerous sources such as IRIS and SDO/HMI, among others, that aggregates important physical quantities from each dataset. The interface allows for the selection and filtering of several key factors, such as particular active regions (organized by NOAA number) and specific time frames, to help refine searches. In addition, the tool provides a clearly organized map detailing the movement of active regions over time. The tool is projected to have several important implications, such as the ability to perform comprehensive statistical studies regarding the evolution of active regions and their chromospheres.

  5. Use of Composite Protein Database including Search Result Sequences for Mass Spectrometric Analysis of Cell Secretome

    PubMed Central

    Shin, Jihye; Kim, Gamin; Kabir, Mohammad Humayun; Park, Seong Jun; Lee, Seoung Taek; Lee, Cheolju

    2015-01-01

    Mass spectrometric (MS) data of human cell secretomes are usually run through the conventional human database for identification. However, the search may result in false identifications due to contamination of the secretome with fetal bovine serum (FBS) proteins. To overcome this challenge, here we provide a composite protein database including human as well as 199 FBS protein sequences for MS data search of human cell secretomes. Searching against the human-FBS database returned more reliable results with fewer false-positive and false-negative identifications compared to using either a human only database or a human-bovine database. Furthermore, the improved results validated our strategy without complex experiments like SILAC. We expect our strategy to improve the accuracy of human secreted protein identification and to also add value for general use. PMID:25822838

  6. REDIportal: a comprehensive database of A-to-I RNA editing events in humans

    PubMed Central

    Picardi, Ernesto; D'Erchia, Anna Maria; Lo Giudice, Claudio; Pesole, Graziano

    2017-01-01

    RNA editing by A-to-I deamination is the prominent co-/post-transcriptional modification in humans. It is carried out by ADAR enzymes and contributes to both transcriptomic and proteomic expansion. RNA editing has pivotal cellular effects and its deregulation has been linked to a variety of human disorders including neurological and neurodegenerative diseases and cancer. Despite its biological relevance, many physiological and functional aspects of RNA editing are yet elusive. Here, we present REDIportal, available online at http://srv00.recas.ba.infn.it/atlas/, the largest and comprehensive collection of RNA editing in humans including more than 4.5 millions of A-to-I events detected in 55 body sites from thousands of RNAseq experiments. REDIportal embeds RADAR database and represents the first editing resource designed to answer functional questions, enabling the inspection and browsing of editing levels in a variety of human samples, tissues and body sites. In contrast with previous RNA editing databases, REDIportal comprises its own browser (JBrowse) that allows users to explore A-to-I changes in their genomic context, empathizing repetitive elements in which RNA editing is prominent. PMID:27587585

  7. [Establishment of a comprehensive database for laryngeal cancer related genes and the miRNAs].

    PubMed

    Li, Mengjiao; E, Qimin; Liu, Jialin; Huang, Tingting; Liang, Chuanyu

    2015-09-01

    By collecting and analyzing the laryngeal cancer related genes and the miRNAs, to build a comprehensive laryngeal cancer-related gene database, which differs from the current biological information database with complex and clumsy structure and focuses on the theme of gene and miRNA, and it could make the research and teaching more convenient and efficient. Based on the B/S architecture, using Apache as a Web server, MySQL as coding language of database design and PHP as coding language of web design, a comprehensive database for laryngeal cancer-related genes was established, providing with the gene tables, protein tables, miRNA tables and clinical information tables of the patients with laryngeal cancer. The established database containsed 207 laryngeal cancer related genes, 243 proteins, 26 miRNAs, and their particular information such as mutations, methylations, diversified expressions, and the empirical references of laryngeal cancer relevant molecules. The database could be accessed and operated via the Internet, by which browsing and retrieval of the information were performed. The database were maintained and updated regularly. The database for laryngeal cancer related genes is resource-integrated and user-friendly, providing a genetic information query tool for the study of laryngeal cancer.

  8. [Current status of Chinese herbal preparations included in LiverTox database].

    PubMed

    Jin, R; Gu, H Y; Li, L L; Sun, L L

    2016-11-20

    Objective: To investigate the contents and features of drug-induced liver injury (DILI) database called LiverTox, as well as 37 herbal preparations included in this database. Methods: Firstly, the source and contents of LiverTox were briefly introduced, including the clinical features, types, severity, and causality assessment scale of DILI. Secondly, detailed information of 37 herbal preparations included in the class of "Herbals and Dietary Supplements" were extracted, including drug name, origin, efficacy, constituents, type of liver injury, and manifestations, to perform a preliminary statistical analysis. Finally, a comparative analysis was performed between such information and current knowledge of Chinese herbal medicine-induced liver injury in China. Results: LiverTox was a DILI database with open access and rich information and provided practical information on treatment, typing, causality assessment, and treatment. Among the 37 herbal preparations, 28 had the risk of liver injury. The most common indication was weight loss, followed by arthritis and constipation. The latency of hepatotoxicity ranged from 4 weeks to 6 months. Compared with the current knowledge in China, there were differences in the varieties and indications for herbal preparations with hepatotoxicity included in LiverTox, and many herbals with acknowledged hepatotoxicity in China were not included. Conclusion: LiverTox database is concise and practical, but there are certain differences between the herbal preparations included in this database and current knowledge in China.

  9. The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters

    PubMed Central

    Blin, Kai; Medema, Marnix H.; Kottmann, Renzo; Lee, Sang Yup; Weber, Tilmann

    2017-01-01

    Secondary metabolites produced by microorganisms are the main source of bioactive compounds that are in use as antimicrobial and anticancer drugs, fungicides, herbicides and pesticides. In the last decade, the increasing availability of microbial genomes has established genome mining as a very important method for the identification of their biosynthetic gene clusters (BGCs). One of the most popular tools for this task is antiSMASH. However, so far, antiSMASH is limited to de novo computing results for user-submitted genomes and only partially connects these with BGCs from other organisms. Therefore, we developed the antiSMASH database, a simple but highly useful new resource to browse antiSMASH-annotated BGCs in the currently 3907 bacterial genomes in the database and perform advanced search queries combining multiple search criteria. antiSMASH-DB is available at http://antismash-db.secondarymetabolites.org/. PMID:27924032

  10. The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters.

    PubMed

    Blin, Kai; Medema, Marnix H; Kottmann, Renzo; Lee, Sang Yup; Weber, Tilmann

    2017-01-04

    Secondary metabolites produced by microorganisms are the main source of bioactive compounds that are in use as antimicrobial and anticancer drugs, fungicides, herbicides and pesticides. In the last decade, the increasing availability of microbial genomes has established genome mining as a very important method for the identification of their biosynthetic gene clusters (BGCs). One of the most popular tools for this task is antiSMASH. However, so far, antiSMASH is limited to de novo computing results for user-submitted genomes and only partially connects these with BGCs from other organisms. Therefore, we developed the antiSMASH database, a simple but highly useful new resource to browse antiSMASH-annotated BGCs in the currently 3907 bacterial genomes in the database and perform advanced search queries combining multiple search criteria. antiSMASH-DB is available at http://antismash-db.secondarymetabolites.org/.

  11. Natural Medicines: A Complementary and Alternative Medicines Tool Combining Natural Standard and the Natural Medicines Comprehensive Database.

    PubMed

    Vardell, Emily

    2015-01-01

    Natural Medicines is a subscription-based database of complementary and alternative medicine information, building on the information previously available within Natural Standard and the Natural Medicines Comprehensive Database. Natural Medicines offers several special features including an Interaction Checker and Effectiveness Checker, as well as tools focused on Nutrient Depletion, Pregnancy & Lactation, and Adverse Effects. This column features a sample search of Natural Medicines, along with descriptions of the special features and how they might be used in practice by health care providers and health sciences information professionals.

  12. A comprehensive clinical research database based on CDISC ODM and i2b2.

    PubMed

    Meineke, Frank A; Stäubert, Sebastian; Löbe, Matthias; Winter, Alfred

    2014-01-01

    We present a working approach for a clinical research database as part of an archival information system. The CDISC ODM standard is target for clinical study and research relevant routine data, thus decoupling the data ingest process from the access layer. The presented research database is comprehensive as it covers annotating, mapping and curation of poorly annotated source data. Besides a conventional relational database the medical data warehouse i2b2 serves as main frontend for end-users. The system we developed is suitable to support patient recruitment, cohort identification and quality assurance in daily routine.

  13. 'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration.

    PubMed

    Ran, Xia; Cai, Wei-Jun; Huang, Xiu-Feng; Liu, Qi; Lu, Fan; Qu, Jia; Wu, Jinyu; Jin, Zi-Bing

    2014-01-01

    Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, 'RetinoGenetics', which contains informative knowledge about all known IRD-related genes and mutations for IRD. 'RetinoGenetics' currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein-protein interaction, mutational annotations and gene-disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, 'RetinoGenetics' could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, 'RetinoGenetics' is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/.

  14. ‘RetinoGenetics’: a comprehensive mutation database for genes related to inherited retinal degeneration

    PubMed Central

    Ran, Xia; Cai, Wei-Jun; Huang, Xiu-Feng; Liu, Qi; Lu, Fan; Qu, Jia; Wu, Jinyu; Jin, Zi-Bing

    2014-01-01

    Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, ‘RetinoGenetics’, which contains informative knowledge about all known IRD-related genes and mutations for IRD. ‘RetinoGenetics’ currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein–protein interaction, mutational annotations and gene–disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, ‘RetinoGenetics’ could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, ‘RetinoGenetics’ is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/. PMID:24939193

  15. Improving pharmaceutical innovation by building a more comprehensive database on drug development and use.

    PubMed

    Daniel, Gregory W; Cazé, Alexis; Romine, Morgan H; Audibert, Céline; Leff, Jonathan S; McClellan, Mark B

    2015-02-01

    New drugs and biologics have had a tremendous impact on the treatment of many diseases. However, available measures suggest that pharmaceutical innovation has remained relatively flat, despite substantial growth in research and development spending. We review recent literature on pharmaceutical innovation to identify limitations in measuring and assessing innovation, and we describe the framework and collaborative approach we are using to develop more comprehensive, publicly available metrics for innovation. Our research teams at the Brookings Institution and Deerfield Institute are collaborating with experts from multiple areas of drug development and regulatory review to identify and collect comprehensive data elements related to key development and regulatory characteristics for each new molecular entity approved over the past several decades in the United States and the European Union. Subsequent phases of our effort will add data on downstream product use and patient outcomes and will also include drugs that have failed or been abandoned in development. Such a database will enable researchers to better analyze the drivers of drug innovation, trends in the output of new medicines, and the effect of policy efforts designed to improve innovation.

  16. Historical seismometry database project: A comprehensive relational database for historical seismic records

    NASA Astrophysics Data System (ADS)

    Bono, Andrea

    2007-01-01

    The recovery and preservation of the patrimony made of the instrumental registrations regarding the historical earthquakes is with no doubt a subject of great interest. This attention, besides being purely historical, must necessarily be also scientific. In fact, the availability of a great amount of parametric information on the seismic activity in a given area is a doubtless help to the seismologic researcher's activities. In this article the project of the Sismos group of the National Institute of Geophysics and Volcanology of Rome new database is presented. In the structure of the new scheme the matured experience of five years of activity is summarized. We consider it useful for those who are approaching to "recovery and reprocess" computer based facilities. In the past years several attempts on Italian seismicity have followed each other. It has almost never been real databases. Some of them have had positive success because they were well considered and organized. In others it was limited in supplying lists of events with their relative hypocentral standards. What makes this project more interesting compared to the previous work is the completeness and the generality of the managed information. For example, it will be possible to view the hypocentral information regarding a given historical earthquake; it will be possible to research the seismograms in raster, digital or digitalized format, the information on times of arrival of the phases in the various stations, the instrumental standards and so on. The relational modern logic on which the archive is based, allows the carrying out of all these operations with little effort. The database described below will completely substitute Sismos' current data bank. Some of the organizational principles of this work are similar to those that inspire the database for the real-time monitoring of the seismicity in use in the principal offices of international research. A modern planning logic in a distinctly historical

  17. Comprehensive database of Manufactured Gas Plant tars. Part B. Aliphatic and aromatic compounds.

    PubMed

    Gallacher, Christopher; Thomas, Russell; Lord, Richard; Kalin, Robert M; Taylor, Chris

    2017-08-15

    Coal tars are a mixture of organic and inorganic compounds that were produced as a by-product from the manufactured gas and coke making industries. The composition of the tar produced varies depending on many factors; these include the temperature of production and the type of retort used. As different production processes produce different tars, a comprehensive database of the compounds present within coal tars from different production processes is a valuable resource. Such a database would help to understand how their chemical properties differ and what hazards the compounds present within these tars might pose. This study focuses on the aliphatic and aromatic compounds present in a database of 16 different tars from five different production processes. Samples of coal tar were extracted using accelerated solvent extraction (ASE) and derivatised post-extraction using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS). The derivatised samples were analysed using two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GCxGC/TOFMS). A total of 198 individual aliphatic and 951 individual aromatic compounds were detected within 16 tar samples produced by five different production processes. The polycyclic aromatic hydrocarbon (PAH) content of coal tars varies greatly depending on the production process used to obtain the tars and this is clearly demonstrated within the results. The aliphatic composition of the tars provided an important piece of analytical information that would have otherwise been missed with the detection of petrogenic compounds such as alkyl cyclohexanes. The aromatic compositions of the tar samples varied greatly between the different production processes investigated and useful analytical information was obtained about the individual production process groups. Alkyl cyclohexanes were detected in all samples from sites known to operate Carbureted Water Gas plants and not detected in

  18. CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database

    USDA-ARS?s Scientific Manuscript database

    The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins, and mutations involved in AMR. CARD is ontologi...

  19. 24 CFR 968.320 - HUD review and approval of comprehensive plan (including five-year action plan).

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... comprehensive plan (including five-year action plan). 968.320 Section 968.320 Housing and Urban Development... approval of comprehensive plan (including five-year action plan). (a) Submission of comprehensive plan. (1... Plan. After HUD approves the Comprehensive Plan (including the Five-Year Action Plan), or any...

  20. microPIR2: a comprehensive database for human–mouse comparative study of microRNA–promoter interactions

    PubMed Central

    Piriyapongsa, Jittima; Bootchai, Chaiwat; Ngamphiw, Chumpol; Tongsima, Sissades

    2014-01-01

    microRNA (miRNA)–promoter interaction resource (microPIR) is a public database containing over 15 million predicted miRNA target sites located within human promoter sequences. These predicted targets are presented along with their related genomic and experimental data, making the microPIR database the most comprehensive repository of miRNA promoter target sites. Here, we describe major updates of the microPIR database including new target predictions in the mouse genome and revised human target predictions. The updated database (microPIR2) now provides ∼80 million human and 40 million mouse predicted target sites. In addition to being a reference database, microPIR2 is a tool for comparative analysis of target sites on the promoters of human–mouse orthologous genes. In particular, this new feature was designed to identify potential miRNA–promoter interactions conserved between species that could be stronger candidates for further experimental validation. We also incorporated additional supporting information to microPIR2 such as nuclear and cytoplasmic localization of miRNAs and miRNA–disease association. Extra search features were also implemented to enable various investigations of targets of interest. Database URL: http://www4a.biotec.or.th/micropir2 PMID:25425035

  1. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

    PubMed Central

    Jia, Baofeng; Raphenya, Amogelang R.; Alcock, Brian; Waglechner, Nicholas; Guo, Peiyao; Tsang, Kara K.; Lago, Briony A.; Dave, Biren M.; Pereira, Sheldon; Sharma, Arjun N.; Doshi, Sachin; Courtot, Mélanie; Lo, Raymond; Williams, Laura E.; Frye, Jonathan G.; Elsayegh, Tariq; Sardar, Daim; Westman, Erin L.; Pawlowski, Andrew C.; Johnson, Timothy A.; Brinkman, Fiona S.L.; Wright, Gerard D.; McArthur, Andrew G.

    2017-01-01

    The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR. CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven and acquired resistance. It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected and hierarchical controlled vocabulary allowing advanced data sharing and organization. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence. Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats. CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis. PMID:27789705

  2. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database.

    PubMed

    Jia, Baofeng; Raphenya, Amogelang R; Alcock, Brian; Waglechner, Nicholas; Guo, Peiyao; Tsang, Kara K; Lago, Briony A; Dave, Biren M; Pereira, Sheldon; Sharma, Arjun N; Doshi, Sachin; Courtot, Mélanie; Lo, Raymond; Williams, Laura E; Frye, Jonathan G; Elsayegh, Tariq; Sardar, Daim; Westman, Erin L; Pawlowski, Andrew C; Johnson, Timothy A; Brinkman, Fiona S L; Wright, Gerard D; McArthur, Andrew G

    2017-01-04

    The Comprehensive Antibiotic Resistance Database (CARD; http://arpcard.mcmaster.ca) is a manually curated resource containing high quality reference data on the molecular basis of antimicrobial resistance (AMR), with an emphasis on the genes, proteins and mutations involved in AMR. CARD is ontologically structured, model centric, and spans the breadth of AMR drug classes and resistance mechanisms, including intrinsic, mutation-driven and acquired resistance. It is built upon the Antibiotic Resistance Ontology (ARO), a custom built, interconnected and hierarchical controlled vocabulary allowing advanced data sharing and organization. Its design allows the development of novel genome analysis tools, such as the Resistance Gene Identifier (RGI) for resistome prediction from raw genome sequence. Recent improvements include extensive curation of additional reference sequences and mutations, development of a unique Model Ontology and accompanying AMR detection models to power sequence analysis, new visualization tools, and expansion of the RGI for detection of emergent AMR threats. CARD curation is updated monthly based on an interplay of manual literature curation, computational text mining, and genome analysis.

  3. The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

    PubMed Central

    Eppig, Janan T.; Blake, Judith A.; Bult, Carol J.; Kadin, James A.; Richardson, Joel E.

    2012-01-01

    The Mouse Genome Database (MGD, http://www.informatics.jax.org) is the international community resource for integrated genetic, genomic and biological data about the laboratory mouse. Data in MGD are obtained through loads from major data providers and experimental consortia, electronic submissions from laboratories and from the biomedical literature. MGD maintains a comprehensive, unified, non-redundant catalog of mouse genome features generated by distilling gene predictions from NCBI, Ensembl and VEGA. MGD serves as the authoritative source for the nomenclature of mouse genes, mutations, alleles and strains. MGD is the primary source for evidence-supported functional annotations for mouse genes and gene products using the Gene Ontology (GO). MGD provides full annotation of phenotypes and human disease associations for mouse models (genotypes) using terms from the Mammalian Phenotype Ontology and disease names from the Online Mendelian Inheritance in Man (OMIM) resource. MGD is freely accessible online through our website, where users can browse and search interactively, access data in bulk using Batch Query or BioMart, download data files or use our web services Application Programming Interface (API). Improvements to MGD include expanded genome feature classifications, inclusion of new mutant allele sets and phenotype associations and extensions of GO to include new relationships and a new stream of annotations via phylogenetic-based approaches. PMID:22075990

  4. The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse.

    PubMed

    Eppig, Janan T; Blake, Judith A; Bult, Carol J; Kadin, James A; Richardson, Joel E

    2012-01-01

    The Mouse Genome Database (MGD, http://www.informatics.jax.org) is the international community resource for integrated genetic, genomic and biological data about the laboratory mouse. Data in MGD are obtained through loads from major data providers and experimental consortia, electronic submissions from laboratories and from the biomedical literature. MGD maintains a comprehensive, unified, non-redundant catalog of mouse genome features generated by distilling gene predictions from NCBI, Ensembl and VEGA. MGD serves as the authoritative source for the nomenclature of mouse genes, mutations, alleles and strains. MGD is the primary source for evidence-supported functional annotations for mouse genes and gene products using the Gene Ontology (GO). MGD provides full annotation of phenotypes and human disease associations for mouse models (genotypes) using terms from the Mammalian Phenotype Ontology and disease names from the Online Mendelian Inheritance in Man (OMIM) resource. MGD is freely accessible online through our website, where users can browse and search interactively, access data in bulk using Batch Query or BioMart, download data files or use our web services Application Programming Interface (API). Improvements to MGD include expanded genome feature classifications, inclusion of new mutant allele sets and phenotype associations and extensions of GO to include new relationships and a new stream of annotations via phylogenetic-based approaches.

  5. Including the Group Quarters Population in the US Synthesized Population Database

    PubMed Central

    Chasteen, Bernadette M.; Wheaton, William D.; Cooley, Philip C.; Ganapathi, Laxminarayana; Wagener, Diane K.

    2011-01-01

    In 2005, RTI International researchers developed methods to generate synthesized population data on US households for the US Synthesized Population Database. These data are used in agent-based modeling, which simulates large-scale social networks to test how changes in the behaviors of individuals affect the overall network. Group quarters are residences where individuals live in close proximity and interact frequently. Although the Synthesized Population Database represents the population living in households, data for the nation’s group quarters residents are not easily quantified because of US Census Bureau reporting methods designed to protect individuals’ privacy. Including group quarters population data can be an important factor in agent-based modeling because the number of residents and the frequency of their interactions are variables that directly affect modeling results. Particularly with infectious disease modeling, the increased frequency of agent interaction may increase the probability of infectious disease transmission between individuals and the probability of disease outbreaks. This report reviews our methods to synthesize data on group quarters residents to match US Census Bureau data. Our goal in developing the Group Quarters Population Database was to enable its use with RTI’s US Synthesized Population Database in the Modeling of Infectious Diseases Agent Study. PMID:21841972

  6. TassDB2 - A comprehensive database of subtle alternative splicing events.

    PubMed

    Sinha, Rileen; Lenser, Thorsten; Jahn, Niels; Gausmann, Ulrike; Friedel, Swetlana; Szafranski, Karol; Huse, Klaus; Rosenstiel, Philip; Hampe, Jochen; Schuster, Stefan; Hiller, Michael; Backofen, Rolf; Platzer, Matthias

    2010-04-29

    Subtle alternative splicing events involving tandem splice sites separated by a short (2-12 nucleotides) distance are frequent and evolutionarily widespread in eukaryotes, and a major contributor to the complexity of transcriptomes and proteomes. However, these events have been either omitted altogether in databases on alternative splicing, or only the cases of experimentally confirmed alternative splicing have been reported. Thus, a database which covers all confirmed cases of subtle alternative splicing as well as the numerous putative tandem splice sites (which might be confirmed once more transcript data becomes available), and allows to search for tandem splice sites with specific features and download the results, is a valuable resource for targeted experimental studies and large-scale bioinformatics analyses of tandem splice sites. Towards this goal we recently set up TassDB (Tandem Splice Site DataBase, version 1), which stores data about alternative splicing events at tandem splice sites separated by 3 nt in eight species. We have substantially revised and extended TassDB. The currently available version 2 contains extensive information about tandem splice sites separated by 2-12 nt for the human and mouse transcriptomes including data on the conservation of the tandem motifs in five vertebrates. TassDB2 offers a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download result datasets. For example, users can search for cases of alternative splicing where the proportion of EST/mRNA evidence supporting the minor isoform exceeds a specific threshold, or where the difference in splice site scores is specified by the user. The predicted impact of each event on the protein is also reported, along with information about being a putative target for the nonsense-mediated decay (NMD) pathway. Links are provided to the UCSC genome browser and other external resources

  7. Comprehensive national database of tree effects on air quality and human health in the United States.

    PubMed

    Hirabayashi, Satoshi; Nowak, David J

    2016-08-01

    Trees remove air pollutants through dry deposition processes depending upon forest structure, meteorology, and air quality that vary across space and time. Employing nationally available forest, weather, air pollution and human population data for 2010, computer simulations were performed for deciduous and evergreen trees with varying leaf area index for rural and urban areas in every county in the conterminous United States. The results populated a national database of annual air pollutant removal, concentration changes, and reductions in adverse health incidences and costs for NO2, O3, PM2.5 and SO2. The developed database enabled a first order approximation of air quality and associated human health benefits provided by trees with any forest configurations anywhere in the conterminous United States over time. Comprehensive national database of tree effects on air quality and human health in the United States was developed.

  8. BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori.

    PubMed

    Zhou, Qiu-Zhong; Zhang, Bindan; Yu, Quan-You; Zhang, Ze

    2016-09-13

    Long non-coding RNAs (lncRNAs) may play critical roles in a wide range of developmental processes of higher organisms. Recently, lncRNAs have been widely identified across eukaryotes and many databases of lncRNAs have been developed for human, mouse, fruit fly, etc. However, there is rare information about them in the only completely domesticated insect, silkworm (Bombyx mori). In this study, we systematically scanned lncRNAs using the available silkworm RNA-seq data and public unigenes. Finally, we identified and collected 6281 lncRNAs in the silkworm. Besides, we also collected 1986 microRNAs (miRNAs) from previous studies. Then, we organized them into a comprehensive and web-based database, BmncRNAdb. This database offers a user-friendly interface for data browse and online analysis as well as the three online tools for users to predict the target genes of lncRNA or miRNA. We have systematically identified and collected the silkworm lncRNAs and constructed a comprehensive database of the silkworm lncRNAs and miRNAs. This work gives a glimpse into lncRNAs of the silkworm and lays foundations for the ncRNAs study of the silkworm and other insects in the future. The BmncRNAdb is freely available at http://gene.cqu.edu.cn/BmncRNAdb/index.php .

  9. Comprehensive Research Synopsis and Systematic Meta-Analyses in Parkinson's Disease Genetics: The PDGene Database

    PubMed Central

    Lill, Christina M.; Roehr, Johannes T.; McQueen, Matthew B.; Kavvoura, Fotini K.; Bagade, Sachin; Schjeide, Brit-Maren M.; Schjeide, Leif M.; Meissner, Esther; Zauft, Ute; Allen, Nicole C.; Liu, Tian; Schilling, Marcel; Anderson, Kari J.; Beecham, Gary; Berg, Daniela; Biernacka, Joanna M.; Brice, Alexis; DeStefano, Anita L.; Do, Chuong B.; Eriksson, Nicholas; Factor, Stewart A.; Farrer, Matthew J.; Foroud, Tatiana; Gasser, Thomas; Hamza, Taye; Hardy, John A.; Heutink, Peter; Hill-Burns, Erin M.; Klein, Christine; Latourelle, Jeanne C.; Maraganore, Demetrius M.; Martin, Eden R.; Martinez, Maria; Myers, Richard H.; Nalls, Michael A.; Pankratz, Nathan; Payami, Haydeh; Satake, Wataru; Scott, William K.; Sharma, Manu; Singleton, Andrew B.; Stefansson, Kari; Toda, Tatsushi; Tung, Joyce Y.; Vance, Jeffery; Wood, Nick W.; Zabetian, Cyrus P.; Young, Peter; Tanzi, Rudolph E.; Khoury, Muin J.; Zipp, Frauke; Lehrach, Hans; Ioannidis, John P. A.; Bertram, Lars

    2012-01-01

    More than 800 published genetic association studies have implicated dozens of potential risk loci in Parkinson's disease (PD). To facilitate the interpretation of these findings, we have created a dedicated online resource, PDGene, that comprehensively collects and meta-analyzes all published studies in the field. A systematic literature screen of ∼27,000 articles yielded 828 eligible articles from which relevant data were extracted. In addition, individual-level data from three publicly available genome-wide association studies (GWAS) were obtained and subjected to genotype imputation and analysis. Overall, we performed meta-analyses on more than seven million polymorphisms originating either from GWAS datasets and/or from smaller scale PD association studies. Meta-analyses on 147 SNPs were supplemented by unpublished GWAS data from up to 16,452 PD cases and 48,810 controls. Eleven loci showed genome-wide significant (P<5×10−8) association with disease risk: BST1, CCDC62/HIP1R, DGKQ/GAK, GBA, LRRK2, MAPT, MCCC1/LAMP3, PARK16, SNCA, STK39, and SYT11/RAB25. In addition, we identified novel evidence for genome-wide significant association with a polymorphism in ITGA8 (rs7077361, OR 0.88, P = 1.3×10−8). All meta-analysis results are freely available on a dedicated online database (www.pdgene.org), which is cross-linked with a customized track on the UCSC Genome Browser. Our study provides an exhaustive and up-to-date summary of the status of PD genetics research that can be readily scaled to include the results of future large-scale genetics projects, including next-generation sequencing studies. PMID:22438815

  10. An X-Ray Analysis Database of Photoionization Cross Sections Including Variable Ionization

    NASA Technical Reports Server (NTRS)

    Wang, Ping; Cohen, David H.; MacFarlane, Joseph J.; Cassinelli, Joseph P.

    1997-01-01

    Results of research efforts in the following areas are discussed: review of the major theoretical and experimental data of subshell photoionization cross sections and ionization edges of atomic ions to assess the accuracy of the data, and to compile the most reliable of these data in our own database; detailed atomic physics calculations to complement the database for all ions of 17 cosmically abundant elements; reconciling the data from various sources and our own calculations; and fitting cross sections with functional approximations and incorporating these functions into a compact computer code.Also, efforts included adapting an ionization equilibrium code, tabulating results, and incorporating them into the overall program and testing the code (both ionization equilibrium and opacity codes) with existing observational data. The background and scientific applications of this work are discussed. Atomic physics cross section models and calculations are described. Calculation results are compared with available experimental data and other theoretical data. The functional approximations used for fitting cross sections are outlined and applications of the database are discussed.

  11. CracidMex1: a comprehensive database of global occurrences of cracids (Aves, Galliformes) with distribution in Mexico

    PubMed Central

    Pinilla-Buitrago, Gonzalo; Martínez-Morales, Miguel Angel; González-García, Fernando; Enríquez, Paula L.; Rangel-Salazar, José Luis; Romero, Carlos Alberto Guichard; Navarro-Sigüenza, Adolfo G.; Monterrubio-Rico, Tiberio César; Escalona-Segura, Griselda

    2014-01-01

    Abstract Cracids are among the most vulnerable groups of Neotropical birds. Almost half of the species of this family are included in a conservation risk category. Twelve taxa occur in Mexico, six of which are considered at risk at national level and two are globally endangered. Therefore, it is imperative that high quality, comprehensive, and high-resolution spatial data on the occurrence of these taxa are made available as a valuable tool in the process of defining appropriate management strategies for conservation at a local and global level. We constructed the CracidMex1 database by collating global records of all cracid taxa that occur in Mexico from available electronic databases, museum specimens, publications, “grey literature”, and unpublished records. We generated a database with 23,896 clean, validated, and standardized geographic records. Database quality control was an iterative process that commenced with the consolidation and elimination of duplicate records, followed by the geo-referencing of records when necessary, and their taxonomic and geographic validation using GIS tools and expert knowledge. We followed the geo-referencing protocol proposed by the Mexican National Commission for the Use and Conservation of Biodiversity. We could not estimate the geographic coordinates of 981 records due to inconsistencies or lack of sufficient information in the description of the locality. Given that current records for most of the taxa have some degree of distributional bias, with redundancies at different spatial scales, the CracidMex1 database has allowed us to detect areas where more sampling effort is required to have a better representation of the global spatial occurrence of these cracids. We also found that particular attention needs to be given to taxa identification in those areas where congeners or conspecifics co-occur in order to avoid taxonomic uncertainty. The construction of the CracidMex1 database represents the first comprehensive

  12. CracidMex1: a comprehensive database of global occurrences of cracids (Aves, Galliformes) with distribution in Mexico.

    PubMed

    Pinilla-Buitrago, Gonzalo; Martínez-Morales, Miguel Angel; González-García, Fernando; Enríquez, Paula L; Rangel-Salazar, José Luis; Romero, Carlos Alberto Guichard; Navarro-Sigüenza, Adolfo G; Monterrubio-Rico, Tiberio César; Escalona-Segura, Griselda

    2014-01-01

    Cracids are among the most vulnerable groups of Neotropical birds. Almost half of the species of this family are included in a conservation risk category. Twelve taxa occur in Mexico, six of which are considered at risk at national level and two are globally endangered. Therefore, it is imperative that high quality, comprehensive, and high-resolution spatial data on the occurrence of these taxa are made available as a valuable tool in the process of defining appropriate management strategies for conservation at a local and global level. We constructed the CracidMex1 database by collating global records of all cracid taxa that occur in Mexico from available electronic databases, museum specimens, publications, "grey literature", and unpublished records. We generated a database with 23,896 clean, validated, and standardized geographic records. Database quality control was an iterative process that commenced with the consolidation and elimination of duplicate records, followed by the geo-referencing of records when necessary, and their taxonomic and geographic validation using GIS tools and expert knowledge. We followed the geo-referencing protocol proposed by the Mexican National Commission for the Use and Conservation of Biodiversity. We could not estimate the geographic coordinates of 981 records due to inconsistencies or lack of sufficient information in the description of the locality. Given that current records for most of the taxa have some degree of distributional bias, with redundancies at different spatial scales, the CracidMex1 database has allowed us to detect areas where more sampling effort is required to have a better representation of the global spatial occurrence of these cracids. We also found that particular attention needs to be given to taxa identification in those areas where congeners or conspecifics co-occur in order to avoid taxonomic uncertainty. The construction of the CracidMex1 database represents the first comprehensive research effort to

  13. PlantNATsDB: a comprehensive database of plant natural antisense transcripts

    PubMed Central

    Chen, Dijun; Yuan, Chunhui; Zhang, Jian; Zhang, Zhao; Bai, Lin; Meng, Yijun; Chen, Ling-Ling; Chen, Ming

    2012-01-01

    Natural antisense transcripts (NATs), as one type of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and pathological processes. Although their important biological functions have been reported widely, a comprehensive database is lacking up to now. Consequently, we constructed a plant NAT database (PlantNATsDB) involving approximately 2 million NAT pairs in 69 plant species. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. PlantNATsDB provides various user-friendly web interfaces to facilitate the presentation of NATs and an integrated, graphical network browser to display the complex networks formed by different NATs. Moreover, a ‘Gene Set Analysis’ module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs. The PlantNATsDB is freely available at http://bis.zju.edu.cn/pnatdb/. PMID:22058132

  14. XML Storage for Magnetotelluric Transfer Functions: Towards a Comprehensive Online Reference Database

    NASA Astrophysics Data System (ADS)

    Kelbert, A.; Blum, C.

    2015-12-01

    Magnetotelluric Transfer Functions (MT TFs) represent most of the information about Earth electrical conductivity found in the raw electromagnetic data, providing inputs for further inversion and interpretation. To be useful for scientific interpretation, they must also contain carefully recorded metadata. Making these data available in a discoverable and citable fashion would provide the most benefit to the scientific community, but such a development requires that the metadata is not only present in the file but is also searchable. The most commonly used MT TF format to date, the historical Society of Exploration Geophysicists Electromagnetic Data Interchange Standard 1987 (EDI), no longer supports some of the needs of modern magnetotellurics, most notably accurate error bars recording. Moreover, the inherent heterogeneity of EDI's and other historic MT TF formats has mostly kept the community away from healthy data sharing practices. Recently, the MT team at Oregon State University in collaboration with IRIS Data Management Center developed a new, XML-based format for MT transfer functions, and an online system for long-term storage, discovery and sharing of MT TF data worldwide (IRIS SPUD; www.iris.edu/spud/emtf). The system provides a query page where all of the MT transfer functions collected within the USArray MT experiment and other field campaigns can be searched for and downloaded; an automatic on-the-fly conversion to the historic EDI format is also included. To facilitate conversion to the new, more comprehensive and sustainable, XML format for MT TFs, and to streamline inclusion of historic data into the online database, we developed a set of open source format conversion tools, which can be used for rotation of MT TFs as well as a general XML <-> EDI converter (https://seiscode.iris.washington.edu/projects/emtf-fcu). Here, we report on the newly established collaboration between the USGS Geomagnetism Program and the Oregon State University to gather

  15. Comprehensive Adolescent Health Programs That Include Sexual and Reproductive Health Services: A Systematic Review

    PubMed Central

    Parekh, Jenita; Tunçalp, Özge; Turke, Shani; Blum, Robert William

    2014-01-01

    We systematically reviewed peer-reviewed and gray literature on comprehensive adolescent health (CAH) programs (1998–2013), including sexual and reproductive health services. We screened 36 119 records and extracted articles using predefined criteria. We synthesized data into descriptive characteristics and assessed quality by evidence level. We extracted data on 46 programs, of which 19 were defined as comprehensive. Ten met all inclusion criteria. Most were US based; others were implemented in Egypt, Ethiopia, and Mexico. Three programs displayed rigorous evidence; 5 had strong and 2 had modest evidence. Those with rigorous or strong evidence directly or indirectly influenced adolescent sexual and reproductive health. The long-term impact of many CAH programs cannot be proven because of insufficient evaluations. Evaluation approaches that take into account the complex operating conditions of many programs are needed to better understand mechanisms behind program effects. PMID:25320876

  16. Development of a comprehensive infrared-material database for the Opticam fabrication system

    NASA Astrophysics Data System (ADS)

    Cerqua-Richardson, Kathleen A.; Schmidt, Stacy; Platt, George R.; Vakiner, John G.

    1993-12-01

    A comprehensive infrared material database has been created to aid in the development of a rule-based deterministic microgrinding process for infrared optics. The process science effort on infrared materials taking place at the University of Central Florida has compiled a concise collation of easily accessible physical property data to more thoroughly understand the material/processing interactions which occur during optical fabrication. The information exists in a user-friendly form whereby designers and system operators utilizing the Opticam system, can quickly and conveniently access and incorporate material property data into the design and fabrication process. We report on the motivation, organization and application of such a database into the Opticim network. The use of the information in establishment of part design, tooling design, machine parameters and predicting the form, figure and surface quality of the resulting optic is presented.

  17. A comprehensive database of verified experimental data on protein folding kinetics

    PubMed Central

    Wagaman, Amy S; Coburn, Aaron; Brand-Thomas, Itai; Dash, Barnali; Jaswal, Sheila S

    2014-01-01

    Insights into protein folding rely increasingly on the synergy between experimental and theoretical approaches. Developing successful computational models requires access to experimental data of sufficient quantity and high quality. We compiled folding rate constants for what initially appeared to be 184 proteins from 15 published collections/web databases. To generate the highest confidence in the dataset, we verified the reported lnkf value and exact experimental construct and conditions from the original experimental report(s). The resulting comprehensive database of 126 verified entries, ACPro, will serve as a freely accessible resource (https://www.ats. amherst.edu/protein/) for the protein folding community to enable confident testing of predictive models. In addition, we provide a streamlined submission form for researchers to add new folding kinetics results, requiring specification of all the relevant experimental information according to the standards proposed in 2005 by the protein folding consortium organized by Plaxco. As the number and diversity of proteins whose folding kinetics are studied expands, our curated database will enable efficient and confident incorporation of new experimental results into a standardized collection. This database will support a more robust symbiosis between experiment and theory, leading ultimately to more rapid and accurate insights into protein folding, stability, and dynamics. PMID:25229122

  18. CoReCG: a comprehensive database of genes associated with colon-rectal cancer

    PubMed Central

    Agarwal, Rahul; Kumar, Binayak; Jayadev, Msk; Raghav, Dhwani; Singh, Ashutosh

    2016-01-01

    Cancer of large intestine is commonly referred as colorectal cancer, which is also the third most frequently prevailing neoplasm across the globe. Though, much of work is being carried out to understand the mechanism of carcinogenesis and advancement of this disease but, fewer studies has been performed to collate the scattered information of alterations in tumorigenic cells like genes, mutations, expression changes, epigenetic alteration or post translation modification, genetic heterogeneity. Earlier findings were mostly focused on understanding etiology of colorectal carcinogenesis but less emphasis were given for the comprehensive review of the existing findings of individual studies which can provide better diagnostics based on the suggested markers in discrete studies. Colon Rectal Cancer Gene Database (CoReCG), contains 2056 colon-rectal cancer genes information involved in distinct colorectal cancer stages sourced from published literature with an effective knowledge based information retrieval system. Additionally, interactive web interface enriched with various browsing sections, augmented with advance search facility for querying the database is provided for user friendly browsing, online tools for sequence similarity searches and knowledge based schema ensures a researcher friendly information retrieval mechanism. Colorectal cancer gene database (CoReCG) is expected to be a single point source for identification of colorectal cancer-related genes, thereby helping with the improvement of classification, diagnosis and treatment of human cancers. Database URL: lms.snu.edu.in/corecg PMID:27114494

  19. Cancer Stem Cells Therapeutic Target Database: The First Comprehensive Database for Therapeutic Targets of Cancer Stem Cells.

    PubMed

    Hu, Xiaoqing; Cong, Ye; Luo, Huizhe Howard; Wu, Sijin; Zhao, Liyuan Eric; Liu, Quentin; Yang, Yongliang

    2017-02-01

    Cancer stem cells (CSCs) are a subpopulation of tumor cells that have strong self-renewal capabilities and may contribute to the failure of conventional cancer therapies. Hence, therapeutics homing in on CSCs represent a novel and promising approach that may eradicate malignant tumors. However, the lack of information on validated targets of CSCs has greatly hindered the development of CSC-directed therapeutics. Herein, we describe the Cancer Stem Cells Therapeutic Target Database (CSCTT), the first online database to provide a rich bioinformatics resource for the display, search, and analysis of structure, function, and related annotation for therapeutic targets of cancer stem cells. CSCTT contains 135 proteins that are potential targets of CSCs, with validated experimental evidence manually curated from existing literatures. Proteins are carefully annotated with a detailed description of protein families, biological process, related diseases, and experimental evidences. In addition, CSCTT has compiled 213 documented therapeutic methods for cancer stem cells, including 118 small molecules and 20 biotherapy methods. The CSCTT may serve as a useful platform for the development of CSC-directed therapeutics against various malignant tumors. The CSCTT database is freely available to the public at http://www.csctt.org/. Stem Cells Translational Medicine 2017;6:331-334.

  20. Sexually transmitted diseases putative drug target database: a comprehensive database of putative drug targets of pathogens identified by comparative genomics.

    PubMed

    Malipatil, Vijayakumari; Madagi, Shivkumar; Bhattacharjee, Biplab

    2013-01-01

    Sexually transmitted diseases (STD) are the serious public health problems and also impose a financial burden on the economy. Sexually transmitted infections are cured with single or multiple antibiotics. However, in many cases the organism showed persistence even after treatment. In the current study, the set of druggable targets in STD pathogens have been identified by comparative genomics. The subtractive genomics scheme exploits the properties of non-homology, essentiality, membrane localization and metabolic pathway uniqueness in identifying the drug targets. To achieve the effective use of data and to understand properties of drug target under single canopy, an integrated knowledge database of drug targets in STD bacteria was created. Data for each drug targets include biochemical pathway, function, cellular localization, essentiality score and structural details. The proteome of STD pathogens yielded 44 membrane associated proteins possessing unique metabolic pathways when subjected to the algorithm. The database can be accessed at http://biomedresearchasia.org/index.html. Diverse data merged in the common framework of this database is expected to be valuable not only for basic studies in clinical bioinformatics, but also for basic studies in immunological, biotechnological and clinical fields.

  1. ARCPHdb: A comprehensive protein database for SF1 and SF2 helicase from archaea.

    PubMed

    Moukhtar, Mirna; Chaar, Wafi; Abdel-Razzak, Ziad; Khalil, Mohamad; Taha, Samir; Chamieh, Hala

    2017-01-01

    Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes. Here we developed an online webserver linked to a specialized protein database named ARCPHdb to provide access for SF1 and SF2 helicase families from archaea. ARCPHdb was implemented using MySQL relational database. Web interfaces were developed using Netbeans. Data were stored according to UniProt accession numbers, NCBI Ref Seq ID, PDB IDs and Entrez Databases. A user-friendly interactive web interface has been developed to browse, search and download archaeal helicase protein sequences, their available 3D structure models, and related documentation available in the literature provided by ARCPHdb. The database provides direct links to matching external databases. The ARCPHdb is the first online database to compile all protein information on SF1 and SF2 helicase from archaea in one platform. This database provides essential resource information for all researchers interested in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

  2. Cancer Stem Cells Therapeutic Target Database: The First Comprehensive Database for Therapeutic Targets of Cancer Stem Cells.

    PubMed

    Hu, Xiaoqing; Cong, Ye; Luo, Huizhe Howard; Wu, Sijin; Zhao, Liyuan Eric; Liu, Quentin; Yang, Yongliang

    2016-09-02

    SummaryCancer stem cells (CSCs) are a subpopulation of tumor cells that have strong self-renewal capabilities and may contribute to the failure of conventional cancer therapies. Hence, therapeutics homing in on CSCs represent a novel and promising approach that may eradicate malignant tumors. However, the lack of information on validated targets of CSCs has greatly hindered the development of CSC-directed therapeutics. Herein, we describe the Cancer Stem Cells Therapeutic Target Database (CSCTT), the first online database to provide a rich bioinformatics resource for the display, search, and analysis of structure, function, and related annotation for therapeutic targets of cancer stem cells. CSCTT contains 135 proteins that are potential targets of CSCs, with validated experimental evidence manually curated from existing literatures. Proteins are carefully annotated with a detailed description of protein families, biological process, related diseases, and experimental evidences. In addition, CSCTT has compiled 213 documented therapeutic methods for cancer stem cells, including 118 small molecules and 20 biotherapy methods. The CSCTT may serve as a useful platform for the development of CSC-directed therapeutics against various malignant tumors. The CSCTT database is freely available to the public at http://www.csctt.org/ SIGNIFICANCE: Although the definition and role of cancer stem cells (CSCs, also called tumor-initiating cells) remain a topic of much debate, increasing evidence suggests that CSCs may be the driving force behind chemotherapy/radiotherapy resistance, as well as metastasis. Consequently, the elimination or differentiation of CSCs is critical for treating malignant tumors and improving clinical outcomes. Unfortunately, the progress of research into the development of anti-CSC therapeutics has been rather slow, and no anti-CSC drugs are yet in clinical use. Hence, there is an urgent need to develop a database that compiles useful information for

  3. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

    PubMed

    Yamasaki, Chisato; Murakami, Katsuhiko; Fujii, Yasuyuki; Sato, Yoshiharu; Harada, Erimi; Takeda, Jun-ichi; Taniya, Takayuki; Sakate, Ryuichi; Kikugawa, Shingo; Shimada, Makoto; Tanino, Motohiko; Koyanagi, Kanako O; Barrero, Roberto A; Gough, Craig; Chun, Hong-Woo; Habara, Takuya; Hanaoka, Hideki; Hayakawa, Yosuke; Hilton, Phillip B; Kaneko, Yayoi; Kanno, Masako; Kawahara, Yoshihiro; Kawamura, Toshiyuki; Matsuya, Akihiro; Nagata, Naoki; Nishikata, Kensaku; Noda, Akiko Ogura; Nurimoto, Shin; Saichi, Naomi; Sakai, Hiroaki; Sanbonmatsu, Ryoko; Shiba, Rie; Suzuki, Mami; Takabayashi, Kazuhiko; Takahashi, Aiko; Tamura, Takuro; Tanaka, Masayuki; Tanaka, Susumu; Todokoro, Fusano; Yamaguchi, Kaori; Yamamoto, Naoyuki; Okido, Toshihisa; Mashima, Jun; Hashizume, Aki; Jin, Lihua; Lee, Kyung-Bum; Lin, Yi-Chueh; Nozaki, Asami; Sakai, Katsunaga; Tada, Masahito; Miyazaki, Satoru; Makino, Takashi; Ohyanagi, Hajime; Osato, Naoki; Tanaka, Nobuhiko; Suzuki, Yoshiyuki; Ikeo, Kazuho; Saitou, Naruya; Sugawara, Hideaki; O'Donovan, Claire; Kulikova, Tamara; Whitfield, Eleanor; Halligan, Brian; Shimoyama, Mary; Twigger, Simon; Yura, Kei; Kimura, Kouichi; Yasuda, Tomohiro; Nishikawa, Tetsuo; Akiyama, Yutaka; Motono, Chie; Mukai, Yuri; Nagasaki, Hideki; Suwa, Makiko; Horton, Paul; Kikuno, Reiko; Ohara, Osamu; Lancet, Doron; Eveno, Eric; Graudens, Esther; Imbeaud, Sandrine; Debily, Marie Anne; Hayashizaki, Yoshihide; Amid, Clara; Han, Michael; Osanger, Andreas; Endo, Toshinori; Thomas, Michael A; Hirakawa, Mika; Makalowski, Wojciech; Nakao, Mitsuteru; Kim, Nam-Soon; Yoo, Hyang-Sook; De Souza, Sandro J; Bonaldo, Maria de Fatima; Niimura, Yoshihito; Kuryshev, Vladimir; Schupp, Ingo; Wiemann, Stefan; Bellgard, Matthew; Shionyu, Masafumi; Jia, Libin; Thierry-Mieg, Danielle; Thierry-Mieg, Jean; Wagner, Lukas; Zhang, Qinghua; Go, Mitiko; Minoshima, Shinsei; Ohtsubo, Masafumi; Hanada, Kousuke; Tonellato, Peter; Isogai, Takao; Zhang, Ji; Lenhard, Boris; Kim, Sangsoo; Chen, Zhu; Hinz, Ursula; Estreicher, Anne; Nakai, Kenta; Makalowska, Izabela; Hide, Winston; Tiffin, Nicola; Wilming, Laurens; Chakraborty, Ranajit; Soares, Marcelo Bento; Chiusano, Maria Luisa; Suzuki, Yutaka; Auffray, Charles; Yamaguchi-Kabata, Yumi; Itoh, Takeshi; Hishiki, Teruyoshi; Fukuchi, Satoshi; Nishikawa, Ken; Sugano, Sumio; Nomura, Nobuo; Tateno, Yoshio; Imanishi, Tadashi; Gojobori, Takashi

    2008-01-01

    Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.

  4. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts*

    PubMed Central

    2008-01-01

    Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein–protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group. PMID:18089548

  5. The Human Intermediate Filament Database: comprehensive information on a gene family involved in many human diseases.

    PubMed

    Szeverenyi, Ildiko; Cassidy, Andrew J; Chung, Cheuk Wang; Lee, Bernett T K; Common, John E A; Ogg, Stephen C; Chen, Huijia; Sim, Shu Yin; Goh, Walter L P; Ng, Kee Woei; Simpson, John A; Chee, Li Lian; Eng, Goi Hui; Li, Bin; Lunny, Declan P; Chuon, Danny; Venkatesh, Aparna; Khoo, Kian Hoe; McLean, W H Irwin; Lim, Yun Ping; Lane, E Birgitte

    2008-03-01

    We describe a revised and expanded database on human intermediate filament proteins, a major component of the eukaryotic cytoskeleton. The family of 70 intermediate filament genes (including those encoding keratins, desmins, and lamins) is now known to be associated with a wide range of diverse diseases, at least 72 distinct human pathologies, including skin blistering, muscular dystrophy, cardiomyopathy, premature aging syndromes, neurodegenerative disorders, and cataract. To date, the database catalogs 1,274 manually-curated pathogenic sequence variants and 170 allelic variants in intermediate filament genes from over 459 peer-reviewed research articles. Unrelated cases were collected from all of the six sequence homology groups and the sequence variations were described at cDNA and protein levels with links to the related diseases and reference articles. The mutations and polymorphisms are presented in parallel with data on protein structure, gene, and chromosomal location and basic information on associated diseases. Detailed statistics relating to the variants records in the database are displayed by homology group, mutation type, affected domain, associated diseases, and nucleic and amino acid substitutions. Multiple sequence alignment algorithms can be run from queries to determine DNA or protein sequence conservation. Literature sources can be interrogated within the database and external links are provided to public databases. The database is freely and publicly accessible online at www.interfil.org (last accessed 13 September 2007). Users can query the database by various keywords and the search results can be downloaded. It is anticipated that the Human Intermediate Filament Database (HIFD) will provide a useful resource to study human genome variations for basic scientists, clinicians, and students alike.

  6. Portfolio of prospective clinical trials including brachytherapy: an analysis of the ClinicalTrials.gov database.

    PubMed

    Cihoric, Nikola; Tsikkinis, Alexandros; Miguelez, Cristina Gutierrez; Strnad, Vratislav; Soldatovic, Ivan; Ghadjar, Pirus; Jeremic, Branislav; Dal Pra, Alan; Aebersold, Daniel M; Lössl, Kristina

    2016-03-22

    To evaluate the current status of prospective interventional clinical trials that includes brachytherapy (BT) procedures. The records of 175,538 (100 %) clinical trials registered at ClinicalTrials.gov were downloaded on September 2014 and a database was established. Trials using BT as an intervention were identified for further analyses. The selected trials were manually categorized according to indication(s), BT source, applied dose rate, primary sponsor type, location, protocol initiator and funding source. We analyzed trials across 8 available trial protocol elements registered within the database. In total 245 clinical trials were identified, 147 with BT as primary investigated treatment modality and 98 that included BT as an optional treatment component or as part of the standard treatment. Academic centers were the most frequent protocol initiators in trials where BT was the primary investigational treatment modality (p < 0.01). High dose rate (HDR) BT was the most frequently investigated type of BT dose rate (46.3 %) followed by low dose rate (LDR) (42.0 %). Prostate was the most frequently investigated tumor entity in trials with BT as the primary treatment modality (40.1 %) followed by breast cancer (17.0 %). BT was rarely the primary investigated treatment modality for cervical cancer (6.8 %). Most clinical trials using BT are predominantly in early phases, investigator-initiated and with low accrual numbers. Current investigational activities that include BT mainly focus on prostate and breast cancers. Important questions concerning the optimal usage of BT will not be answered in the near future.

  7. Phenol-Explorer: an online comprehensive database on polyphenol contents in foods

    PubMed Central

    Neveu, V.; Perez-Jiménez, J.; Vos, F.; Crespy, V.; du Chaffaut, L.; Mennen, L.; Knox, C.; Eisner, R.; Cruz, J.; Wishart, D.; Scalbert, A.

    2010-01-01

    A number of databases on the plant metabolome describe the chemistry and biosynthesis of plant chemicals. However, no such database is specifically focused on foods and more precisely on polyphenols, one of the major classes of phytochemicals. As antoxidants, polyphenols influence human health and may play a role in the prevention of a number of chronic diseases such as cardiovascular diseases, some cancers or type 2 diabetes. To determine polyphenol intake in populations and study their association with health, it is essential to have detailed information on their content in foods. However this information is not easily collected due to the variety of their chemical structures and the variability of their content in a given food. Phenol-Explorer is the first comprehensive web-based database on polyphenol content in foods. It contains more than 37 000 original data points collected from 638 scientific articles published in peer-reviewed journals. The quality of these data has been evaluated before they were aggregated to produce final representative mean content values for 502 polyphenols in 452 foods. The web interface allows making various queries on the aggregated data to identify foods containing a given polyphenol or polyphenols present in a given food. For each mean content value, it is possible to trace all original content values and their literature sources. Phenol-Explorer is a major step forward in the development of databases on food constituents and the food metabolome. It should help researchers to better understand the role of phytochemicals in the technical and nutritional quality of food, and food manufacturers to develop tailor-made healthy foods. Database URL: http://www.phenol-explorer.eu PMID:20428313

  8. A comprehensive change detection method for updating the National Land Cover Database to circa 2011

    USGS Publications Warehouse

    Jin, Suming; Yang, Limin; Danielson, Patrick; Homer, Collin G.; Fry, Joyce; Xian, George

    2013-01-01

    The importance of characterizing, quantifying, and monitoring land cover, land use, and their changes has been widely recognized by global and environmental change studies. Since the early 1990s, three U.S. National Land Cover Database (NLCD) products (circa 1992, 2001, and 2006) have been released as free downloads for users. The NLCD 2006 also provides land cover change products between 2001 and 2006. To continue providing updated national land cover and change datasets, a new initiative in developing NLCD 2011 is currently underway. We present a new Comprehensive Change Detection Method (CCDM) designed as a key component for the development of NLCD 2011 and the research results from two exemplar studies. The CCDM integrates spectral-based change detection algorithms including a Multi-Index Integrated Change Analysis (MIICA) model and a novel change model called Zone, which extracts change information from two Landsat image pairs. The MIICA model is the core module of the change detection strategy and uses four spectral indices (CV, RCVMAX, dNBR, and dNDVI) to obtain the changes that occurred between two image dates. The CCDM also includes a knowledge-based system, which uses critical information on historical and current land cover conditions and trends and the likelihood of land cover change, to combine the changes from MIICA and Zone. For NLCD 2011, the improved and enhanced change products obtained from the CCDM provide critical information on location, magnitude, and direction of potential change areas and serve as a basis for further characterizing land cover changes for the nation. An accuracy assessment from the two study areas show 100% agreement between CCDM mapped no-change class with reference dataset, and 18% and 82% disagreement for the change class for WRS path/row p22r39 and p33r33, respectively. The strength of the CCDM is that the method is simple, easy to operate, widely applicable, and capable of capturing a variety of natural and

  9. Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources.

    PubMed

    Wu, Linhuan; Sun, Qinglan; Sugawara, Hideaki; Yang, Song; Zhou, Yuguang; McCluskey, Kevin; Vasilenko, Alexander; Suzuki, Ken-Ichiro; Ohkuma, Moriya; Lee, Yeonhee; Robert, Vincent; Ingsriswang, Supawadee; Guissart, François; Philippe, Desmeth; Ma, Juncai

    2013-12-30

    Throughout the long history of industrial and academic research, many microbes have been isolated, characterized and preserved (whenever possible) in culture collections. With the steady accumulation in observational data of biodiversity as well as microbial sequencing data, bio-resource centers have to function as data and information repositories to serve academia, industry, and regulators on behalf of and for the general public. Hence, the World Data Centre for Microorganisms (WDCM) started to take its responsibility for constructing an effective information environment that would promote and sustain microbial research data activities, and bridge the gaps currently present within and outside the microbiology communities. Strain catalogue information was collected from collections by online submission. We developed tools for automatic extraction of strain numbers and species names from various sources, including Genbank, Pubmed, and SwissProt. These new tools connect strain catalogue information with the corresponding nucleotide and protein sequences, as well as to genome sequence and references citing a particular strain. All information has been processed and compiled in order to create a comprehensive database of microbial resources, and was named Global Catalogue of Microorganisms (GCM). The current version of GCM contains information of over 273,933 strains, which includes 43,436 bacterial, fungal and archaea species from 52 collections in 25 countries and regions.A number of online analysis and statistical tools have been integrated, together with advanced search functions, which should greatly facilitate the exploration of the content of GCM. A comprehensive dynamic database of microbial resources has been created, which unveils the resources preserved in culture collections especially for those whose informatics infrastructures are still under development, which should foster cumulative research, facilitating the activities of microbiologists world

  10. Global catalogue of microorganisms (gcm): a comprehensive database and information retrieval, analysis, and visualization system for microbial resources

    PubMed Central

    2013-01-01

    Background Throughout the long history of industrial and academic research, many microbes have been isolated, characterized and preserved (whenever possible) in culture collections. With the steady accumulation in observational data of biodiversity as well as microbial sequencing data, bio-resource centers have to function as data and information repositories to serve academia, industry, and regulators on behalf of and for the general public. Hence, the World Data Centre for Microorganisms (WDCM) started to take its responsibility for constructing an effective information environment that would promote and sustain microbial research data activities, and bridge the gaps currently present within and outside the microbiology communities. Description Strain catalogue information was collected from collections by online submission. We developed tools for automatic extraction of strain numbers and species names from various sources, including Genbank, Pubmed, and SwissProt. These new tools connect strain catalogue information with the corresponding nucleotide and protein sequences, as well as to genome sequence and references citing a particular strain. All information has been processed and compiled in order to create a comprehensive database of microbial resources, and was named Global Catalogue of Microorganisms (GCM). The current version of GCM contains information of over 273,933 strains, which includes 43,436bacterial, fungal and archaea species from 52 collections in 25 countries and regions. A number of online analysis and statistical tools have been integrated, together with advanced search functions, which should greatly facilitate the exploration of the content of GCM. Conclusion A comprehensive dynamic database of microbial resources has been created, which unveils the resources preserved in culture collections especially for those whose informatics infrastructures are still under development, which should foster cumulative research, facilitating the

  11. A European Flood Database: facilitating comprehensive flood research beyond administrative boundaries

    NASA Astrophysics Data System (ADS)

    Hall, J.; Arheimer, B.; Aronica, G. T.; Bilibashi, A.; Boháč, M.; Bonacci, O.; Borga, M.; Burlando, P.; Castellarin, A.; Chirico, G. B.; Claps, P.; Fiala, K.; Gaál, L.; Gorbachova, L.; Gül, A.; Hannaford, J.; Kiss, A.; Kjeldsen, T.; Kohnová, S.; Koskela, J. J.; Macdonald, N.; Mavrova-Guirguinova, M.; Ledvinka, O.; Mediero, L.; Merz, B.; Merz, R.; Molnar, P.; Montanari, A.; Osuch, M.; Parajka, J.; Perdigão, R. A. P.; Radevski, I.; Renard, B.; Rogger, M.; Salinas, J. L.; Sauquet, E.; Šraj, M.; Szolgay, J.; Viglione, A.; Volpi, E.; Wilson, D.; Zaimi, K.; Blöschl, G.

    2015-06-01

    The current work addresses one of the key building blocks towards an improved understanding of flood processes and associated changes in flood characteristics and regimes in Europe: the development of a comprehensive, extensive European flood database. The presented work results from ongoing cross-border research collaborations initiated with data collection and joint interpretation in mind. A detailed account of the current state, characteristics and spatial and temporal coverage of the European Flood Database, is presented. At this stage, the hydrological data collection is still growing and consists at this time of annual maximum and daily mean discharge series, from over 7000 hydrometric stations of various data series lengths. Moreover, the database currently comprises data from over 50 different data sources. The time series have been obtained from different national and regional data sources in a collaborative effort of a joint European flood research agreement based on the exchange of data, models and expertise, and from existing international data collections and open source websites. These ongoing efforts are contributing to advancing the understanding of regional flood processes beyond individual country boundaries and to a more coherent flood research in Europe.

  12. Development of a Publicly Available, Comprehensive Database of Fiber and Health Outcomes: Rationale and Methods

    PubMed Central

    Livingston, Kara A.; Chung, Mei; Sawicki, Caleigh M.; Lyle, Barbara J.; Wang, Ding Ding; Roberts, Susan B.; McKeown, Nicola M.

    2016-01-01

    Background Dietary fiber is a broad category of compounds historically defined as partially or completely indigestible plant-based carbohydrates and lignin with, more recently, the additional criteria that fibers incorporated into foods as additives should demonstrate functional human health outcomes to receive a fiber classification. Thousands of research studies have been published examining fibers and health outcomes. Objectives (1) Develop a database listing studies testing fiber and physiological health outcomes identified by experts at the Ninth Vahouny Conference; (2) Use evidence mapping methodology to summarize this body of literature. This paper summarizes the rationale, methodology, and resulting database. The database will help both scientists and policy-makers to evaluate evidence linking specific fibers with physiological health outcomes, and identify missing information. Methods To build this database, we conducted a systematic literature search for human intervention studies published in English from 1946 to May 2015. Our search strategy included a broad definition of fiber search terms, as well as search terms for nine physiological health outcomes identified at the Ninth Vahouny Fiber Symposium. Abstracts were screened using a priori defined eligibility criteria and a low threshold for inclusion to minimize the likelihood of rejecting articles of interest. Publications then were reviewed in full text, applying additional a priori defined exclusion criteria. The database was built and published on the Systematic Review Data Repository (SRDR™), a web-based, publicly available application. Conclusions A fiber database was created. This resource will reduce the unnecessary replication of effort in conducting systematic reviews by serving as both a central database archiving PICO (population, intervention, comparator, outcome) data on published studies and as a searchable tool through which this data can be extracted and updated. PMID:27348733

  13. dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock.

    PubMed

    Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar; Mishra, Barada Kanta

    2016-01-01

    Microalgae have attracted wide attention as one of the most versatile renewable feedstocks for production of biofuel. To develop genetically engineered high lipid yielding algal strains, a thorough understanding of the lipid biosynthetic pathway and the underpinning enzymes is essential. In this work, we have systematically mined the genomes of fifteen diverse algal species belonging to Chlorophyta, Heterokontophyta, Rhodophyta, and Haptophyta, to identify and annotate the putative enzymes of lipid metabolic pathway. Consequently, we have also developed a database, dEMBF (Database of Enzymes of Microalgal Biofuel Feedstock), which catalogues the complete list of identified enzymes along with their computed annotation details including length, hydrophobicity, amino acid composition, subcellular location, gene ontology, KEGG pathway, orthologous group, Pfam domain, intron-exon organization, transmembrane topology, and secondary/tertiary structural data. Furthermore, to facilitate functional and evolutionary study of these enzymes, a collection of built-in applications for BLAST search, motif identification, sequence and phylogenetic analysis have been seamlessly integrated into the database. dEMBF is the first database that brings together all enzymes responsible for lipid synthesis from available algal genomes, and provides an integrative platform for enzyme inquiry and analysis. This database will be extremely useful for algal biofuel research. It can be accessed at http://bbprof.immt.res.in/embf.

  14. dEMBF: A Comprehensive Database of Enzymes of Microalgal Biofuel Feedstock

    PubMed Central

    Misra, Namrata; Panda, Prasanna Kumar; Parida, Bikram Kumar; Mishra, Barada Kanta

    2016-01-01

    Microalgae have attracted wide attention as one of the most versatile renewable feedstocks for production of biofuel. To develop genetically engineered high lipid yielding algal strains, a thorough understanding of the lipid biosynthetic pathway and the underpinning enzymes is essential. In this work, we have systematically mined the genomes of fifteen diverse algal species belonging to Chlorophyta, Heterokontophyta, Rhodophyta, and Haptophyta, to identify and annotate the putative enzymes of lipid metabolic pathway. Consequently, we have also developed a database, dEMBF (Database of Enzymes of Microalgal Biofuel Feedstock), which catalogues the complete list of identified enzymes along with their computed annotation details including length, hydrophobicity, amino acid composition, subcellular location, gene ontology, KEGG pathway, orthologous group, Pfam domain, intron-exon organization, transmembrane topology, and secondary/tertiary structural data. Furthermore, to facilitate functional and evolutionary study of these enzymes, a collection of built-in applications for BLAST search, motif identification, sequence and phylogenetic analysis have been seamlessly integrated into the database. dEMBF is the first database that brings together all enzymes responsible for lipid synthesis from available algal genomes, and provides an integrative platform for enzyme inquiry and analysis. This database will be extremely useful for algal biofuel research. It can be accessed at http://bbprof.immt.res.in/embf. PMID:26727469

  15. Feasibility of including green tea products for an analytically verified dietary supplement database

    USDA-ARS?s Scientific Manuscript database

    The Dietary Supplement Ingredient Database (DSID) is a federally-funded, publically-accessible dietary supplement database that currently contains analytically derived information on micronutrients in selected adult and children’s multivitamin and mineral (MVM) supplements. Other constituents in di...

  16. WATCHDOG: A COMPREHENSIVE ALL-SKY DATABASE OF GALACTIC BLACK HOLE X-RAY BINARIES

    SciTech Connect

    Tetarenko, B. E.; Sivakoff, G. R.; Heinke, C. O.; Gladstone, J. C.

    2016-02-15

    With the advent of more sensitive all-sky instruments, the transient universe is being probed in greater depth than ever before. Taking advantage of available resources, we have established a comprehensive database of black hole (and black hole candidate) X-ray binary (BHXB) activity between 1996 and 2015 as revealed by all-sky instruments, scanning surveys, and select narrow-field X-ray instruments on board the INTErnational Gamma-Ray Astrophysics Laboratory, Monitor of All-Sky X-ray Image, Rossi X-ray Timing Explorer, and Swift telescopes; the Whole-sky Alberta Time-resolved Comprehensive black-Hole Database Of the Galaxy or WATCHDOG. Over the past two decades, we have detected 132 transient outbursts, tracked and classified behavior occurring in 47 transient and 10 persistently accreting BHs, and performed a statistical study on a number of outburst properties across the Galactic population. We find that outbursts undergone by BHXBs that do not reach the thermally dominant accretion state make up a substantial fraction (∼40%) of the Galactic transient BHXB outburst sample over the past ∼20 years. Our findings suggest that this “hard-only” behavior, observed in transient and persistently accreting BHXBs, is neither a rare nor recent phenomenon and may be indicative of an underlying physical process, relatively common among binary BHs, involving the mass-transfer rate onto the BH remaining at a low level rather than increasing as the outburst evolves. We discuss how the larger number of these “hard-only” outbursts and detected outbursts in general have significant implications for both the luminosity function and mass-transfer history of the Galactic BHXB population.

  17. An Expanded UV Irradiance Database from TOMS Including the Effects of Ozone, Clouds, and Aerosol Attenuation

    NASA Technical Reports Server (NTRS)

    Herman, J.; Krotkov, N.

    2003-01-01

    The TOMS UV irradiance database (1978 to 2003) has been expanded to include five new products (noon irradiance at 305,310,324, and 380 nm, and noon erythemal-weighted irradiance), in addition to the existing erythemal daily exposure, that permit direct comparisons with ground-based measurements from spectrometers and broadband instruments. The new data are available on http://toms.gsfc.nasa.gov/>http://toms.gsfc.nasa.gov. Comparisons of the TOMS estimated irradiances with ground-based instruments are given along with a review of the sources of known errors, especially the recent improvements in accounting for aerosol attenuation. Trend estimations from the new TOMS irradiances permit the clear separation of changes caused by ozone and those caused by aerosols and clouds. Systematic differences in cloud cover are shown to be the most important factor in determining regional differences in UV radiation reaching the ground for locations at the same latitude (e.g., the summertime differences between Australia and the US southwest).

  18. An automated DICOM database capable of arbitrary data mining (including radiation dose indicators) for quality monitoring.

    PubMed

    Wang, Shanshan; Pavlicek, William; Roberts, Catherine C; Langer, Steve G; Zhang, Muhong; Hu, Mengqi; Morin, Richard L; Schueler, Beth A; Wellnitz, Clinton V; Wu, Teresa

    2011-04-01

    The U.S. National Press has brought to full public discussion concerns regarding the use of medical radiation, specifically x-ray computed tomography (CT), in diagnosis. A need exists for developing methods whereby assurance is given that all diagnostic medical radiation use is properly prescribed, and all patients' radiation exposure is monitored. The "DICOM Index Tracker©" (DIT) transparently captures desired digital imaging and communications in medicine (DICOM) tags from CT, nuclear imaging equipment, and other DICOM devices across an enterprise. Its initial use is recording, monitoring, and providing automatic alerts to medical professionals of excursions beyond internally determined trigger action levels of radiation. A flexible knowledge base, aware of equipment in use, enables automatic alerts to system administrators of newly identified equipment models or software versions so that DIT can be adapted to the new equipment or software. A dosimetry module accepts mammography breast organ dose, skin air kerma values from XA modalities, exposure indices from computed radiography, etc. upon receipt. The American Association of Physicists in Medicine recommended a methodology for effective dose calculations which are performed with CT units having DICOM structured dose reports. Web interface reporting is provided for accessing the database in real-time. DIT is DICOM-compliant and, thus, is standardized for international comparisons. Automatic alerts currently in use include: email, cell phone text message, and internal pager text messaging. This system extends the utility of DICOM for standardizing the capturing and computing of radiation dose as well as other quality measures.

  19. A Comprehensive List of Items to be Included on a Pediatric Drug Monograph.

    PubMed

    Kelly, Lauren E; Ito, Shinya; Woods, David; Nunn, Anthony J; Taketomo, Carol; de Hoog, Matthijs; Offringa, Martin

    2017-01-01

    Children require special considerations for drug prescribing. Drug information summarized in a formulary containing drug monographs is essential for safe and effective prescribing. Currently, little is known about the information needs of those who prescribe and administer medicines to children. Our primary objective was to identify a list of important and relevant items to be included in a pediatric drug monograph. Following the establishment of an expert steering committee and an environmental scan of adult and pediatric formulary monograph items, 46 participants from 25 countries were invited to complete a 2-round Delphi survey. Questions regarding source of prescribing information and importance of items were recorded. An international consensus meeting to vote on and finalize the items list with the steering committee followed. Pediatric formularies are most commonly the first resource consulted for information on medication used in children by 31 Delphi participants. After the Delphi rounds, 116 items were identified to be included in a comprehensive pediatric drug monograph, including general information, adverse drug reactions, dosages, precautions, drug-drug interactions, formulation, and drug properties. Health care providers identified 116 monograph items as important for prescribing medicines for children by an international consensus-based process. This information will assist in setting standards for the creation of new pediatric drug monographs for international application and for those involved in pediatric formulary development.

  20. A Comprehensive List of Items to be Included on a Pediatric Drug Monograph

    PubMed Central

    Ito, Shinya; Woods, David; Nunn, Anthony J.; Taketomo, Carol; de Hoog, Matthijs; Offringa, Martin

    2017-01-01

    OBJECTIVES Children require special considerations for drug prescribing. Drug information summarized in a formulary containing drug monographs is essential for safe and effective prescribing. Currently, little is known about the information needs of those who prescribe and administer medicines to children. Our primary objective was to identify a list of important and relevant items to be included in a pediatric drug monograph. METHODS Following the establishment of an expert steering committee and an environmental scan of adult and pediatric formulary monograph items, 46 participants from 25 countries were invited to complete a 2-round Delphi survey. Questions regarding source of prescribing information and importance of items were recorded. An international consensus meeting to vote on and finalize the items list with the steering committee followed. RESULTS Pediatric formularies are most commonly the first resource consulted for information on medication used in children by 31 Delphi participants. After the Delphi rounds, 116 items were identified to be included in a comprehensive pediatric drug monograph, including general information, adverse drug reactions, dosages, precautions, drug-drug interactions, formulation, and drug properties. CONCLUSIONS Health care providers identified 116 monograph items as important for prescribing medicines for children by an international consensus-based process. This information will assist in setting standards for the creation of new pediatric drug monographs for international application and for those involved in pediatric formulary development.

  1. The Modern Black Hole X-Ray Binary Database: A Comprehensive All-Sky Observational Study

    NASA Astrophysics Data System (ADS)

    Tetarenko, Bailey; Sivakoff, Gregory R.; Heinke, Craig O.; Gladstone, Jeanette C

    2014-08-01

    Stellar mass black holes accreting in binary systems provide valuable insight into how binary systems evolve and how mass is transferred via accretion. With the advent of more sensitive all-sky X-ray instruments like the Swift Burst Alert Transient Monitor (BAT) and the Monitor of All-Sky X-ray Image (MAXI) telescope, the transient X-ray Universe is being probed in greater depth than ever before. Taking advantage of these resources, we have established a comprehensive database of black hole (and black hole candidate) X-ray binary activity over the last 18 years as revealed by all-sky X-ray instruments and scanning surveys. As a result, we have detected over 90 outbursts occurring in 43 transient BHXRBs, and estimate that current instruments can detect ~ 6-12 transient BHXRB outbursts every year, more than a factor of three larger than is commonly assumed. Most significantly, we find that the outbursts undergone by BHXRBs that do not complete the canonical pattern make up ~ 50% of all outbursts occurring in Galactic BHXRBs. Such a high fraction of "failed" outbursts challenges the standard paradigm for accretion behaviour in transient BHXRBs. We present the detailed findings of our database and discuss how both the larger number of these so-called "failed" outbursts and the BHXRB outbursts in general have significant implications for the mass-transfer history of the Galactic BHXRB population.

  2. The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources.

    PubMed

    Arnaud, Martha B; Cerqueira, Gustavo C; Inglis, Diane O; Skrzypek, Marek S; Binkley, Jonathan; Chibucos, Marcus C; Crabtree, Jonathan; Howarth, Clinton; Orvis, Joshua; Shah, Prachi; Wymore, Farrell; Binkley, Gail; Miyasato, Stuart R; Simison, Matt; Sherlock, Gavin; Wortman, Jennifer R

    2012-01-01

    The Aspergillus Genome Database (AspGD; http://www.aspgd.org) is a freely available, web-based resource for researchers studying fungi of the genus Aspergillus, which includes organisms of clinical, agricultural and industrial importance. AspGD curators have now completed comprehensive review of the entire published literature about Aspergillus nidulans and Aspergillus fumigatus, and this annotation is provided with streamlined, ortholog-based navigation of the multispecies information. AspGD facilitates comparative genomics by providing a full-featured genomics viewer, as well as matched and standardized sets of genomic information for the sequenced aspergilli. AspGD also provides resources to foster interaction and dissemination of community information and resources. We welcome and encourage feedback at aspergillus-curator@lists.stanford.edu.

  3. The Global Paleomagnetic Database Should Include Specimen-Level Demagnetization Data

    NASA Astrophysics Data System (ADS)

    Kirschvink, J. L.; Kazansky, A.

    2002-12-01

    In their description of the paleomagnetic database, McElhinny and Smethurst [1] provided a reasonable description of the status quo in terms of compiling and storing a quantitative summary of the results from the past 50 years of paleomagnetic investigation. However, recent developments in science and technology have far outpaced the response of the paleomagnetic community on the issue of data archive and storage, and as a consequence this field risks being left in the dust. It is our opinion that the database should be expanded to include the entire set of specimen-level demagnetization data that go into a paleomagnetic study, along with the interpretation made by the authors. A simple back-of-the-envelope estimate suggests that all the raw paleomagnetic demagnetization data generated in the past 50 years would fit easily on a single hard drive of a personal computer. Other fields are doing precisely this type of the data archiving -- for example, nothing is accepted for publication in the good, peer-reviewed molecular genetics journals until the raw sequence data have been deposited in one of the internationally-accepted genetic databanks. As we feel that geophysics is in no way inferior to genetics, we should have no fear of archiving our data and making it publicly available in a similar fashion. The actual process of measuring and demagnetizing typical paleomagnetic materials has not changed much in the 30 years since the introduction of superconducting magnetometers, with most studies still utilizing some combination of alternating field, thermal, microwave, or chemical demagnetization to isolate the principal magnetic components (although the number of demagnetization steps per specimen has certainly improved with the increasing use of automation). In contrast, techniques for the analysis of paleomagnetic data have improved substantially (e.g., [2,3]). Hence, public access to the archived raw demagnetization data would not only allow independent scrutiny of

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

    PubMed Central

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

    2015-01-01

    With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com PMID:25887162

  5. Comprehensive database of Manufactured Gas Plant tars. Part C. Heterocyclic and hydroxylated polycyclic aromatic hydrocarbons.

    PubMed

    Gallacher, Christopher; Thomas, Russell; Lord, Richard; Kalin, Robert M; Taylor, Chris

    2017-08-15

    Coal tars are a mixture of organic and inorganic compounds that were by-products from the manufactured gas and coke making industries. The tar compositions varied depending on many factors such as the temperature of production and the type of retort used. For this reason a comprehensive database of the compounds found in different tar types is of value to understand both how their compositions differ and what potential chemical hazards are present. This study focuses on the heterocyclic and hydroxylated compounds present in a database produced from 16 different tars from five different production processes. Samples of coal tar were extracted using accelerated solvent extraction (ASE) and derivatized post-extraction using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) with 1% trimethylchlorosilane (TMCS). The derivatized samples were analysed using two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GCxGC/TOFMS). A total of 865 heterocyclic compounds and 359 hydroxylated polycyclic aromatic hydrocarbons (PAHs) were detected in 16 tar samples produced by five different processes. The contents of both heterocyclic and hydroxylated PAHs varied greatly with the production process used, with the heterocyclic compounds giving information about the feedstock used. Of the 359 hydroxylated PAHs detected the majority would not have been be detected without the use of derivatization. Coal tars produced using different production processes and feedstocks yielded tars with significantly different heterocyclic and hydroxylated contents. The concentrations of the individual heterocyclic compounds varied greatly even within the different production processes and provided information about the feedstock used to produce the tars. The hydroxylated PAH content of the samples provided important analytical information that would otherwise not have been obtained without the use of derivatization and GCxGC/TOFMS. Copyright © 2017 John Wiley & Sons, Ltd.

  6. A Comprehensive Opacities/Atomic Database for the Analysis of Astrophysical Spectra and Modeling

    NASA Technical Reports Server (NTRS)

    Pradhan, Anil K. (Principal Investigator)

    1997-01-01

    The main goals of this ADP award have been accomplished. The electronic database TOPBASE, consisting of the large volume of atomic data from the Opacity Project, has been installed and is operative at a NASA site at the Laboratory for High Energy Astrophysics Science Research Center (HEASRC) at the Goddard Space Flight Center. The database will be continually maintained and updated by the PI and collaborators. TOPBASE is publicly accessible from IP: topbase.gsfc.nasa.gov. During the last six months (since the previous progress report), considerable work has been carried out to: (1) put in the new data for low ionization stages of iron: Fe I - V, beginning with Fe II, (2) high-energy photoionization cross sections computed by Dr. Hong Lin Zhang (consultant on the Project) were 'merged' with the current Opacity Project data and input into TOPbase; (3) plans laid out for a further extension of TOPbase to include TIPbase, the database for collisional data to complement the radiative data in TOPbase.

  7. Feasibility of Including Green Tea Products for an Analytically Verified Dietary Supplement Database

    PubMed Central

    Saldanha, Leila; Dwyer, Johanna; Andrews, Karen; Betz, Joseph; Harnely, James; Pehrsson, Pamela; Rimmer, Catherine; Savarala, Sushma

    2015-01-01

    The Dietary Supplement Ingredient Database (DSID) is a federally funded, publicly accessible dietary supplement database that currently contains analytically-derived information on micronutrients in selected adult and children’s multivitamin and mineral (MVM) supplements. Other constituents in dietary supplement products such as botanicals are also of interest and thus are being considered for inclusion in the DSID. Thirty-eight constituents, mainly botanicals were identified and prioritized by a federal interagency committee. Green tea was selected from this list as the botanical for expansion of the DSID. This paper describes the process for prioritizing dietary ingredients in the DSID. It also discusses the criteria for inclusion of these ingredients, and the approach for selecting and testing products for the green tea pilot study. PMID:25817236

  8. Chemical composition of ferromanganese crusts in the world ocean: a review and comprehensive database

    USGS Publications Warehouse

    Manheim, Frank T.; Lane-Bostwick, Candice M.

    1989-01-01

    A comprehensive database of chemical and mineralogical properties for ferromanganese crusts collected throughout the Atlantic, Pacific, and Indian Oceans, and has been assembled from published and unpublished sources which provide collection and analytical information for these samples. These crusts, their chemical compositions and natural distribution, have been a topic of interest to scientific research, as well as to industrial and military applications. Unlike abyssal ferromanganese nodules, which form in areas of low disturbance and high sediment accumulation, crusts have been found to contain three to five times more cobalt than these nodules, and can be found on harder, steeper substrates which can be too steep for permanent sediment accumulation. They have also been documented on seamounts and plateaus within the U.S. exclusive economic zone in both Pacific and Atlantic Oceans, and these are therefore of strategic importance to the United States Government, as well as to civilian mining and metallurgical industries. The data tables provided in this report have been digitized and previously uploaded to the National Oceanic and Atmospheric Administration National Geophysical Data Center in 1991 for online distribution, and were provided in plain text format. The 2014 update to the original U.S. Geological Survey open-file report published in 1989 provides these data tables in a slightly reformatted version to make them easier to ingest into geographic information system software, converted to shapefiles, and have completed metadata written and associated with them.

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

    PubMed

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

    2017-04-01

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

  10. Developing a comprehensive database management system for organization and evaluation of mammography datasets.

    PubMed

    Wu, Yirong; Rubin, Daniel L; Woods, Ryan W; Elezaby, Mai; Burnside, Elizabeth S

    2014-01-01

    We aimed to design and develop a comprehensive mammography database system (CMDB) to collect clinical datasets for outcome assessment and development of decision support tools. A Health Insurance Portability and Accountability Act (HIPAA) compliant CMDB was created to store multi-relational datasets of demographic risk factors and mammogram results using the Breast Imaging Reporting and Data System (BI-RADS) lexicon. The CMDB collected both biopsy pathology outcomes, in a breast pathology lexicon compiled by extending BI-RADS, and our institutional breast cancer registry. The audit results derived from the CMDB were in accordance with Mammography Quality Standards Act (MQSA) audits and national benchmarks. The CMDB has managed the challenges of multi-level organization demanded by the complexity of mammography practice and lexicon development in pathology. We foresee that the CMDB will be useful for efficient quality assurance audits and development of decision support tools to improve breast cancer diagnosis. Our procedure of developing the CMDB provides a framework to build a detailed data repository for breast imaging quality control and research, which has the potential to augment existing resources.

  11. Developing a Comprehensive Database Management System for Organization and Evaluation of Mammography Datasets

    PubMed Central

    Wu, Yirong; Rubin, Daniel L; Woods, Ryan W; Elezaby, Mai; Burnside, Elizabeth S

    2014-01-01

    We aimed to design and develop a comprehensive mammography database system (CMDB) to collect clinical datasets for outcome assessment and development of decision support tools. A Health Insurance Portability and Accountability Act (HIPAA) compliant CMDB was created to store multi-relational datasets of demographic risk factors and mammogram results using the Breast Imaging Reporting and Data System (BI-RADS) lexicon. The CMDB collected both biopsy pathology outcomes, in a breast pathology lexicon compiled by extending BI-RADS, and our institutional breast cancer registry. The audit results derived from the CMDB were in accordance with Mammography Quality Standards Act (MQSA) audits and national benchmarks. The CMDB has managed the challenges of multi-level organization demanded by the complexity of mammography practice and lexicon development in pathology. We foresee that the CMDB will be useful for efficient quality assurance audits and development of decision support tools to improve breast cancer diagnosis. Our procedure of developing the CMDB provides a framework to build a detailed data repository for breast imaging quality control and research, which has the potential to augment existing resources. PMID:25368510

  12. EpiFactors: a comprehensive database of human epigenetic factors and complexes

    PubMed Central

    Medvedeva, Yulia A.; Lennartsson, Andreas; Ehsani, Rezvan; Kulakovskiy, Ivan V.; Vorontsov, Ilya E.; Panahandeh, Pouda; Khimulya, Grigory; Kasukawa, Takeya; Drabløs, Finn

    2015-01-01

    Epigenetics refers to stable and long-term alterations of cellular traits that are not caused by changes in the DNA sequence per se. Rather, covalent modifications of DNA and histones affect gene expression and genome stability via proteins that recognize and act upon such modifications. Many enzymes that catalyse epigenetic modifications or are critical for enzymatic complexes have been discovered, and this is encouraging investigators to study the role of these proteins in diverse normal and pathological processes. Rapidly growing knowledge in the area has resulted in the need for a resource that compiles, organizes and presents curated information to the researchers in an easily accessible and user-friendly form. Here we present EpiFactors, a manually curated database providing information about epigenetic regulators, their complexes, targets and products. EpiFactors contains information on 815 proteins, including 95 histones and protamines. For 789 of these genes, we include expressions values across several samples, in particular a collection of 458 human primary cell samples (for approximately 200 cell types, in many cases from three individual donors), covering most mammalian cell steady states, 255 different cancer cell lines (representing approximately 150 cancer subtypes) and 134 human postmortem tissues. Expression values were obtained by the FANTOM5 consortium using Cap Analysis of Gene Expression technique. EpiFactors also contains information on 69 protein complexes that are involved in epigenetic regulation. The resource is practical for a wide range of users, including biologists, pharmacologists and clinicians. Database URL: http://epifactors.autosome.ru PMID:26153137

  13. GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis

    PubMed Central

    Araki, Hiromitsu; Knapp, Christoph; Tsai, Peter; Print, Cristin

    2012-01-01

    Most “omics” experiments require comprehensive interpretation of the biological meaning of gene lists. To address this requirement, a number of gene set analysis (GSA) tools have been developed. Although the biological value of GSA is strictly limited by the breadth of the gene sets used, very few methods exist for simultaneously analysing multiple publically available gene set databases. Therefore, we constructed GeneSetDB (http://genesetdb.auckland.ac.nz/haeremai.html), a comprehensive meta-database, which integrates 26 public databases containing diverse biological information with a particular focus on human disease and pharmacology. GeneSetDB enables users to search for gene sets containing a gene identifier or keyword, generate their own gene sets, or statistically test for enrichment of an uploaded gene list across all gene sets, and visualise gene set enrichment and overlap using a clustered heat map. PMID:23650583

  14. GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis.

    PubMed

    Araki, Hiromitsu; Knapp, Christoph; Tsai, Peter; Print, Cristin

    2012-01-01

    Most "omics" experiments require comprehensive interpretation of the biological meaning of gene lists. To address this requirement, a number of gene set analysis (GSA) tools have been developed. Although the biological value of GSA is strictly limited by the breadth of the gene sets used, very few methods exist for simultaneously analysing multiple publically available gene set databases. Therefore, we constructed GeneSetDB (http://genesetdb.auckland.ac.nz/haeremai.html), a comprehensive meta-database, which integrates 26 public databases containing diverse biological information with a particular focus on human disease and pharmacology. GeneSetDB enables users to search for gene sets containing a gene identifier or keyword, generate their own gene sets, or statistically test for enrichment of an uploaded gene list across all gene sets, and visualise gene set enrichment and overlap using a clustered heat map.

  15. A User’s Guide to the Comprehensive Water Quality Database for Groundwater in the Vicinity of the Nevada Test Site, Rev. No.: 1

    SciTech Connect

    Farnham, Irene

    2006-09-01

    This water quality database (viz.GeochemXX.mdb) has been developed as part of the Underground Test Area (UGTA) Program with the cooperation of several agencies actively participating in ongoing evaluation and characterization activities under contract to the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Site Office (NNSA/NSO). The database has been constructed to provide up-to-date, comprehensive, and quality controlled data in a uniform format for the support of current and future projects. This database provides a valuable tool for geochemical and hydrogeologic evaluations of the Nevada Test Site (NTS) and surrounding region. Chemistry data have been compiled for groundwater within the NTS and the surrounding region. These data include major ions, organic compounds, trace elements, radionuclides, various field parameters, and environmental isotopes. Colloid data are also included in the database. The GeochemXX.mdb database is distributed on an annual basis. The extension ''XX'' within the database title is replaced by the last two digits of the release year (e.g., Geochem06 for the version released during the 2006 fiscal year). The database is distributed via compact disc (CD) and is also uploaded to the Common Data Repository (CDR) in order to make it available to all agencies with DOE intranet access. This report provides an explanation of the database configuration and summarizes the general content and utility of the individual data tables. In addition to describing the data, subsequent sections of this report provide the data user with an explanation of the quality assurance/quality control (QA/QC) protocols for this database.

  16. InDiaMed: A Comprehensive Database of Indian Medicinal plants for Diabetes

    PubMed Central

    Tota, Kumudini; Rayabarapu, Nihar; Moosa, Sowmya; Talla, Venu; Bhyravbhatla, Balaji; Rao, Srinivasa

    2013-01-01

    According to International Diabetes Federation (IDF), India has 62.4 million people with diabetes and by 2030 it is predicted that the number will rise to 100 million. Studies claim that there are around 410 experimentally proven Indian medicinal plants which have anti-diabetic activity, of which the mechanism of action of 109 plants has been elucidated or reported. So, the need of the hour is to explore the claims of Indian medicinal flora and open up the facets of many Indian plants which are being examined for their beneficial role in diabetes. So, we created a database (InDiaMed) of Indian medicinal plants that captures their role in anti-diabetic activity. InDiaMed's features include chemical, pharmacological, biochemical and geographical information of the medicinal plant, scientifically relevant information of the plant, and the coherent research done on it in the field of diabetes. The database also includes the list of poly-herbal formulations which are used for treatment of diabetes in India. Availability http://www.indiamed.info PMID:23750084

  17. A comprehensive database of quality-rated fossil ages for Sahul’s Quaternary vertebrates

    PubMed Central

    Rodríguez-Rey, Marta; Herrando-Pérez, Salvador; Brook, Barry W.; Saltré, Frédérik; Alroy, John; Beeton, Nicholas; Bird, Michael I.; Cooper, Alan; Gillespie, Richard; Jacobs, Zenobia; Johnson, Christopher N.; Miller, Gifford H.; Prideaux, Gavin J.; Roberts, Richard G.; Turney, Chris S.M.; Bradshaw, Corey J.A.

    2016-01-01

    The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery. PMID:27434208

  18. A comprehensive database of quality-rated fossil ages for Sahul's Quaternary vertebrates.

    PubMed

    Rodríguez-Rey, Marta; Herrando-Pérez, Salvador; Brook, Barry W; Saltré, Frédérik; Alroy, John; Beeton, Nicholas; Bird, Michael I; Cooper, Alan; Gillespie, Richard; Jacobs, Zenobia; Johnson, Christopher N; Miller, Gifford H; Prideaux, Gavin J; Roberts, Richard G; Turney, Chris S M; Bradshaw, Corey J A

    2016-07-19

    The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.

  19. The MiST2 database: a comprehensive genomics resource on microbial signal transduction

    PubMed Central

    Ulrich, Luke E.; Zhulin, Igor B.

    2010-01-01

    The MiST2 database (http://mistdb.com) identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. Signal transduction systems regulate the majority of cellular activities including the metabolism, development, host-recognition, biofilm production, virulence, and antibiotic resistance of human pathogens. Thus, knowledge of the proteins and interactions that comprise these communication networks is an essential component to furthering biomedical discovery. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. Compared to the previous version of the database, MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface. MiST2 currently contains 966 complete and 157 draft bacterial and archaeal genomes, which collectively contain more than 245 000 signal transduction proteins. The majority (66%) of these are one-component systems, followed by two-component proteins (26%), chemotaxis (6%), and finally ECF factors (2%). PMID:19900966

  20. The MiST2 database: a comprehensive genomics resource on microbial signal transduction.

    PubMed

    Ulrich, Luke E; Zhulin, Igor B

    2010-01-01

    The MiST2 database (http://mistdb.com) identifies and catalogs the repertoire of signal transduction proteins in microbial genomes. Signal transduction systems regulate the majority of cellular activities including the metabolism, development, host-recognition, biofilm production, virulence, and antibiotic resistance of human pathogens. Thus, knowledge of the proteins and interactions that comprise these communication networks is an essential component to furthering biomedical discovery. These are identified by searching protein sequences for specific domain profiles that implicate a protein in signal transduction. Compared to the previous version of the database, MiST2 contains a host of new features and improvements including the following: draft genomes; extracytoplasmic function (ECF) sigma factor protein identification; enhanced classification of signaling proteins; novel, high-quality domain models for identifying histidine kinases and response regulators; neighboring two-component genes; gene cart; better search capabilities; enhanced taxonomy browser; advanced genome browser; and a modern, biologist-friendly web interface. MiST2 currently contains 966 complete and 157 draft bacterial and archaeal genomes, which collectively contain more than 245 000 signal transduction proteins. The majority (66%) of these are one-component systems, followed by two-component proteins (26%), chemotaxis (6%), and finally ECF factors (2%).

  1. A comprehensive database of quality-rated fossil ages for Sahul’s Quaternary vertebrates

    NASA Astrophysics Data System (ADS)

    Rodríguez-Rey, Marta; Herrando-Pérez, Salvador; Brook, Barry W.; Saltré, Frédérik; Alroy, John; Beeton, Nicholas; Bird, Michael I.; Cooper, Alan; Gillespie, Richard; Jacobs, Zenobia; Johnson, Christopher N.; Miller, Gifford H.; Prideaux, Gavin J.; Roberts, Richard G.; Turney, Chris S. M.; Bradshaw, Corey J. A.

    2016-07-01

    The study of palaeo-chronologies using fossil data provides evidence for past ecological and evolutionary processes, and is therefore useful for predicting patterns and impacts of future environmental change. However, the robustness of inferences made from fossil ages relies heavily on both the quantity and quality of available data. We compiled Quaternary non-human vertebrate fossil ages from Sahul published up to 2013. This, the FosSahul database, includes 9,302 fossil records from 363 deposits, for a total of 478 species within 215 genera, of which 27 are from extinct and extant megafaunal species (2,559 records). We also provide a rating of reliability of individual absolute age based on the dating protocols and association between the dated materials and the fossil remains. Our proposed rating system identified 2,422 records with high-quality ages (i.e., a reduction of 74%). There are many applications of the database, including disentangling the confounding influences of hypothetical extinction drivers, better spatial distribution estimates of species relative to palaeo-climates, and potentially identifying new areas for fossil discovery.

  2. C2Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships

    PubMed Central

    2012-01-01

    Background Network pharmacology has emerged as a new topic of study in recent years. It aims to study the myriad relationships among proteins, drugs, and disease phenotypes. The concept of molecular connectivity maps has been proposed to establish comprehensive knowledge links between molecules of interest in a given biological context. Molecular connectivity maps between drugs and genes/proteins in specific disease contexts can be particularly valuable, since the functional approach with these maps helps researchers gain global perspectives on both the therapeutic profiles and toxicological profiles of candidate drugs. Methods To assess drug pharmacological effect, we assume that "ideal" drugs for a patient can treat or prevent the disease by modulating gene expression profiles of this patient to the similar level with those in healthy people. Starting from this hypothesis, we build comprehensive disease-gene-drug connectivity relationships with drug-protein directionality (inhibit/activate) information based on a computational connectivity maps (C2Maps) platform. An interactive interface for directionality annotation of drug-protein pairs with literature evidences from PubMed has been added to the new version of C2Maps. We also upload the curated directionality information of drug-protein pairs specific for three complex diseases - breast cancer, colorectal cancer and Alzheimer disease. Results For relevant drug-protein pairs with directionality information, we use breast cancer as a case study to demonstrate the functionality of disease-specific searching. Based on the results obtained from searching, we perform pharmacological effect evaluation for two important breast cancer drugs on treating patients diagnosed with different breast cancer subtypes. The evaluation is performed on a well-studied breast cancer gene expression microarray dataset to portray how useful the updated C2Maps is in assessing drug efficacy and toxicity information. Conclusions The C2Maps

  3. Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation

    PubMed Central

    Medvar, Barbara; Raghuram, Viswanathan; Pisitkun, Trairak; Sarkar, Abhijit

    2016-01-01

    Aquaporin-2 (AQP2) is regulated in part via vasopressin-mediated changes in protein half-life that are in turn dependent on AQP2 ubiquitination. Here we addressed the question, “What E3 ubiquitin ligase is most likely to be responsible for AQP2 ubiquitination?” using large-scale data integration based on Bayes' rule. The first step was to bioinformatically identify all E3 ligase genes coded by the human genome. The 377 E3 ubiquitin ligases identified in the human genome, consisting predominant of HECT, RING, and U-box proteins, have been used to create a publically accessible and downloadable online database (https://hpcwebapps.cit.nih.gov/ESBL/Database/E3-ligases/). We also curated a second database of E3 ligase accessory proteins that included BTB domain proteins, cullins, SOCS-box proteins, and F-box proteins. Using Bayes' theorem to integrate information from multiple large-scale proteomic and transcriptomic datasets, we ranked these 377 E3 ligases with respect to their probability of interaction with AQP2. Application of Bayes' rule identified the E3 ligases most likely to interact with AQP2 as (in order of probability): NEDD4 and NEDD4L (tied for first), AMFR, STUB1, ITCH, ZFPL1. Significantly, the two E3 ligases tied for top rank have also been studied extensively in the reductionist literature as regulatory proteins in renal tubule epithelia. The concordance of conclusions from reductionist and systems-level data provides strong motivation for further studies of the roles of NEDD4 and NEDD4L in the regulation of AQP2 protein turnover. PMID:27199454

  4. CENTRAL, PEDro, PubMed, and EMBASE are the most comprehensive databases indexing randomized controlled trials of physical therapy interventions.

    PubMed

    Michaleff, Zoe A; Costa, Leonardo O P; Moseley, Anne M; Maher, Christopher G; Elkins, Mark R; Herbert, Robert D; Sherrington, Catherine

    2011-02-01

    Many bibliographic databases index research studies evaluating the effects of health care interventions. One study has concluded that the Physiotherapy Evidence Database (PEDro) has the most complete indexing of reports of randomized controlled trials of physical therapy interventions, but the design of that study may have exaggerated estimates of the completeness of indexing by PEDro. The purpose of this study was to compare the completeness of indexing of reports of randomized controlled trials of physical therapy interventions by 8 bibliographic databases. This study was an audit of bibliographic databases. Prespecified criteria were used to identify 400 reports of randomized controlled trials from the reference lists of systematic reviews published in 2008 that evaluated physical therapy interventions. Eight databases (AMED, CENTRAL, CINAHL, EMBASE, Hooked on Evidence, PEDro, PsycINFO, and PubMed) were searched for each trial report. The proportion of the 400 trial reports indexed by each database was calculated. The proportions of the 400 trial reports indexed by the databases were as follows: CENTRAL, 95%; PEDro, 92%; PubMed, 89%; EMBASE, 88%; CINAHL, 53%; AMED, 50%; Hooked on Evidence, 45%; and PsycINFO, 6%. Almost all of the trial reports (99%) were found in at least 1 database, and 88% were indexed by 4 or more databases. Four trial reports were uniquely indexed by a single database only (2 in CENTRAL and 1 each in PEDro and PubMed). The results are only applicable to searching for English-language published reports of randomized controlled trials evaluating physical therapy interventions. The 4 most comprehensive databases of trial reports evaluating physical therapy interventions were CENTRAL, PEDro, PubMed, and EMBASE. Clinicians seeking quick answers to clinical questions could search any of these databases knowing that all are reasonably comprehensive. PEDro, unlike the other 3 most complete databases, is specific to physical therapy, so studies not

  5. The development of a comprehensive regional digital geospatial database for geothermal exploration in the West-Central Great Basin, U.S.A.

    SciTech Connect

    Nash, G.D.; Hernandez, M.W.

    1996-08-01

    The Earth Sciences and Resources Institute, Geomatics Laboratory, (EGL), Department of Civil and Environmental Engineering, University of Utah, has compiled and initiated the use of a comprehensive digital geospatial database for geothermal exploration in the west-central Great Basin, U.S.A. The database consists of hydrothermal alteration, lineament, recent earthquake, aeromagnetic, gravity, hot spring, mining district, heat flow, geochemical, and geologic unit digital maps in a GIS format. Several problems were encountered during the development of this geospatial database. These primarily included (1) data availability and coverage of the study area, (2) data accuracy (both spatial and thematic), (3) inconsistent data formats, and (4) a lack of metadata. These problems were all overcome satisfactorily. The data are currently being used to create a regional geothermal potential model for the study area.

  6. Circ2Traits: a comprehensive database for circular RNA potentially associated with disease and traits

    PubMed Central

    Ghosal, Suman; Das, Shaoli; Sen, Rituparno; Basak, Piyali; Chakrabarti, Jayprokas

    2013-01-01

    Circular RNAs are new players in regulation of post transcriptional gene expression. Animal genomes express many circular RNAs from diverse genomic locations. A recent study has validated a fairly large number of circular RNAs in human, mouse, and nematode. Circular RNAs play a crucial role in fine tuning the level of miRNA mediated regulation of gene expression by sequestering the miRNAs. Their interaction with disease associated miRNAs indicates that circular RNAs are important for disease regulation. In this paper we studied the potential association of circular RNAs (circRNA) with human diseases in two different ways. Firstly, the interactions of circRNAs with disease associated miRNAs were identified, following which the likelihood of a circRNA being associated with a disease was calculated. For the miRNAs associated with individual diseases, we constructed a network of predicted interactions between the miRNAs and protein coding, long non-coding and circular RNA genes. We carried out gene ontology (GO) enrichment analysis on the set of protein coding genes in the miRNA- circRNA interactome of individual diseases to check the enrichment of genes associated with particular biological processes. Secondly, disease associated SNPs were mapped on circRNA loci, and Argonaute (Ago) interaction sites on circular RNAs were identified. We compiled a database of disease-circRNA association in Circ2Traits (http://gyanxet-beta.com/circdb/), the first comprehensive knowledgebase of potential association of circular RNAs with diseases in human. PMID:24339831

  7. PlaMoM: a comprehensive database compiles plant mobile macromolecules

    PubMed Central

    Guan, Daogang; Yan, Bin; Thieme, Christoph; Hua, Jingmin; Zhu, Hailong; Boheler, Kenneth R.; Zhao, Zhongying; Kragler, Friedrich; Xia, Yiji; Zhang, Shoudong

    2017-01-01

    In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets. To facilitate study of the mobile signaling macromolecules, we compiled the PlaMoM (Plant Mobile Macromolecules) database, a resource that provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM contains detailed information such as nucleotide/amino acid sequences, ortholog partners, related experiments, gene functions and literature. For the model plant Arabidopsis thaliana, protein–protein interactions of mobile transcripts are presented as interactive molecular networks. Furthermore, PlaMoM provides a built-in tool to identify potential RNA mobility signals such as tRNA-like structures. The current version of PlaMoM compiles a total of 17 991 mobile macromolecules from 14 plant species/ecotypes from published data and literature. PlaMoM is available at http://www.systembioinfo.org/plamom/. PMID:27924044

  8. Cortrak-Assisted Feeding Tube Insertion: A Comprehensive Review of Adverse Events in the MAUDE Database.

    PubMed

    Bourgault, Annette M; Aguirre, Lillian; Ibrahim, Joseph

    2017-03-01

    Electromagnetic devices to guide feeding tube placement such as the CORTRAK Enteral Access System have shown promising results; however, researchers in recent studies have expressed concern that a higher level of user expertise may be required for safe use. To review adverse events related to CORTRAK-assisted feeding tube insertion reported in the Food and Drug Administration's Manufacturer and User Facility Device Experience (MAUDE) database. A retrospective, secondary analysis of the MAUDE database was performed to evaluate adverse events (ie, injury or death of patient) related to CORTRAK. Fifty-four adverse events between January 1, 2006 and February 29, 2016 were identified and reviewed. Most events (98%) involved feeding tube placement in the lungs (37%, left lung; 46%, right lung; 15%, not specified). Lung complications included pneumothorax (77%) and pneumonitis (21%). Death occurred in 17% of lung placements. Clinicians failed to recognize placement in 89% of CORTRAK insertion tracings reviewed. Lung placement is not unique to CORTRAK and is an inherent risk of all feeding tube insertions. In known or suspected lung placement, feeding tubes should be removed and radiography performed to assess for pneumothorax. Clinicians must observe closely for lung placement and discriminate lung from gastric placement on insertion tracings. Clinicians require specialized training and experience to develop competency in using the CORTRAK device, although the exact amount of experience needed is unknown. ©2017 American Association of Critical-Care Nurses.

  9. Development of a comprehensive Blast-Related Auditory Injury Database (BRAID).

    PubMed

    Joseph, Antony R; Horton, Jaime L; Clouser, Mary C; MacGregor, Andrew J; Louie, Michelle; Galarneau, Michael R

    2016-01-01

    The Department of Defense Hearing Conservation Program provides specific guidance for service components to prevent occupational hearing loss; however, it does not specifically contend with the unique noise exposures observed in the theater of war, such as blasts and explosions. In order to examine the effects of blast injury on hearing sensitivity, we developed a large database composed of demographic, audiometric, point of injury, and medical outcome data, with the primary aim of developing a long-standing and integrated capability for the surveillance, assessment, and investigation of blast-related hearing outcomes. Methods used to develop the dataset are described. Encompassing more than 16,500 Navy and Marine Corps personnel, the Blast-Related Auditory Injury Database (BRAID) includes individuals with a blast-related injury and nonblast control subjects. Using baseline and postdeployment hearing threshold data, a retrospective analysis of the cohort revealed that the rate of hearing loss for the injured servicemembers was 39%. The BRAID will be useful for studies that assess hearing patterns following deployment-related injury, such as blast exposures, that facilitate exploration of health outcomes and whether they are predictive of audiometric disposition and that help establish hearing loss prevention strategies and program policies for affected military commands and servicemembers.

  10. Including additional controls from public databases improves the power of a genome-wide association study.

    PubMed

    Mukherjee, Semanti; Simon, Jennifer; Bayuga, Sharon; Ludwig, Emmy; Yoo, Sarah; Orlow, Irene; Viale, Agnes; Offit, Kenneth; Kurtz, Robert C; Olson, Sara H; Klein, Robert J

    2011-01-01

    Though genome-wide association studies (GWAS) have identified numerous susceptibility loci for common diseases, their use is limited due to the expense of genotyping large cohorts of individuals. One potential solution is to use 'additional controls', or genotype data from control individuals deposited in public repositories. While this approach has been used by several groups, the genetically heterogeneous nature of the population of the United States makes this approach potentially problematic. We empirically investigated the utility of this approach in a US-based GWAS. In a small GWAS of pancreatic cancer in New York, we observed clear population structure differences relative to controls from the database of Genotypes and Phenotypes (dbGaP). When we conduct the GWAS using these additional controls, we find large inflation of the test statistic that is properly corrected by using eigenvectors from principal components analysis as covariates. To deal with errors introduced due to different sources, we propose simultaneously genotyping a small number of controls along with cases and then comparing this group to the additional controls. We show that removing SNPs that show differences between these control groups reduces false-positive findings. Thus, through an empirical approach, this report provides practical guidance for using additional controls from publicly available datasets. Copyright © 2011 S. Karger AG, Basel.

  11. RIDOM: Comprehensive and public sequence database for identification of Mycobacterium species

    PubMed Central

    Harmsen, Dag; Dostal, Stefan; Roth, Andreas; Niemann, Stefan; Rothgänger, Jörg; Sammeth, Michael; Albert, Jürgen; Frosch, Matthias; Richter, Elvira

    2003-01-01

    Background Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The information content of the 5' end of the 16S ribosomal RNA gene (16S rDNA) is sufficient for identification of most bacterial species. However, reliable sequence-based identification is hampered by many faulty and some missing sequence entries in publicly accessible databases. Methods In order to establish an improved 16S rDNA sequence database for the identification of clinical and environmental isolates, we sequenced both strands of the 5' end of 16S rDNA (Escherichia coli positions 54 to 510) from 199 mycobacterial culture collection isolates. All validly described species (n = 89; up to March 21, 2000) and nearly all published sequevar variants were included. If the 16S rDNA sequences were not discriminatory, the internal transcribed spacer (ITS) region sequences (n = 84) were also determined. Results Using 5'-16S rDNA sequencing a total of 64 different mycobacterial species (71.9%) could be identified. With the additional input of the ITS sequence, a further 16 species or subspecies could be differentiated. Only Mycobacterium tuberculosis complex species, M. marinum / M. ulcerans and the M. avium subspecies could not be differentiated using 5'-16S rDNA or ITS sequencing. A total of 77 culture collection strain sequences, exhibiting an overlap of at least 80% and identical by strain number to the isolates used in this study, were found in the GenBank. Comparing these with our sequences revealed that an average of 4.31 nucleotide differences (SD ± 0.57) were present. Conclusions The data from this analysis show that it is possible to differentiate most mycobacterial species by sequence analysis of partial 16S rDNA. The high-quality sequences reported here, together with ancillary information (e.g., taxonomic, medical), are available in a public database, which is currently being

  12. PlaMoM: a comprehensive database compiles plant mobile macromolecules.

    PubMed

    Guan, Daogang; Yan, Bin; Thieme, Christoph; Hua, Jingmin; Zhu, Hailong; Boheler, Kenneth R; Zhao, Zhongying; Kragler, Friedrich; Xia, Yiji; Zhang, Shoudong

    2017-01-04

    In plants, various phloem-mobile macromolecules including noncoding RNAs, mRNAs and proteins are suggested to act as important long-distance signals in regulating crucial physiological and morphological transition processes such as flowering, plant growth and stress responses. Given recent advances in high-throughput sequencing technologies, numerous mobile macromolecules have been identified in diverse plant species from different plant families. However, most of the identified mobile macromolecules are not annotated in current versions of species-specific databases and are only available as non-searchable datasheets. To facilitate study of the mobile signaling macromolecules, we compiled the PlaMoM (Plant Mobile Macromolecules) database, a resource that provides convenient and interactive search tools allowing users to retrieve, to analyze and also to predict mobile RNAs/proteins. Each entry in the PlaMoM contains detailed information such as nucleotide/amino acid sequences, ortholog partners, related experiments, gene functions and literature. For the model plant Arabidopsis thaliana, protein-protein interactions of mobile transcripts are presented as interactive molecular networks. Furthermore, PlaMoM provides a built-in tool to identify potential RNA mobility signals such as tRNA-like structures. The current version of PlaMoM compiles a total of 17 991 mobile macromolecules from 14 plant species/ecotypes from published data and literature. PlaMoM is available at http://www.systembioinfo.org/plamom/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. A comprehensive approach including a new enlargement technique to prevent complications after De Quervain tendinopathy surgery.

    PubMed

    Perno-Ioanna, D; Papaloïzos, M

    2016-06-01

    The goal of this study was to evaluate the outcome of our surgical approach aimed at preventing complications following surgery for De Quervain tendinopathy. Our stepwise surgical procedure is described in detail. We reviewed 56 cases operated by a senior surgeon over 5years, and re-evaluated them with a minimum 15months' follow-up. Complications mentioned in the literature (poor wound healing, adhesions, nerve injury, incomplete decompression, tendon subluxation) were not present in any of the cases; the satisfaction rate was very high. Slight residual discomfort was noted in 16 cases. Among them, 13 had an associated pathology. In summary, the outcome after the comprehensive approach presented here is highly predictable. Properly applied, good to excellent results can be expected in most patients. Potential postoperative complications are effectively prevented. Some caution is needed in cases of associated pathologies. Copyright © 2016 SFCM. Published by Elsevier Masson SAS. All rights reserved.

  14. The National Deep-Sea Coral and Sponge Database: A Comprehensive Resource for United States Deep-Sea Coral and Sponge Records

    NASA Astrophysics Data System (ADS)

    Dornback, M.; Hourigan, T.; Etnoyer, P.; McGuinn, R.; Cross, S. L.

    2014-12-01

    Research on deep-sea corals has expanded rapidly over the last two decades, as scientists began to realize their value as long-lived structural components of high biodiversity habitats and archives of environmental information. The NOAA Deep Sea Coral Research and Technology Program's National Database for Deep-Sea Corals and Sponges is a comprehensive resource for georeferenced data on these organisms in U.S. waters. The National Database currently includes more than 220,000 deep-sea coral records representing approximately 880 unique species. Database records from museum archives, commercial and scientific bycatch, and from journal publications provide baseline information with relatively coarse spatial resolution dating back as far as 1842. These data are complemented by modern, in-situ submersible observations with high spatial resolution, from surveys conducted by NOAA and NOAA partners. Management of high volumes of modern high-resolution observational data can be challenging. NOAA is working with our data partners to incorporate this occurrence data into the National Database, along with images and associated information related to geoposition, time, biology, taxonomy, environment, provenance, and accuracy. NOAA is also working to link associated datasets collected by our program's research, to properly archive them to the NOAA National Data Centers, to build a robust metadata record, and to establish a standard protocol to simplify the process. Access to the National Database is provided through an online mapping portal. The map displays point based records from the database. Records can be refined by taxon, region, time, and depth. The queries and extent used to view the map can also be used to download subsets of the database. The database, map, and website is already in use by NOAA, regional fishery management councils, and regional ocean planning bodies, but we envision it as a model that can expand to accommodate data on a global scale.

  15. Establishment of the most comprehensive ITS2 barcode database to date of the traditional medicinal plant Rhodiola (Crassulacaee).

    PubMed

    Zhu, Ruo-Wei; Li, Yuan-Cong; Zhong, Da-Lv; Zhang, Jian-Qiang

    2017-08-30

    The roots and rhizomes of Rhodiola crenulata and R. rosea have been used worldwide as adaptogens for hundreds of years. However, rapid growth in demand has resulted in merchants using other species of Rhodiola as adulterants. Here, we surveyed 518 individuals representing 47 of the 55 species in the genus, including 253 R. crenulata individuals from 16 populations and 98 R. rosea individuals from 11 populations, to evaluate the utility of the internal transcribed spacer 2 (ITS2) barcode for identification of Rhodiola species. We detected six haplotypes in R. crenulata and only one haplotype in R. rosea. An obvious overlap between intra- and inter-specific distance was detected, and the authentication efficacy of ITS2, which was assessed by BLAST1, a nearest distance method, and a tree test, was much lower than in other groups. However, R. crenulata and R. rosea could be exactly identified. Analysis showed that the secondary structure of ITS2 differs in R. crenulata and its closest relatives. Our results demonstrated that both a mini barcode from ITS2 and the structure of ITS2 are effective markers for the identification of R. crenulata and R. rosea. This study represents the most comprehensive database of ITS2 barcodes in Rhodiola to date and will be useful in Rhodiola species identification.

  16. GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.

    PubMed

    Worth, Catherine L; Kreuchwig, Annika; Kleinau, Gunnar; Krause, Gerd

    2011-05-23

    G protein-coupled receptors (GPCRs) transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. The data provided by GPCR-SSFE are useful for investigating general and detailed sequence-structure-function relationships

  17. A comprehensive database of the geographic spread of past human Ebola outbreaks

    PubMed Central

    Mylne, Adrian; Brady, Oliver J.; Huang, Zhi; Pigott, David M.; Golding, Nick; Kraemer, Moritz U.G.; Hay, Simon I.

    2014-01-01

    Ebola is a zoonotic filovirus that has the potential to cause outbreaks of variable magnitude in human populations. This database collates our existing knowledge of all known human outbreaks of Ebola for the first time by extracting details of their suspected zoonotic origin and subsequent human-to-human spread from a range of published and non-published sources. In total, 22 unique Ebola outbreaks were identified, composed of 117 unique geographic transmission clusters. Details of the index case and geographic spread of secondary and imported cases were recorded as well as summaries of patient numbers and case fatality rates. A brief text summary describing suspected routes and means of spread for each outbreak was also included. While we cannot yet include the ongoing Guinea and DRC outbreaks until they are over, these data and compiled maps can be used to gain an improved understanding of the initial spread of past Ebola outbreaks and help evaluate surveillance and control guidelines for limiting the spread of future epidemics. PMID:25984346

  18. Dental Health Services Research Utilizing Comprehensive Clinical Databases and Information Technology.

    ERIC Educational Resources Information Center

    Hayden, William J.

    1997-01-01

    Argues that dental schools are the logical location for development of valid, reliable, and acceptable health services research methods and databases, and describes development of an insurance claims database to demonstrate the types of research possible, as well as weaknesses and shortcomings of pure administrative data. Considers implications…

  19. 41 CFR 302-12.105 - Must we have a contract with a RSC that includes a comprehensive homesale program?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 41 Public Contracts and Property Management 4 2013-07-01 2012-07-01 true Must we have a contract with a RSC that includes a comprehensive homesale program? 302-12.105 Section 302-12.105 Public... TRANSACTION ALLOWANCES 12-USE OF A RELOCATION SERVICES COMPANY Agency's Use of a Relocation Services Company...

  20. 41 CFR 302-12.105 - Must we have a contract with a RSC that includes a comprehensive homesale program?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 41 Public Contracts and Property Management 4 2012-07-01 2012-07-01 false Must we have a contract with a RSC that includes a comprehensive homesale program? 302-12.105 Section 302-12.105 Public... TRANSACTION ALLOWANCES 12-USE OF A RELOCATION SERVICES COMPANY Agency's Use of a Relocation Services Company...

  1. 41 CFR 302-12.105 - Must we have a contract with a RSC that includes a comprehensive homesale program?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 41 Public Contracts and Property Management 4 2014-07-01 2014-07-01 false Must we have a contract with a RSC that includes a comprehensive homesale program? 302-12.105 Section 302-12.105 Public... TRANSACTION ALLOWANCES 12-USE OF A RELOCATION SERVICES COMPANY Agency's Use of a Relocation Services Company...

  2. MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota

    PubMed Central

    Blanco-Míguez, Aitor; Gutiérrez-Jácome, Alberto; Fdez-Riverola, Florentino; Lourenço, Anália; Sánchez, Borja

    2017-01-01

    The Mechanism of Action of the Human Microbiome (MAHMI) database is a unique resource that provides comprehensive information about the sequence of potential immunomodulatory and antiproliferative peptides encrypted in the proteins produced by the human gut microbiota. Currently, MAHMI database contains over 300 hundred million peptide entries, with detailed information about peptide sequence, sources and potential bioactivity. The reference peptide data section is curated manually by domain experts. The in silico peptide data section is populated automatically through the systematic processing of publicly available exoproteomes of the human microbiome. Bioactivity prediction is based on the global alignment of the automatically processed peptides with experimentally validated immunomodulatory and antiproliferative peptides, in the reference section. MAHMI provides researchers with a comparative tool for inspecting the potential immunomodulatory or antiproliferative bioactivity of new amino acidic sequences and identifying promising peptides to be further investigated. Moreover, researchers are welcome to submit new experimental evidence on peptide bioactivity, namely, empiric and structural data, as a proactive, expert means to keep the database updated and improve the implemented bioactivity prediction method. Bioactive peptides identified by MAHMI have a huge biotechnological potential, including the manipulation of aberrant immune responses and the design of new functional ingredients/foods based on the genetic sequences of the human microbiome. Hopefully, the resources provided by MAHMI will be useful to those researching gastrointestinal disorders of autoimmune and inflammatory nature, such as Inflammatory Bowel Diseases. MAHMI database is routinely updated and is available free of charge. Database URL: http://mahmi.org/ PMID:28077565

  3. ECO: a generic eutrophication model including comprehensive sediment-water interaction.

    PubMed

    Smits, Johannes G C; van Beek, Jan K L

    2013-01-01

    The content and calibration of the comprehensive generic 3D eutrophication model ECO for water and sediment quality is presented. Based on a computational grid for water and sediment, ECO is used as a tool for water quality management to simulate concentrations and mass fluxes of nutrients (N, P, Si), phytoplankton species, detrital organic matter, electron acceptors and related substances. ECO combines integral simulation of water and sediment quality with sediment diagenesis and closed mass balances. Its advanced process formulations for substances in the water column and the bed sediment were developed to allow for a much more dynamic calculation of the sediment-water exchange fluxes of nutrients as resulting from steep concentration gradients across the sediment-water interface than is possible with other eutrophication models. ECO is to more accurately calculate the accumulation of organic matter and nutrients in the sediment, and to allow for more accurate prediction of phytoplankton biomass and water quality in response to mitigative measures such as nutrient load reduction. ECO was calibrated for shallow Lake Veluwe (The Netherlands). Due to restoration measures this lake underwent a transition from hypertrophic conditions to moderately eutrophic conditions, leading to the extensive colonization by submerged macrophytes. ECO reproduces observed water quality well for the transition period of ten years. The values of its process coefficients are in line with ranges derived from literature. ECO's calculation results underline the importance of redox processes and phosphate speciation for the nutrient return fluxes. Among other things, the results suggest that authigenic formation of a stable apatite-like mineral in the sediment can contribute significantly to oligotrophication of a lake after a phosphorus load reduction.

  4. ECO: A Generic Eutrophication Model Including Comprehensive Sediment-Water Interaction

    PubMed Central

    Smits, Johannes G. C.; van Beek, Jan K. L.

    2013-01-01

    The content and calibration of the comprehensive generic 3D eutrophication model ECO for water and sediment quality is presented. Based on a computational grid for water and sediment, ECO is used as a tool for water quality management to simulate concentrations and mass fluxes of nutrients (N, P, Si), phytoplankton species, detrital organic matter, electron acceptors and related substances. ECO combines integral simulation of water and sediment quality with sediment diagenesis and closed mass balances. Its advanced process formulations for substances in the water column and the bed sediment were developed to allow for a much more dynamic calculation of the sediment-water exchange fluxes of nutrients as resulting from steep concentration gradients across the sediment-water interface than is possible with other eutrophication models. ECO is to more accurately calculate the accumulation of organic matter and nutrients in the sediment, and to allow for more accurate prediction of phytoplankton biomass and water quality in response to mitigative measures such as nutrient load reduction. ECO was calibrated for shallow Lake Veluwe (The Netherlands). Due to restoration measures this lake underwent a transition from hypertrophic conditions to moderately eutrophic conditions, leading to the extensive colonization by submerged macrophytes. ECO reproduces observed water quality well for the transition period of ten years. The values of its process coefficients are in line with ranges derived from literature. ECO’s calculation results underline the importance of redox processes and phosphate speciation for the nutrient return fluxes. Among other things, the results suggest that authigenic formation of a stable apatite-like mineral in the sediment can contribute significantly to oligotrophication of a lake after a phosphorus load reduction. PMID:23844160

  5. A comprehensive database of published tDCS clinical trials (2005-2016).

    PubMed

    Lefaucheur, Jean-Pascal

    2016-12-01

    Transcranial direct current stimulation (tDCS) is a technique of noninvasive cortical stimulation allowing significant modification of brain functions. Clinical application of this technique was reported for the first time in March 2005. This paper presents a detailed list of the 340 articles (excluding single case reports) which have assessed the clinical effect of tDCS in patients, at least when delivered to cortical targets. The reviewed conditions were: pain syndromes, Parkinson's disease, dystonia, cerebral palsy, post-stroke limb motor impairment, post-stroke neglect, post-stroke dysphagia, post-stroke aphasia, primary progressive aphasia, multiple sclerosis, epilepsy, consciousness disorders, Alzheimer's disease and other types of dementia, tinnitus, depression, auditory hallucinations and negative symptoms of schizophrenia, addiction and craving, autism, and attention disorders. The following data were collected: (i) clinical condition; (ii) study design; (iii) sample size; (iv) anode and cathode locations; (v) stimulation intensity and electrode area; (vi) number and duration of sessions; (vii) clinical outcome measures and results. This article does not include any meta-analysis and aims simply at providing a comprehensive overview of the raw data reported in this field to date, as an aid to researchers. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  6. Toxic Substances Control Act (TSCA) TSCATS (test submissions database) comprehensive update (raw data file)

    SciTech Connect

    1999-09-01

    TSCATS (Toxic Substances Control Act Test Submissions) is an online index to unpublished, nonconfidential studies covering chemical testing results and adverse effects of chemicals on health and ecological systems. The studies are submitted by US industry to EPA under several sections of the Toxic Substances Control Act (TSCA). There are four types of documents in the database: Section 4 chemical testing results, Section 8(d) health and safety studies, Section 8(e) substantial risk of injury to health or the environment notices, and voluntary documents submitted to EPA known as a For Your Information (FYI) notice. TSCATS contains information that is pertinent to the risk assessment and hazard evaluation processes. The information can be used in conjunction with published material and is a valuable source along with or in the absence of published data. The data are used by federal and state agencies, researchers, toxicologists, risk assessors, the regulated industry, attorneys, trade and professional associations. TSCATS was developed to make ongoing and completed chemical testing studies available to the public and includes chemical exposure studies, epidemiology, environmental fate, monitoring, episodic incidents, such as spills and case reports. There are 81,000 studies on 6,700 unique chemical substances contained in 23,000 documents. On average three or four individual studies are extracted from each document. Studies are indexed under three broad categories: health effects, ecological effects and environmental fate. Additional controlled vocabulary terms are assigned to describe the experimental protocol and test observations. A TSCATS record also includes: the chemical name, CAS (Chemical Abstracts Service) Registry Number, Section of TSCA, title, document number, microfiche number, submitting organization, and performing organization. A select number of studies also have abstracts. Microfiche copies of the full-text documents of the unpublished reports

  7. MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.

    PubMed

    Zhai, Peng; Yang, Longshu; Guo, Xiao; Wang, Zhe; Guo, Jiangtao; Wang, Xiaoqi; Zhu, Huaiqiu

    2017-10-02

    During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community. We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples. MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis

  8. Toxic Substances Control Act (TSCA) TSCATS (test submissions database) comprehensive update, August 1999

    SciTech Connect

    1999-08-01

    TSCATS (Toxic Substances Control Act Test Submissions) is an online index to unpublished, nonconfidential studies covering chemical testing results and adverse effects of chemicals on health and ecological systems. There are four types of documents in the database: Section 4 chemical testing results, Section 8(d) health and safety studies, Section 8(e) substantial risk of injury to health or the environment notices, and voluntary documents submitted to EPA known as a For Your Information (FYI) notice. TSCATS contains information that is pertinent to the risk assessment and hazard evaluation processes. The information can be used in conjunction with published material and is a valuable source along with or in the absence of published data. The data are used by federal and state agencies, researchers, toxicologists, risk assessors, the regulated industry, attorneys, trade and professional associations. TSCATS was developed to make ongoing and completed chemical testing studies available to the public.There are 81,000 studies on 6,700 unique chemical substances are contained in 23,000 documents. Studies are indexed under three broad categories: health effects, ecological effects and environmental fate. Additional controlled vocabulary terms are assigned to describe the experimental protocol and test observations. A TSCATS record also includes: the chemical name, CAS (Chemical Abstracts Service) Registry Number, Section of TSCA, title, document number, microfiche number, submitting organization, and performing organization. A select number of studies also have abstracts. Microfiche copies of the full-text documents of the unpublished reports referenced by TSCATS are directly available from NTIS. The titles of these 23,000 unpublished reports can be searched directly on the NTIS web site at www.ntis.gov/yellowbk/1nty834.htm.

  9. Comprehensive evaluation of long-term trends in occupational exposure: Part 1. Description of the database

    PubMed Central

    Symanski, E.; Kupper, L. L.; Rappaport, S. M.

    1998-01-01

    OBJECTIVES: To conduct a comprehensive evaluation of long term changes in occupational exposure among a broad cross section of industries worldwide. METHODS: A review of the scientific literature identified studies that reported historical changes in exposure. About 700 sets of data from 119 published and several unpublished sources were compiled. Data were published over a 30 year period in 25 journals that spanned a range of disciplines. For each data set, the average exposure level was compiled for each period and details on the contaminant, the industry and location, changes in the threshold limit value (TLV), as well as the type of sampling method were recorded. Spearman rank correlation coefficients were used to identify monotonic changes in exposure over time and simple linear regression analyses were used to characterise trends in exposure. RESULTS: About 78% of the natural log transformed data showed linear trends towards lower exposure levels whereas 22% indicated increasing trends. (The Spearman rank correlation analyses produced a similar breakdown between exposures monotonically increasing or decreasing over time.) Although the rates of reduction for the data showing downward trends ranged from -1% to -62% per year, most exposures declined at rates between -4% and -14% per year (the interquartile range), with a median value of -8% per year. Exposures seemed to increase at rates that were slightly lower than those of exposures which have declined over time. Data sets that showed downward (versus upward) trends were influenced by several factors including type and carcinogenicity of the contaminant, type of monitoring, historical changes in the threshold limit values (TLVs), and period of sampling. CONCLUSIONS: This review supports the notion that occupational exposures are generally lower today than they were years or decades ago. However, such trends seem to have been affected by factors related to the contaminant, as well as to the period and type of

  10. BtoxDB: a comprehensive database of protein structural data on toxin-antitoxin systems.

    PubMed

    Barbosa, Luiz Carlos Bertucci; Garrido, Saulo Santesso; Marchetto, Reinaldo

    2015-03-01

    Toxin-antitoxin (TA) systems are diverse and abundant genetic modules in prokaryotic cells that are typically formed by two genes encoding a stable toxin and a labile antitoxin. Because TA systems are able to repress growth or kill cells and are considered to be important actors in cell persistence (multidrug resistance without genetic change), these modules are considered potential targets for alternative drug design. In this scenario, structural information for the proteins in these systems is highly valuable. In this report, we describe the development of a web-based system, named BtoxDB, that stores all protein structural data on TA systems. The BtoxDB database was implemented as a MySQL relational database using PHP scripting language. Web interfaces were developed using HTML, CSS and JavaScript. The data were collected from the PDB, UniProt and Entrez databases. These data were appropriately filtered using specialized literature and our previous knowledge about toxin-antitoxin systems. The database provides three modules ("Search", "Browse" and "Statistics") that enable searches, acquisition of contents and access to statistical data. Direct links to matching external databases are also available. The compilation of all protein structural data on TA systems in one platform is highly useful for researchers interested in this content. BtoxDB is publicly available at http://www.gurupi.uft.edu.br/btoxdb. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Persistence at 1 year of oral antiosteoporotic drugs: a prospective study in a comprehensive health insurance database.

    PubMed

    Confavreux, Cyrille B; Canoui-Poitrine, Florence; Schott, Anne-Marie; Ambrosi, Véronique; Tainturier, Valérie; Chapurlat, Roland D

    2012-04-01

    Treatments against osteoporosis have demonstrated fracture risk reduction but persistence to therapy remains a major issue. Intermittent regimens have been developed to improve persistence. The aim of this 1-year prospective study was to compare, in the general population, the persistence of various oral regimens of antiosteoporotic treatment. We conducted this prospective study in the French comprehensive public health insurance database of the Rhône-Alpes region. Women aged 45 years or older who had a first reimbursement of an oral antiosteoporotic treatment during February 2007 composed the study cohort. Persistence was defined by the proportion of patients refilling a prescription in the pharmacist delivery register (ERASME). Using statistical analyses like Kaplan-Meier survival curves and log-rank tests, we compared the treatment persistence of strontium ranelate, raloxifene, and daily-, weekly-, and monthly bisphosphonates. Two thousand four hundred and nineteen patients were included over a period of 1 month and followed up for 12 months. Two hundred and eighty-nine (11.9%) patients were treated with monthly bisphosphonates, 1298 (53.7%) with weekly bisphosphonates, and 832 (34.4%) with daily treatments (526 strontium ranelate (21.7%), 296 raloxifene (12.2%), and 10 bisphosphonates (0.4%)). At 1 year, overall persistence was 34%. Fifty percent of patients on monthly bisphosphonates were still persistent while only 37% of patients on weekly bisphosphonates, 34% on raloxifene, and 16% on strontium ranelate were persistent. Therapy monitoring with biochemical markers or bone mineral density was associated with improved persistence. Overall persistence at 1 year was low, but intermittent regimens were associated with higher persistence rates, along with women who had therapy monitoring.

  12. Comprehensive functional characterization of murine infantile Batten disease including Parkinson-like behavior and dopaminergic markers

    PubMed Central

    Dearborn, Joshua T.; Harmon, Steven K.; Fowler, Stephen C.; O’Malley, Karen L.; Taylor, George T.; Sands, Mark S.; Wozniak, David F.

    2015-01-01

    Infantile neuronal ceroid lipofuscinosis (INCL, Infantile Batten disease) is a neurodegenerative lysosomal storage disease caused by a deficiency in palmitoyl protein thioesterase-1 (PPT1). The PPT1-deficient mouse (Cln1−/−) is a useful phenocopy of human INCL. Cln1−/− mice display retinal dysfunction, seizures, motor deficits, and die at ~8 months of age. However, little is known about the cognitive and behavioral functions of Cln1−/− mice during disease progression. In the present study, younger (~1–2 months of age) Cln1−/− mice showed minor deficits in motor/sensorimotor functions while older (~5–6 months of age) Cln1−/− mice exhibited more severe impairments, including decreased locomotor activity, inferior cued water maze performance, decreased running wheel ability, and altered auditory cue conditioning. Unexpectedly, certain cognitive functions such as some learning and memory capabilities seemed intact in older Cln1−/− mice. Younger and older Cln1−/− mice presented with walking initiation defects, gait abnormalities, and slowed movements, which are analogous to some symptoms reported in INCL and parkinsonism. However, there was no evidence of alterations in dopaminergic markers in Cln1−/− mice. Results from this study demonstrate quantifiable changes in behavioral functions during progression of murine INCL and suggest that Parkinson-like motor/sensorimotor deficits in Cln1−/− mice are not mediated by dopamine deficiency. PMID:26238334

  13. Designing and recruiting to UK autism spectrum disorder research databases: do they include representative children with valid ASD diagnoses?

    PubMed Central

    Warnell, F; George, B; McConachie, H; Johnson, M; Hardy, R; Parr, J R

    2015-01-01

    Objectives (1) Describe how the Autism Spectrum Database-UK (ASD-UK) was established; (2) investigate the representativeness of the first 1000 children and families who participated, compared to those who chose not to; (3) investigate the reliability of the parent-reported Autism Spectrum Disorder (ASD) diagnoses, and present evidence about the validity of diagnoses, that is, whether children recruited actually have an ASD; (4) present evidence about the representativeness of the ASD-UK children and families, by comparing their characteristics with the first 1000 children and families from the regional Database of children with ASD living in the North East (Daslne), and children and families identified from epidemiological studies. Setting Recruitment through a network of 50 UK child health teams and self-referral. Patients Parents/carers with a child with ASD, aged 2–16 years, completed questionnaires about ASD and some gave professionals’ reports about their children. Results 1000 families registered with ASD-UK in 30 months. Children of families who participated, and of the 208 who chose not to, were found to be very similar on: gender ratio, year of birth, ASD diagnosis and social deprivation score. The reliability of parent-reported ASD diagnoses of children was very high when compared with clinical reports (over 96%); no database child without ASD was identified. A comparison of gender, ASD diagnosis, age at diagnosis, school placement, learning disability, and deprivation score of children and families from ASD-UK with 1084 children and families from Daslne, and families from population studies, showed that ASD-UK families are representative of families of children with ASD overall. Conclusions ASD-UK includes families providing parent-reported data about their child and family, who appear to be broadly representative of UK children with ASD. Families continue to join the databases and more than 3000 families can now be contacted by researchers

  14. Comprehensive database of diameter-based biomass regressions for North American tree species

    Treesearch

    Jennifer C. Jenkins; David C. Chojnacky; Linda S. Heath; Richard A. Birdsey

    2004-01-01

    A database consisting of 2,640 equations compiled from the literature for predicting the biomass of trees and tree components from diameter measurements of species found in North America. Bibliographic information, geographic locations, diameter limits, diameter and biomass units, equation forms, statistical errors, and coefficients are provided for each equation,...

  15. SU-E-T-153: Establish a Comprehensive Patient-Specific Plan QA Database for Instituitional Quality Control Program

    SciTech Connect

    Ding, X; Olszanski, A; Scheuermann, R; Bellerive, M; Solberg, T

    2014-06-01

    Purpose: Since the publication of TG-119, several new treatment techniques requiring new QA devices have been implemented in the clinic. To monitor and analyze our institutional QA performance, we have created a comprehensive QA database using Research Electronic Data Capture (REDCap). The database will also assist us in creating IMRT QA Analysis practice guidelines. Methods: Since Oct. 2013, 336 patient plan QA results were entered into the database. Plan parameters such as plan ID, treatment site, technique, energy, optimization constraints, modulation factor, leaf speed, leaf opening.etc were automatically extracted from the Varian Eclipse database to allow us to refine our evaluation and analysis method. Specific QA device, LINAC-related information, and measurement and analysis results were manually entered by the QA team. IMRT plans were measured using MapCHECK2 while RapidArc plans were measured using ArcCHECK. Distance-To-Agreement 3%/3mm without global maximum normalization was used. Results: The data indicates that different treatment techniques might benefit from a different site-specific action level(AL) depending on the complexity of the plan and optimization parameter used (e.g., breast IMRT QA= 97.8% and pelvis IMRT QA=93.1%). Different QA devices may also benefit from a different AL (MapCHECK2 = 94.1% while ArcCHECK = 83.0%). The relationship between the parameters and passing rate suggests that the complexity of each plan, characterized by leaf travel, leaf opening and modulation factor, affect the passing rate significantly. The database is reviewed regularly, and any abnormal point of the QA result or a trend of lower QA passing rate on a specific LINAC is further investigated. Conclusion: Establishing a comprehensive QA database provides an overview of the quality assurance program. It not only helps in answering the question “what is a reasonable and achievable standard for each institution”, but also saves time in monitoring and

  16. Clostridium-DT(DB): a comprehensive database for potential drug targets of Clostridium difficile.

    PubMed

    Jadhav, Ankush; Ezhilarasan, Vijayalakshmi; Prakash Sharma, Om; Pan, Archana

    2013-05-01

    Clostridium difficile is considered to be one of the most important causes of health care-associated infections currently. The prevalence and severity of C. difficile infection have increased significantly worldwide in the past decade which has led to the increased research interest. Here, using comparative genomics strategy coupled with bioinformatics tools we have identified potential drug targets in C. difficile and determined their three-dimensional structures in order to develop a database, named Clostridium-DT(DB). Currently, the database comprises the potential drug targets with their structural information from three strains of C. difficile, namely hypervirulent PCR-ribotype 027 strain R20291, PCR-ribotype 012 strain 630, and PCR-ribotype 027 strain CD196. Copyright © 2013 Elsevier Ltd. All rights reserved.

  17. Characteristics of comprehensive Chemical Industry Database CD-NET : Centered around chemical product information file

    NASA Astrophysics Data System (ADS)

    Takano, Hideo

    This paper describes Chemical Product Information File of Chemical Industry Database, CD-NET provided by Chemical Data Service Inc.. It defines "information" first, then explains file organization and presents how Chemical product Information File is located in CD-NET. Mentioning its complementary relation with JICST's JOIS-F the author defines the File as chemical product information for business purpose. All of the information items in the File emphasize that it is exactly a type of business and practical database. To distinguish general items from important items by product, all of the information is categorized into II classes by general chemical product and by area. The scope and emphasized items under each class are described in detail.

  18. Volcanic hazard in Mexico: a comprehensive on-line database for risk mitigation

    NASA Astrophysics Data System (ADS)

    Manea, Marina; Constantin Manea, Vlad; Capra, Lucia; Bonasia, Rosanna

    2013-04-01

    Researchers are currently working on several key aspects of the Mexican volcanoes, such as remote sensing, field data of old and recent volcaniclastic deposits, structural framework, monitoring (rainfall data and visual observation of lahars), and laboratory experiment (analogue models and numerical simulations - fall3D, titan2D). Each investigation is focused on specific processes, but it is fundamental to visualize the global status of the volcano in order to understand its behavior and to mitigate future hazards. The Mexican Volcanoes @nline represents a novel initiative aimed to collect, on a systematic basis, the complete set of data obtained so far on the volcanoes, and to continuously update the database with new data. All the information is compiled from published works and updated frequently. Maps, such as the geological map of the Mexican volcanos and the associated hazard zonation, as well as point data, such as stratigraphic sections, sedimentology and diagrams of rainfall intensities, are presented in Google Earth format in order to be easily accessed by the scientific community and the general public. An important section of this online database is the presentation of numerical simulations results for ash dispersion associated with the principal Mexican active volcanoes. Daily prediction of ash flow dispersion (based on real-time data from CENAPRED and the Mexican Meteorological Service), as well as large-scale high-resolution subduction simulations performed on HORUS (the Computational Geodynamics Laboratory's supercomputer) represent a central part of the Mexican Volcanos @nline database. The Mexican Volcanoes @nline database is maintained by the Computational Geodynamics Laboratory and it is based entirely on Open Source software. The website can be visited at: http://www.geociencias.unam.mx/mexican_volcanoes.

  19. A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria

    PubMed Central

    Gaby, John Christian; Buckley, Daniel H.

    2014-01-01

    We describe a nitrogenase gene sequence database that facilitates analysis of the evolution and ecology of nitrogen-fixing organisms. The database contains 32 954 aligned nitrogenase nifH sequences linked to phylogenetic trees and associated sequence metadata. The database includes 185 linked multigene entries including full-length nifH, nifD, nifK and 16S ribosomal RNA (rRNA) gene sequences. Evolutionary analyses enabled by the multigene entries support an ancient horizontal transfer of nitrogenase genes between Archaea and Bacteria and provide evidence that nifH has a different history of horizontal gene transfer from the nifDK enzyme core. Further analyses show that lineages in nitrogenase cluster I and cluster III have different rates of substitution within nifD, suggesting that nifD is under different selection pressure in these two lineages. Finally, we find that that the genetic divergence of nifH and 16S rRNA genes does not correlate well at sequence dissimilarity values used commonly to define microbial species, as stains having <3% sequence dissimilarity in their 16S rRNA genes can have up to 23% dissimilarity in nifH. The nifH database has a number of uses including phylogenetic and evolutionary analyses, the design and assessment of primers/probes and the evaluation of nitrogenase sequence diversity. Database URL: http://www.css.cornell.edu/faculty/buckley/nifh.htm PMID:24501396

  20. A comprehensive database and analysis framework to incorporate multiscale data types and enable integrated analysis of bioactive polyphenols.

    PubMed

    Pasinetti, Giulio M; Ho, Lap; Cheng, Haoxiang; Wang, Jun; Simon, James E; Wu, Qing-Li; Zhao, Danyue; Carry, Eileen; Ferruzzi, Mario G; Faith, Jeremiah; Valcarcel, Breanna; Hao, Ke

    2017-06-30

    The development of a given botanical preparation for eventual clinical application requires extensive, detailed characterizations of the chemical composition, as well as the biological availability, biological activity and safety profiles of the botanical. These issues are typically addressed using diverse experimental protocols and model systems. Based on this consideration, in this study we established a comprehensive database and analysis framework for the collection, collation and integrative analysis of diverse, multiscale data sets. Using this framework, we conducted an integrative analysis of heterogeneous data from in vivo and in vitro investigation of a complex bioactive dietary polyphenol-rich preparation (BDPP) and built an integrated network linking datasets generated from this multitude of diverse experimental paradigms. We established a comprehensive database and analysis framework as well as a systematic and logical means to catalogue and collate the diverse array of information gathered, which is securely stored and added to in a standardized manner to enable fast query. We demonstrated the utility of the database in: (1) a statistical ranking scheme to prioritize response to treatments and (2) in depth reconstruction of functionality studies. By examination of these datasets, the system allows analytical querying of heterogeneous data and the access of information related to interactions, mechanism of actions, functions, etc., which ultimately provide a global overview of complex biological responses. Collectively, we present an integrative analysis framework that leads to novel insights on the biological activities of a complex botanical such as BDPP that is based on data-driven characterizations of interactions between BDPP-derived phenolic metabolites, their mechanisms of action, as well as synergism and/or potential cancellation of biological functions. Out integrative analytical approach provides novel means for a systematic integrative

  1. Designing and recruiting to UK autism spectrum disorder research databases: do they include representative children with valid ASD diagnoses?

    PubMed

    Warnell, F; George, B; McConachie, H; Johnson, M; Hardy, R; Parr, J R

    2015-09-04

    (1) Describe how the Autism Spectrum Database-UK (ASD-UK) was established; (2) investigate the representativeness of the first 1000 children and families who participated, compared to those who chose not to; (3) investigate the reliability of the parent-reported Autism Spectrum Disorder (ASD) diagnoses, and present evidence about the validity of diagnoses, that is, whether children recruited actually have an ASD; (4) present evidence about the representativeness of the ASD-UK children and families, by comparing their characteristics with the first 1000 children and families from the regional Database of children with ASD living in the North East (Dasl(n)e), and children and families identified from epidemiological studies. Recruitment through a network of 50 UK child health teams and self-referral. Parents/carers with a child with ASD, aged 2-16 years, completed questionnaires about ASD and some gave professionals' reports about their children. 1000 families registered with ASD-UK in 30 months. Children of families who participated, and of the 208 who chose not to, were found to be very similar on: gender ratio, year of birth, ASD diagnosis and social deprivation score. The reliability of parent-reported ASD diagnoses of children was very high when compared with clinical reports (over 96%); no database child without ASD was identified. A comparison of gender, ASD diagnosis, age at diagnosis, school placement, learning disability, and deprivation score of children and families from ASD-UK with 1084 children and families from Dasl(n)e, and families from population studies, showed that ASD-UK families are representative of families of children with ASD overall. ASD-UK includes families providing parent-reported data about their child and family, who appear to be broadly representative of UK children with ASD. Families continue to join the databases and more than 3000 families can now be contacted by researchers about UK autism research. Published by the BMJ

  2. Comprehensibility.

    ERIC Educational Resources Information Center

    Pettersson, Rune

    This paper addresses the difficulty involved in creating easily understood information. The act of communicating is not complete until the message has been both received and understood by the audience. Messages must always be comprehensible, otherwise they will have no effect. The readability, legibility, and reading value of a graphic message is…

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

    PubMed Central

    Arjunan, Selvam; Sastri, Narayan P.; Chandra, Nagasuma

    2016-01-01

    Dengue virus (DENV) is a human pathogen and its etiology has been widely established. There are many interactions between DENV and human proteins that have been reported in literature. However, no publicly accessible resource for efficiently retrieving the information is yet available. In this study, we mined all publicly available dengue–human interactions that have been reported in the literature into a database called DenHunt. We retrieved 682 direct interactions of human proteins with dengue viral components, 382 indirect interactions and 4120 differentially expressed human genes in dengue infected cell lines and patients. We have illustrated the importance of DenHunt by mapping the dengue–human interactions on to the host interactome and observed that the virus targets multiple host functional complexes of important cellular processes such as metabolism, immune system and signaling pathways suggesting a potential role of these interactions in viral pathogenesis. We also observed that 7 percent of the dengue virus interacting human proteins are also associated with other infectious and non-infectious diseases. Finally, the understanding that comes from such analyses could be used to design better strategies to counteract the diseases caused by dengue virus. The whole dataset has been catalogued in a searchable database, called DenHunt (http://proline.biochem.iisc.ernet.in/DenHunt/). PMID:27618709

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

    PubMed

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

    2016-09-01

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

  5. 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

  6. 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.

  7. AT_CHLORO, a Comprehensive Chloroplast Proteome Database with Subplastidial Localization and Curated Information on Envelope Proteins*

    PubMed Central

    Ferro, Myriam; Brugière, Sabine; Salvi, Daniel; Seigneurin-Berny, Daphné; Court, Magali; Moyet, Lucas; Ramus, Claire; Miras, Stéphane; Mellal, Mourad; Le Gall, Sophie; Kieffer-Jaquinod, Sylvie; Bruley, Christophe; Garin, Jérôme; Joyard, Jacques; Masselon, Christophe; Rolland, Norbert

    2010-01-01

    Recent advances in the proteomics field have allowed a series of high throughput experiments to be conducted on chloroplast samples, and the data are available in several public databases. However, the accurate localization of many chloroplast proteins often remains hypothetical. This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. LC-MS/MS-based analyses first allowed building the AT_CHLORO database (http://www.grenoble.prabi.fr/protehome/grenoble-plant-proteomics/), a comprehensive repertoire of the 1323 proteins, identified by 10,654 unique peptide sequences, present in highly purified chloroplasts and their subfractions prepared from Arabidopsis thaliana leaves. This database also provides extensive proteomics information (peptide sequences and molecular weight, chromatographic retention times, MS/MS spectra, and spectral count) for a unique chloroplast protein accurate mass and time tag database gathering identified peptides with their respective and precise analytical coordinates, molecular weight, and retention time. We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). These data together with an in-depth investigation of the literature were compiled to provide accurate subplastidial localization of previously known and newly identified proteins. A unique knowledge base containing extensive information on the proteins identified in envelope fractions was thus obtained, allowing new insights into this membrane system to be revealed. Altogether, the data we obtained provide unexpected information about plastidial or subplastidial localization of some proteins that were not suspected to be associated to this membrane system. The spectral counting-based strategy was further

  8. Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes

    PubMed Central

    Kurotani, Atsushi; Yamada, Yutaka

    2017-01-01

    Algae are smaller organisms than land plants and offer clear advantages in research over terrestrial species in terms of rapid production, short generation time and varied commercial applications. Thus, studies investigating the practical development of effective algal production are important and will improve our understanding of both aquatic and terrestrial plants. In this study we estimated multiple physicochemical and secondary structural properties of protein sequences, the predicted presence of post-translational modification (PTM) sites, and subcellular localization using a total of 510,123 protein sequences from the proteomes of 31 algal and three plant species. Algal species were broadly selected from green and red algae, glaucophytes, oomycetes, diatoms and other microalgal groups. The results were deposited in the Algal Protein Annotation Suite database (Alga-PrAS; http://alga-pras.riken.jp/), which can be freely accessed online. PMID:28069893

  9. Alga-PrAS (Algal Protein Annotation Suite): A Database of Comprehensive Annotation in Algal Proteomes.

    PubMed

    Kurotani, Atsushi; Yamada, Yutaka; Sakurai, Tetsuya

    2017-01-01

    Algae are smaller organisms than land plants and offer clear advantages in research over terrestrial species in terms of rapid production, short generation time and varied commercial applications. Thus, studies investigating the practical development of effective algal production are important and will improve our understanding of both aquatic and terrestrial plants. In this study we estimated multiple physicochemical and secondary structural properties of protein sequences, the predicted presence of post-translational modification (PTM) sites, and subcellular localization using a total of 510,123 protein sequences from the proteomes of 31 algal and three plant species. Algal species were broadly selected from green and red algae, glaucophytes, oomycetes, diatoms and other microalgal groups. The results were deposited in the Algal Protein Annotation Suite database (Alga-PrAS; http://alga-pras.riken.jp/), which can be freely accessed online. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

  10. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

    PubMed

    Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

  11. Tocilizumab use in pregnancy: Analysis of a global safety database including data from clinical trials and post-marketing data.

    PubMed

    Hoeltzenbein, Maria; Beck, Evelin; Rajwanshi, Richa; Gøtestam Skorpen, Carina; Berber, Erhan; Schaefer, Christof; Østensen, Monika

    2016-10-01

    Analyze the cumulative evidence for pregnancy outcomes after maternal exposure to tocilizumab, an anti-interleukin-6-receptor monoclonal antibody used for the treatment of rheumatoid arthritis and juvenile idiopathic arthritis. At present, published experience on tocilizumab use during pregnancy is very limited. We have analyzed all pregnancy-related reports documented in the Roche Global Safety Database until December 31, 2014 (n = 501). After exclusion of ongoing pregnancies, duplicates, and cases retrieved from the literature, 399 women were found to have been exposed to tocilizumab shortly before or during pregnancy, with pregnancy outcomes being reported in 288 pregnancies (72.2%). Of these 288 pregnancies, 180 were prospectively reported resulting in 109 live births (60.6%), 39 spontaneous abortions (21.7%), 31 elective terminations of pregnancy (17.2%), and 1 stillbirth. The rate of malformations was 4.5%. Co-medications included methotrexate in 21.1% of the prospectively ascertained cases. Compared to the general population, an increased rate of preterm birth (31.2%) was observed. Retrospectively reported pregnancies (n = 108) resulted in 55 live births (50.9%), 31 spontaneous abortions (28.7%), and 22 elective terminations (20.4%). Three infants/fetuses with congenital anomalies were reported in this group. No increased risks for adverse pregnancy outcomes were observed after paternal exposure in 13 pregnancies with known outcome. No indication for a substantially increased malformation risk was observed. Considering the limitations of global safety databases, the data do not yet prove safety, but provide information for physicians and patients to make informed decisions. This is particularly important after inadvertent exposure to tocilizumab, shortly before or during early pregnancy. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Human Transporter Database: Comprehensive Knowledge and Discovery Tools in the Human Transporter Genes

    PubMed Central

    Ye, Adam Y.; Liu, Qing-Rong; Li, Chuan-Yun; Zhao, Min; Qu, Hong

    2014-01-01

    Transporters are essential in homeostatic exchange of endogenous and exogenous substances at the systematic, organic, cellular, and subcellular levels. Gene mutations of transporters are often related to pharmacogenetics traits. Recent developments in high throughput technologies on genomics, transcriptomics and proteomics allow in depth studies of transporter genes in normal cellular processes and diverse disease conditions. The flood of high throughput data have resulted in urgent need for an updated knowledgebase with curated, organized, and annotated human transporters in an easily accessible way. Using a pipeline with the combination of automated keywords query, sequence similarity search and manual curation on transporters, we collected 1,555 human non-redundant transporter genes to develop the Human Transporter Database (HTD) (http://htd.cbi.pku.edu.cn). Based on the extensive annotations, global properties of the transporter genes were illustrated, such as expression patterns and polymorphisms in relationships with their ligands. We noted that the human transporters were enriched in many fundamental biological processes such as oxidative phosphorylation and cardiac muscle contraction, and significantly associated with Mendelian and complex diseases such as epilepsy and sudden infant death syndrome. Overall, HTD provides a well-organized interface to facilitate research communities to search detailed molecular and genetic information of transporters for development of personalized medicine. PMID:24558441

  13. Citrus sinensis Annotation Project (CAP): A Comprehensive Database for Sweet Orange Genome

    PubMed Central

    Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/. PMID:24489955

  14. CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state

    PubMed Central

    Monzon, Alexander Miguel; Rohr, Cristian Oscar; Fornasari, María Silvina; Parisi, Gustavo

    2016-01-01

    CoDNaS (conformational diversity of the native state) is a protein conformational diversity database. Conformational diversity describes structural differences between conformers that define the native state of proteins. It is a key concept to understand protein function and biological processes related to protein functions. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function. Database URL: http://ufq.unq.edu.ar/codnas PMID:27022160

  15. CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state.

    PubMed

    Monzon, Alexander Miguel; Rohr, Cristian Oscar; Fornasari, María Silvina; Parisi, Gustavo

    2016-01-01

    CoDNaS (conformational diversity of the native state) is a protein conformational diversity database. Conformational diversity describes structural differences between conformers that define the native state of proteins. It is a key concept to understand protein function and biological processes related to protein functions. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function. Database URL:http://ufq.unq.edu.ar/codnas.

  16. Increasing resource allocation and research into tobacco control activities: a comprehensive approach including primary prevention, treatment and brief intervention.

    PubMed

    Richmond, R

    1993-01-01

    The range of tobacco control activities should be viewed as essential parts of a complex multi-component puzzle. Intervention strategies designed to address tobacco control should be comprehensive and include both primary and secondary prevention activities and be multi-faceted and capable of bringing about change at both the individual and broader social and cultural levels. In this paper I argue for a mutually inclusive framework in which the various components contribute in important and different ways. I examine the prevalence of smoking and identify the high risk groups, then I examine the range of available strategies and present the evidence for their success. I discuss the primary prevention approaches such as warning labels, taxes, price increases, workplace bans, education in schools, mass media and self-help materials, as well as brief interventions and treatment strategies which are conducted at the worksite, general practice and specialized cessation clinics. The areas for future research are delineated for increased resource allocation and include: the best ways to disseminate brief interventions to smokers, methods to motivate smokers; training of health professionals to deliver brief interventions; enhancing quitting and access to existing treatment resources among specific disadvantaged minority groups, e.g. migrants, unemployed youth, the effect on smoking prevalence of warning labels on cigarette packets and price rises on cigarettes.

  17. Using open-access taxonomic and spatial information to create a comprehensive database for the study of mammalian and avian livestock and pet infections.

    PubMed

    McIntyre, K M; Setzkorn, C; Wardeh, M; Hepworth, P J; Radford, A D; Baylis, M

    2014-10-01

    What are all the species of pathogen that affect our livestock? As 6 out of every 10 human pathogens came from animals, with a good number from livestock and pets, it seems likely that the majority that emerge in the future, and which could threaten or devastate human health, will come from animals. Only 10 years ago, the first comprehensive pathogen list was compiled for humans; we still have no equivalent for animals. Here we describe the creation of a novel pathogen database, and present outputs from the database that demonstrate its value. The ENHanCEd Infectious Diseases database (EID2) is open-access and evidence-based, and it describes the pathogens of humans and animals, their host and vector species, and also their global occurrence. The EID2 systematically collates information on pathogens into a single resource using evidence from the NCBI Taxonomy database, the NCBI Nucleotide database, the NCBI MeSH (Medical Subject Headings) library and PubMed. Information about pathogens is assigned using data-mining of meta-data and semi-automated literature searches. Here we focus on 47 mammalian and avian hosts, including humans and animals commonly used in Europe as food or kept as pets. Currently, the EID2 evidence suggests that: • Within these host species, 793 (30.5%) pathogens were bacteria species, 395 (15.2%) fungi, 705 (27.1%) helminths, 372 (14.3%) protozoa and 332 (12.8%) viruses. • The odds of pathogens being emerging compared to not emerging differed by taxonomic division, and increased when pathogens had greater numbers of host species associated with them, and were zoonotic rather than non-zoonotic. • The odds of pathogens being zoonotic compared to non-zoonotic differed by taxonomic division and also increased when associated with greater host numbers. • The pathogens affecting the greatest number of hosts included: Escherichia coli, Giardia intestinalis, Toxoplasma gondii, Anaplasma phagocytophilum, Cryptosporidium parvum, Rabies virus

  18. Adherence to osteoporosis medicines in Estonia-a comprehensive 15-year retrospective prescriptions database study.

    PubMed

    Laius, Ott; Pisarev, Heti; Maasalu, Katre; Kõks, Sulev; Märtson, Aare

    2017-12-01

    Some patients do not take medicines as they are supposed to. Our research showed that in Estonia, one fifth of patients did not start treatment with osteoporosis medicines and only 20% used the medicines for at least 3 years as they should. This induces unnecessary costs to the healthcare system. Medication non-adherence is the number one reason for not obtaining the expected clinical effect of medicines. With osteoporosis treatment, it has been shown that both implementation of treatment and persistence influence the risk of fractures significantly. Long-term adherence to medication in Estonia is to be determined with this study. A 15-year retrospective study was carried out in order to establish initiation, implementation, and persistence of Estonian patients. All new users of osteoporosis medicines were analyzed for all prescriptions they received during the study period. Sufficient adherence to treatment was defined as a patient being dispensed 80% or more prescribed doses for at least 1 year. The study period was from 2001 to 2015. Patients (24,652) were included in the study. Of the patients, 93.7% (n = 23,091) were women and 6.3% (n = 1564) were men. Eighteen percent (4636) were dispensed only one prescription. Of the patients, 44.2% included in the study had medication possession ratio (MPR) ≥80% over follow-up period; 8922 (36.2%) who were prescribed from 2001 to 2015 persisted for 1 year with MPR ≥80% and 19.8% persisted for 3 years. Forty percent of expenditure on osteoporosis medication was made for treatment courses with insufficient adherence. There is room for improvement in Estonia with medication adherence relating to all three aspects that determine adherence-initiation, implementation, and persistence. This means further efforts are to be made to educate patients and healthcare professionals on realizing the importance of good adherence.

  19. A comprehensive analysis of electron conical distributions from multi-satellite databases

    NASA Technical Reports Server (NTRS)

    Menietti, J. Douglas

    1993-01-01

    This report consists of a copy of a paper that has been submitted to the 'Journal of Geophysical Research', entitled 'DE 1 and Viking Observations Associated With Electron Conical Distributions,' and an abstract of another paper (included as an appendix to the report) that is about to be submitted to the same journal entitled 'Perpendicular Electron Heating by Absorption of Auroral Kilometric Radiation.' A bibliography of other papers that have been published as a result of this project follows. The purpose of this project was to use the DE 1 and Viking particle and wave data to better understand the source mechanism of electron conical distributions. We have shown that electron conics are often associated with upper hybrid waves in the nightside auroral region. We have also shown that electron conics are observed near auroral kilometric radiation (AKR) source regions and may be the result of perpendicular heating due to waves. We have completed a statistical study of electron conics observed by DE-l and Viking. The study shows the occurrence frequency and location of electron conical distributions; there are some differences between the results of DE and Viking perhaps due to different regions sampled.

  20. The Antimicrobial Index: a comprehensive literature-based antimicrobial database and reference work

    PubMed Central

    Amirkia, Vafa David; Qiubao, Pan

    2011-01-01

    Although the ever-growing usage of antimicrobials in the fields of medicine, pharmacology, and microbiology have undoubtedly allowed for unprecedented advances in the scientific world, these advances are nevertheless accompanied by unprecedented challenges. Sharp increases in antibiotic usages have led to inefficient and wasteful usage practices. Bacterial resistances have dramatically increased and therefore hindered the effectiveness of traditional antibiotics, thus forcing many life-science professionals to turn to plant extracts and synthetic chemicals [1]. The Antimicrobial Index (TAMI) seeks to alleviate some of these mounting difficulties through the collection and centralization of relevant antimicrobial susceptibility data from journals. Data compiled for antimicrobials include: method of action, physical properties, resistance genes, side effects, and minimal inhibitory concentrations (MIC50, MIC90 and/or ranges). TAMI currently contains data on 960 antimicrobials and over 24,000 microorganisms (3,500 unique strains) which were collected from over 400 pieces of published literature. Volume and scope of the index have been and will continue to increase and it is hoped that such an index will further foster international cooperation and communication of antimicrobial-related knowledge. TAMI can be accessed at: http://antibiotics.toku-e.com/. PMID:21383924

  1. A comprehensive database of high-throughput sequencing-based RNA secondary structure probing data (Structure Surfer).

    PubMed

    Berkowitz, Nathan D; Silverman, Ian M; Childress, Daniel M; Kazan, Hilal; Wang, Li-San; Gregory, Brian D

    2016-05-17

    RNA molecules fold into complex three-dimensional shapes, guided by the pattern of hydrogen bonding between nucleotides. This pattern of base pairing, known as RNA secondary structure, is critical to their cellular function. Recently several diverse methods have been developed to assay RNA secondary structure on a transcriptome-wide scale using high-throughput sequencing. Each approach has its own strengths and caveats, however there is no widely available tool for visualizing and comparing the results from these varied methods. To address this, we have developed Structure Surfer, a database and visualization tool for inspecting RNA secondary structure in six transcriptome-wide data sets from human and mouse ( http://tesla.pcbi.upenn.edu/strucuturesurfer/ ). The data sets were generated using four different high-throughput sequencing based methods. Each one was analyzed with a scoring pipeline specific to its experimental design. Users of Structure Surfer have the ability to query individual loci as well as detect trends across multiple sites. Here, we describe the included data sets and their differences. We illustrate the database's function by examining known structural elements and we explore example use cases in which combined data is used to detect structural trends. In total, Structure Surfer provides an easy-to-use database and visualization interface for allowing users to interrogate the currently available transcriptome-wide RNA secondary structure information for mammals.

  2. Automated Identification of Medically Important Bacteria by 16S rRNA Gene Sequencing Using a Novel Comprehensive Database, 16SpathDB▿

    PubMed Central

    Woo, Patrick C. Y.; Teng, Jade L. L.; Yeung, Juilian M. Y.; Tse, Herman; Lau, Susanna K. P.; Yuen, Kwok-Yung

    2011-01-01

    Despite the increasing use of 16S rRNA gene sequencing, interpretation of 16S rRNA gene sequence results is one of the most difficult problems faced by clinical microbiologists and technicians. To overcome the problems we encountered in the existing databases during 16S rRNA gene sequence interpretation, we built a comprehensive database, 16SpathDB (http://147.8.74.24/16SpathDB) based on the 16S rRNA gene sequences of all medically important bacteria listed in the Manual of Clinical Microbiology and evaluated its use for automated identification of these bacteria. Among 91 nonduplicated bacterial isolates collected in our clinical microbiology laboratory, 71 (78%) were reported by 16SpathDB as a single bacterial species having >98.0% nucleotide identity with the query sequence, 19 (20.9%) were reported as more than one bacterial species having >98.0% nucleotide identity with the query sequence, and 1 (1.1%) was reported as no match. For the 71 bacterial isolates reported as a single bacterial species, all results were identical to their true identities as determined by a polyphasic approach. For the 19 bacterial isolates reported as more than one bacterial species, all results contained their true identities as determined by a polyphasic approach and all of them had their true identities as the “best match in 16SpathDB.” For the isolate (Gordonibacter pamelaeae) reported as no match, the bacterium has never been reported to be associated with human disease and was not included in the Manual of Clinical Microbiology. 16SpathDB is an automated, user-friendly, efficient, accurate, and regularly updated database for 16S rRNA gene sequence interpretation in clinical microbiology laboratories. PMID:21389154

  3. Comprehensive mollusk acute toxicity database improves the use of Interspecies Correlation Estimation (ICE) models to predict toxicity of untested freshwater and endangered mussel species

    EPA Science Inventory

    Interspecies correlation estimation (ICE) models extrapolate acute toxicity data from surrogate test species to untested taxa. A suite of ICE models developed from a comprehensive database is available on the US Environmental Protection Agency’s web-based application, Web-I...

  4. Comprehensive mollusk acute toxicity database improves the use of Interspecies Correlation Estimation (ICE) models to predict toxicity of untested freshwater and endangered mussel species

    EPA Science Inventory

    Interspecies correlation estimation (ICE) models extrapolate acute toxicity data from surrogate test species to untested taxa. A suite of ICE models developed from a comprehensive database is available on the US Environmental Protection Agency’s web-based application, Web-I...

  5. 24 CFR 968.320 - HUD review and approval of comprehensive plan (including five-year action plan).

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ...) Contradiction of local government certification or PHA resolution. (c) Effect of HUD approval of Comprehensive... under this part. HUD shall allocate such funds to PHAs and IHAs participating in the CGP in accordance...

  6. Asthma exacerbations and traffic: examining relationships using link-based traffic metrics and a comprehensive patient database.

    PubMed

    Lindgren, Paula; Johnson, Jean; Williams, Allan; Yawn, Barbara; Pratt, Gregory C

    2016-11-03

    The Rochester Epidemiology Project (REP) is a unique community-based medical record data linkage system that provides individual patient address, diagnosis and visit information for all hospitalizations, as well as emergency department, urgent care and outpatient clinic visits for asthma. Proximity to traffic is known to be associated with asthma exacerbations and severity. Our null hypothesis was that there is no association between residential proximity to traffic and asthma exacerbations over eleven years of REP data. Spatial coordinates of the homes of 19,915 individuals diagnosed with asthma were extracted from the REP database. Three metrics of traffic exposure at residences were calculated from link-based traffic count data. We used exploratory statistics as well as logistic and Poisson regression to examine associations between three traffic metrics at the home address and asthma exacerbations. Asthma exacerbations increased as traffic levels near the home increased. Proximity to traffic was a significant predictor of asthma exacerbations in logistic and Poisson regressions controlling for age, gender and block group poverty. Over eleven years in a comprehensive county-wide data set of asthma patients, and after controlling for demographic effects, we found evidence that living in proximity to traffic increased the risk of asthma exacerbations.

  7. Subject and authorship of records related to the Organization for Tropical Studies (OTS) in BINABITROP, a comprehensive database about Costa Rican biology.

    PubMed

    Monge-Nájera, Julián; Nielsen-Muñoz, Vanessa; Azofeifa-Mora, Ana Beatriz

    2013-06-01

    BINABITROP is a bibliographical database of more than 38000 records about the ecosystems and organisms of Costa Rica. In contrast with commercial databases, such as Web of Knowledge and Scopus, which exclude most of the scientific journals published in tropical countries, BINABITROP is a comprehensive record of knowledge on the tropical ecosystems and organisms of Costa Rica. We analyzed its contents in three sites (La Selva, Palo Verde and Las Cruces) and recorded scientific field, taxonomic group and authorship. We found that most records dealt with ecology and systematics, and that most authors published only one article in the study period (1963-2011). Most research was published in four journals: Biotropica, Revista de Biología Tropical/ International Journal of Tropical Biology and Conservation, Zootaxa and Brenesia. This may be the first study of a such a comprehensive database for any case of tropical biology literature.

  8. Potash: a global overview of evaporate-related potash resources, including spatial databases of deposits, occurrences, and permissive tracts: Chapter S in Global mineral resource assessment

    USGS Publications Warehouse

    Orris, Greta J.; Cocker, Mark D.; Dunlap, Pamela; Wynn, Jeff C.; Spanski, Gregory T.; Briggs, Deborah A.; Gass, Leila; Bliss, James D.; Bolm, Karen S.; Yang, Chao; Lipin, Bruce R.; Ludington, Stephen; Miller, Robert J.; Słowakiewicz, Mirosław

    2014-01-01

    This report describes a global, evaporite-related potash deposits and occurrences database and a potash tracts database. Chapter 1 summarizes potash resource history and use. Chapter 2 describes a global potash deposits and occurrences database, which contains more than 900 site records. Chapter 3 describes a potash tracts database, which contains 84 tracts with geology permissive for the presence of evaporite-hosted potash resources, including areas with active evaporite-related potash production, areas with known mineralization that has not been quantified or exploited, and areas with potential for undiscovered potash resources. Chapter 4 describes geographic information system (GIS) data files that include (1) potash deposits and occurrences data, (2) potash tract data, (3) reference databases for potash deposit and tract data, and (4) representative graphics of geologic features related to potash tracts and deposits. Summary descriptive models for stratabound potash-bearing salt and halokinetic potash-bearing salt are included in appendixes A and B, respectively. A glossary of salt- and potash-related terms is contained in appendix C and a list of database abbreviations is given in appendix D. Appendix E describes GIS data files, and appendix F is a guide to using the geodatabase.

  9. Spanish public awareness regarding DNA profile databases in forensic genetics: what type of DNA profiles should be included?

    PubMed Central

    Gamero, Joaquín J; Romero, Jose‐Luis; Peralta, Juan‐Luis; Carvalho, Mónica; Corte‐Real, Francisco

    2007-01-01

    The importance of non‐codifying DNA polymorphism for the administration of justice is now well known. In Spain, however, this type of test has given rise to questions in recent years: (a) Should consent be obtained before biological samples are taken from an individual for DNA analysis? (b) Does society perceive these techniques and methods of analysis as being reliable? (c) There appears to be lack of knowledge concerning the basic norms that regulate databases containing private or personal information and the protection that information of this type must be given. This opinion survey and the subsequent analysis of the results in ethical terms may serve to reveal the criteria and the degree of information that society has with regard to DNA databases. In the study, 73.20% (SE 1.12%) of the population surveyed was in favour of specific legislation for computer files in which DNA analysis results for forensic purposes are stored. PMID:17906059

  10. SUPERSITES INTEGRATED RELATIONAL DATABASE (SIRD)

    EPA Science Inventory

    As part of EPA's Particulate Matter (PM) Supersites Program (Program), the University of Maryland designed and developed the Supersites Integrated Relational Database (SIRD). Measurement data in SIRD include comprehensive air quality data from the 7 Supersite program locations f...

  11. SUPERSITES INTEGRATED RELATIONAL DATABASE (SIRD)

    EPA Science Inventory

    As part of EPA's Particulate Matter (PM) Supersites Program (Program), the University of Maryland designed and developed the Supersites Integrated Relational Database (SIRD). Measurement data in SIRD include comprehensive air quality data from the 7 Supersite program locations f...

  12. Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C₂H₂ zinc fingers and engineered zinc finger arrays.

    PubMed

    Fu, Fengli; Voytas, Daniel F

    2013-01-01

    ZiFDB (Zinc Finger Database, http://zifdb.msi.umn.edu) is a web-accessible database that houses information on individual C(2)H(2) zinc fingers (ZFs) and engineered zinc finger arrays (ZFAs). ZiFDB serves as a resource for biologists interested in engineering ZFAs for use as sequence-specific DNA-binding reagents. Here, we describe four new features of ZiFDB: (i) the database allows users to input new ZFs and ZFAs; (ii) a shadow database temporarily stores user-submitted data, pending approval by the database curator and subsequent loading into the persistent database; (iii) ZiFDB contains 181 Context-Dependent Assembly (CoDA) ZFAs, which were generated by this newly described ZFA engineering platform; and (iv) the database also now contains 319 F1F2 CoDA units and 334 F2F3 CoDA units that can be used to construct CoDA arrays. In total, the new release of ZiFDB contains 1226 ZFs and 1123 ZFAs.

  13. 24 CFR 968.320 - HUD review and approval of comprehensive plan (including five-year action plan).

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... REGULATIONS RELATING TO HOUSING AND URBAN DEVELOPMENT (CONTINUED) OFFICE OF ASSISTANT SECRETARY FOR PUBLIC AND INDIAN HOUSING, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT PUBLIC HOUSING MODERNIZATION Comprehensive Grant Program (for PHAs That Own or Operate 250 or More Public Housing Units) § 968.320 HUD review and...

  14. Teach Someone to Read. A Step-by-Step Guide for Literacy Tutors, Including Diagnostic Phonics and Comprehension Assessments.

    ERIC Educational Resources Information Center

    Rosenthal, Nadine

    This guide gives new tutors who are not professional teachers some techniques for teaching others to read and write. A comprehension-based approach to literacy training is used. Part 1 presents a variety of background information on illiteracy. It also gives some guidelines useful for the new tutor. Part 2 is composed of two diagnostic…

  15. Comprehensive Approach to Pupil Planning: Stage II - Planning and Placement (Includes Planning and Placement Team Meeting Agenda). Experimental Edition.

    ERIC Educational Resources Information Center

    Vlasak, Frances Stetson; Kaufman, Martin J.

    Presented is Stage II of the Comprehensive Approach to Pupil Planning (CAPP) System, a three-stage model for planning educational interventions in the regular and special education classrooms and for guiding placement decisions. The guide focuses on the evaluation services performed by the Planning and Placement Team (PPT) with sections on the…

  16. Alaska Geochemical Database, Version 2.0 (AGDB2)--including “best value” data compilations for rock, sediment, soil, mineral, and concentrate sample media

    USGS Publications Warehouse

    Granitto, Matthew; Schmidt, Jeanine M.; Shew, Nora B.; Gamble, Bruce M.; Labay, Keith A.

    2013-01-01

    The Alaska Geochemical Database Version 2.0 (AGDB2) contains new geochemical data compilations in which each geologic material sample has one “best value” determination for each analyzed species, greatly improving speed and efficiency of use. Like the Alaska Geochemical Database (AGDB, http://pubs.usgs.gov/ds/637/) before it, the AGDB2 was created and designed to compile and integrate geochemical data from Alaska in order to facilitate geologic mapping, petrologic studies, mineral resource assessments, definition of geochemical baseline values and statistics, environmental impact assessments, and studies in medical geology. This relational database, created from the Alaska Geochemical Database (AGDB) that was released in 2011, serves as a data archive in support of present and future Alaskan geologic and geochemical projects, and contains data tables in several different formats describing historical and new quantitative and qualitative geochemical analyses. The analytical results were determined by 85 laboratory and field analytical methods on 264,095 rock, sediment, soil, mineral and heavy-mineral concentrate samples. Most samples were collected by U.S. Geological Survey personnel and analyzed in U.S. Geological Survey laboratories or, under contracts, in commercial analytical laboratories. These data represent analyses of samples collected as part of various U.S. Geological Survey programs and projects from 1962 through 2009. In addition, mineralogical data from 18,138 nonmagnetic heavy-mineral concentrate samples are included in this database. The AGDB2 includes historical geochemical data originally archived in the U.S. Geological Survey Rock Analysis Storage System (RASS) database, used from the mid-1960s through the late 1980s and the U.S. Geological Survey PLUTO database used from the mid-1970s through the mid-1990s. All of these data are currently maintained in the National Geochemical Database (NGDB). Retrievals from the NGDB were used to generate

  17. No identifiable Hb1Ac or lifestyle change after a comprehensive diabetes programme including motivational interviewing: A cluster randomised trial

    PubMed Central

    2013-01-01

    Abstract Objective To study the effectiveness of a comprehensive diabetes programme in general practice that integrates patient-centred lifestyle counselling into structured diabetes care. Design and setting Cluster randomised trial in general practices. Intervention Nurse-led structured diabetes care with a protocol, record keeping, reminders, and feedback, plus training in motivational interviewing and agenda setting. Subjects Primary care nurses in 58 general practices and their 940 type 2 diabetes patients with an HbA1c concentration above 7%, and a body mass index (BMI) above 25 kg/m2. Main outcome measures HbA1c, diet, and physical activity (medical records and patient questionnaires). Results Multilevel linear and logistic regression analyses adjusted for baseline outcomes showed that despite active nurse participation in the intervention, the comprehensive programme was no more effective than usual care after 14 months, as shown by HbA1c levels (difference between groups = 0.13; CI 20.8–0.35) and diet (fat (difference between groups = 0.19; CI 20.82–1.21); vegetables (difference between groups = 0.10; CI-0.21–0.41); fruit (difference between groups = 20.02; CI 20.26–0.22)), and physical activity (difference between groups = 21.15; CI 212.26–9.97), or any of the other measures of clinical parameters, patient's readiness to change, or quality of life. Conclusion A comprehensive programme that integrated lifestyle counselling based on motivational interviewing principles integrated into structured diabetes care did not alter HbA1c or the lifestyle related to diet and physical activity. We thus question the impact of motivational interviewing in terms of its ability to improve routine diabetes care in general practice. PMID:23659710

  18. A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening.

    PubMed

    Broughton, H B

    2000-06-01

    Second-generation methods for docking ligands into their biological receptors, such as FLOG, provide for flexibility of the ligand but not of the receptor. Molecular dynamics based methods, such as free energy perturbation, account for flexibility, solvent effects, etc., but are very time consuming. We combined the use of statistical analysis of conformational samples from short-run protein molecular dynamics with grid-based docking protocols and demonstrated improved performance in two test cases. Our statistical analysis explores the importance of the average strength of a potential interaction with the biological target and optionally applies a weighting depending on the variability in the strength of the interaction seen during dynamics simulation. Using these methods, we improved the num-top-ranked 10% of a database of drug-like molecules, in searches based on the three-dimensional structure of the protein. These methods are able to match the ability of manual docking to assess likely inactivity on steric grounds and indeed to rank order ligands from a homologous series of cyclooxygenase-2 inhibitors with good correlation to their true activity. Furthermore, these methods reduce the need for human intervention in setting up molecular docking experiments.

  19. 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 (σ1) and sigma-2 (σ2). The two receptor subtypes have specific drug actions, pharmacological profiles and molecular characteristics. The σ2 receptor is overexpressed in several tumor cell lines, and its ligands are currently under investigation for their role in tumor diagnosis and treatment. The σ2 receptor structure has not been disclosed, and researchers rely on σ2 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 σ2 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 σ2 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.

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

    PubMed

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

    2016-08-05

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

  1. A Comprehensive Electronic Health Record Based Patient Navigation Module Including Technology Driven Colorectal Cancer Outreach and Education.

    PubMed

    Ajeesh, Sunny; Luis, Rustveld

    2017-02-10

    The purpose of this concept paper is to propose an innovative multifaceted patient navigation module embedded in the Electronic Health Record (EHR) to address barriers to efficient and effective colorectal cancer (CRC) care. The EHR-based CRC patient navigation module will include several patient navigation features: (1) CRC screening registry; (2) patient navigation data, including CRC screening data, outcomes of patient navigation including navigation status (CRC screening referrals, fecal occult blood test (FOBT) completed, colonoscopy scheduled and completed, cancelations, reschedules, and no-shows); (3) CRC counseling aid; and 4) Web-based CRC education application including interactive features such as a standardized colonoscopy preparation guide, modifiable CRC risk factors, and links to existing resources. An essential component of health informatics is the use of EHR systems to not only provide a system for storing and retrieval of patient health data but can also be used to enhance patient decision-making both from a provider and patient perspective.

  2. Glia Open Access Database (GOAD): A comprehensive gene expression encyclopedia of glia cells in health and disease.

    PubMed

    Holtman, Inge R; Noback, Michiel; Bijlsma, Marieke; Duong, Kim N; van der Geest, Marije A; Ketelaars, Peer T; Brouwer, Nieske; Vainchtein, Ilia D; Eggen, Bart J L; Boddeke, Hendrikus W G M

    2015-09-01

    Recently, the number of genome-wide transcriptome profiles of pure populations of glia cells has drastically increased, resulting in an unprecedented amount of data that offer opportunities to study glia phenotypes and functions in health and disease. To make genome-wide transcriptome data easily accessible, we developed the Glia Open Access Database (GOAD), available via www.goad.education. GOAD contains a collection of previously published and unpublished transcriptome data, including datasets from isolated microglia, astrocytes and oligodendrocytes both at homeostatic and pathological conditions. It contains an intuitive web-based interface that consists of three features that enable searching, browsing, analyzing, and downloading of the data. The first feature is differential gene expression (DE) analysis that provides genes that are significantly up and down-regulated with the associated fold changes and p-values between two conditions of interest. In addition, an interactive Venn diagram is generated to illustrate the overlap and differences between several DE gene lists. The second feature is quantitative gene expression (QE) analysis, to investigate which genes are expressed in a particular glial cell type and to what degree. The third feature is a search utility, which can be used to find a gene of interest and depict its expression in all available expression data sets by generating a gene card. In addition, quality guidelines and relevant concepts for transcriptome analysis are discussed. Finally, GOAD is discussed in relation to several online transcriptome tools developed in neuroscience and immunology. In conclusion, GOAD is a unique platform to facilitate integration of bioinformatics in glia biology. © 2015 Wiley Periodicals, Inc.

  3. GreekLex 2: A comprehensive lexical database with part-of-speech, syllabic, phonological, and stress information.

    PubMed

    Kyparissiadis, Antonios; van Heuven, Walter J B; Pitchford, Nicola J; Ledgeway, Timothy

    2017-01-01

    Databases containing lexical properties on any given orthography are crucial for psycholinguistic research. In the last ten years, a number of lexical databases have been developed for Greek. However, these lack important part-of-speech information. Furthermore, the need for alternative procedures for calculating syllabic measurements and stress information, as well as combination of several metrics to investigate linguistic properties of the Greek language are highlighted. To address these issues, we present a new extensive lexical database of Modern Greek (GreekLex 2) with part-of-speech information for each word and accurate syllabification and orthographic information predictive of stress, as well as several measurements of word similarity and phonetic information. The addition of detailed statistical information about Greek part-of-speech, syllabification, and stress neighbourhood allowed novel analyses of stress distribution within different grammatical categories and syllabic lengths to be carried out. Results showed that the statistical preponderance of stress position on the pre-final syllable that is reported for Greek language is dependent upon grammatical category. Additionally, analyses showed that a proportion higher than 90% of the tokens in the database would be stressed correctly solely by relying on stress neighbourhood information. The database and the scripts for orthographic and phonological syllabification as well as phonetic transcription are available at http://www.psychology.nottingham.ac.uk/greeklex/.

  4. GreekLex 2: A comprehensive lexical database with part-of-speech, syllabic, phonological, and stress information

    PubMed Central

    van Heuven, Walter J. B.; Pitchford, Nicola J.; Ledgeway, Timothy

    2017-01-01

    Databases containing lexical properties on any given orthography are crucial for psycholinguistic research. In the last ten years, a number of lexical databases have been developed for Greek. However, these lack important part-of-speech information. Furthermore, the need for alternative procedures for calculating syllabic measurements and stress information, as well as combination of several metrics to investigate linguistic properties of the Greek language are highlighted. To address these issues, we present a new extensive lexical database of Modern Greek (GreekLex 2) with part-of-speech information for each word and accurate syllabification and orthographic information predictive of stress, as well as several measurements of word similarity and phonetic information. The addition of detailed statistical information about Greek part-of-speech, syllabification, and stress neighbourhood allowed novel analyses of stress distribution within different grammatical categories and syllabic lengths to be carried out. Results showed that the statistical preponderance of stress position on the pre-final syllable that is reported for Greek language is dependent upon grammatical category. Additionally, analyses showed that a proportion higher than 90% of the tokens in the database would be stressed correctly solely by relying on stress neighbourhood information. The database and the scripts for orthographic and phonological syllabification as well as phonetic transcription are available at http://www.psychology.nottingham.ac.uk/greeklex/. PMID:28231303

  5. New Comprehensive Cytogenetic Scoring System for Primary Myelodysplastic Syndromes (MDS) and Oligoblastic Acute Myeloid Leukemia After MDS Derived From an International Database Merge

    PubMed Central

    Schanz, Julie; Tüchler, Heinz; Solé, Francesc; Mallo, Mar; Luño, Elisa; Cervera, José; Granada, Isabel; Hildebrandt, Barbara; Slovak, Marilyn L.; Ohyashiki, Kazuma; Steidl, Christian; Fonatsch, Christa; Pfeilstöcker, Michael; Nösslinger, Thomas; Valent, Peter; Giagounidis, Aristoteles; Aul, Carlo; Lübbert, Michael; Stauder, Reinhard; Krieger, Otto; Garcia-Manero, Guillermo; Faderl, Stefan; Pierce, Sherry; Le Beau, Michelle M.; Bennett, John M.; Greenberg, Peter; Germing, Ulrich; Haase, Detlef

    2012-01-01

    Purpose The karyotype is a strong independent prognostic factor in myelodysplastic syndromes (MDS). Since the implementation of the International Prognostic Scoring System (IPSS) in 1997, knowledge concerning the prognostic impact of abnormalities has increased substantially. The present study proposes a new and comprehensive cytogenetic scoring system based on an international data collection of 2,902 patients. Patients and Methods Patients were included from the German-Austrian MDS Study Group (n = 1,193), the International MDS Risk Analysis Workshop (n = 816), the Spanish Hematological Cytogenetics Working Group (n = 849), and the International Working Group on MDS Cytogenetics (n = 44) databases. Patients with primary MDS and oligoblastic acute myeloid leukemia (AML) after MDS treated with supportive care only were evaluated for overall survival (OS) and AML evolution. Internal validation by bootstrap analysis and external validation in an independent patient cohort were performed to confirm the results. Results In total, 19 cytogenetic categories were defined, providing clear prognostic classification in 91% of all patients. The abnormalities were classified into five prognostic subgroups (P < .001): very good (median OS, 61 months; hazard ratio [HR], 0.5; n = 81); good (49 months; HR, 1.0 [reference category]; n = 1,809); intermediate (26 months; HR, 1.6; n = 529); poor (16 months; HR, 2.6; n = 148); and very poor (6 months; HR, 4.2; n = 187). The internal and external validations confirmed the results of the score. Conclusion In conclusion, these data should contribute to the ongoing efforts to update the IPSS by refining the cytogenetic risk categories. PMID:22331955

  6. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine.

    PubMed

    Stenson, Peter D; Mort, Matthew; Ball, Edward V; Shaw, Katy; Phillips, Andrew; Cooper, David N

    2014-01-01

    The Human Gene Mutation Database (HGMD®) is a comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. By June 2013, the database contained over 141,000 different lesions detected in over 5,700 different genes, with new mutation entries currently accumulating at a rate exceeding 10,000 per annum. HGMD was originally established in 1996 for the scientific study of mutational mechanisms in human genes. However, it has since acquired a much broader utility as a central unified disease-oriented mutation repository utilized by human molecular geneticists, genome scientists, molecular biologists, clinicians and genetic counsellors as well as by those specializing in biopharmaceuticals, bioinformatics and personalized genomics. The public version of HGMD (http://www.hgmd.org) is freely available to registered users from academic institutions/non-profit organizations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via BIOBASE GmbH.

  7. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies.

    PubMed

    Stenson, Peter D; Mort, Matthew; Ball, Edward V; Evans, Katy; Hayden, Matthew; Heywood, Sally; Hussain, Michelle; Phillips, Andrew D; Cooper, David N

    2017-03-27

    The Human Gene Mutation Database (HGMD(®)) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD ( http://www.hgmd.org ) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.

  8. Comprehensive detection and identification of human coronaviruses, including the SARS-associated coronavirus, with a single RT-PCR assay.

    PubMed

    Adachi, D; Johnson, G; Draker, R; Ayers, M; Mazzulli, T; Talbot, P J; Tellier, R

    2004-12-01

    The SARS-associated human coronavirus (SARS-HCoV) is a newly described, emerging virus conclusively established as the etiologic agent of the severe acute respiratory syndrome (SARS). This study presents a single-tube RT-PCR assay that can detect with high analytical sensitivity the SARS-HCoV, as well as several other coronaviruses including other known human respiratory coronaviruses (HCoV-OC43 and HCoV-229E). Species identification is provided by sequencing the amplicon, although a rapid screening test by restriction enzyme analysis has proved to be very useful for the analysis of samples obtained during the SARS outbreak in Toronto, Canada.

  9. A comprehensive model for reproductive and developmental toxicity hazard identification: I. Development of a weight of evidence QSAR database.

    PubMed

    Matthews, Edwin J; Kruhlak, Naomi L; Daniel Benz, R; Contrera, Joseph F

    2007-03-01

    A weight of evidence (WOE) reproductive and developmental toxicology (reprotox) database was constructed that is suitable for quantitative structure-activity relationship (QSAR) modeling and human hazard identification of untested chemicals. The database was derived from multiple publicly available reprotox databases and consists of more than 10,000 individual rat, mouse, or rabbit reprotox tests linked to 2134 different organic chemical structures. The reprotox data were classified into seven general classes (male reproductive toxicity, female reproductive toxicity, fetal dysmorphogenesis, functional toxicity, mortality, growth, and newborn behavioral toxicity), and 90 specific categories as defined in the source reprotox databases. Each specific category contained over 500 chemicals, but the percentage of active chemicals was low, generally only 0.1-10%. The mathematical WOE model placed greater significance on confirmatory observations from repeat experiments, chemicals with multiple findings within a category, and the categorical relatedness of the findings. Using the weighted activity scores, statistical analyses were performed for specific data sets to identify clusters of categories that were correlated, containing similar profiles of active and inactive chemicals. The analysis revealed clusters of specific categories that contained chemicals that were active in two or more mammalian species (trans-species). Such chemicals are considered to have the highest potential risk to humans. In contrast, some specific categories exhibited only single species-specific activities. Results also showed that the rat and mouse were more susceptible to dysmorphogenesis than rabbits (6.1- and 3.6-fold, respectively).

  10. Data-based Decision-making: Teachers' Comprehension of Curriculum-based Measurement Progress-monitoring Graphs

    ERIC Educational Resources Information Center

    van den Bosch, Roxette M.; Espin, Christine A.; Chung, Siuman; Saab, Nadira

    2017-01-01

    Teachers have difficulty using data from Curriculum-based Measurement (CBM) progress graphs of students with learning difficulties for instructional decision-making. As a first step in unraveling those difficulties, we studied teachers' comprehension of CBM graphs. Using think-aloud methodology, we examined 23 teachers' ability to…

  11. Data-based Decision-making: Teachers' Comprehension of Curriculum-based Measurement Progress-monitoring Graphs

    ERIC Educational Resources Information Center

    van den Bosch, Roxette M.; Espin, Christine A.; Chung, Siuman; Saab, Nadira

    2017-01-01

    Teachers have difficulty using data from Curriculum-based Measurement (CBM) progress graphs of students with learning difficulties for instructional decision-making. As a first step in unraveling those difficulties, we studied teachers' comprehension of CBM graphs. Using think-aloud methodology, we examined 23 teachers' ability to…

  12. Antiphospholipid antibody testing for the antiphospholipid syndrome: a comprehensive practical review including a synopsis of challenges and recent guidelines.

    PubMed

    Favaloro, Emmanuel J; Wong, Richard C W

    2014-10-01

    The antiphospholipid (antibody) syndrome (APS) is an autoimmune condition characterised by a wide range of clinical features, but primarily identified as thrombotic and/or obstetric related adverse events. APS is associated with the presence of antiphospholipid antibodies (aPL), including the so-called lupus anticoagulant (LA). These aPL are heterogeneous in nature, detected with varying sensitivity and specificity by a diverse range of laboratory tests. All these tests are unfortunately imperfect, suffer from poor assay reproducibility (inter-method and inter-laboratory) and a lack of standardisation and harmonisation. Clinicians and laboratory personnel may struggle to keep abreast of these factors, as well as the expanding range of available aPL tests, and consequent result interpretation. Therefore, APS remains a significant diagnostic challenge for many clinicians across a wide range of clinical specialities, due to these issues related to laboratory testing as well as the ever-expanding range of reported clinical manifestations. This review is primarily focussed on issues related to laboratory testing for APS in regards to the currently available assays, and summarises recent international consensus guidelines for aPL testing, both for the liquid phase functional LA assays and the solid phase assays (anticardiolipin and anti-beta-2-Glycoprotein-I).

  13. Comprehensive capacitance-voltage analysis including quantum effects for high-k interfaces on germanium and other alternative channel materials

    NASA Astrophysics Data System (ADS)

    Anwar, Sarkar R. M.

    High mobility alternative channel materials to silicon are critical to the continued scaling of metal oxide semiconductor (MOS) devices. However, before they can be incorporated into advanced devices, some major issues need to be solved. The high mobility materials suffer from lower allowable thermal budgets compared to Si (before desorption and defect formation becomes an issue) and the absence of a good quality native oxide has further increased the interest in the use of high-k dielectrics. However, the high interface state density and high electric fields at these semiconductor/high-k interfaces can significantly impact the capacitance-voltage (C-V) profile, and current C-V modeling software cannot account for these effects. This in turn affects the parameters extracted from the C-V data of the high mobility semiconductor/high-k interface, which are crucial to fully understand the interface properties and expedite process development. To address this issue, we developed a model which takes into account quantum corrections which can be applied to a number of these alternative channel materials including SixGe1-x, Ge, InGaAs, and GaAs. The C-V simulation using this QM correction model is orders of magnitude faster compared to a full band Schrodinger-Poisson solver. The simulated C-V is directly benchmarked to a self consistent Schrodinger-Poisson solution for each bulk semiconductor material, and from the benchmarking process the QM correction parameters are extracted. The full program, C-V Alternative Channel Extraction (CV ACE), incorporates a quantum mechanical correction model, along with the interface state density model, and can extract device parameters such as equivalent oxide thickness (EOT), doping density and flat band voltage (Vfb) as well as the interface state density profile using multiple measurements performed at different frequencies and temperatures, simultaneously. The program was used to analyze experimentally measured C-V profiles and the

  14. MOPED 2.5—An Integrated Multi-Omics Resource: Multi-Omics Profiling Expression Database Now Includes Transcriptomics Data

    PubMed Central

    Montague, Elizabeth; Stanberry, Larissa; Higdon, Roger; Janko, Imre; Lee, Elaine; Anderson, Nathaniel; Choiniere, John; Stewart, Elizabeth; Yandl, Gregory; Broomall, William; Kolker, Natali

    2014-01-01

    Abstract Multi-omics data-driven scientific discovery crucially rests on high-throughput technologies and data sharing. Currently, data are scattered across single omics repositories, stored in varying raw and processed formats, and are often accompanied by limited or no metadata. The Multi-Omics Profiling Expression Database (MOPED, http://moped.proteinspire.org) version 2.5 is a freely accessible multi-omics expression database. Continual improvement and expansion of MOPED is driven by feedback from the Life Sciences Community. In order to meet the emergent need for an integrated multi-omics data resource, MOPED 2.5 now includes gene relative expression data in addition to protein absolute and relative expression data from over 250 large-scale experiments. To facilitate accurate integration of experiments and increase reproducibility, MOPED provides extensive metadata through the Data-Enabled Life Sciences Alliance (DELSA Global, http://delsaglobal.org) metadata checklist. MOPED 2.5 has greatly increased the number of proteomics absolute and relative expression records to over 500,000, in addition to adding more than four million transcriptomics relative expression records. MOPED has an intuitive user interface with tabs for querying different types of omics expression data and new tools for data visualization. Summary information including expression data, pathway mappings, and direct connection between proteins and genes can be viewed on Protein and Gene Details pages. These connections in MOPED provide a context for multi-omics expression data exploration. Researchers are encouraged to submit omics data which will be consistently processed into expression summaries. MOPED as a multi-omics data resource is a pivotal public database, interdisciplinary knowledge resource, and platform for multi-omics understanding. PMID:24910945

  15. Device failures associated with patient injuries during robot-assisted laparoscopic surgeries: a comprehensive review of FDA MAUDE database.

    PubMed

    Andonian, Sero; Okeke, Zeph; Okeke, Deidre A; Rastinehad, Ardeshir; Vanderbrink, Brian A; Richstone, Lee; Lee, Benjamin R

    2008-02-01

    Robot-assisted laparoscopic surgery has increased in the areas of cardiac and urologic surgery. We sought to determine the number of reported device malfunctions leading to patient injuries. We performed a review of the MAUDE database of the FDA. Adverse events (AE) were defined as potential and actual product use errors and product quality problems. All incidents involving the ZEUS and da Vinci surgical robots were analyzed. The MAUDE database was last accessed on August 27, 2007. A total of 189 AEs were reported from 2000 to August 27, 2007. Assuming that 50,000 robotic-assisted laparoscopic cases have been performed, this represents 0.38% overall estimated failure rate. Twenty-one malfunctions were reported for the ZEUS robotic system between 2001 and 2003, while 168 malfunctions were reported for the da Vinci robotic system between 2000 and 2007. The rate of open conversions due to device malfunction decreased from 94% in 2003 to 16% in 2007. Of the 189 reported device malfunctions, only 9 (4.8%) were associated with patient injury. The increasing use of robotic-assisted surgery has led to an increase in the number of reported device malfunctions, albeit at a very small estimated rate of 0.38%. With experience, the rate of open conversions due to device malfunction decreased. Only a small percentage of these adverse occurrences were associated with patient injury.

  16. 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

  17. Expanding the MTM1 mutational spectrum: novel variants including the first multi-exonic duplication and development of a locus-specific database

    PubMed Central

    Oliveira, Jorge; Oliveira, Márcia E; Kress, Wolfram; Taipa, Ricardo; Pires, Manuel Melo; Hilbert, Pascale; Baxter, Peter; Santos, Manuela; Buermans, Henk; den Dunnen, Johan T; Santos, Rosário

    2013-01-01

    Myotubular myopathy (MIM#310400), the X-linked form of Centronuclear myopathy (CNM) is mainly characterized by neonatal hypotonia and inability to maintain unassisted respiration. The MTM1 gene, responsible for this disease, encodes myotubularin – a lipidic phosphatase involved in vesicle trafficking regulation and maturation. Recently, it was shown that myotubularin interacts with desmin, being a major regulator of intermediate filaments. We report the development of a locus-specific database for MTM1 using the Leiden Open Variation database software (http://www.lovd.nl/MTM1), with data collated for 474 mutations identified in 472 patients (by June 2012). Among the entries are a total of 25 new mutations, including a large deletion encompassing introns 2–15. During database implementation it was noticed that no large duplications had been reported. We tested a group of eight uncharacterized CNM patients for this specific type of mutation, by multiple ligation-dependent probe amplification (MLPA) analysis. A large duplication spanning exons 1–5 was identified in a boy with a mild phenotype, with results pointing toward possible somatic mosaicism. Further characterization revealed that this duplication causes an in-frame deletion at the mRNA level (r.343_444del). Results obtained with a next generation sequencing approach suggested that the duplication extends into the neighboring MAMLD1 gene and subsequent cDNA analysis detected the presence of a MTM1/MAMLD1 fusion transcript. A complex rearrangement involving the duplication of exon 10 has since been reported, with detection also enabled by MLPA analysis. It is thus conceivable that large duplications in MTM1 may account for a number of CNM cases that have remained genetically unresolved. PMID:22968136

  18. VPDB: Viral Protein Structural Database

    PubMed Central

    Sharma, Om Prakash; Jadhav, Ankush; Hussain, Afzal; Kumar, Muthuvel Suresh

    2011-01-01

    Viral Protein Database is an interactive database for three dimensional viral proteins. Our aim is to provide a comprehensive resource to the community of structural virology, with an emphasis on the description of derived data from structural biology. Currently, VPDB includes ˜1,670 viral protein structures from >277 viruses with more than 465 virus strains. The whole database can be easily accessed through the user convenience text search. Interactivity has been enhanced by using Jmol, WebMol and Strap to visualize the viral protein molecular structure. Availability The database is available for free at http://www.vpdb.bicpu.edu.in PMID:21769196

  19. [Update the wood dust exposure values included in the job-exposure matrix MatEmESp by making use of the WOODEX database].

    PubMed

    Ramoneda Paniagua, Alex; van der Haar, Rudolf

    2016-01-01

    To revise and complete information on prevalence and intensity of wood dust exposure among Spanish workers in the MatEmESp job-exposure matrix, based on data from the WOODEX database. Exposure groups by economic activity in WOODEX were linked to the occupations in MatEmESp. The WOODEX data were then used to calculate new values of exposure prevalence and intensity for the occupations included in MatEmESp. A total of 18 occupations in MatEmESp were linked to exposure groups in the WOODEX database. This allowed estimation of new exposure intensity values for these 18 occupations and calculation of new exposure prevalence values for 16 of them. In addition, a new at-risk occupation, previously not in MatEmESp, was identified. The occupations with the highest prevalence values are sawmill operators (CNO-94 code 8141) and operators of machinery for making wood products (CNO-94 code 8340). The new calculations indicate that 10.5% of at-risk workers in MatEmESp are exposed to concentrations above 5 mg/m3. The WOODEX data provided more detailed information about exposure profiles to wood dust and are mainly based on Spanish data. In contrast, 95% of the data on wood dust exposure inMatEmESp is based on extrapolations from other countries or on expert considerations. Copyright belongs to the Societat Catalana de Salut Laboral.

  20. Isotopic reconstruction of ancient human migrations: A comprehensive Sr isotope reference database for France and the first case study at Tumulus de Sables, south-western France

    NASA Astrophysics Data System (ADS)

    Willmes, M.; Boel, C.; Grün, R.; Armstrong, R.; Chancerel, A.; Maureille, B.; Courtaud, P.

    2012-04-01

    Strontium isotope ratios (87Sr/86Sr) can be used for the reconstruction of human and animal migrations across geologically different terrains. Sr isotope ratios in rocks are a product of age and composition and thus vary between geologic units. From the eroding environment Sr is transported into the soils, plants and rivers of a region. Humans and animals incorporate Sr from their diet into their bones and teeth, where it substitutes for calcium. Tooth enamel contains Sr isotope signatures acquired during childhood and is most resistant to weathering and overprinting, while the dentine is often diagenetically altered towards the local Sr signature. For the reconstruction of human and animal migrations the tooth enamel 87Sr/86Sr ratio is compared to the Sr isotope signature in the vicinity of the burial site and the surrounding area. This study focuses on the establishment of a comprehensive reference map of bioavailable 87Sr/86Sr ratios for France. In a next step we will compare human and animal teeth from key archaeological sites to this reference map to investigate mobility. So far, we have analysed plant and soil samples from ~200 locations across France including the Aquitaine basin, the western and northern parts of the Paris basin, as well as three transects through the Pyrenees Mountains. The isotope data, geologic background information (BRGM 1:1M), field images, and detailed method descriptions are available through our online database iRhum (http://rses.anu.edu.au/research/ee). This database can also be used in forensic studies and food sciences. As an archaeological case study teeth from 16 adult and 8 juvenile individuals were investigated from an early Bell Beaker (2500-2000 BC) site at Le Tumulus des Sables, south-west France (Gironde). The teeth were analysed for Sr isotope ratios using laser ablation ICP-MS. Four teeth were also analysed using solution ICP-MS, which showed a significant offset to the laser ablation results. This requires further

  1. A Comprehensive Software and Database Management System for Glomerular Filtration Rate Estimation by Radionuclide Plasma Sampling and Serum Creatinine Methods.

    PubMed

    Jha, Ashish Kumar

    2015-01-01

    Glomerular filtration rate (GFR) estimation by plasma sampling method is considered as the gold standard. However, this method is not widely used because the complex technique and cumbersome calculations coupled with the lack of availability of user-friendly software. The routinely used Serum Creatinine method (SrCrM) of GFR estimation also requires the use of online calculators which cannot be used without internet access. We have developed user-friendly software "GFR estimation software" which gives the options to estimate GFR by plasma sampling method as well as SrCrM. We have used Microsoft Windows(®) as operating system and Visual Basic 6.0 as the front end and Microsoft Access(®) as database tool to develop this software. We have used Russell's formula for GFR calculation by plasma sampling method. GFR calculations using serum creatinine have been done using MIRD, Cockcroft-Gault method, Schwartz method, and Counahan-Barratt methods. The developed software is performing mathematical calculations correctly and is user-friendly. This software also enables storage and easy retrieval of the raw data, patient's information and calculated GFR for further processing and comparison. This is user-friendly software to calculate the GFR by various plasma sampling method and blood parameter. This software is also a good system for storing the raw and processed data for future analysis.

  2. The Danish Testicular Cancer database.

    PubMed

    Daugaard, Gedske; Kier, Maria Gry Gundgaard; Bandak, Mikkel; Mortensen, Mette Saksø; Larsson, Heidi; Søgaard, Mette; Toft, Birgitte Groenkaer; Engvad, Birte; Agerbæk, Mads; Holm, Niels Vilstrup; Lauritsen, Jakob

    2016-01-01

    The nationwide Danish Testicular Cancer database consists of a retrospective research database (DaTeCa database) and a prospective clinical database (Danish Multidisciplinary Cancer Group [DMCG] DaTeCa database). The aim is to improve the quality of care for patients with testicular cancer (TC) in Denmark, that is, by identifying risk factors for relapse, toxicity related to treatment, and focusing on late effects. All Danish male patients with a histologically verified germ cell cancer diagnosis in the Danish Pathology Registry are included in the DaTeCa databases. Data collection has been performed from 1984 to 2007 and from 2013 onward, respectively. The retrospective DaTeCa database contains detailed information with more than 300 variables related to histology, stage, treatment, relapses, pathology, tumor markers, kidney function, lung function, etc. A questionnaire related to late effects has been conducted, which includes questions regarding social relationships, life situation, general health status, family background, diseases, symptoms, use of medication, marital status, psychosocial issues, fertility, and sexuality. TC survivors alive on October 2014 were invited to fill in this questionnaire including 160 validated questions. Collection of questionnaires is still ongoing. A biobank including blood/sputum samples for future genetic analyses has been established. Both samples related to DaTeCa and DMCG DaTeCa database are included. The prospective DMCG DaTeCa database includes variables regarding histology, stage, prognostic group, and treatment. The DMCG DaTeCa database has existed since 2013 and is a young clinical database. It is necessary to extend the data collection in the prospective database in order to answer quality-related questions. Data from the retrospective database will be added to the prospective data. This will result in a large and very comprehensive database for future studies on TC patients.

  3. Nuclear Science References Database

    SciTech Connect

    Pritychenko, B.; Běták, E.; Singh, B.; Totans, J.

    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 Energy Agency (http://www-nds.iaea.org/nsr)

  4. Color Comprehension and Color Categories among Blind Students: A Multi-Sensory Approach in Implementing Concrete Language to Include All Students in Advanced Writing Classes

    ERIC Educational Resources Information Center

    Antarasena, Salinee

    2009-01-01

    This study investigates teaching methods regarding color comprehension and color categorization among blind students, as compared to their non-blind peers and whether they understand and represent the same color comprehension and color categories. Then after digit codes for color comprehension teaching and assistive technology for the blind had…

  5. Color Comprehension and Color Categories among Blind Students: A Multi-Sensory Approach in Implementing Concrete Language to Include All Students in Advanced Writing Classes

    ERIC Educational Resources Information Center

    Antarasena, Salinee

    2009-01-01

    This study investigates teaching methods regarding color comprehension and color categorization among blind students, as compared to their non-blind peers and whether they understand and represent the same color comprehension and color categories. Then after digit codes for color comprehension teaching and assistive technology for the blind had…

  6. Clinical profile of 266 Filipino patients with rheumatoid arthritis included in the rheumatoid arthritis database and registry (RADAR) of the Philippine General Hospital.

    PubMed

    Penserga, Ester G; Natividad, Therese Aileen L; Salido, Evelyn S

    2015-05-01

    To describe Filipino patients with rheumatoid arthritis (RA) entered in the Rheumatoid arthritis database and registry (RADAR) of the Philippine General Hospital. Cases entered to RADAR from 2010-2012 were included. All fulfilled the 1987 American College of Rheumatology criteria for classification of RA. Included cases gave written infomed consent. Data extracted were demographics, clinical presentation, laboratory tests, treatment and disease course. Means and proportions were used for population characteristics. Two hundred and sixty-six cases were included. Mean age was 44 years, with 9 : 1 female preponderance and mean diagnosis time of 5 years. There was symmetrical polyarthritis with high tender and swollen joint count and mean Disease Activity Score of 28 joints, erythrocyte sedimentation rate of 5.27 (3.39, 8.13). Rheumatoid factor was positive in 2/3 of cases. Hypertension, tuberculosis and diabetes were important co-morbidities. Treatment included prednisone, non-steroidal anti-inflammatory drugs and methotrexate. At 12 months of treatment, evaluable cases (< 20%) showed improvement from high to moderate disease activity. Methotrexate average dose was 8.6 mg/week. Nine cases received biologic agents. Factors affecting treatment included access to rheumatology centers, low socioeconomic status, presence of co-morbid diseases and treatment adverse events. This study reports a cohort of Filipino RA patients seen in a government arthritis unit whose disease characteristics are similar to what is reported worldwide. This cohort differs from most studies in having a high female to male ratio, a long delay in diagnosis, and high attrition rate. Mean methotrexate dose was low and there was less access to biologic disease-modifying anti-rheumatic drugs. © 2014 Asia Pacific League of Associations for Rheumatology and Wiley Publishing Asia Pty Ltd.

  7. The CEBAF Element Database and Related Operational Software

    SciTech Connect

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

    2015-09-01

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

  8. Development of a comprehensive survey of sexuality issues including a self-report version of the International Spinal Cord Injury sexual function basic data sets.

    PubMed

    New, P W; Currie, K E

    2016-08-01

    Questionnaire development, validation and completion. Develop comprehensive survey of sexuality issues including validated self-report versions of the International Spinal Cord Injury male sexual function and female sexual and reproductive function basic data sets (SR-iSCI-sexual function). People with spinal cord damage (SCD) living in the community, Australia from August 2013 to June 2014. An iterative process involving rehabilitation medicine clinicians, a nurse specialising in sexuality issues in SCD and people with SCD who developed a comprehensive survey that included the SR-iSCI-sexual function. Participants recruitment through spinal rehabilitation review clinic and community organisations that support people with SCD. Surveys completed by 154 people. Most were male (n=101, 65.6%). Respondents' median age was 50 years (interquartile range (IQR) 38-58), and they were a median of 10 years (IQR 4-20) after the onset of SCD. Sexual problems unrelated to SCD were reported by 12 (8%) respondents, and 114 (n=75.5%) reported sexual problems because of SCD. Orgasms were much less likely (χ(2)=13.1, P=0.006) to be normal in males (n=5, 5%) compared with females (n=11, 22%). Males had significantly worse (χ(2)=26.0, P=0.001) psychogenic genital functioning (normal n=9, 9%) than females (normal n=13, 26%) and worse (χ(2)=10.8, P=0.013) reflex genital functioning. Normal ejaculation was reported in only three (3%) men. Most (n=26, 52%) women reported reduced or absent menstruation pattern since SCD. The SR-iSCI-sexual function provides a useful tool for researchers and clinicians to collect information regarding patient-reported sexual functioning after SCD and to facilitate comparative studies.

  9. Characteristics and comprehensiveness of adult HIV care and treatment programmes in Asia-Pacific, sub-Saharan Africa and the Americas: results of a site assessment conducted by the International epidemiologic Databases to Evaluate AIDS (IeDEA) Collaboration

    PubMed Central

    Duda, Stephany N; Farr, Amanda M; Lindegren, Mary Lou; Blevins, Meridith; Wester, C William; Wools-Kaloustian, Kara; Ekouevi, Didier K; Egger, Matthias; Hemingway-Foday, Jennifer; Cooper, David A; Moore, Richard D; McGowan, Catherine C; Nash, Denis

    2014-01-01

    Introduction HIV care and treatment programmes worldwide are transforming as they push to deliver universal access to essential prevention, care and treatment services to persons living with HIV and their communities. The characteristics and capacity of these HIV programmes affect patient outcomes and quality of care. Despite the importance of ensuring optimal outcomes, few studies have addressed the capacity of HIV programmes to deliver comprehensive care. We sought to describe such capacity in HIV programmes in seven regions worldwide. Methods Staff from 128 sites in 41 countries participating in the International epidemiologic Databases to Evaluate AIDS completed a site survey from 2009 to 2010, including sites in the Asia-Pacific region (n=20), Latin America and the Caribbean (n=7), North America (n=7), Central Africa (n=12), East Africa (n=51), Southern Africa (n=16) and West Africa (n=15). We computed a measure of the comprehensiveness of care based on seven World Health Organization-recommended essential HIV services. Results Most sites reported serving urban (61%; region range (rr): 33–100%) and both adult and paediatric populations (77%; rr: 29–96%). Only 45% of HIV clinics that reported treating children had paediatricians on staff. As for the seven essential services, survey respondents reported that CD4+ cell count testing was available to all but one site, while tuberculosis (TB) screening and community outreach services were available in 80 and 72%, respectively. The remaining four essential services – nutritional support (82%), combination antiretroviral therapy adherence support (88%), prevention of mother-to-child transmission (PMTCT) (94%) and other prevention and clinical management services (97%) – were uniformly available. Approximately half (46%) of sites reported offering all seven services. Newer sites and sites in settings with low rankings on the UN Human Development Index (HDI), especially those in the President's Emergency Plan

  10. Characteristics and comprehensiveness of adult HIV care and treatment programmes in Asia-Pacific, sub-Saharan Africa and the Americas: results of a site assessment conducted by the International epidemiologic Databases to Evaluate AIDS (IeDEA) Collaboration.

    PubMed

    Duda, Stephany N; Farr, Amanda M; Lindegren, Mary Lou; Blevins, Meridith; Wester, C William; Wools-Kaloustian, Kara; Ekouevi, Didier K; Egger, Matthias; Hemingway-Foday, Jennifer; Cooper, David A; Moore, Richard D; McGowan, Catherine C; Nash, Denis

    2014-01-01

    HIV care and treatment programmes worldwide are transforming as they push to deliver universal access to essential prevention, care and treatment services to persons living with HIV and their communities. The characteristics and capacity of these HIV programmes affect patient outcomes and quality of care. Despite the importance of ensuring optimal outcomes, few studies have addressed the capacity of HIV programmes to deliver comprehensive care. We sought to describe such capacity in HIV programmes in seven regions worldwide. Staff from 128 sites in 41 countries participating in the International epidemiologic Databases to Evaluate AIDS completed a site survey from 2009 to 2010, including sites in the Asia-Pacific region (n=20), Latin America and the Caribbean (n=7), North America (n=7), Central Africa (n=12), East Africa (n=51), Southern Africa (n=16) and West Africa (n=15). We computed a measure of the comprehensiveness of care based on seven World Health Organization-recommended essential HIV services. Most sites reported serving urban (61%; region range (rr): 33-100%) and both adult and paediatric populations (77%; rr: 29-96%). Only 45% of HIV clinics that reported treating children had paediatricians on staff. As for the seven essential services, survey respondents reported that CD4+ cell count testing was available to all but one site, while tuberculosis (TB) screening and community outreach services were available in 80 and 72%, respectively. The remaining four essential services - nutritional support (82%), combination antiretroviral therapy adherence support (88%), prevention of mother-to-child transmission (PMTCT) (94%) and other prevention and clinical management services (97%) - were uniformly available. Approximately half (46%) of sites reported offering all seven services. Newer sites and sites in settings with low rankings on the UN Human Development Index (HDI), especially those in the President's Emergency Plan for AIDS Relief focus countries

  11. Risk of Mortality (Including Sudden Cardiac Death) and Major Cardiovascular Events in Atypical and Typical Antipsychotic Users: A Study with the General Practice Research Database

    PubMed Central

    Murray-Thomas, Tarita; Jones, Meghan E.; Patel, Deven; Brunner, Elizabeth; Shatapathy, Chetan C.; Motsko, Stephen; Van Staa, Tjeerd P.

    2013-01-01

    Objective. Antipsychotics have been associated with increased cardiac events including mortality. This study assessed cardiac events including mortality among antipsychotic users relative to nonusers. Methods. The General Practice Research Database (GPRD) was used to identify antipsychotic users, matched general population controls, and psychiatric diseased nonusers. Outcomes included cardiac mortality, sudden cardiac death (SCD), all-cause mortality (excluding suicide), coronary heart disease (CHD), and ventricular arrhythmias (VA). Sensitivity analyses were conducted for age, dose, duration, antipsychotic type, and psychiatric disease. Results. 183,392 antipsychotic users (115,491 typical and 67,901 atypical), 544,726 general population controls, and 193,920 psychiatric nonusers were identified. Nonusers with schizophrenia, dementia, or bipolar disorder had increased risks of all-cause mortality compared to general population controls, while nonusers with major depression had comparable risks. Relative to psychiatric nonusers, the adjusted relative ratios (aRR) of all-cause mortality in antipsychotic users was 1.75 (95% CI: 1.64–1.87); cardiac mortality 1.72 (95% CI: 1.42–2.07); SCD primary definition 5.76 (95% CI: 2.90–11.45); SCD secondary definition 2.15 (95% CI: 1.64–2.81); CHD 1.16 (95% CI: 0.94–1.44); and VA 1.16 (95% CI: 1.02–1.31). aRRs of the various outcomes were lower for atypical versus typical antipsychotics (all-cause mortality 0.83 (95% CI: 0.80–0.85); cardiac mortality 0.89 (95% CI: 0.82–0.97); and SCD secondary definition 0.76 (95% CI: 0.55–1.04). Conclusions. Antipsychotic users had an increased risk of cardiac mortality, all-cause mortality, and SCD compared to a psychiatric nonuser cohort. PMID:24455199

  12. THE ECOTOX DATABASE

    EPA Science Inventory

    The database provides chemical-specific toxicity information for aquatic life, terrestrial plants, and terrestrial wildlife. ECOTOX is a comprehensive ecotoxicology database and is therefore essential for providing and suppoirting high quality models needed to estimate population...

  13. THE ECOTOX DATABASE

    EPA Science Inventory

    The database provides chemical-specific toxicity information for aquatic life, terrestrial plants, and terrestrial wildlife. ECOTOX is a comprehensive ecotoxicology database and is therefore essential for providing and suppoirting high quality models needed to estimate population...

  14. The Comprehensive, Powerful, Academic Database (CPAD): An Evaluative Study of a Predictive Tool Designed for Elementary School Personnel in Identifying At-Risk Students through Progress, Curriculum, and Performance Monitoring

    ERIC Educational Resources Information Center

    Chavez-Gibson, Sarah

    2013-01-01

    The purpose of this study is to exam in-depth, the Comprehensive, Powerful, Academic Database (CPAD), a data decision-making tool that determines and identifies students at-risk of dropping out of school, and how the CPAD assists administrators and teachers at an elementary campus to monitor progress, curriculum, and performance to improve student…

  15. The Comprehensive, Powerful, Academic Database (CPAD): An Evaluative Study of a Predictive Tool Designed for Elementary School Personnel in Identifying At-Risk Students through Progress, Curriculum, and Performance Monitoring

    ERIC Educational Resources Information Center

    Chavez-Gibson, Sarah

    2013-01-01

    The purpose of this study is to exam in-depth, the Comprehensive, Powerful, Academic Database (CPAD), a data decision-making tool that determines and identifies students at-risk of dropping out of school, and how the CPAD assists administrators and teachers at an elementary campus to monitor progress, curriculum, and performance to improve student…

  16. Caenorhabditis elegans par2.1/mtssb-1 is essential for mitochondrial DNA replication and its defect causes comprehensive transcriptional alterations including a hypoxia response

    SciTech Connect

    Sugimoto, Tomoko; Mori, Chihiro; Takanami, Takako; Sasagawa, Yohei; Saito, Rumiko; Ichiishi, Eiichiro; Higashitani, Atsushi

    2008-01-01

    DNA polymerase {gamma} and mtSSB are key components of the mtDNA replication machinery. To study the biological influences of defects in mtDNA replication, we used RNAi to deplete the gene for a putative mtSSB, par2.1, in Caenorhabditis elegans. In previous systematic RNAi screens, downregulation of this gene has not caused any clearly defective phenotypes. Here, we continuously fed a dsRNA targeting par2.1 to C. elegans over generations. Seventy-nine percent of F1 progeny produced 60-72 h after feeding grew to adulthood but were completely sterile, with an arrest of germline cell proliferation. Analyses of mtDNA copy number and cell cytology indicated that the sterile hermaphrodites had fewer mitochondria. These results indicated that par2.1 essentially functions for germline cell proliferation through mtDNA replication; we therefore termed it mtssb-1. Comprehensive transcriptional alterations including hypoxia response induction dependent on and independent of hif-1 function, occurred by RNAi depletion of mtssb-1. Treatment with ethidium bromide, which impairs mtDNA replication and transcription, caused similar transcriptional alterations. In addition, the frequency of apoptosis in the germline cells was reduced in fertile progeny with a partial RNAi effect. These suggest that RNAi depletion of C. elegans mtssb-1 is useful as a model system of mitochondrial dysfunction.

  17. Comprehensive processing of high throughput small RNA sequencing data including quality checking, normalization and differential expression analysis using the UEA sRNA Workbench.

    PubMed

    Beckers, Matthew L; Mohorianu, Irina; Stocks, Matthew B; Applegate, Christopher; Dalmay, Tamas; Moulton, Vincent

    2017-03-13

    Recently High Throughput Sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20-25 nt non-coding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved. To enable a comprehensive study of differential expression in sRNA datasets we present a new interactive pipeline that guides researchers through the various stages of data pre-processing and analysis. This includes various tools, some of which we specifically developed for sRNA analysis, for quality checking and normalization of sRNA samples as well as tools for the detection of differentially expressed sRNAs and identification of the resulting expression patterns. The pipeline is available within the UEA sRNA Workbench, a user-friendly software package for the processing of sRNA datasets. We demonstrate the use of the pipeline on a H. sapiens dataset; additional examples on a B. terrestris dataset and on an A. thaliana dataset are described in the supplementary information. A comparison with existing approaches is also included, which exemplifies some of the issues that need to be addressed for sRNA analysis, and how the new pipeline may be used to do this.

  18. Marine and Hydrokinetic Technology Database

    DOE Data Explorer

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

  19. Leading-edge forensic DNA analyses and the necessity of including crime scene investigators, police officers and technicians in a DNA elimination database.

    PubMed

    Lapointe, Martine; Rogic, Anita; Bourgoin, Sarah; Jolicoeur, Christine; Séguin, Diane

    2015-11-01

    In recent years, sophisticated technology has significantly increased the sensitivity and analytical power of genetic analyses so that very little starting material may now produce viable genetic profiles. This sensitivity however, has also increased the risk of detecting unknown genetic profiles assumed to be that of the perpetrator, yet originate from extraneous sources such as from crime scene workers. These contaminants may mislead investigations, keeping criminal cases active and unresolved for long spans of time. Voluntary submission of DNA samples from crime scene workers is fairly low, therefore we have created a promotional method for our staff elimination database that has resulted in a significant increase in voluntary samples since 2011. Our database enforces privacy safeguards and allows for optional anonymity to all staff members. We also offer information sessions at various police precincts to advise crime scene workers of the importance and success of our staff elimination database. This study, a pioneer in its field, has obtained 327 voluntary submissions from crime scene workers to date, of which 46 individual profiles (14%) have been matched to 58 criminal cases. By implementing our methods and respect for individual privacy, forensic laboratories everywhere may see similar growth and success in explaining unidentified genetic profiles in stagnate criminal cases.

  20. Incorporating a Comprehensive Drama Unit including a Theatre of the Absurd Component within the Advanced Placement English Program for Senior Level Students.

    ERIC Educational Resources Information Center

    Konaxis, Antoinette

    This practicum was designed to increase the experiences in the genre of world drama, to further develop student understanding of its evolution and impact on subsequently created drama, and to proffer a diverse collection of drama for senior level students pursuing the Advanced Placement (AP) English literature program. A comprehensive curriculum,…

  1. Human Mitochondrial Protein Database

    National Institute of Standards and Technology Data Gateway

    SRD 131 Human Mitochondrial Protein Database (Web, free access)   The Human Mitochondrial Protein Database (HMPDb) provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function. This database consolidates information from SwissProt, LocusLink, Protein Data Bank (PDB), GenBank, Genome Database (GDB), Online Mendelian Inheritance in Man (OMIM), Human Mitochondrial Genome Database (mtDB), MITOMAP, Neuromuscular Disease Center and Human 2-D PAGE Databases. This database is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases.

  2. Insight into residues critical for antithrombin function from analysis of an expanded database of sequences that includes frog, turtle, and ostrich antithrombins.

    PubMed

    Backovic, Marija; Gettins, Peter G W

    2002-01-01

    Complete sequences were determined for frog, turtle, and ostrich antithrombins. Protein sequence comparisons with the other 10 known antithrombin sequences and with sequences of other serpins have provided striking evidence for the conservation of the heparin activation mechanism and new insight into those residues important for heparin binding, for heparin activation, and for reactive center loop function, as well as an indication of which glycosylation sites might be needed for function. Importantly, an understanding of, as yet, poorly understood antithrombin-protein interactions will be greatly aided by this expanded database and comparative analysis.

  3. Protein ligand interaction database (PLID).

    PubMed

    Reddy, A Srinivas; Amarnath, H S Durga; Bapi, Raju S; Sastry, G Madhavi; Sastry, G Narahari

    2008-10-01

    A comprehensive database named, protein ligand interaction database (PLID), is created with 6295 ligands bound to proteins extracted from the protein data bank (PDB). This is by far the most comprehensive database of physico-chemical properties, quantum mechanical descriptors and the residues present in the active site of proteins. It is a publicly available web-based database (via the Internet) at http://203.199.182.73/gnsmmg/databases/plid/.

  4. Genome databases

    SciTech Connect

    Courteau, J.

    1991-10-11

    Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

  5. Aviation Safety Issues Database

    NASA Technical Reports Server (NTRS)

    Morello, Samuel A.; Ricks, Wendell R.

    2009-01-01

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

  6. gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes.

    PubMed

    Nakagawa, So; Takahashi, Mahoko Ueda

    2016-01-01

    In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species.Database URL: http://geve.med.u-tokai.ac.jp.

  7. gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes

    PubMed Central

    Nakagawa, So; Takahashi, Mahoko Ueda

    2016-01-01

    In mammals, approximately 10% of genome sequences correspond to endogenous viral elements (EVEs), which are derived from ancient viral infections of germ cells. Although most EVEs have been inactivated, some open reading frames (ORFs) of EVEs obtained functions in the hosts. However, EVE ORFs usually remain unannotated in the genomes, and no databases are available for EVE ORFs. To investigate the function and evolution of EVEs in mammalian genomes, we developed EVE ORF databases for 20 genomes of 19 mammalian species. A total of 736,771 non-overlapping EVE ORFs were identified and archived in a database named gEVE (http://geve.med.u-tokai.ac.jp). The gEVE database provides nucleotide and amino acid sequences, genomic loci and functional annotations of EVE ORFs for all 20 genomes. In analyzing RNA-seq data with the gEVE database, we successfully identified the expressed EVE genes, suggesting that the gEVE database facilitates studies of the genomic analyses of various mammalian species. Database URL: http://geve.med.u-tokai.ac.jp PMID:27242033

  8. Overlap in Bibliographic Databases.

    ERIC Educational Resources Information Center

    Hood, William W.; Wilson, Concepcion S.

    2003-01-01

    Examines the topic of Fuzzy Set Theory to determine the overlap of coverage in bibliographic databases. Highlights include examples of comparisons of database coverage; frequency distribution of the degree of overlap; records with maximum overlap; records unique to one database; intra-database duplicates; and overlap in the top ten databases.…

  9. SEISMIC-REFLECTOR DATABASE SOFTWARE.

    USGS Publications Warehouse

    Wright, Evelyn L.; Hosom, John-Paul; ,

    1986-01-01

    The seismic data analysis (SDA) software system facilitates generation of marine seismic reflector databases composed of reflector depths, travel times, root-mean-square and interval velocities, geographic coordinates, and identifying information. System processes include digitizing of seismic profiles and velocity semblance curves, merging of velocity and navigation data with profile travel-time data, calculation of reflector depths in meters, profile and map graphic displays, data editing and smoothing, and entry of finalized data into a comprehensive database. An overview of concepts, file structures, and programs is presented.

  10. Applying Various Comprehension Strategies. Learning Package No. 8.

    ERIC Educational Resources Information Center

    Simic, Marge; Smith, Carl, Comp.

    Originally developed for the Department of Defense Schools (DoDDS) system, this learning package on applying various comprehension strategies is designed for teachers who wish to upgrade or expand their teaching skills on their own. The package includes a comprehensive search of the ERIC database; a lecture giving an overview on the topic; the…

  11. The latissimus dorsi-groin-lymph node compound flap: A comprehensive technique with three features including skin coverage, restoration of motor function, and prevention of upper limb lymphedema.

    PubMed

    Nicoli, Fabio; Orfaniotis, Georgios; Lazzeri, Davide; Lim, Seong Yoon; Kiranantawat, Kidakorn; Chen, Pei-Yu; Ciudad, Pedro; Chilgar, Ram M; Sapountzis, Stamatis; Sacak, Bulent; Chen, Hung-Chi

    2016-11-01

    Reconstruction of complex upper extremity defects requires a need for multiple tissue components. The supercharged latissimus dorsi (LD)-groin compound flap is an option that can provide a large skin paddle with simultaneous functional muscle transfer. It is necessary to supercharge the flap with the superficial circumflex iliac pedicle to ensure the viability of its groin extension. In this report, we present a case of a supercharged LD-groin flap in combination with vascularized inguinal lymph nodes, which was used for upper limb reconstruction in a young male patient, following excision of high-grade liposarcoma. Resection resulted in a 28 cm × 15 cm skin defect extending from the upper arm to the proximal forearm, also involving the triceps muscle, a segment of the ulnar nerve and the axillary lymph nodes. Restoration of triceps function was achieved with transfer of the innervated LD muscle. Part of the ulnar nerve was resected and repaired with sural nerve grafts. Post-operatively, the flap survived fully with no partial necrosis, and no complications at both the recipient and donor sites. At 1-year follow up, the patient had a well-healed wound with good elbow extension (against resistance), no tumor recurrence, and no signs of lymphedema. We believe this comprehensive approach may represent a valuable technique, for not only the oncological reconstruction of upper extremity, but also for the prevention of lymphedema. © 2015 Wiley Periodicals, Inc. Microsurgery 36:689-694, 2016. © 2015 Wiley Periodicals, Inc.

  12. Implementation of a comprehensive program including psycho-social and treatment literacy activities to improve adherence to HIV care and treatment for a pediatric population in Kenya

    PubMed Central

    Van Winghem, Joelle; Telfer, Barbara; Reid, Tony; Ouko, Judith; Mutunga, Angela; Jama, Zaina; Vakil, Shobha

    2008-01-01

    Background To achieve good clinical outcomes with HAART, patient adherence to treatment and care is a key factor. Since the literature on how to care for pediatric HIV patients is limited, we describe here adherence interventions implemented in our comprehensive care program in a resource-limited setting in Kenya. Methods We based our program on factors reported to influence adherence to HIV care and treatment. We describe, in detail, our program with respect to how we adapted our clinical settings, implemented psycho-social support activities for children and their caregivers and developed treatment literacy for children and teenagers living with HIV/AIDS. Results This paper focused on the details of the program, with the treatment outcomes as secondary. However, our program appeared to have been effective; for 648 children under 15 years of age who were started on HAART, the Kaplan-Meier mortality survival estimate was 95.27% (95%CI 93.16–96.74) at 12 months after the time of initiation of HAART. Conclusion Our model of pediatric HIV/AIDS care, focused on a child-centered approach with inclusion of caregivers and extended family, addressed the main factors influencing treatment adherence. It appeared to produce good results and is replicable in resource-limited settings. PMID:19025581

  13. Towards a comprehensive electronic database of polycyclic aromatic hydrocarbons and its application in constraining the identities of possible carriers of the diffuse interstellar bands

    NASA Astrophysics Data System (ADS)

    Tan, Xiaofeng

    2009-01-01

    A theoretical approach is developed to pre-select individual polycyclic aromatic hydrocarbons (PAHs) as possible carriers of the diffuse interstellar bands (DIBs). In this approach, a computer program is used to enumerate all PAH molecules with up to a specific number of fused benzene rings. Fast quantum chemical calculations are then employed to calculate the electronic transition energies, oscillator strengths, and rotational constants of these molecules. An electronic database of all PAHs with up to any specific number of benzene rings can be constructed this way. Comparison of the electronic transition energies, oscillator strengths, and rotational band contours of all PAHs in the database with astronomical spectra allows one to constrain the identities of individual PAHs as possible carriers of some of the intense narrow DIBs. Using the current database containing up to 10 benzene rings we have pre-selected 8 closed-shell PAHs as possible carriers of the famous λ6614 DIB.

  14. Comprehensive review of the evidence regarding the effectiveness of community-based primary health care in improving maternal, neonatal and child health: 1. rationale, methods and database description.

    PubMed

    Perry, Henry B; Rassekh, Bahie M; Gupta, Sundeep; Wilhelm, Jess; Freeman, Paul A

    2017-06-01

    concerned education about warning signs of pregnancy and safe delivery; promotion and/or provision of antenatal care; promotion and/or provision of safe delivery by a trained birth attendant, screening and treatment for HIV infection and other maternal infections; family planning, and; HIV prevention and treatment. The neonatal and child health interventions that were assessed concerned promotion or provision of good nutrition and immunizations; promotion of healthy household behaviors and appropriate utilization of health services, diagnosis and treatment of acute neonatal and child illness; and provision and/or promotion of safe water, sanitation and hygiene. Two-thirds of assessments (63.0%) were for projects implementing three or fewer interventions in relatively small populations for relatively brief periods; half of the assessments involved fewer than 5000 women or children, and 62.9% of the assessments were for projects lasting less than 3 years. One-quarter (26.6%) of the projects were from three countries in South Asia: India, Bangladesh and Nepal. The number of reports has grown markedly during the past decade. A small number of funders supported most of the assessments, led by the United States Agency for International Development. The reviewers judged the methodology for 90% of the assessments to be adequate. The evidence regarding the effectiveness of community-based interventions to improve the health of mothers, neonates, and children younger than 5 years of age is growing rapidly. The database created for this review serves as the basis for a series of articles that follow this one on the effectiveness of CBPHC in improving MNCH published in the Journal of Global Health. These findings, together with recommendations provided by an Expert Panel which has guided this review, that are included as the last paper in this series, will help to provide the rationale for building stronger community-based platforms for delivering evidence-based interventions in high

  15. The androgen receptor gene mutations database.

    PubMed

    Patterson, M N; Hughes, I A; Gottlieb, B; Pinsky, L

    1994-09-01

    The androgen receptor gene mutations database is a comprehensive listing of mutations published in journals and meetings proceedings. The majority of mutations are point mutations identified in patients with androgen insensitivity syndrome. Information is included regarding the phenotype, the nature and location of the mutations, as well as the effects of the mutations on the androgen binding activity of the receptor. The current version of the database contains 149 entries, of which 114 are unique mutations. The database is available from EMBL (NetServ@EMBL-Heidelberg.DE) or as a Macintosh Filemaker file (mc33001@musica.mcgill.ca).

  16. Tautomerism in large databases

    PubMed Central

    Sitzmann, Markus; Ihlenfeldt, Wolf-Dietrich

    2010-01-01

    We have used the Chemical Structure DataBase (CSDB) of the NCI CADD Group, an aggregated collection of over 150 small-molecule databases totaling 103.5 million structure records, to conduct tautomerism analyses on one of the largest currently existing sets of real (i.e. not computer-generated) compounds. This analysis was carried out using calculable chemical structure identifiers developed by the NCI CADD Group, based on hash codes available in the chemoinformatics toolkit CACTVS and a newly developed scoring scheme to define a canonical tautomer for any encountered structure. CACTVS’s tautomerism definition, a set of 21 transform rules expressed in SMIRKS line notation, was used, which takes a comprehensive stance as to the possible types of tautomeric interconversion included. Tautomerism was found to be possible for more than 2/3 of the unique structures in the CSDB. A total of 680 million tautomers were calculated from, and including, the original structure records. Tautomerism overlap within the same individual database (i.e. at least one other entry was present that was really only a different tautomeric representation of the same compound) was found at an average rate of 0.3% of the original structure records, with values as high as nearly 2% for some of the databases in CSDB. Projected onto the set of unique structures (by FICuS identifier), this still occurred in about 1.5% of the cases. Tautomeric overlap across all constituent databases in CSDB was found for nearly 10% of the records in the collection. PMID:20512400

  17. Tautomerism in large databases

    NASA Astrophysics Data System (ADS)

    Sitzmann, Markus; Ihlenfeldt, Wolf-Dietrich; Nicklaus, Marc C.

    2010-06-01

    We have used the Chemical Structure DataBase (CSDB) of the NCI CADD Group, an aggregated collection of over 150 small-molecule databases totaling 103.5 million structure records, to conduct tautomerism analyses on one of the largest currently existing sets of real (i.e. not computer-generated) compounds. This analysis was carried out using calculable chemical structure identifiers developed by the NCI CADD Group, based on hash codes available in the chemoinformatics toolkit CACTVS and a newly developed scoring scheme to define a canonical tautomer for any encountered structure. CACTVS's tautomerism definition, a set of 21 transform rules expressed in SMIRKS line notation, was used, which takes a comprehensive stance as to the possible types of tautomeric interconversion included. Tautomerism was found to be possible for more than 2/3 of the unique structures in the CSDB. A total of 680 million tautomers were calculated from, and including, the original structure records. Tautomerism overlap within the same individual database (i.e. at least one other entry was present that was really only a different tautomeric representation of the same compound) was found at an average rate of 0.3% of the original structure records, with values as high as nearly 2% for some of the databases in CSDB. Projected onto the set of unique structures (by FICuS identifier), this still occurred in about 1.5% of the cases. Tautomeric overlap across all constituent databases in CSDB was found for nearly 10% of the records in the collection.

  18. A reservoir morphology database for the conterminous United States

    USGS Publications Warehouse

    Rodgers, Kirk D.

    2017-09-13

    The U.S. Geological Survey, in cooperation with the Reservoir Fisheries Habitat Partnership, combined multiple national databases to create one comprehensive national reservoir database and to calculate new morphological metrics for 3,828 reservoirs. These new metrics include, but are not limited to, shoreline development index, index of basin permanence, development of volume, and other descriptive metrics based on established morphometric formulas. The new database also contains modeled chemical and physical metrics. Because of the nature of the existing databases used to compile the Reservoir Morphology Database and the inherent missing data, some metrics were not populated. One comprehensive database will assist water-resource managers in their understanding of local reservoir morphology and water chemistry characteristics throughout the continental United States.

  19. Managing Rock and Paleomagnetic Data Flow with the MagIC Database: from Measurement and Analysis to Comprehensive Archive and Visualization

    NASA Astrophysics Data System (ADS)

    Koppers, A. A.; Minnett, R. C.; Tauxe, L.; Constable, C.; Donadini, F.

    2008-12-01

    The Magnetics Information Consortium (MagIC) is commissioned to implement and maintain an online portal to a relational database populated by rock and paleomagnetic data. The goal of MagIC is to archive all measurements and derived properties for studies of paleomagnetic directions (inclination, declination) and intensities, and for rock magnetic experiments (hysteresis, remanence, susceptibility, anisotropy). Organizing data for presentation in peer-reviewed publications or for ingestion into databases is a time-consuming task, and to facilitate these activities, three tightly integrated tools have been developed: MagIC-PY, the MagIC Console Software, and the MagIC Online Database. A suite of Python scripts is available to help users port their data into the MagIC data format. They allow the user to add important metadata, perform basic interpretations, and average results at the specimen, sample and site levels. These scripts have been validated for use as Open Source software under the UNIX, Linux, PC and Macintosh© operating systems. We have also developed the MagIC Console Software program to assist in collating rock and paleomagnetic data for upload to the MagIC database. The program runs in Microsoft Excel© on both Macintosh© computers and PCs. It performs routine consistency checks on data entries, and assists users in preparing data for uploading into the online MagIC database. The MagIC website is hosted under EarthRef.org at http://earthref.org/MAGIC/ and has two search nodes, one for paleomagnetism and one for rock magnetism. Both nodes provide query building based on location, reference, methods applied, material type and geological age, as well as a visual FlashMap interface to browse and select locations. Users can also browse the database by data type (inclination, intensity, VGP, hysteresis, susceptibility) or by data compilation to view all contributions associated with previous databases, such as PINT, GMPDB or TAFI or other user

  20. Solubility Database

    National Institute of Standards and Technology Data Gateway

    SRD 106 IUPAC-NIST Solubility Database (Web, free access)   These solubilities are compiled from 18 volumes (Click here for List) of the International Union for Pure and Applied Chemistry(IUPAC)-NIST Solubility Data Series. The database includes liquid-liquid, solid-liquid, and gas-liquid systems. Typical solvents and solutes include water, seawater, heavy water, inorganic compounds, and a variety of organic compounds such as hydrocarbons, halogenated hydrocarbons, alcohols, acids, esters and nitrogen compounds. There are over 67,500 solubility measurements and over 1800 references.

  1. Databases: Beyond the Basics.

    ERIC Educational Resources Information Center

    Whittaker, Robert

    This presented paper offers an elementary description of database characteristics and then provides a survey of databases that may be useful to the teacher and researcher in Slavic and East European languages and literatures. The survey focuses on commercial databases that are available, usable, and needed. Individual databases discussed include:…

  2. Databases: Beyond the Basics.

    ERIC Educational Resources Information Center

    Whittaker, Robert

    This presented paper offers an elementary description of database characteristics and then provides a survey of databases that may be useful to the teacher and researcher in Slavic and East European languages and literatures. The survey focuses on commercial databases that are available, usable, and needed. Individual databases discussed include:…

  3. More Publications about Databases.

    ERIC Educational Resources Information Center

    Tenopir, Carol

    1983-01-01

    Reviews recent publications in online database literature including three newsletters ("Database Update,""Database Alert," and "Information Hotline"), a directory ("Guide to Online Databases"), and a textbook ("Online Reference and Information Retrieval" by Roger C. Palmer). The new "Guide to Searching ONTAP ABI/INFORM" is noted. (EJS)

  4. Pigmented spindle cell nevus: clues for differentiating it from spindle cell malignant melanoma. A comprehensive survey including clinicopathologic, immunohistochemical, and FISH studies.

    PubMed

    Díaz, Alba; Valera, Alexandra; Carrera, Cristina; Hakim, Sofía; Aguilera, Paula; García, Adriana; Palou, Josep; Puig, Susana; Malvehy, Josep; Alos, Llúcia

    2011-11-01

    Pigmented spindle cell nevus (PSCN), also known as Reed nevus, is a distinctive melanocytic tumor that can show worrisome clinical and histologic features mimicking a malignant melanoma. From a series of 46 pigmented spindle cell melanocytic lesions, including 22 PSCN and 24 spindle cell malignant melanomas (SCMMs), we collected clinical and histopathologic characteristics and evaluated cell cycle and apoptosis regulators by immunohistochemistry. Moreover, fluorescence in situ hybridization (FISH) using probes targeting 6p25 (RREB1), 11q13 (CCND1), 6q23 (MYB), and centromere 6 was performed. PSCN presented in younger people, frequently in women, and were small lesions under 7 mm in diameter affecting the lower limbs, whereas SCMMs arose more frequently in the trunk, upper limbs, and head and neck region. Histologically, symmetry, good lateral demarcation, and uniformity of cellular nests were significantly differential features of PSCN, whereas pagetoid and adnexal spread were frequently seen in both tumors. Immunohistochemical markers that significantly differed from melanomas were Ki-67, cyclin D1, and survivin. FISH was positive in 1 of 15 PSCN and was negative in 4 of 15 SCMMs. These results correlated to a sensitivity of 73% and a specificity of 93%. In conclusion, in the evaluation of pigmented spindle cell melanocytic tumors, the integration of clinical and histologic assessment is essential. However, ancillary techniques such as proliferation antigen Ki-67, cyclin D1, survivin, and FISH can be useful as adjunctive tools.

  5. Trace elements in sediments, blue spotted tilapia Oreochromis leucostictus (Trewavas, 1933) and its parasite Contracaecum multipapillatum from Lake Naivasha, Kenya, including a comprehensive health risk analysis.

    PubMed

    Otachi, Elick O; Körner, Wilfried; Avenant-Oldewage, Annemariè; Fellner-Frank, Christine; Jirsa, Franz

    2014-06-01

    This study presents the distribution of 15 major and trace elements in sediments and fish and their pericardial parasites from Lake Naivasha, Kenya. The lake is one of the few freshwater lakes in the Great Rift Valley and is under strong anthropogenic pressure mainly due to agricultural activities. Its fish provide a valuable protein source for approximately 100,000 people in the area. Fish and their parasites have been acknowledged as indicators of environmental quality due to their accumulation potential for both essential and nonessential trace elements. A total of 34 specimens of the blue spotted tilapia Oreochromis leucostictus and pooled samples of their pericardial parasite, the anisakid nematode Contracaecum multipapillatum (larvae 3), were examined. Element concentrations were determined by inductively coupled plasma-optical emission spectroscopy (ICP-OES) and graphite furnace atomic absorption spectrometry (GF-AAS). The concentrations of elements in the sediments reflected the geology of the area and did not point to pollution: none of the investigated trace elements, including Pb, Cd, Cu, and Zn, showed elevated values. In contrast, concentrations in the fish muscle were elevated for Li, Sr, Cd, and Zn, with high target hazard quotients (THQ > 0.1) indicating a potential health risk to the consumers of this fish. Fish liver showed significantly higher concentrations of the trace elements Fe, Mn, Cd, and Cu compared to the muscle and C. multipapillatum. In the parasite, Zn had the highest concentration, but the worms only minimally accumulated trace elements in relation to their fish host.

  6. YMDB: the Yeast Metabolome Database

    PubMed Central

    Jewison, Timothy; Knox, Craig; Neveu, Vanessa; Djoumbou, Yannick; Guo, An Chi; Lee, Jacqueline; Liu, Philip; Mandal, Rupasri; Krishnamurthy, Ram; Sinelnikov, Igor; Wilson, Michael; Wishart, David S.

    2012-01-01

    The Yeast Metabolome Database (YMDB, http://www.ymdb.ca) is a richly annotated ‘metabolomic’ database containing detailed information about the metabolome of Saccharomyces cerevisiae. Modeled closely after the Human Metabolome Database, the YMDB contains >2000 metabolites with links to 995 different genes/proteins, including enzymes and transporters. The information in YMDB has been gathered from hundreds of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the YMDB also contains an extensive collection of experimental intracellular and extracellular metabolite concentration data compiled from detailed Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR) metabolomic analyses performed in our lab. This is further supplemented with thousands of NMR and MS spectra collected on pure, reference yeast metabolites. Each metabolite entry in the YMDB contains an average of 80 separate data fields including comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, intracellular/extracellular concentrations, growth conditions and substrates, pathway information, enzyme data, gene/protein sequence data, as well as numerous hyperlinks to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of S. cervesiae's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers, but also to yeast biologists, systems biologists, the industrial fermentation industry, as well as the beer, wine and spirit industry. PMID:22064855

  7. DMTB: the magnetotactic bacteria database

    NASA Astrophysics Data System (ADS)

    Pan, Y.; Lin, W.

    2012-12-01

    Magnetotactic bacteria (MTB) are of interest in biogeomagnetism, rock magnetism, microbiology, biomineralization, and advanced magnetic materials because of their ability to synthesize highly ordered intracellular nano-sized magnetic minerals, magnetite or greigite. Great strides for MTB studies have been made in the past few decades. More than 600 articles concerning MTB have been published. These rapidly growing data are stimulating cross disciplinary studies in such field as biogeomagnetism. We have compiled the first online database for MTB, i.e., Database of Magnestotactic Bacteria (DMTB, http://database.biomnsl.com). It contains useful information of 16S rRNA gene sequences, oligonucleotides, and magnetic properties of MTB, and corresponding ecological metadata of sampling sites. The 16S rRNA gene sequences are collected from the GenBank database, while all other data are collected from the scientific literature. Rock magnetic properties for both uncultivated and cultivated MTB species are also included. In the DMTB database, data are accessible through four main interfaces: Site Sort, Phylo Sort, Oligonucleotides, and Magnetic Properties. References in each entry serve as links to specific pages within public databases. The online comprehensive DMTB will provide a very useful data resource for researchers from various disciplines, e.g., microbiology, rock magnetism and paleomagnetism, biogeomagnetism, magnetic material sciences and others.

  8. Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs

    PubMed Central

    Jimenez-Infante, Francy; Ngugi, David Kamanda; Vinu, Manikandan; Alam, Intikhab; Kamau, Allan Anthony; Blom, Jochen; Bajic, Vladimir B.

    2015-01-01

    The OM43 clade within the family Methylophilaceae of Betaproteobacteria represents a group of methylotrophs that play important roles in the metabolism of C1 compounds in marine environments and other aquatic environments around the globe. Using dilution-to-extinction cultivation techniques, we successfully isolated a novel species of this clade (here designated MBRS-H7) from the ultraoligotrophic open ocean waters of the central Red Sea. Phylogenomic analyses indicate that MBRS-H7 is a novel species that forms a distinct cluster together with isolate KB13 from Hawaii (Hawaii-Red Sea [H-RS] cluster) that is separate from the cluster represented by strain HTCC2181 (from the Oregon coast). Phylogenetic analyses using the robust 16S-23S internal transcribed spacer revealed a potential ecotype separation of the marine OM43 clade members, which was further confirmed by metagenomic fragment recruitment analyses that showed trends of higher abundance in low-chlorophyll and/or high-temperature provinces for the H-RS cluster but a preference for colder, highly productive waters for the HTCC2181 cluster. This potential environmentally driven niche differentiation is also reflected in the metabolic gene inventories, which in the case of the H-RS cluster include those conferring resistance to high levels of UV irradiation, temperature, and salinity. Interestingly, we also found different energy conservation modules between these OM43 subclades, namely, the existence of the NADH:quinone oxidoreductase complex I (NUO) system in the H-RS cluster and the nonhomologous NADH:quinone oxidoreductase (NQR) system in the HTCC2181 cluster, which might have implications for their overall energetic yields. PMID:26655752

  9. Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase-a comprehensive drug target database for Lymphatic filariasis

    PubMed Central

    Sharma, Om Prakash; Kumar, Muthuvel Suresh

    2016-01-01

    Lymphatic filariasis (Lf) is one of the oldest and most debilitating tropical diseases. Millions of people are suffering from this prevalent disease. It is estimated to infect over 120 million people in at least 80 nations of the world through the tropical and subtropical regions. More than one billion people are in danger of getting affected with this life-threatening disease. Several studies were suggested its emerging limitations and resistance towards the available drugs and therapeutic targets for Lf. Therefore, better medicine and drug targets are in demand. We took an initiative to identify the essential proteins of Wolbachia endosymbiont of Brugia malayi, which are indispensable for their survival and non-homologous to human host proteins. In this current study, we have used proteome subtractive approach to screen the possible therapeutic targets for wBm. In addition, numerous literatures were mined in the hunt for potential drug targets, drugs, epitopes, crystal structures, and expressed sequence tag (EST) sequences for filarial causing nematodes. Data obtained from our study were presented in a user friendly database named FiloBase. We hope that information stored in this database may be used for further research and drug development process against filariasis. URL: http://filobase.bicpu.edu.in. PMID:26806463

  10. Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase-a comprehensive drug target database for Lymphatic filariasis

    NASA Astrophysics Data System (ADS)

    Sharma, Om Prakash; Kumar, Muthuvel Suresh

    2016-01-01

    Lymphatic filariasis (Lf) is one of the oldest and most debilitating tropical diseases. Millions of people are suffering from this prevalent disease. It is estimated to infect over 120 million people in at least 80 nations of the world through the tropical and subtropical regions. More than one billion people are in danger of getting affected with this life-threatening disease. Several studies were suggested its emerging limitations and resistance towards the available drugs and therapeutic targets for Lf. Therefore, better medicine and drug targets are in demand. We took an initiative to identify the essential proteins of Wolbachia endosymbiont of Brugia malayi, which are indispensable for their survival and non-homologous to human host proteins. In this current study, we have used proteome subtractive approach to screen the possible therapeutic targets for wBm. In addition, numerous literatures were mined in the hunt for potential drug targets, drugs, epitopes, crystal structures, and expressed sequence tag (EST) sequences for filarial causing nematodes. Data obtained from our study were presented in a user friendly database named FiloBase. We hope that information stored in this database may be used for further research and drug development process against filariasis. URL: http://filobase.bicpu.edu.in.

  11. Comprehensibility maximization and humanly comprehensible representations

    NASA Astrophysics Data System (ADS)

    Kamimura, Ryotaro

    2012-04-01

    In this paper, we propose a new information-theoretic method to measure the comprehensibility of network configurations in competitive learning. Comprehensibility is supposed to be measured by information contained in components in competitive networks. Thus, the increase in information corresponds to the increase in comprehensibility of network configurations. One of the most important characteristics of the method is that parameters can be explicitly determined so as to produce a state where the different types of comprehensibility can be mutually increased. We applied the method to two problems, namely an artificial data set and the ionosphere data from the well-known machine learning database. In both problems, we showed that improved performance could be obtained in terms of all types of comprehensibility and quantization errors. For the topographic errors, we found that updating connection weights prevented them from increasing. Then, the optimal values of comprehensibility could be explicitly determined, and clearer class boundaries were generated.

  12. Choosing among the physician databases.

    PubMed

    Heller, R H

    1988-04-01

    Prudent examination and knowing how to ask the "right questions" can enable hospital marketers and planners to find the most accurate and appropriate database. The author compares the comprehensive AMA physician database with the less expensive MEDEC database to determine their strengths and weaknesses.

  13. One year of anaesthesia in France: A comprehensive survey based on the national medical information (PMSI) database. Part 1: In-hospital patients.

    PubMed

    Dadure, Christophe; Marie, Anaïs; Seguret, Fabienne; Capdevila, Xavier

    2015-08-01

    Anaesthesia has evolved in France since the last epidemiologic survey in 1996. The national database program for medical information systems (the PMSI) can be used to track specific knowledge concerning anaesthesia for a selected period of time. The goal of this study was to perform a contemporary epidemiological description of anaesthesia in France for the year 2010. The data concerning private or public hospital stays were collected from the national PMSI database. All surgical/medical institutions performing anaesthesia in France and French Overseas Departments and Territories were queried concerning the number of anaesthesias, patient age, sex ratios, institution characteristics, hospitalization types, the duration of hospital stays, and the surgical procedures performed. In 2010, the number of anaesthesia procedures performed was 11,323,630 during 8,568,630 hospital stays. We found that 9,544,326 (84.3%) anaesthetic procedures were performed in adults (> 18 years of age; excluding childbirth), 845,568 (7.5%) were related to childbirth and 933,736 (8.2%) were acts in children (up to 18 years of age). The mean duration of hospital stay was 5.7±8.2 days. 56.5% of adults and 39.5% of children were managed as inpatient hospital stays. The male/female sex ratio and mean age were 42/58 and 54±19 years, respectively. In adults, anaesthesia was predominantly performed for abdominal surgery (24.5%), orthopaedics (16.7%), gynaecology (10.3%), ophthalmology (9.7%) and vascular surgeries (7.1%). For paediatric populations, the main surgical activities were Ear-Nose-Throat surgery (43.1%), orthopaedic surgery (15.1%) and urological surgeries (12.8%). The number of anaesthesias performed in France has dramatically increased (42.7%) since the last major epidemiological survey. Anaesthesia in the 21th century has been adapted to associated demographic changes: an older population with more comorbidities and fewer in-hospital procedures. Copyright © 2015 Société fran

  14. 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).

  15. Building a Comprehensive Mill-Level Database for the Industrial Sectors Integrated Solutions (ISIS) Model of the U.S. Pulp and Paper Sector

    PubMed Central

    Modak, Nabanita; Spence, Kelley; Sood, Saloni; Rosati, Jacky Ann

    2015-01-01

    Air emissions from the U.S. pulp and paper sector have been federally regulated since 1978; however, regulations are periodically reviewed and revised to improve efficiency and effectiveness of existing emission standards. The Industrial Sectors Integrated Solutions (ISIS) model for the pulp and paper sector is currently under development at the U.S. Environmental Protection Agency (EPA), and can be utilized to facilitate multi-pollutant, sector-based analyses that are performed in conjunction with regulatory development. The model utilizes a multi-sector, multi-product dynamic linear modeling framework that evaluates the economic impact of emission reduction strategies for multiple air pollutants. The ISIS model considers facility-level economic, environmental, and technical parameters, as well as sector-level market data, to estimate the impacts of environmental regulations on the pulp and paper industry. Specifically, the model can be used to estimate U.S. and global market impacts of new or more stringent air regulations, such as impacts on product price, exports and imports, market demands, capital investment, and mill closures. One major challenge to developing a representative model is the need for an extensive amount of data. This article discusses the collection and processing of data for use in the model, as well as the methods used for building the ISIS pulp and paper database that facilitates the required analyses to support the air quality management of the pulp and paper sector. PMID:25806516

  16. Qualitative Alterations of Bacterial Metabolome after Exposure to Metal Nanoparticles with Bactericidal Properties: A Comprehensive Workflow Based on (1)H NMR, UHPLC-HRMS, and Metabolic Databases.

    PubMed

    Chatzimitakos, Theodoros G; Stalikas, Constantine D

    2016-09-02

    Metal nanoparticles (NPs) have proven to be more toxic than bulk analogues of the same chemical composition due to their unique physical properties. The NPs, lately, have drawn the attention of researchers because of their antibacterial and biocidal properties. In an effort to shed light on the mechanism through which the bacteria elimination is achieved and the metabolic changes they undergo, an untargeted metabolomic fingerprint study was carried out on Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria species. The (1)H NMR spectroscopy, in conjunction with high resolution mass-spectrometry (HRMS) and an unsophisticated data processing workflow were implemented. The combined NMR/HRMS data, supported by an open-access metabolomic database, proved to be efficacious in the process of assigning a putative annotation to a wide range of metabolite signals and is a useful tool to appraise the metabolome alterations, as a consequence of bacterial response to NPs. Interestingly, not all the NPs diminished the intracellular metabolites; bacteria treated with iron NPs produced metabolites not present in the nonexposed bacteria sample, implying the activation of previously inactive metabolic pathways. In contrast, copper and iron-copper NPs reduced the annotated metabolites, alluding to the conclusion that the metabolic pathways (mainly alanine, aspartate, and glutamate metabolism, beta-alanine metabolism, glutathione metabolism, and arginine and proline metabolism) were hindered by the interactions of NPs with the intracellular metabolites.

  17. Building a comprehensive mill-level database for the Industrial Sectors Integrated Solutions (ISIS) model of the U.S. pulp and paper sector.

    PubMed

    Modak, Nabanita; Spence, Kelley; Sood, Saloni; Rosati, Jacky Ann

    2015-01-01

    Air emissions from the U.S. pulp and paper sector have been federally regulated since 1978; however, regulations are periodically reviewed and revised to improve efficiency and effectiveness of existing emission standards. The Industrial Sectors Integrated Solutions (ISIS) model for the pulp and paper sector is currently under development at the U.S. Environmental Protection Agency (EPA), and can be utilized to facilitate multi-pollutant, sector-based analyses that are performed in conjunction with regulatory development. The model utilizes a multi-sector, multi-product dynamic linear modeling framework that evaluates the economic impact of emission reduction strategies for multiple air pollutants. The ISIS model considers facility-level economic, environmental, and technical parameters, as well as sector-level market data, to estimate the impacts of environmental regulations on the pulp and paper industry. Specifically, the model can be used to estimate U.S. and global market impacts of new or more stringent air regulations, such as impacts on product price, exports and imports, market demands, capital investment, and mill closures. One major challenge to developing a representative model is the need for an extensive amount of data. This article discusses the collection and processing of data for use in the model, as well as the methods used for building the ISIS pulp and paper database that facilitates the required analyses to support the air quality management of the pulp and paper sector.

  18. bioDBnet - Biological Database Network

    Cancer.gov

    bioDBnet is a comprehensive resource of most of the biological databases available from different sites like NCBI, Uniprot, EMBL, Ensembl, Affymetrix. It provides a queryable interface to all the databases available, converts identifiers from one database into another and generates comprehensive reports.

  19. The Transporter Classification Database (TCDB): recent advances

    PubMed Central

    Saier, Milton H.; Reddy, Vamsee S.; Tsu, Brian V.; Ahmed, Muhammad Saad; Li, Chun; Moreno-Hagelsieb, Gabriel

    2016-01-01

    The Transporter Classification Database (TCDB; http://www.tcdb.org) is a freely accessible reference database for transport protein research, which provides structural, functional, mechanistic, evolutionary and disease/medical information about transporters from organisms of all types. TCDB is the only transport protein classification database adopted by the International Union of Biochemistry and Molecular Biology (IUBMB). It consists of more than 10 000 non-redundant transport systems with more than 11 000 reference citations, classified into over 1000 transporter families. Transporters in TCDB can be single or multi-component systems, categorized in a functional/phylogenetic hierarchical system of classes, subclasses, families, subfamilies and transport systems. TCDB also includes updated software designed to analyze the distinctive features of transport proteins, extending its usefulness. Here we present a comprehensive update of the database contents and features and summarize recent discoveries recorded in TCDB. PMID:26546518

  20. FlyBase: a Drosophila database. Flybase Consortium.

    PubMed Central

    1998-01-01

    FlyBase (http://flybase.bio.indiana.edu/) is a comprehensive database of genetic and molecular data concerning Drosophila . FlyBase is maintained as a relational database (in Sybase) and is made available as html documents and flat files. The scope of FlyBase includes: genes, alleles (with phenotypes), aberrations, transposons, pointers to sequence data, gene products, maps, clones, stock lists, Drosophila workers and bibliographic references. PMID:9399806

  1. Aero/fluids database system

    NASA Technical Reports Server (NTRS)

    Reardon, John E.; Violett, Duane L., Jr.

    1991-01-01

    The AFAS Database System was developed to provide the basic structure of a comprehensive database system for the Marshall Space Flight Center (MSFC) Structures and Dynamics Laboratory Aerophysics Division. The system is intended to handle all of the Aerophysics Division Test Facilities as well as data from other sources. The system was written for the DEC VAX family of computers in FORTRAN-77 and utilizes the VMS indexed file system and screen management routines. Various aspects of the system are covered, including a description of the user interface, lists of all code structure elements, descriptions of the file structures, a description of the security system operation, a detailed description of the data retrieval tasks, a description of the session log, and a description of the archival system.

  2. Scopus database: a review.

    PubMed

    Burnham, Judy F

    2006-03-08

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs.

  3. Scopus database: a review

    PubMed Central

    Burnham, Judy F

    2006-01-01

    The Scopus database provides access to STM journal articles and the references included in those articles, allowing the searcher to search both forward and backward in time. The database can be used for collection development as well as for research. This review provides information on the key points of the database and compares it to Web of Science. Neither database is inclusive, but complements each other. If a library can only afford one, choice must be based in institutional needs. PMID:16522216

  4. Comprehension of Connected Discourse.

    ERIC Educational Resources Information Center

    Mosberg, Ludwig; Shima, Fred

    A rationale was developed for researching reading comprehension based on information gain. Previous definitions of comprehension which were reviewed included operational vs. nonoperational and skills vs. processes. Comprehension was viewed as an informational processing event which includes a constellation of cognitive and learning processes. Two…

  5. Clinical decision support tools: personal digital assistant versus online dietary supplement databases.

    PubMed

    Clauson, Kevin A; Polen, Hyla H; Peak, Amy S; Marsh, Wallace A; DiScala, Sandra L

    2008-11-01

    Clinical decision support tools (CDSTs) on personal digital assistants (PDAs) and online databases assist healthcare practitioners who make decisions about dietary supplements. To assess and compare the content of PDA dietary supplement databases and their online counterparts used as CDSTs. A total of 102 question-and-answer pairs were developed within 10 weighted categories of the most clinically relevant aspects of dietary supplement therapy. PDA versions of AltMedDex, Lexi-Natural, Natural Medicines Comprehensive Database, and Natural Standard and their online counterparts were assessed by scope (percent of correct answers present), completeness (3-point scale), ease of use, and a composite score integrating all 3 criteria. Descriptive statistics and inferential statistics, including a chi(2) test, Scheffé's multiple comparison test, McNemar's test, and the Wilcoxon signed rank test were used to analyze data. The scope scores for PDA databases were: Natural Medicines Comprehensive Database 84.3%, Natural Standard 58.8%, Lexi-Natural 50.0%, and AltMedDex 36.3%, with Natural Medicines Comprehensive Database statistically superior (p < 0.01). Completeness scores were: Natural Medicines Comprehensive Database 78.4%, Natural Standard 51.0%, Lexi-Natural 43.5%, and AltMedDex 29.7%. Lexi-Natural was superior in ease of use (p < 0.01). Composite scores for PDA databases were: Natural Medicines Comprehensive Database 79.3, Natural Standard 53.0, Lexi-Natural 48.0, and AltMedDex 32.5, with Natural Medicines Comprehensive Database superior (p < 0.01). There was no difference between the scope for PDA and online database pairs with Lexi-Natural (50.0% and 53.9%, respectively) or Natural Medicines Comprehensive Database (84.3% and 84.3%, respectively) (p > 0.05), whereas differences existed for AltMedDex (36.3% vs 74.5%, respectively) and Natural Standard (58.8% vs 80.4%, respectively) (p < 0.01). For composite scores, AltMedDex and Natural Standard online were better than

  6. BIAdb: A curated database of benzylisoquinoline alkaloids

    PubMed Central

    2010-01-01

    Background Benzylisoquinoline is the structural backbone of many alkaloids with a wide variety of structures including papaverine, noscapine, codeine, morphine, apomorphine, berberine, protopine and tubocurarine. Many benzylisoquinoline alkaloids have been reported to show therapeutic properties and to act as novel medicines. Thus it is important to collect and compile benzylisoquinoline alkaloids in order to explore their usage in medicine. Description We extract information about benzylisoquinoline alkaloids from various sources like PubChem, KEGG, KNApSAcK and manual curation from literature. This information was processed and compiled in order to create a comprehensive database of benzylisoquinoline alkaloids, called BIAdb. The current version of BIAdb contains information about 846 unique benzylisoquinoline alkaloids, with multiple entries in term of source, function leads to total number of 2504 records. One of the major features of this database is that it provides data about 627 different plant species as a source of benzylisoquinoline and 114 different types of function performed by these compounds. A large number of online tools have been integrated, which facilitate user in exploring full potential of BIAdb. In order to provide additional information, we give external links to other resources/databases. One of the important features of this database is that it is tightly integrated with Drugpedia, which allows managing data in fixed/flexible format. Conclusions A database of benzylisoquinoline compounds has been created, which provides comprehensive information about benzylisoquinoline alkaloids. This database will be very useful for those who are working in the field of drug discovery based on natural products. This database will also serve researchers working in the field of synthetic biology, as developing medicinally important alkaloids using synthetic process are one of important challenges. This database is available from http

  7. National Databases for Neurosurgical Outcomes Research: Options, Strengths, and Limitations.

    PubMed

    Karhade, Aditya V; Larsen, Alexandra M G; Cote, David J; Dubois, Heloise M; Smith, Timothy R

    2017-08-05

    Quality improvement, value-based care delivery, and personalized patient care depend on robust clinical, financial, and demographic data streams of neurosurgical outcomes. The neurosurgical literature lacks a comprehensive review of large national databases. To assess the strengths and limitations of various resources for outcomes research in neurosurgery. A review of the literature was conducted to identify surgical outcomes studies using national data sets. The databases were assessed for the availability of patient demographics and clinical variables, longitudinal follow-up of patients, strengths, and limitations. The number of unique patients contained within each data set ranged from thousands (Quality Outcomes Database [QOD]) to hundreds of millions (MarketScan). Databases with both clinical and financial data included PearlDiver, Premier Healthcare Database, Vizient Clinical Data Base and Resource Manager, and the National Inpatient Sample. Outcomes collected by databases included patient-reported outcomes (QOD); 30-day morbidity, readmissions, and reoperations (National Surgical Quality Improvement Program); and disease incidence and disease-specific survival (Surveillance, Epidemiology, and End Results-Medicare). The strengths of large databases included large numbers of rare pathologies and multi-institutional nationally representative sampling; the limitations of these databases included variable data veracity, variable data completeness, and missing disease-specific variables. The improvement of existing large national databases and the establishment of new registries will be crucial to the future of neurosurgical outcomes research.

  8. America: History and Life--A Wide Ranging Database.

    ERIC Educational Resources Information Center

    Sweetland, James H.

    1983-01-01

    Description of America: History and Life (AHL)--database including references from over 2,000 periodicals in literature, philosophy, religion, art, sociology, other disciplines of historical value--highlights structure; document treatment; access points; comparison of dissertation coverage between AHL and Comprehensive Dissertation Abstracts;…

  9. MIPS: a database for protein sequences and complete genomes.

    PubMed Central

    Mewes, H W; Hani, J; Pfeiffer, F; Frishman, D

    1998-01-01

    The MIPS group [Munich Information Center for Protein Sequences of the German National Center for Environment and Health (GSF)] at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, is involved in a number of data collection activities, including a comprehensive database of the yeast genome, a database reflecting the progress in sequencing the Arabidopsis thaliana genome, the systematic analysis of other small genomes and the collection of protein sequence data within the framework of the PIR-International Protein Sequence Database (described elsewhere in this volume). Through its WWW server (http://www.mips.biochem.mpg.de ) MIPS provides access to a variety of generic databases, including a database of protein families as well as automatically generated data by the systematic application of sequence analysis algorithms. The yeast genome sequence and its related information was also compiled on CD-ROM to provide dynamic interactive access to the 16 chromosomes of the first eukaryotic genome unraveled. PMID:9399795

  10. Geologic map and map database of northeastern San Francisco Bay region, California, [including] most of Solano County and parts of Napa, Marin, Contra Costa, San Joaquin, Sacramento, Yolo, and Sonoma Counties

    USGS Publications Warehouse

    Graymer, Russell Walter; Jones, David Lawrence; Brabb, Earl E.

    2002-01-01

    This digital map database, compiled from previously published and unpublished data, and new mapping by the authors, represents the general distribution of bedrock and surficial deposits in the mapped area. Together with the accompanying text file (nesfmf.ps, nesfmf.pdf, nesfmf.txt), it provides current information on the geologic structure and stratigraphy of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:62,500 or smaller.

  11. A Chronostratigraphic Relational Database Ontology

    NASA Astrophysics Data System (ADS)

    Platon, E.; Gary, A.; Sikora, P.

    2005-12-01

    A chronostratigraphic research database was donated by British Petroleum to the Stratigraphy Group at the Energy and Geoscience Institute (EGI), University of Utah. These data consists of over 2,000 measured sections representing over three decades of research into the application of the graphic correlation method. The data are global and includes both microfossil (foraminifera, calcareous nannoplankton, spores, pollen, dinoflagellate cysts, etc) and macrofossil data. The objective of the donation was to make the research data available to the public in order to encourage additional chronostratigraphy studies, specifically regarding graphic correlation. As part of the National Science Foundation's Cyberinfrastructure for the Geosciences (GEON) initiative these data have been made available to the public at http://css.egi.utah.edu. To encourage further research using the graphic correlation method, EGI has developed a software package, StrataPlot that will soon be publicly available from the GEON website as a standalone software download. The EGI chronostratigraphy research database, although relatively large, has many data holes relative to some paleontological disciplines and geographical areas, so the challenge becomes how do we expand the data available for chronostratigrahic studies using graphic correlation. There are several public or soon-to-be public databases available to chronostratigraphic research, but they have their own data structures and modes of presentation. The heterogeneous nature of these database schemas hinders their integration and makes it difficult for the user to retrieve and consolidate potentially valuable chronostratigraphic data. The integration of these data sources would facilitate rapid and comprehensive data searches, thus helping advance studies in chronostratigraphy. The GEON project will host a number of databases within the geology domain, some of which contain biostratigraphic data. Ontologies are being developed to provide

  12. AmphibiaChina: an online database of Chinese Amphibians.

    PubMed

    Che, Jing; Wang, Kai

    2016-01-18

    AmphibiaChina, an open-access, web-based database, is designed to provide comprehensive and up-to-date information on Chinese amphibians. It offers an integrated module with six major sections. Compared to other known databases including AmphibiaWeb and Amphibian Species of the World, AmphibiaChina has the following new functions: (1) online species identification based on DNA barcode sequences; (2) comparisons and discussions of different major taxonomic systems; and (3) phylogenetic progress on Chinese amphibians. This database offers a window for the world to access available information of Chinese amphibians. AmphibiaChina with its Chinese version can be accessed at http://www.amphibiachina.org.

  13. A snapshot in time - the new TRUplanner database

    SciTech Connect

    Estill, Wesley Gordon; Crawford, Beverly; Van Soest, Greg

    2010-01-01

    A new database was developed to augment transuranic (TRU) waste inventory information already captured within the Comprehensive Inventory Database (CID). This new database, known as the TRUplanner, includes information focused on site capability for TRU waste certification and availability to ship to either the Waste Isolation Pilot Plant (WIPP) or Idaho National Laboratory for final characterization and certification before coming to WIPP. Waste stream specific data is imported from the CID to the TRUplanner, and additional data is collected and entered as a result of interviews and site visits. This data is continuously updated as sites are visited.

  14. Biofuel Database

    National Institute of Standards and Technology Data Gateway

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

  15. Inorganic Crystal Structure Database (ICSD)

    National Institute of Standards and Technology Data Gateway

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

  16. Central Asia Active Fault Database

    NASA Astrophysics Data System (ADS)

    Mohadjer, Solmaz; Ehlers, Todd A.; Kakar, Najibullah

    2014-05-01

    The ongoing collision of the Indian subcontinent with Asia controls active tectonics and seismicity in Central Asia. This motion is accommodated by faults that have historically caused devastating earthquakes and continue to pose serious threats to the population at risk. Despite international and regional efforts to assess seismic hazards in Central Asia, little attention has been given to development of a comprehensive database for active faults in the region. To address this issue and to better understand the distribution and level of seismic hazard in Central Asia, we are developing a publically available database for active faults of Central Asia (including but not limited to Afghanistan, Tajikistan, Kyrgyzstan, northern Pakistan and western China) using ArcGIS. The database is designed to allow users to store, map and query important fault parameters such as fault location, displacement history, rate of movement, and other data relevant to seismic hazard studies including fault trench locations, geochronology constraints, and seismic studies. Data sources integrated into the database include previously published maps and scientific investigations as well as strain rate measurements and historic and recent seismicity. In addition, high resolution Quickbird, Spot, and Aster imagery are used for selected features to locate and measure offset of landforms associated with Quaternary faulting. These features are individually digitized and linked to attribute tables that provide a description for each feature. Preliminary observations include inconsistent and sometimes inaccurate information for faults documented in different studies. For example, the Darvaz-Karakul fault which roughly defines the western margin of the Pamir, has been mapped with differences in location of up to 12 kilometers. The sense of motion for this fault ranges from unknown to thrust and strike-slip in three different studies despite documented left-lateral displacements of Holocene and late

  17. Common hyperspectral image database design

    NASA Astrophysics Data System (ADS)

    Tian, Lixun; Liao, Ningfang; Chai, Ali

    2009-11-01

    This paper is to introduce Common hyperspectral image database with a demand-oriented Database design method (CHIDB), which comprehensively set ground-based spectra, standardized hyperspectral cube, spectral analysis together to meet some applications. The paper presents an integrated approach to retrieving spectral and spatial patterns from remotely sensed imagery using state-of-the-art data mining and advanced database technologies, some data mining ideas and functions were associated into CHIDB to make it more suitable to serve in agriculture, geological and environmental areas. A broad range of data from multiple regions of the electromagnetic spectrum is supported, including ultraviolet, visible, near-infrared, thermal infrared, and fluorescence. CHIDB is based on dotnet framework and designed by MVC architecture including five main functional modules: Data importer/exporter, Image/spectrum Viewer, Data Processor, Parameter Extractor, and On-line Analyzer. The original data were all stored in SQL server2008 for efficient search, query and update, and some advance Spectral image data Processing technology are used such as Parallel processing in C#; Finally an application case is presented in agricultural disease detecting area.

  18. Database Administrator

    ERIC Educational Resources Information Center

    Moore, Pam

    2010-01-01

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

  19. FIREMON Database

    Treesearch

    John F. Caratti

    2006-01-01

    The FIREMON database software allows users to enter data, store, analyze, and summarize plot data, photos, and related documents. The FIREMON database software consists of a Java application and a Microsoft® Access database. The Java application provides the user interface with FIREMON data through data entry forms, data summary reports, and other data management tools...

  20. Database Administrator

    ERIC Educational Resources Information Center

    Moore, Pam

    2010-01-01

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

  1. The NCBI Taxonomy database.

    PubMed

    Federhen, Scott

    2012-01-01

    The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC's nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community.

  2. IDPredictor: predict database links in biomedical database.

    PubMed

    Mehlhorn, Hendrik; Lange, Matthias; Scholz, Uwe; Schreiber, Falk

    2012-06-26

    Knowledge found in biomedical databases, in particular in Web information systems, is a major bioinformatics resource. In general, this biological knowledge is worldwide represented in a network of databases. These data is spread among thousands of databases, which overlap in content, but differ substantially with respect to content detail, interface, formats and data structure. To support a functional annotation of lab data, such as protein sequences, metabolites or DNA sequences as well as a semi-automated data exploration in information retrieval environments, an integrated view to databases is essential. Search engines have the potential of assisting in data retrieval from these structured sources, but fall short of providing a comprehensive knowledge except out of the interlinked databases. A prerequisite of supporting the concept of an integrated data view is to acquire insights into cross-references among database entities. This issue is being hampered by the fact, that only a fraction of all possible cross-references are explicitely tagged in the particular biomedical informations systems. In this work, we investigate to what extend an automated construction of an integrated data network is possible. We propose a method that predicts and extracts cross-references from multiple life science databases and possible referenced data targets. We study the retrieval quality of our method and report on first, promising results. The method is implemented as the tool IDPredictor, which is published under the DOI 10.5447/IPK/2012/4 and is freely available using the URL: http://dx.doi.org/10.5447/IPK/2012/4.

  3. ADAM: another database of abbreviations in MEDLINE.

    PubMed

    Zhou, Wei; Torvik, Vetle I; Smalheiser, Neil R

    2006-11-15

    Abbreviations are an important type of terminology in the biomedical domain. Although several groups have already created databases of biomedical abbreviations, these are either not public, or are not comprehensive, or focus exclusively on acronym-type abbreviations. We have created another abbreviation database, ADAM, which covers commonly used abbreviations and their definitions (or long-forms) within MEDLINE titles and abstracts, including both acronym and non-acronym abbreviations. A model of recognizing abbreviations and their long-forms from titles and abstracts of MEDLINE (2006 baseline) was employed. After grouping morphological variants, 59 405 abbreviation/long-form pairs were identified. ADAM shows high precision (97.4%) and includes most of the frequently used abbreviations contained in the Unified Medical Language System (UMLS) Lexicon and the Stanford Abbreviation Database. Conversely, one-third of abbreviations in ADAM are novel insofar as they are not included in either database. About 19% of the novel abbreviations are non-acronym-type and these cover at least seven different types of short-form/long-form pairs. A free, public query interface to ADAM is available at http://arrowsmith.psych.uic.edu, and the entire database can be downloaded as a text file.

  4. E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

    PubMed Central

    Boutselakis, H.; Dimitropoulos, D.; Fillon, J.; Golovin, A.; Henrick, K.; Hussain, A.; Ionides, J.; John, M.; Keller, P. A.; Krissinel, E.; McNeil, P.; Naim, A.; Newman, R.; Oldfield, T.; Pineda, J.; Rachedi, A.; Copeland, J.; Sitnov, A.; Sobhany, S.; Suarez-Uruena, A.; Swaminathan, J.; Tagari, M.; Tate, J.; Tromm, S.; Velankar, S.; Vranken, W.

    2003-01-01

    The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool. PMID:12520052

  5. The RESID Database of protein structure modifications and the NRL-3D Sequence-Structure Database.

    PubMed

    Garavelli, J S; Hou, Z; Pattabiraman, N; Stephens, R M

    2001-01-01

    The RESID Database is a comprehensive collection of annotations and structures for protein post-translational modifications including N-terminal, C-terminal and peptide chain cross-link modifications. The RESID Database includes systematic and frequently observed alternate names, Chemical Abstracts Service registry numbers, atomic formulas and weights, enzyme activities, taxonomic range, keywords, literature citations with database cross-references, structural diagrams and molecular models. The NRL-3D Sequence-Structure Database is derived from the three-dimensional structure of proteins deposited with the Research Collaboratory for Structural Bioinformatics Protein Data Bank. The NRL-3D Database includes standardized and frequently observed alternate names, sources, keywords, literature citations, experimental conditions and searchable sequences from model coordinates. These databases are freely accessible through the National Cancer Institute-Frederick Advanced Biomedical Computing Center at these web sites: http://www. ncifcrf.gov/RESID, http://www.ncifcrf.gov/NRL-3D; or at these National Biomedical Research Foundation Protein Information Resource web sites: http://pir.georgetown.edu/pirwww/dbinfo/resid .html, http://pir.georgetown.edu/pirwww/dbinfo/nrl3d .html

  6. The Danish Prostate Cancer Database

    PubMed Central

    Nguyen-Nielsen, Mary; Høyer, Søren; Friis, Søren; Hansen, Steinbjørn; Brasso, Klaus; Jakobsen, Erik Breth; Moe, Mette; Larsson, Heidi; Søgaard, Mette; Nakano, Anne; Borre, Michael

    2016-01-01

    Aim of database The Danish Prostate Cancer Database (DAPROCAdata) is a nationwide clinical cancer database that has prospectively collected data on patients with incident prostate cancer in Denmark since February 2010. The overall aim of the DAPROCAdata is to improve the quality of prostate cancer care in Denmark by systematically collecting key clinical variables for the purposes of health care monitoring, quality improvement, and research. Study population All Danish patients with histologically verified prostate cancer are included in the DAPROCAdata. Main variables The DAPROCAdata registers clinical data and selected characteristics for patients with prostate cancer at diagnosis. Data are collected from the linkage of nationwide health registries and supplemented with online registration of key clinical variables by treating physicians at urological and oncological departments. Main variables include Gleason scores, cancer staging, prostate-specific antigen values, and therapeutic measures (active surveillance, surgery, radiotherapy, endocrine therapy, and chemotherapy). Descriptive data In total, 22,332 patients with prostate cancer were registered in DAPROCAdata as of April 2015. A key feature of DAPROCAdata is the routine collection of patient-reported outcome measures (PROM), including data on quality-of-life (pain levels, physical activity, sexual function, depression, urine and fecal incontinence) and lifestyle factors (smoking, alcohol consumption, and body mass index). PROM data are derived from questionnaires distributed at diagnosis and at 1-year and 3-year follow-up. Hitherto, the PROM data have been limited by low completeness (26% among newly diagnosed patients in 2014). Conclusion DAPROCAdata is a comprehensive, yet still young clinical database. Efforts to improve data collection, data validity, and completeness are ongoing and of high priority. PMID:27843346

  7. RNAcentral: A vision for an international database of RNA sequences

    PubMed Central

    Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A.; Bujnicki, Janusz M.; Cochrane, Guy; Cole, James R.; Dinger, Marcel E.; Enright, Anton J.; Gardner, Paul P.; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H.; Huang, Hsien-Da; Kelly, Krystyna A.; Kersey, Paul; Kozomara, Ana; Lowe, Todd M.; Marz, Manja; Moxon, Simon; Pruitt, Kim D.; Samuelsson, Tore; Stadler, Peter F.; Vilella, Albert J.; Vogel, Jan-Hinnerk; Williams, Kelly P.; Wright, Mathew W.; Zwieb, Christian

    2011-01-01

    During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor. PMID:21940779

  8. RNAcentral: A vision for an international database of RNA sequences.

    PubMed

    Bateman, Alex; Agrawal, Shipra; Birney, Ewan; Bruford, Elspeth A; Bujnicki, Janusz M; Cochrane, Guy; Cole, James R; Dinger, Marcel E; Enright, Anton J; Gardner, Paul P; Gautheret, Daniel; Griffiths-Jones, Sam; Harrow, Jen; Herrero, Javier; Holmes, Ian H; Huang, Hsien-Da; Kelly, Krystyna A; Kersey, Paul; Kozomara, Ana; Lowe, Todd M; Marz, Manja; Moxon, Simon; Pruitt, Kim D; Samuelsson, Tore; Stadler, Peter F; Vilella, Albert J; Vogel, Jan-Hinnerk; Williams, Kelly P; Wright, Mathew W; Zwieb, Christian

    2011-11-01

    During the last decade there has been a great increase in the number of noncoding RNA genes identified, including new classes such as microRNAs and piRNAs. There is also a large growth in the amount of experimental characterization of these RNA components. Despite this growth in information, it is still difficult for researchers to access RNA data, because key data resources for noncoding RNAs have not yet been created. The most pressing omission is the lack of a comprehensive RNA sequence database, much like UniProt, which provides a comprehensive set of protein knowledge. In this article we propose the creation of a new open public resource that we term RNAcentral, which will contain a comprehensive collection of RNA sequences and fill an important gap in the provision of biomedical databases. We envision RNA researchers from all over the world joining a federated RNAcentral network, contributing specialized knowledge and databases. RNAcentral would centralize key data that are currently held across a variety of databases, allowing researchers instant access to a single, unified resource. This resource would facilitate the next generation of RNA research and help drive further discoveries, including those that improve food production and human and animal health. We encourage additional RNA database resources and research groups to join this effort. We aim to obtain international network funding to further this endeavor.

  9. 2010 Worldwide Gasification Database

    DOE Data Explorer

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

  10. DPTEdb, an integrative database of transposable elements in dioecious plants

    PubMed Central

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

    2016-01-01

    Dioecious plants usually harbor ‘young’ sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants. Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php PMID:27173524

  11. DPTEdb, an integrative database of transposable elements in dioecious plants.

    PubMed

    Li, Shu-Fen; Zhang, Guo-Jun; Zhang, Xue-Jin; Yuan, Jin-Hong; Deng, Chuan-Liang; Gu, Lian-Feng; Gao, Wu-Jun

    2016-01-01

    Dioecious plants usually harbor 'young' sex chromosomes, providing an opportunity to study the early stages of sex chromosome evolution. Transposable elements (TEs) are mobile DNA elements frequently found in plants and are suggested to play important roles in plant sex chromosome evolution. The genomes of several dioecious plants have been sequenced, offering an opportunity to annotate and mine the TE data. However, comprehensive and unified annotation of TEs in these dioecious plants is still lacking. In this study, we constructed a dioecious plant transposable element database (DPTEdb). DPTEdb is a specific, comprehensive and unified relational database and web interface. We used a combination of de novo, structure-based and homology-based approaches to identify TEs from the genome assemblies of previously published data, as well as our own. The database currently integrates eight dioecious plant species and a total of 31 340 TEs along with classification information. DPTEdb provides user-friendly web interfaces to browse, search and download the TE sequences in the database. Users can also use tools, including BLAST, GetORF, HMMER, Cut sequence and JBrowse, to analyze TE data. Given the role of TEs in plant sex chromosome evolution, the database will contribute to the investigation of TEs in structural, functional and evolutionary dynamics of the genome of dioecious plants. In addition, the database will supplement the research of sex diversification and sex chromosome evolution of dioecious plants.Database URL: http://genedenovoweb.ticp.net:81/DPTEdb/index.php.

  12. CERCLIS (Superfund) ASCII Text Format - CPAD Database

    EPA Pesticide Factsheets

    The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access Database (CPAD) 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 Project Plan (QAPP).

  13. Advanced transportation system studies. Alternate propulsion subsystem concepts: Propulsion database

    NASA Technical Reports Server (NTRS)

    Levack, Daniel

    1993-01-01

    The Advanced Transportation System Studies alternate propulsion subsystem concepts propulsion database interim report is presented. The objective of the database development task is to produce a propulsion database which is easy to use and modify while also being comprehensive in the level of detail available. The database is to be available on the Macintosh computer system. The task is to extend across all three years of the contract. Consequently, a significant fraction of the effort in this first year of the task was devoted to the development of the database structure to ensure a robust base for the following years' efforts. Nonetheless, significant point design propulsion system descriptions and parametric models were also produced. Each of the two propulsion databases, parametric propulsion database and propulsion system database, are described. The descriptions include a user's guide to each code, write-ups for models used, and sample output. The parametric database has models for LOX/H2 and LOX/RP liquid engines, solid rocket boosters using three different propellants, a hybrid rocket booster, and a NERVA derived nuclear thermal rocket engine.

  14. Dictionary as Database.

    ERIC Educational Resources Information Center

    Painter, Derrick

    1996-01-01

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

  15. A Quality System Database

    NASA Technical Reports Server (NTRS)

    Snell, William H.; Turner, Anne M.; Gifford, Luther; Stites, William

    2010-01-01

    A quality system database (QSD), and software to administer the database, were developed to support recording of administrative nonconformance activities that involve requirements for documentation of corrective and/or preventive actions, which can include ISO 9000 internal quality audits and customer complaints.

  16. Specialist Bibliographic Databases

    PubMed Central

    2016-01-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls. PMID:27134485

  17. Specialist Bibliographic Databases.

    PubMed

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

    2016-05-01

    Specialist bibliographic databases offer essential online tools for researchers and authors who work on specific subjects and perform comprehensive and systematic syntheses of evidence. This article presents examples of the established specialist databases, which may be of interest to those engaged in multidisciplinary science communication. Access to most specialist databases is through subscription schemes and membership in professional associations. Several aggregators of information and database vendors, such as EBSCOhost and ProQuest, facilitate advanced searches supported by specialist keyword thesauri. Searches of items through specialist databases are complementary to those through multidisciplinary research platforms, such as PubMed, Web of Science, and Google Scholar. Familiarizing with the functional characteristics of biomedical and nonbiomedical bibliographic search tools is mandatory for researchers, authors, editors, and publishers. The database users are offered updates of the indexed journal lists, abstracts, author profiles, and links to other metadata. Editors and publishers may find particularly useful source selection criteria and apply for coverage of their peer-reviewed journals and grey literature sources. These criteria are aimed at accepting relevant sources with established editorial policies and quality controls.

  18. Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses.

    PubMed

    Park, Heejin; Bae, Junwoo; Kim, Hyunwoo; Kim, Sangok; Kim, Hokeun; Mun, Dong-Gi; Joh, Yoonsung; Lee, Wonyeop; Chae, Sehyun; Lee, Sanghyuk; Kim, Hark Kyun; Hwang, Daehee; Lee, Sang-Won; Paek, Eunok

    2014-12-01

    In proteogenomic analysis, construction of a compact, customized database from mRNA-seq data and a sensitive search of both reference and customized databases are essential to accurately determine protein abundances and structural variations at the protein level. However, these tasks have not been systematically explored, but rather performed in an ad-hoc fashion. Here, we present an effective method for constructing a compact database containing comprehensive sequences of sample-specific variants--single nucleotide variants, insertions/deletions, and stop-codon mutations derived from Exome-seq and RNA-seq data. It, however, occupies less space by storing variant peptides, not variant proteins. We also present an efficient search method for both customized and reference databases. The separate searches of the two databases increase the search time, and a unified search is less sensitive to identify variant peptides due to the smaller size of the customized database, compared to the reference database, in the target-decoy setting. Our method searches the unified database once, but performs target-decoy validations separately. Experimental results show that our approach is as fast as the unified search and as sensitive as the separate searches. Our customized database includes mutation information in the headers of variant peptides, thereby facilitating the inspection of peptide-spectrum matches.

  19. Maize databases

    USDA-ARS?s Scientific Manuscript database

    This chapter is a succinct overview of maize data held in the species-specific database MaizeGDB (the Maize Genomics and Genetics Database), and selected multi-species data repositories, such as Gramene/Ensembl Plants, Phytozome, UniProt and the National Center for Biotechnology Information (NCBI), ...

  20. Database Manager

    ERIC Educational Resources Information Center

    Martin, Andrew

    2010-01-01

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

  1. Image Databases.

    ERIC Educational Resources Information Center

    Pettersson, Rune

    Different kinds of pictorial databases are described with respect to aims, user groups, search possibilities, storage, and distribution. Some specific examples are given for databases used for the following purposes: (1) labor markets for artists; (2) document management; (3) telling a story; (4) preservation (archives and museums); (5) research;…

  2. Database Manager

    ERIC Educational Resources Information Center

    Martin, Andrew

    2010-01-01

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

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

    PubMed Central

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

    2017-01-01

    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

  4. HHMD: the human histone modification database.

    PubMed

    Zhang, Yan; Lv, Jie; Liu, Hongbo; Zhu, Jiang; Su, Jianzhong; Wu, Qiong; Qi, Yunfeng; Wang, Fang; Li, Xia

    2010-01-01

    Histone modifications play important roles in chromatin remodeling, gene transcriptional regulation, stem cell maintenance and differentiation. Alterations in histone modifications may be linked to human diseases especially cancer. Histone modifications including methylation, acetylation and ubiquitylation probed by ChIP-seq, ChIP-chip and qChIP have become widely available. Mining and integration of histone modification data can be beneficial to novel biological discoveries. There has been no comprehensive data repository that is exclusive for human histone modifications. Therefore, we developed a relatively comprehensive database for human histone modifications. Human Histone Modification Database (HHMD, http://bioinfo.hrbmu.edu.cn/hhmd) focuses on the storage and integration of histone modification datasets that were obtained from laboratory experiments. The latest release of HHMD incorporates 43 location-specific histone modifications in human. To facilitate data extraction, flexible search options are built in HHMD. It can be searched by histone modification, gene ID, functional categories, chromosome location and cancer name. HHMD also includes a user-friendly visualization tool named HisModView, by which genome-wide histone modification map can be shown. HisModView facilitates the acquisition and visualization of histone modifications. The database also has manually curated information of histone modification dysregulation in nine human cancers.

  5. Cascadia Tsunami Deposit Database

    USGS Publications Warehouse

    Peters, Robert; Jaffe, Bruce; Gelfenbaum, Guy; Peterson, Curt

    2003-01-01

    The Cascadia Tsunami Deposit Database contains data on the location and sedimentological properties of tsunami deposits found along the Cascadia margin. Data have been compiled from 52 studies, documenting 59 sites from northern California to Vancouver Island, British Columbia that contain known or potential tsunami deposits. Bibliographical references are provided for all sites included in the database. Cascadia tsunami deposits are usually seen as anomalous sand layers in coastal marsh or lake sediments. The studies cited in the database use numerous criteria based on sedimentary characteristics to distinguish tsunami deposits from sand layers deposited by other processes, such as river flooding and storm surges. Several studies cited in the database contain evidence for more than one tsunami at a site. Data categories include age, thickness, layering, grainsize, and other sedimentological characteristics of Cascadia tsunami deposits. The database documents the variability observed in tsunami deposits found along the Cascadia margin.

  6. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - NPL Sites

    EPA Pesticide Factsheets

    National Priorities List (NPL) Sites - 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 QAPP

  7. RCDB: Renal Cancer Gene Database.

    PubMed

    Ramana, Jayashree

    2012-05-18

    Renal cell carcinoma or RCC is one of the common and most lethal urological cancers, with 40% of the patients succumbing to death because of metastatic progression of the disease. Treatment of metastatic RCC remains highly challenging because of its resistance to chemotherapy as well as radiotherapy, besides surgical resection. Whereas RCC comprises tumors with differing histological types, clear cell RCC remains the most common. A major problem in the clinical management of patients presenting with localized ccRCC is the inability to determine tumor aggressiveness and accurately predict the risk of metastasis following surgery. As a measure to improve the diagnosis and prognosis of RCC, researchers have identified several molecular markers through a number of techniques. However the wealth of information available is scattered in literature and not easily amenable to data-mining. To reduce this gap, this work describes a comprehensive repository called Renal Cancer Gene Database, as an integrated gateway to study renal cancer related data. Renal Cancer Gene Database is a manually curated compendium of 240 protein-coding and 269 miRNA genes contributing to the etiology and pathogenesis of various forms of renal cell carcinomas. The protein coding genes have been classified according to the kind of gene alteration observed in RCC. RCDB also includes the miRNAsdysregulated in RCC, along with the corresponding information regarding the type of RCC and/or metastatic or prognostic significance. While some of the miRNA genes showed an association with other types of cancers few were unique to RCC. Users can query the database using keywords, category and chromosomal location of the genes. The knowledgebase can be freely accessed via a user-friendly web interface at http://www.juit.ac.in/attachments/jsr/rcdb/homenew.html. It is hoped that this database would serve as a useful complement to the existing public resources and as a good starting point for researchers and

  8. GMDD: a database of GMO detection methods

    PubMed Central

    Dong, Wei; Yang, Litao; Shen, Kailin; Kim, Banghyun; Kleter, Gijs A; Marvin, Hans JP; Guo, Rong; Liang, Wanqi; Zhang, Dabing

    2008-01-01

    Background Since more than one hundred events of genetically modified organisms (GMOs) have been developed and approved for commercialization in global area, the GMO analysis methods are essential for the enforcement of GMO labelling regulations. Protein and nucleic acid-based detection techniques have been developed and utilized for GMOs identification and quantification. However, the information for harmonization and standardization of GMO analysis methods at global level is needed. Results GMO Detection method Database (GMDD) has collected almost all the previous developed and reported GMOs detection methods, which have been grouped by different strategies (screen-, gene-, construct-, and event-specific), and also provide a user-friendly search service of the detection methods by GMO event name, exogenous gene, or protein information, etc. In this database, users can obtain the sequences of exogenous integration, which will facilitate PCR primers and probes design. Also the information on endogenous genes, certified reference materials, reference molecules, and the validation status of developed methods is included in this database. Furthermore, registered users can also submit new detection methods and sequences to this database, and the newly submitted information will be released soon after being checked. Conclusion GMDD contains comprehensive information of GMO detection methods. The database will make the GMOs analysis much easier. PMID:18522755

  9. GMDD: a database of GMO detection methods.

    PubMed

    Dong, Wei; Yang, Litao; Shen, Kailin; Kim, Banghyun; Kleter, Gijs A; Marvin, Hans J P; Guo, Rong; Liang, Wanqi; Zhang, Dabing

    2008-06-04

    Since more than one hundred events of genetically modified organisms (GMOs) have been developed and approved for commercialization in global area, the GMO analysis methods are essential for the enforcement of GMO labelling regulations. Protein and nucleic acid-based detection techniques have been developed and utilized for GMOs identification and quantification. However, the information for harmonization and standardization of GMO analysis methods at global level is needed. GMO Detection method Database (GMDD) has collected almost all the previous developed and reported GMOs detection methods, which have been grouped by different strategies (screen-, gene-, construct-, and event-specific), and also provide a user-friendly search service of the detection methods by GMO event name, exogenous gene, or protein information, etc. In this database, users can obtain the sequences of exogenous integration, which will facilitate PCR primers and probes design. Also the information on endogenous genes, certified reference materials, reference molecules, and the validation status of developed methods is included in this database. Furthermore, registered users can also submit new detection methods and sequences to this database, and the newly submitted information will be released soon after being checked. GMDD contains comprehensive information of GMO detection methods. The database will make the GMOs analysis much easier.

  10. Livestock Anaerobic Digester Database

    EPA Pesticide Factsheets

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

  11. The plant organelles database (PODB): a collection of visualized plant organelles and protocols for plant organelle research.

    PubMed

    Mano, Shoji; Miwa, Tomoki; Nishikawa, Shuh-ichi; Mimura, Tetsuro; Nishimura, Mikio

    2008-01-01

    The plant organelles database (PODB; http://podb.nibb.ac.jp/Organellome) was built to promote a comprehensive understanding of organelle dynamics, including organelle function, biogenesis, differentiation, movement and interactions with other organelles. This database consists of three individual parts, the organellome database, the functional analysis database and external links to other databases and homepages. The organellome database provides images of various plant organelles that were visualized with fluorescent and nonfluorescent probes in various tissues of several plant species at different developmental stages. The functional analysis database is a collection of protocols for plant organelle research. External links give access primarily to other databases and Web pages with information on transcriptomes and proteomes. All the data and protocols in the organellome database and the functional analysis database are populated by direct submission of experimentally determined data from plant researchers and can be freely downloaded. Our database promotes the exchange of information between plant organelle researchers for the comprehensive study of the organelle dynamics that support integrated functions in higher plants. We would also appreciate contributions of data and protocols from all plant researchers to maximize the usefulness of the database.

  12. Phase Equilibria Diagrams Database

    National Institute of Standards and Technology Data Gateway

    SRD 31 NIST/ACerS Phase Equilibria Diagrams Database (PC database for purchase)   The Phase Equilibria Diagrams Database contains commentaries and more than 21,000 diagrams for non-organic systems, including those published in all 21 hard-copy volumes produced as part of the ACerS-NIST Phase Equilibria Diagrams Program (formerly titled Phase Diagrams for Ceramists): Volumes I through XIV (blue books); Annuals 91, 92, 93; High Tc Superconductors I & II; Zirconium & Zirconia Systems; and Electronic Ceramics I. Materials covered include oxides as well as non-oxide systems such as chalcogenides and pnictides, phosphates, salt systems, and mixed systems of these classes.

  13. DRAG: a database for recognition and analasys of gait

    NASA Astrophysics Data System (ADS)

    Kuchi, Prem; Hiremagalur, Raghu Ram V.; Huang, Helen; Carhart, Michael; He, Jiping; Panchanathan, Sethuraman

    2003-11-01

    A novel approach is proposed for creating a standardized and comprehensive database for gait analysis. The field of gait analysis is gaining increasing attention for applications such as visual surveillance, human-computer interfaces, and gait recognition and rehabilitation. Numerous algorithms have been developed for analyzing and processing gait data; however, a standard database for their systematic evaluation does not exist. Instead, existing gait databases consist of subsets of kinematic, kinetic, and electromyographic activity recordings by different investigators, at separate laboratories, and under varying conditions. Thus, the existing databases are neither homogenous nor sufficiently populated to statistically validate the algorithms. In this paper, a methodology for creating a database is presented, which can be used as a common ground to test the performance of algorithms that rely upon external marker data, ground reaction loading data, and/or video images. The database consists of: (1) synchronized motion-capture data (3D marker data) obtained using external markers, (2) computed joint angles, and (3) ground reaction loading acquired with plantar pressure insoles. This database could be easily expanded to include synchronized video, which will facilitate further development of video-based algorithms for motion tracking. This eventually could lead to the realization of markerless gait tracking. Such a system would have extensive applications in gait recognition, as well as gait rehabilitation. The entire database (marker, angle, and force data) will be placed in the public domain, and made available for downloads over the World Wide Web.

  14. National Database of Geriatrics

    PubMed Central

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

    2016-01-01

    Aim of database The aim of the National Database of Geriatrics is to monitor the quality of interdisciplinary diagnostics and treatment of patients admitted to a geriatric hospital unit. Study population The database population consists of patients who were admitted to a geriatric hospital unit. Geriatric patients cannot be defined by specific diagnoses. A geriatric patient is typically a frail multimorbid elderly patient with decreasing functional ability and social challenges. The database includes 14–15,000 admissions per year, and the database completeness has been stable at 90% during the past 5 years. Main variables An important part of the geriatric approach is the interdisciplinary collaboration. Indicators, therefore, reflect the combined efforts directed toward the geriatric patient. The indicators include Barthel index, body mass index, de Morton Mobility Index, Chair Stand, percentage of discharges with a rehabilitation plan, and the part of cases where an interdisciplinary conference has taken place. Data are recorded by doctors, nurses, and therapists in a database and linked to the Danish National Patient Register. Descriptive data Descriptive patient-related data include information about home, mobility aid, need of fall and/or cognitive diagnosing, and categorization of cause (general geriatric, orthogeriatric, or neurogeriatric). Conclusion The National Database of Geriatrics covers ∼90% of geriatric admissions in Danish hospitals and provides valuable information about a large and increasing patient population in the health care system. PMID:27822120

  15. Who's Gonna Pay the Piper for Free Online Databases?

    ERIC Educational Resources Information Center

    Jacso, Peter

    1996-01-01

    Discusses new pricing models for some online services and considers the possibilities for the traditional online database market. Topics include multimedia music databases, including copyright implications; other retail-oriented databases; and paying for free databases with advertising. (LRW)

  16. Bcipep: A database of B-cell epitopes

    PubMed Central

    Saha, Sudipto; Bhasin, Manoj; Raghava, Gajendra PS

    2005-01-01

    Background Bcipep is a database of experimentally determined linear B-cell epitopes of varying immunogenicity collected from literature and other publicly available databases. Results The current version of Bcipep database contains 3031 entries that include 763 immunodominant, 1797 immunogenic and 471 null-immunogenic epitopes. It covers a wide range of pathogenic organisms like viruses, bacteria, protozoa, and fungi. The database provides a set of tools for the analysis and extraction of data that includes keyword search, peptide mapping and BLAST search. It also provides hyperlinks to various databases such as GenBank, PDB, SWISS-PROT and MHCBN. Conclusion A comprehensive database of B-cell epitopes called Bcipep has been developed that covers information on epitopes from a wide range of pathogens. The Bcipep will be source of information for investigators involved in peptide-based vaccine design, disease diagnosis and research in allergy. It should also be a promising data source for the development and evaluation of methods for prediction of B-cell epitopes. The database is available at . PMID:15921533

  17. Version 3 of the GEOMAGIA50 Paleomagnetic Database

    NASA Astrophysics Data System (ADS)

    Brown, M. C.; Donadini, F.; Nilsson, A.; Korte, M. C.; Panovska, S.; Frank, U.; Korhonen, K.; Lodge, A.; Lengyel, S. N.; Schuberth, M.; Constable, C.

    2015-12-01

    Version 3 of GEOMAGIA50 is the product of an international collaboration to develop a comprehensive online database that allows easy access to published paleomagnetic and chronological data from the past 50 ka. The overarching scientific goal is to improve our understanding of changes in the geomagnetic field, with applications ranging from the deep Earth, to past environments and climate, to the interaction of the geomagnetic field with the space environment. We present the large range of modifications made to the database since its initial release in 2006. The most significant is the addition of paleomagnetic, rock magnetic and chronological data obtained from lake and marine sediments. An emphasis has been placed on geochronological data from sediments and the database includes comprehensive radiocarbon age data, oxygen isotope data, varve ages and tephra ages. In the archeomagnetic and volcanic database, the amount of declination, inclination and paleointensity data has been increased greatly and now exceeds 15,000. In addition, a number of new metadata fields have been added, e.g., more specific information about the archaeological or volcanic sites the data were obtained from. Finally, the web interface has been updated. This includes a new query form for the sediment database and improved functionality of the archeomagnetic and volcanic query form. The webpage can be found at found at http://geomagia.gfz-potsdam.de.

  18. RNAcentral: an international database of ncRNA sequences

    DOE PAGES

    Williams, Kelly Porter

    2014-10-28

    The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

  19. Expert systems identify fossils and manage large paleontological databases

    SciTech Connect

    Beightol, D.S. ); Conrad, M.A.

    1988-02-01

    EXPAL is a computer program permitting creation and maintenance of comprehensive databases in marine paleontology. It is designed to assist specialists and non-specialists. EXPAL includes a powerful expert system based on the morphological descriptors specific to a given group of fossils. The expert system may be used, for example, to describe and automatically identify an unknown specimen. EXPAL was first applied to Dasycladales (Calcareous green algae). Projects are under way for corresponding expert systems and databases on planktonic foraminifers and calpionellids. EXPAL runs on an IBM XT or compatible microcomputer.

  20. RNAcentral: an international database of ncRNA sequences

    SciTech Connect

    Williams, Kelly Porter

    2014-10-28

    The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

  1. RNAcentral: an international database of ncRNA sequences

    PubMed Central

    2015-01-01

    The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species. PMID:25352543

  2. Experiment Databases

    NASA Astrophysics Data System (ADS)

    Vanschoren, Joaquin; Blockeel, Hendrik

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

  3. A Spanish American War Database.

    ERIC Educational Resources Information Center

    Hands, Edmund

    1992-01-01

    Discusses a database used by honors high school U.S. history students learning about the Spanish-American War. Reports that the students compiled the database. Includes some of the historical background of the war, questions for study, a database key, and a table showing U.S. senators' votes relating to the War. (SG)

  4. Working with Existing Databases

    PubMed Central

    Murphy, Melissa; Alavi, Karim; Maykel, Justin

    2013-01-01

    Outcomes research has established itself as an integral part of surgical research as physicians and hospitals are increasingly required to demonstrate attainment of performance markers and surgical safety indicators. Large-volume and clinical and administrative databases are used to study regional practice pattern variations, health care disparities, and resource utilization. Understanding the unique strengths and limitations of these large databases is critical to performing quality surgical outcomes research. In the current work, we review the currently available large-volume databases including selection processes, modes of analyses, data application, and limitations. PMID:24436641

  5. Online interactive U.S. Reservoir Sedimentation Survey Database

    USGS Publications Warehouse

    Gray, J.B.; Bernard, J.M.; Schwarz, G.E.; Stewart, D.W.; Ray, K.T.

    2009-01-01

    In April 2009, the U.S. Geological Survey and the Natural Resources Conservation Service (prior to 1994, the Soil Conservation Service) created the Reservoir Sedimentation Survey Database (RESSED) and Web site, the most comprehensive compilation of data from reservoir bathymetric and dry basin surveys in the United States. RESSED data can be useful for a number of purposes, including calculating changes in reservoir storage characteristics, quantifying rates of sediment delivery to reservoirs, and estimating erosion rates in a reservoir's watershed.

  6. Human mapping databases.

    PubMed

    Talbot, C; Cuticchia, A J

    2001-05-01

    This unit concentrates on the data contained within two human genome databasesGDB (Genome Database) and OMIM (Online Mendelian Inheritance in Man)and includes discussion of different methods for submitting and accessing data. An understanding of electronic mail, FTP, and the use of a World Wide Web (WWW) navigational tool such as Netscape or Internet Explorer is a prerequisite for utilizing the information in this unit.

  7. The ribosomal database project.

    PubMed

    Larsen, N; Olsen, G J; Maidak, B L; McCaughey, M J; Overbeek, R; Macke, T J; Marsh, T L; Woese, C R

    1993-07-01

    The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software packages for handling, analyzing and displaying alignments and trees. The data are available via ftp and electronic mail. Certain analytic services are also provided by the electronic mail server.

  8. The ribosomal database project.

    PubMed Central

    Larsen, N; Olsen, G J; Maidak, B L; McCaughey, M J; Overbeek, R; Macke, T J; Marsh, T L; Woese, C R

    1993-01-01

    The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software packages for handling, analyzing and displaying alignments and trees. The data are available via ftp and electronic mail. Certain analytic services are also provided by the electronic mail server. PMID:8332524

  9. Glycoproteomic and glycomic databases.

    PubMed

    Baycin Hizal, Deniz; Wolozny, Daniel; Colao, Joseph; Jacobson, Elena; Tian, Yuan; Krag, Sharon S; Betenbaugh, Michael J; Zhang, Hui

    2014-01-01

    Protein glycosylation serves critical roles in the cellular and biological processes of many organisms. Aberrant glycosylation has been associated with many illnesses such as hereditary and chronic diseases like cancer, cardiovascular diseases, neurological disorders, and immunological disorders. Emerging mass spectrometry (MS) technologies that enable the high-throughput identification of glycoproteins and glycans have accelerated the analysis and made possible the creation of dynamic and expanding databases. Although glycosylation-related databases have been established by many laboratories and institutions, they are not yet widely known in the community. Our study reviews 15 different publicly available databases and identifies their key elements so that users can identify the most applicable platform for their analytical needs. These databases include biological information on the experimentally identified glycans and glycopeptides from various cells and organisms such as human, rat, mouse, fly and zebrafish. The features of these databases - 7 for glycoproteomic data, 6 for glycomic data, and 2 for glycan binding proteins are summarized including the enrichment techniques that are used for glycoproteome and glycan identification. Furthermore databases such as Unipep, GlycoFly, GlycoFish recently established by our group are introduced. The unique features of each database, such as the analytical methods used and bioinformatical tools available are summarized. This information will be a valuable resource for the glycobiology community as it presents the analytical methods and glycosylation related databases together in one compendium. It will also represent a step towards the desired long term goal of integrating the different databases of glycosylation in order to characterize and categorize glycoproteins and glycans better for biomedical research.

  10. National Database of Geriatrics.

    PubMed

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

    2016-01-01

    The aim of the National Database of Geriatrics is to monitor the quality of interdisciplinary diagnostics and treatment of patients admitted to a geriatric hospital unit. The database population consists of patients who were admitted to a geriatric hospital unit. Geriatric patients cannot be defined by specific diagnoses. A geriatric patient is typically a frail multimorbid elderly patient with decreasing functional ability and social challenges. The database includes 14-15,000 admissions per year, and the database completeness has been stable at 90% during the past 5 years. An important part of the geriatric approach is the interdisciplinary collaboration. Indicators, therefore, reflect the combined efforts directed toward the geriatric patient. The indicators include Barthel index, body mass index, de Morton Mobility Index, Chair Stand, percentage of discharges with a rehabilitation plan, and the part of cases where an interdisciplinary conference has taken place. Data are recorded by doctors, nurses, and therapists in a database and linked to the Danish National Patient Register. Descriptive patient-related data include information about home, mobility aid, need of fall and/or cognitive diagnosing, and categorization of cause (general geriatric, orthogeriatric, or neurogeriatric). The National Database of Geriatrics covers ∼90% of geriatric admissions in Danish hospitals and provides valuable information about a large and increasing patient population in the health care system.

  11. Glaucoma database.

    PubMed

    K, Rangachari; M, Dhivya; Pj, Eswari Pandaranayaka; N, Prasanthi; P, Sundaresan; Sr, Krishnadas; S, Krishnaswamy

    2011-02-07

    Glaucoma, a complex heterogenous disease, is the leading cause for optic nerve-related blindness worldwide. Primary open angle glaucoma (POAG) is the most common subset and by the year 2020 it is estimated that approximately 60 million people will be affected. MYOC, OPTN, CYP1B1 and WDR36 are the important candidate genes. Nearly 4% of the glaucoma patients have mutation in any one of these genes. Mutation in any of these genes causes disease either directly or indirectly and the severity of the disease varies according to position of the genes. We have compiled all the related mutations and SNPs in the above genes and developed a database, to help access statistical and clinical information of particular mutation. This database is available online at http:bicmku.in:8081/glaucoma The database, constructed using SQL, contains data pertaining to the SNPs and mutation information involved in the above genes and relevant study data. The database is available for free at http:bicmku.in:8081/glaucoma.

  12. 78 FR 60861 - Native American Tribal Insignia Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-02

    ... United States Patent and Trademark Office Native American Tribal Insignia Database ACTION: Proposed... maintain an accurate and comprehensive database containing the official insignia of all federally and state... Appropriations directed the USPTO to create this database. The USPTO database of official tribal insignias...

  13. 75 FR 65611 - Native American Tribal Insignia Database

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-26

    ... Patent and Trademark Office Native American Tribal Insignia Database ACTION: Proposed collection; comment... recommendations made in the report was that the USPTO create and maintain an accurate and comprehensive database... database. The USPTO database of official tribal insignias assists trademark attorneys in their examination...

  14. Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

    PubMed

    Shao, Wei; Shan, Jigui; Kearney, Mary F; Wu, Xiaolin; Maldarelli, Frank; Mellors, John W; Luke, Brian; Coffin, John M; Hughes, Stephen H

    2016-07-04

    The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. https://rid.ncifcrf.gov ; or http://home.ncifcrf.gov/hivdrp/resources.htm .

  15. ECOTOX database; new additions and future direction

    EPA Science Inventory

    The ECOTOXicology database (ECOTOX) is a comprehensive, publicly available knowledgebase developed and maintained by ORD/NHEERL. It is used for environmental toxicity data on aquatic life, terrestrial plants and wildlife. Publications are identified for potential applicability af...

  16. ECOTOX database; new additions and future direction

    EPA Science Inventory

    The ECOTOXicology database (ECOTOX) is a comprehensive, publicly available knowledgebase developed and maintained by ORD/NHEERL. It is used for environmental toxicity data on aquatic life, terrestrial plants and wildlife. Publications are identified for potential applicability af...

  17. ResPlan Database

    NASA Technical Reports Server (NTRS)

    Zellers, Michael L.

    2003-01-01

    The main project I was involved in was new application development for the existing CIS0 Database (ResPlan). This database application was developed in Microsoft Access. Initial meetings with Greg Follen, Linda McMillen, Griselle LaFontaine and others identified a few key weaknesses with the existing database. The weaknesses centered around that while the database correctly modeled the structure of Programs, Projects and Tasks, once the data was entered, the database did not capture any dynamic status information, and as such was of limited usefulness. After the initial meetings my goals were identified as follows: Enhance the ResPlan Database to include qualitative and quantitative status information about the Programs, Projects and Tasks Train staff members about the ResPlan database from both the user perspective and the developer perspective Give consideration to a Web Interface for reporting. Initially, the thought was that there would not be adequate time to actually develop the Web Interface, Greg wanted it understood that this was an eventual goal and as such should be a consideration throughout the development process.

  18. The NCBI Taxonomy database

    PubMed Central

    Federhen, Scott

    2012-01-01

    The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC’s nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community. PMID:22139910

  19. BGDB: a database of bivalent genes.

    PubMed

    Li, Qingyan; Lian, Shuabin; Dai, Zhiming; Xiang, Qian; Dai, Xianhua

    2013-01-01

    Bivalent gene is a gene marked with both H3K4me3 and H3K27me3 epigenetic modification in the same area, and is proposed to play a pivotal role related to pluripotency in embryonic stem (ES) cells. Identification of these bivalent genes and understanding their functions are important for further research of lineage specification and embryo development. So far, lots of genome-wide histone modification data were generated in mouse and human ES cells. These valuable data make it possible to identify bivalent genes, but no comprehensive data repositories or analysis tools are available for bivalent genes currently. In this work, we develop BGDB, the database of bivalent genes. The database contains 6897 bivalent genes in human and mouse ES cells, which are manually collected from scientific literature. Each entry contains curated information, including genomic context, sequences, gene ontology and other relevant information. The web services of BGDB database were implemented with PHP + MySQL + JavaScript, and provide diverse query functions. Database URL: http://dailab.sysu.edu.cn/bgdb/

  20. HCSD: the human cancer secretome database.

    PubMed

    Feizi, Amir; Banaei-Esfahani, Amir; Nielsen, Jens

    2015-01-01

    The human cancer secretome database (HCSD) is a comprehensive database for human cancer secretome data. The cancer secretome describes proteins secreted by cancer cells and structuring information about the cancer secretome will enable further analysis of how this is related with tumor biology. The secreted proteins from cancer cells are believed to play a deterministic role in cancer progression and therefore may be the key to find novel therapeutic targets and biomarkers for many cancers. Consequently, huge data on cancer secretome have been generated in recent years and the lack of a coherent database is limiting the ability to query the increasing community knowledge. We therefore developed the Human Cancer Secretome Database (HCSD) to fulfil this gap. HCSD contains >80 000 measurements for about 7000 nonredundant human proteins collected from up to 35 high-throughput studies on 17 cancer types. It has a simple and user friendly query system for basic and advanced search based on gene name, cancer type and data type as the three main query options. The results are visualized in an explicit and interactive manner. An example of a result page includes annotations, cross references, cancer secretome data and secretory features for each identified protein. © The Author(s) 2015. Published by Oxford University Press.

  1. PanSNPdb: the Pan-Asian SNP genotyping database.

    PubMed

    Ngamphiw, Chumpol; Assawamakin, Anunchai; Xu, Shuhua; Shaw, Philip J; Yang, Jin Ok; Ghang, Ho; Bhak, Jong; Liu, Edison; Tongsima, Sissades

    2011-01-01

    The HUGO Pan-Asian SNP consortium conducted the largest survey to date of human genetic diversity among Asians by sampling 1,719 unrelated individuals among 71 populations from China, India, Indonesia, Japan, Malaysia, the Philippines, Singapore, South Korea, Taiwan, and Thailand. We have constructed a database (PanSNPdb), which contains these data and various new analyses of them. PanSNPdb is a research resource in the analysis of the population structure of Asian peoples, including linkage disequilibrium patterns, haplotype distributions, and copy number variations. Furthermore, PanSNPdb provides an interactive comparison with other SNP and CNV databases, including HapMap3, JSNP, dbSNP and DGV and thus provides a comprehensive resource of human genetic diversity. The information is accessible via a widely accepted graphical interface used in many genetic variation databases. Unrestricted access to PanSNPdb and any associated files is available at: http://www4a.biotec.or.th/PASNP.

  2. Comprehensive Care

    MedlinePlus

    Emergency & Disaster Resources If you or a loved one have been affected—or may be affected—by a hurricane, ... our comprehensive information and resources on emergency and disaster planning . We can also connect you to emergency ...

  3. The Transporter Classification Database

    PubMed Central

    Saier, Milton H.; Reddy, Vamsee S.; Tamang, Dorjee G.; Västermark, Åke

    2014-01-01

    The Transporter Classification Database (TCDB; http://www.tcdb.org) serves as a common reference point for transport protein research. The database contains more than 10 000 non-redundant proteins that represent all currently recognized families of transmembrane molecular transport systems. Proteins in TCDB are organized in a five level hierarchical system, where the first two levels are the class and subclass, the second two are the family and subfamily, and the last one is the transport system. Superfamilies that contain multiple families are included as hyperlinks to the five tier TC hierarchy. TCDB includes proteins from all types of living organisms and is the only transporter classification system that is both universal and recognized by the International Union of Biochemistry and Molecular Biology. It has been expanded by manual curation, contains extensive text descriptions providing structural, functional, mechanistic and evolutionary information, is supported by unique software and is interconnected to many other relevant databases. TCDB is of increasing usefulness to the international scientific community and can serve as a model for the expansion of database technologies. This manuscript describes an update of the database descriptions previously featured in NAR database issues. PMID:24225317

  4. Chemical Kinetics Database

    National Institute of Standards and Technology Data Gateway

    SRD 17 NIST Chemical Kinetics Database (Web, free access)   The NIST Chemical Kinetics Database includes essentially all reported kinetics results for thermal gas-phase chemical reactions. The database is designed to be searched for kinetics data based on the specific reactants involved, for reactions resulting in specified products, for all the reactions of a particular species, or for various combinations of these. In addition, the bibliography can be searched by author name or combination of names. The database contains in excess of 38,000 separate reaction records for over 11,700 distinct reactant pairs. These data have been abstracted from over 12,000 papers with literature coverage through early 2000.

  5. Drinking Water Treatability Database (Database)

    EPA Science Inventory

    The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

  6. ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

    DOE Data Explorer

    Loots, Gabriela G. [LLNL; Ovcharenko, I. [LLNL

    Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. This database of evolutionary conserved regions (ECRs) in vertebrate genomes features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a comprehensive collection of promoters in all vertebrate genomes generated using multiple sources of gene annotation. The database also contains a collection of annotated transcription factor binding sites (TFBSs) in evolutionary conserved and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and fugu genomes. (taken from paper in Journal: Bioinformatics, November 7, 2006, pp. 122-124

  7. The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.

    PubMed

    Liolios, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Kyrpides, Nikos C

    2006-01-01

    The Genomes On Line Database (GOLD) is a web resource for comprehensive access to information regarding complete and ongoing genome sequencing projects worldwide. The database currently incorporates information on over 1500 sequencing projects, of which 294 have been completed and the data deposited in the public databases. GOLD v.2 has been expanded to provide information related to organism properties such as phenotype, ecotype and disease. Furthermore, project relevance and availability information is now included. GOLD is available at http://www.genomesonline.org. It is also mirrored at the Institute of Molecular Biology and Biotechnology, Crete, Greece at http://gold.imbb.forth.gr/

  8. OxDBase: a database of oxygenases involved in biodegradation

    PubMed Central

    Arora, Pankaj K; Kumar, Manish; Chauhan, Archana; Raghava, Gajendra PS; Jain, Rakesh K

    2009-01-01

    Background Oxygenases belong to the oxidoreductive group of enzymes (E.C. Class 1), which oxidize the substrates by transferring oxygen from molecular oxygen (O2) and utilize FAD/NADH/NADPH as the co-substrate. Oxygenases can further be grouped into two categories i.e. monooxygenases and dioxygenases on the basis of number of oxygen atoms used for oxidation. They play a key role in the metabolism of organic compounds by increasing their reactivity or water solubility or bringing about cleavage of the aromatic ring. Findings We compiled a database of biodegradative oxygenases (OxDBase) which provides a compilation of the oxygenase data as sourced from primary literature in the form of web accessible database. There are two separate search engines for searching into the database i.e. mono and dioxygenases database respectively. Each enzyme entry contains its common name and synonym, reaction in which enzyme is involved, family and subfamily, structure and gene link and literature citation. The entries are also linked to several external database including BRENDA, KEGG, ENZYME and UM-BBD providing wide background information. At present the database contains information of over 235 oxygenases including both dioxygenases and monooxygenases. This database is freely available online at . Conclusion OxDBase is the first database that is dedicated only to oxygenases and provides comprehensive information about them. Due to the importance of the oxygenases in chemical synthesis of drug intermediates and oxidation of xenobiotic compounds, OxDBase database would be very useful tool in the field of synthetic chemistry as well as bioremediation. PMID:19405962

  9. Comprehensive Epidemiologic Data Resource (CEDR) (Poster)

    SciTech Connect

    Oak Ridge Institute for Science and Education

    2012-12-12

    This poster introduces the Comprehensive Epidemiologic Data Resource (CEDR), an electronic database with demographic, health outcome, and exposure information for over a million DOE nuclear plant and laboratory workers.

  10. FishTraits Database

    USGS Publications Warehouse

    Angermeier, Paul L.; Frimpong, Emmanuel A.

    2009-01-01

    The need for integrated and widely accessible sources of species traits data to facilitate studies of ecology, conservation, and management has motivated development of traits databases for various taxa. In spite of the increasing number of traits-based analyses of freshwater fishes in the United States, no consolidated database of traits of this group exists publicly, and much useful information on these species is documented only in obscure sources. The largely inaccessible and unconsolidated traits information makes large-scale analysis involving many fishes and/or traits particularly challenging. FishTraits is a database of >100 traits for 809 (731 native and 78 exotic) fish species found in freshwaters of the conterminous United States, including 37 native families and 145 native genera. The database contains information on four major categories of traits: (1) trophic ecology, (2) body size and reproductive ecology (life history), (3) habitat associations, and (4) salinity and temperature tolerances. Information on geographic distribution and conservation status is also included. Together, we refer to the traits, distribution, and conservation status information as attributes. Descriptions of attributes are available here. Many sources were consulted to compile attributes, including state and regional species accounts and other databases.

  11. Drinking Water Database

    NASA Technical Reports Server (NTRS)

    Murray, ShaTerea R.

    2004-01-01

    This summer I had the opportunity to work in the Environmental Management Office (EMO) under the Chemical Sampling and Analysis Team or CS&AT. This team s mission is to support Glenn Research Center (GRC) and EM0 by providing chemical sampling and analysis services and expert consulting. Services include sampling and chemical analysis of water, soil, fbels, oils, paint, insulation materials, etc. One of this team s major projects is the Drinking Water Project. This is a project that is done on Glenn s water coolers and ten percent of its sink every two years. For the past two summers an intern had been putting together a database for this team to record the test they had perform. She had successfully created a database but hadn't worked out all the quirks. So this summer William Wilder (an intern from Cleveland State University) and I worked together to perfect her database. We began be finding out exactly what every member of the team thought about the database and what they would change if any. After collecting this data we both had to take some courses in Microsoft Access in order to fix the problems. Next we began looking at what exactly how the database worked from the outside inward. Then we began trying to change the database but we quickly found out that this would be virtually impossible.

  12. The Validity of Reading Comprehension Rate: Reading Speed, Comprehension, and Comprehension Rates

    ERIC Educational Resources Information Center

    Skinner, Christopher H.; Williams, Jacqueline L.; Morrow, Jennifer Ann; Hale, Andre D.; Neddenriep, Christine E.; Hawkins, Renee O.

    2009-01-01

    This article describes a secondary analysis of a brief reading comprehension rate measure, percent comprehension questions correct per minute spent reading (%C/M). This measure includes reading speed (seconds to read) in the denominator and percentage of comprehension questions answered correctly in the numerator. Participants were 22 4th-, 29…

  13. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

    PubMed

    Pruitt, Kim D; Tatusova, Tatiana; Maglott, Donna R

    2005-01-01

    The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database (http://www.ncbi.nlm.nih.gov/RefSeq/) provides a non-redundant collection of sequences representing genomic data, transcripts and proteins. Although the goal is to provide a comprehensive dataset representing the complete sequence information for any given species, the database pragmatically includes sequence data that are currently publicly available in the archival databases. The database incorporates data from over 2400 organisms and includes over one million proteins representing significant taxonomic diversity spanning prokaryotes, eukaryotes and viruses. Nucleotide and protein sequences are explicitly linked, and the sequences are linked to other resources including the NCBI Map Viewer and Gene. Sequences are annotated to include coding regions, conserved domains, variation, references, names, database cross-references, and other features using a combined approach of collaboration and other input from the scientific community, automated annotation, propagation from GenBank and curation by NCBI staff.

  14. A survey of population-based drug databases in Canada.

    PubMed Central

    Miller, E; Blatman, B; Einarson, T R

    1996-01-01

    OBJECTIVE: To identify the population-based drug databases in Canada and to determine their comprehensiveness and accessibility for performing pharmacoepidemiologic and outcomes research. DESIGN: Survey (four-part mailed questionnaire). SETTING: Public and private third-party drug plans across Canada. PARTICIPANTS: All provincial and territorial drug plan or pharmacare managers as well as selected private plan managers including health benefit consultants, group insurers and claims adjudicators/pharmacy benefit managers (CA/PBMs). OUTCOME MEASURES: Patient, drug and pharmacy information; potential for electronic linkages to other provincial databases (e.g., physician, hospital, vital statistics); accessibility of information; population profile. RESULTS: Of the 32 recipients of the questionnaire 29 (91%) responded and 18 (56%) completed the survey. Most databases were reported to contain patient information (e.g., patient identification number, age, sex and medication history) and prescription drug information (e.g., drug identification number, strength, quantity and cost). Six provinces and one territory reported the capability to link to other databases (e.g., hospital and physician databases). One CA/PBM reported some links to selected long-term disability data. All of the government databases except those in British Columbia and the Yukon Territory allowed use of the data for research purposes. Manitoba and Saskatchewan included all residents of the province in their database; the others included selected groups (e.g., residents 65 years of age or older, people on social assistance or people covered by private group insurance). CONCLUSION: A number of public and private population-based databases are available for use in pharmacoepidemiologic and outcomes research. PMID:8653645

  15. Enabling heterogenous multi-scale database for emergency service functions through geoinformation technologies

    NASA Astrophysics Data System (ADS)

    Bhanumurthy, V.; Venugopala Rao, K.; Srinivasa Rao, S.; Ram Mohan Rao, K.; Chandra, P. Satya; Vidhyasagar, J.; Diwakar, P. G.; Dadhwal, V. K.

    2014-11-01

    Geographical Information Science (GIS) is now graduated from traditional desktop system to Internet system. Internet GIS is emerging as one of the most promising technologies for addressing Emergency Management. Web services with different privileges are playing an important role in dissemination of the emergency services to the decision makers. Spatial database is one of the most important components in the successful implementation of Emergency Management. It contains spatial data in the form of raster, vector, linked with non-spatial information. Comprehensive data is required to handle emergency situation in different phases. These database elements comprise core data, hazard specific data, corresponding attribute data, and live data coming from the remote locations. Core data sets are minimum required data including base, thematic, infrastructure layers to handle disasters. Disaster specific information is required to handle a particular disaster situation like flood, cyclone, forest fire, earth quake, land slide, drought. In addition to this Emergency Management require many types of data with spatial and temporal attributes that should be made available to the key players in the right format at right time. The vector database needs to be complemented with required resolution satellite imagery for visualisation and analysis in disaster management. Therefore, the database is interconnected and comprehensive to meet the requirement of an Emergency Management. This kind of integrated, comprehensive and structured database with appropriate information is required to obtain right information at right time for the right people. However, building spatial database for Emergency Management is a challenging task because of the key issues such as availability of data, sharing policies, compatible geospatial standards, data interoperability etc. Therefore, to facilitate using, sharing, and integrating the spatial data, there is a need to define standards to build

  16. Hanford Site technical baseline database

    SciTech Connect

    Porter, P.E., Westinghouse Hanford

    1996-05-10

    This document includes a cassette tape that contains the Hanford specific files that make up the Hanford Site Technical Baseline Database as of May 10, 1996. The cassette tape also includes the delta files that delineate the differences between this revision and revision 3 (April 10, 1996) of the Hanford Site Technical Baseline Database.

  17. Atomic Databases

    NASA Astrophysics Data System (ADS)

    Mendoza, Claudio

    2000-10-01

    Atomic and molecular data are required in a variety of fields ranging from the traditional astronomy, atmospherics and fusion research to fast growing technologies such as lasers, lighting, low-temperature plasmas, plasma assisted etching and radiotherapy. In this context, there are some research groups, both theoretical and experimental, scattered round the world that attend to most of this data demand, but the implementation of atomic databases has grown independently out of sheer necessity. In some cases the latter has been associated with the data production process or with data centers involved in data collection and evaluation; but sometimes it has been the result of individual initiatives that have been quite successful. In any case, the development and maintenance of atomic databases call for a number of skills and an entrepreneurial spirit that are not usually associated with most physics researchers. In the present report we present some of the highlights in this area in the past five years and discuss what we think are some of the main issues that have to be addressed.

  18. A snapshot in time - the new TRUplanner database - 10400

    SciTech Connect

    Estill, Wes; Crawford, Beverly A; Van Soest, Gregory D

    2009-01-01

    A new database was developed to augment transuranic (TRU) waste inventory information already captured within the Comprehensive Inventory Database (CID). This new database, known as the TRUplanner, includes information focused on site capability for TRU waste certification and availability to ship to either the Waste Isolation Pilot Plant (WIPP) or Idaho National Laboratory for final characterization and certification before coming to WIPP. Waste stream specific data is imported from the CID to the TRUplanner, and additional data is collected and entered as a result of interviews and site visits. This data is continuously updated as sites are visited. TRU waste information such as facility, equipment, and container information for waste streams, has been captured within the TRUplanner, and supports the Department of Energy, Carlsbad Field Office (CBFO) decision making and strategic planning activities. This infonnation is delivered via three built-in TRUplanner reports that are provided to CBFO management, Acceptable Knowledge (AK) Experts and the TRU Waste Inventory Team.

  19. Comprehension Clinchers

    ERIC Educational Resources Information Center

    Marcell, Barclay

    2006-01-01

    This author, an academic achievement teacher for second and third grade reading and math at Theodore Roosevelt Elementary School in Park Ridge, Illinois, contends that since fluency is such a measurable skill, over-emphasizing decoding and de-emphasizing comprehension results in short-changing students. In this article, she shares several reading…

  20. Navigating through the Jungle of Allergens: Features and Applications of Allergen Databases.

    PubMed

    Radauer, Christian

    2017-01-01

    The increasing number of available data on allergenic proteins demanded the establishment of structured, freely accessible allergen databases. In this review article, features and applications of 6 of the most widely used allergen databases are discussed. The WHO/IUIS Allergen Nomenclature Database is the official resource of allergen designations. Allergome is the most comprehensive collection of data on allergens and allergen sources. AllergenOnline is aimed at providing a peer-reviewed database of allergen sequences for prediction of allergenicity of proteins, such as those planned to be inserted into genetically modified crops. The Structural Database of Allergenic Proteins (SDAP) provides a database of allergen sequences, structures, and epitopes linked to bioinformatics tools for sequence analysis and comparison. The Immune Epitope Database (IEDB) is the largest repository of T-cell, B-cell, and major histocompatibility complex protein epitopes including epitopes of allergens. AllFam classifies allergens into families of evolutionarily related proteins using definitions from the Pfam protein family database. These databases contain mostly overlapping data, but also show differences in terms of their targeted users, the criteria for including allergens, data shown for each allergen, and the availability of bioinformatics tools. © 2017 S. Karger AG, Basel.

  1. The Histone Database: an integrated resource for histones and histone fold-containing proteins

    PubMed Central

    Mariño-Ramírez, Leonardo; Levine, Kevin M.; Morales, Mario; Zhang, Suiyuan; Moreland, R. Travis; Baxevanis, Andreas D.; Landsman, David

    2011-01-01

    Eukaryotic chromatin is composed of DNA and protein components—core histones—that act to compactly pack the DNA into nucleosomes, the fundamental building blocks of chromatin. These nucleosomes are connected to adjacent nucleosomes by linker histones. Nucleosomes are highly dynamic and, through various core histone post-translational modifications and incorporation of diverse histone variants, can serve as epigenetic marks to control processes such as gene expression and recombination. The Histone Sequence Database is a curated collection of sequences and structures of histones and non-histone proteins containing histone folds, assembled from major public databases. Here, we report a substantial increase in the number of sequences and taxonomic coverage for histone and histone fold-containing proteins available in the database. Additionally, the database now contains an expanded dataset that includes archaeal histone sequences. The database also provides comprehensive multiple sequence alignments for each of the four core histones (H2A, H2B, H3 and H4), the linker histones (H1/H5) and the archaeal histones. The database also includes current information on solved histone fold-containing structures. The Histone Sequence Database is an inclusive resource for the analysis of chromatin structure and function focused on histones and histone fold-containing proteins. Database URL: The Histone Sequence Database is freely available and can be accessed at http://research.nhgri.nih.gov/histones/. PMID:22025671

  2. Benefits of an International Database for UF6 Cylinders

    SciTech Connect

    Babcock, R A; Whitaker, J M; Murphy, J; Oakberg, J

    2008-06-30

    A reasonable expectation regarding the nuclear energy renaissance is that the location of fuel cycle nuclear materials throughout the world will be known. We ask--would an international system for uranium hexafluoride (UF{sub 6}) cylinders provide the effective assurances expected for international fuel supply and of the international fuel centers? This paper introduces the question and discusses the potential benefits of tracking UF{sub 6} cylinders through the development of an international database. The nonproliferation benefits of an international database for UF{sub 6} cylinders being used in the fuel cycle include an enhanced capability to reconcile nuclear material imports and exports. Currently, import and export declarations only require the reporting of total 'rolled up' quantities of nuclear materials contained in all items--not the quantities of materials in individual items like individual UF{sub 6} cylinders. The database could provide supplier countries with more assurance on the location of the UF{sub 6} cylinders they export. Additionally, a comprehensive database on all declared cylinders would be a valuable resource in detecting and recognizing undeclared cylinders. The database could potentially be administered by the IAEA and be accessible to authorized countries around the world. During the nuclear renaissance, the general public, as well as the participants will expect transparency and quality information about movement of nuclear fuel cycle nuclear materials. We will discuss the potential benefits of such a database for the suppliers, inspectorates, and general public.

  3. Patent Family Databases.

    ERIC Educational Resources Information Center

    Simmons, Edlyn S.

    1985-01-01

    Reports on retrieval of patent information online and includes definition of patent family, basic and equivalent patents, "parents and children" applications, designated states, patent family databases--International Patent Documentation Center, World Patents Index, APIPAT (American Petroleum Institute), CLAIMS (IFI/Plenum). A table…

  4. Stackfile Database

    NASA Technical Reports Server (NTRS)

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

    2013-01-01

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

  5. Database Technology in Digital Libraries.

    ERIC Educational Resources Information Center

    Preston, Carole; Lin, Binshan

    2002-01-01

    Reviews issues relating to database technology and digital libraries. Highlights include resource sharing; ongoing digital library projects; metadata; user interfaces; query processing; interoperability; data quality; copyright infringement; and managerial implications, including electronic versus printed materials, accessibility,…

  6. Comprehensive rotorcraft analysis methods

    NASA Technical Reports Server (NTRS)

    Stephens, Wendell B.; Austin, Edward E.

    1988-01-01

    The development and application of comprehensive rotorcraft analysis methods in the field of rotorcraft technology are described. These large scale analyses and the resulting computer programs are intended to treat the complex aeromechanical phenomena that describe the behavior of rotorcraft. They may be used to predict rotor aerodynamics, acoustic, performance, stability and control, handling qualities, loads and vibrations, structures, dynamics, and aeroelastic stability characteristics for a variety of applications including research, preliminary and detail design, and evaluation and treatment of field problems. The principal comprehensive methods developed or under development in recent years and generally available to the rotorcraft community because of US Army Aviation Research and Technology Activity (ARTA) sponsorship of all or part of the software systems are the Rotorcraft Flight Simulation (C81), Dynamic System Coupler (DYSCO), Coupled Rotor/Airframe Vibration Analysis Program (SIMVIB), Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics (CAMRAD), General Rotorcraft Aeromechanical Stability Program (GRASP), and Second Generation Comprehensive Helicopter Analysis System (2GCHAS).

  7. The RIKEN integrated database of mammals

    PubMed Central

    Masuya, Hiroshi; Makita, Yuko; Kobayashi, Norio; Nishikata, Koro; Yoshida, Yuko; Mochizuki, Yoshiki; Doi, Koji; Takatsuki, Terue; Waki, Kazunori; Tanaka, Nobuhiko; Ishii, Manabu; Matsushima, Akihiro; Takahashi, Satoshi; Hijikata, Atsushi; Kozaki, Kouji; Furuichi, Teiichi; Kawaji, Hideya; Wakana, Shigeharu; Nakamura, Yukio; Yoshiki, Atsushi; Murata, Takehide; Fukami-Kobayashi, Kaoru; Mohan, Sujatha; Ohara, Osamu; Hayashizaki, Yoshihide; Mizoguchi, Riichiro; Obata, Yuichi; Toyoda, Tetsuro

    2011-01-01

    The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN’s original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists’ Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information. PMID:21076152

  8. The RIKEN integrated database of mammals.

    PubMed

    Masuya, Hiroshi; Makita, Yuko; Kobayashi, Norio; Nishikata, Koro; Yoshida, Yuko; Mochizuki, Yoshiki; Doi, Koji; Takatsuki, Terue; Waki, Kazunori; Tanaka, Nobuhiko; Ishii, Manabu; Matsushima, Akihiro; Takahashi, Satoshi; Hijikata, Atsushi; Kozaki, Kouji; Furuichi, Teiichi; Kawaji, Hideya; Wakana, Shigeharu; Nakamura, Yukio; Yoshiki, Atsushi; Murata, Takehide; Fukami-Kobayashi, Kaoru; Mohan, Sujatha; Ohara, Osamu; Hayashizaki, Yoshihide; Mizoguchi, Riichiro; Obata, Yuichi; Toyoda, Tetsuro

    2011-01-01

    The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.

  9. Usefulness of In Vivo and In Vitro Diagnostic Tests in the Diagnosis of Hypersensitivity Reactions to Quinolones and in the Evaluation of Cross-Reactivity: A Comprehensive Study Including the Latest Quinolone Gemifloxacin

    PubMed Central

    Gelincik, Asli; Akdeniz, Nilgun; Aktas-Cetin, Esin; Olgac, Muge; Unal, Derya; Ertek, Belkis; Coskun, Raif; Colakoğlu, Bahattin; Deniz, Gunnur; Buyukozturk, Suna

    2017-01-01

    Purpose Reports evaluating diagnosis and cross reactivity of quinolone hypersensitivity have revealed contradictory results. Furthermore, there are no reports investigating the cross-reactivity between gemifloxacin (GFX) and the others. We aimed to detect the usefulness of diagnostic tests of hypersensitivity reactions to quinolones and to evaluate the cross reactivity between different quinolones including the latest quinolone GFX. Methods We studied 54 patients (mean age 42.31±10.39 years; 47 female) with 57 hypersensitivity reactions due to different quinolones and 10 nonatopic quinolone tolerable control subjects. A detailed clinical history, skin test (ST), and single-blind placebo-controlled drug provocation test (SBPCDPT), as well as basophil activation test (BAT) and lymphocyte transformation test (LTT) were performed with the culprit and alternative quinolones including ciprofloxacin (CFX), moxifloxacin (MFX), levofloxacin (LFX), ofloxacin (OFX), and GFX. Results The majority (75.9%) of the patients reported immediate type reactions to various quinolones. The most common culprit drug was CFX (52.6%) and the most common reaction type was urticaria (26.3%). A quarter of the patients (24.1%) reacted to SBPCDPTs, although their STs were negative; while false ST positivity was 3.5% and ST/SBPCDPTs concordance was only 1.8%. Both BAT and LTT were not found useful in quinolone hypersensitivity. Cross-reactivity was primarily observed between LFX and OFX (50.0%), whereas it was the least between MFX and the others, and in GFX hypersensitive patients the degree of cross-reactivity to the other quinolones was 16.7%. Conclusions These results suggest that STs, BAT, and LTT are not supportive in the diagnosis of a hypersensitivity reaction to quinolone as well as in the prediction of cross-reactivity. Drug provocation tests (DPTs) are necessary to identify both culprit and alternative quinolones. PMID:28497922

  10. Usefulness of In Vivo and In Vitro Diagnostic Tests in the Diagnosis of Hypersensitivity Reactions to Quinolones and in the Evaluation of Cross-Reactivity: A Comprehensive Study Including the Latest Quinolone Gemifloxacin.

    PubMed

    Demir, Semra; Gelincik, Asli; Akdeniz, Nilgun; Aktas-Cetin, Esin; Olgac, Muge; Unal, Derya; Ertek, Belkis; Coskun, Raif; Colakoğlu, Bahattin; Deniz, Gunnur; Buyukozturk, Suna

    2017-07-01

    Reports evaluating diagnosis and cross reactivity of quinolone hypersensitivity have revealed contradictory results. Furthermore, there are no reports investigating the cross-reactivity between gemifloxacin (GFX) and the others. We aimed to detect the usefulness of diagnostic tests of hypersensitivity reactions to quinolones and to evaluate the cross reactivity between different quinolones including the latest quinolone GFX. We studied 54 patients (mean age 42.31±10.39 years; 47 female) with 57 hypersensitivity reactions due to different quinolones and 10 nonatopic quinolone tolerable control subjects. A detailed clinical history, skin test (ST), and single-blind placebo-controlled drug provocation test (SBPCDPT), as well as basophil activation test (BAT) and lymphocyte transformation test (LTT) were performed with the culprit and alternative quinolones including ciprofloxacin (CFX), moxifloxacin (MFX), levofloxacin (LFX), ofloxacin (OFX), and GFX. The majority (75.9%) of the patients reported immediate type reactions to various quinolones. The most common culprit drug was CFX (52.6%) and the most common reaction type was urticaria (26.3%). A quarter of the patients (24.1%) reacted to SBPCDPTs, although their STs were negative; while false ST positivity was 3.5% and ST/SBPCDPTs concordance was only 1.8%. Both BAT and LTT were not found useful in quinolone hypersensitivity. Cross-reactivity was primarily observed between LFX and OFX (50.0%), whereas it was the least between MFX and the others, and in GFX hypersensitive patients the degree of cross-reactivity to the other quinolones was 16.7%. These results suggest that STs, BAT, and LTT are not supportive in the diagnosis of a hypersensitivity reaction to quinolone as well as in the prediction of cross-reactivity. Drug provocation tests (DPTs) are necessary to identify both culprit and alternative quinolones.

  11. A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

    PubMed

    Senis, Yotis A; Tomlinson, Michael G; García, Angel; Dumon, Stephanie; Heath, Victoria L; Herbert, John; Cobbold, Stephen P; Spalton, Jennifer C; Ayman, Sinem; Antrobus, Robin; Zitzmann, Nicole; Bicknell, Roy; Frampton, Jon; Authi, Kalwant S; Martin, Ashley; Wakelam, Michael J O; Watson, Stephen P

    2007-03-01

    The platelet surface is poorly characterized due to the low abundance of many membrane proteins and the lack of specialist tools for their investigation. In this study we identified novel human platelet and mouse megakaryocyte membrane proteins using specialist proteomics and genomics approaches. Three separate methods were used to enrich platelet surface proteins prior to identification by liquid chromatography and tandem mass spectrometry: lectin affinity chromatography, biotin/NeutrAvidin affinity chromatography, and free flow electrophoresis. Many known, abundant platelet surface transmembrane proteins and several novel proteins were identified using each receptor enrichment strategy. In total, two or more unique peptides were identified for 46, 68, and 22 surface membrane, intracellular membrane, and membrane proteins of unknown subcellular localization, respectively. The majority of these were single transmembrane proteins. To complement the proteomics studies, we analyzed the transcriptome of a highly purified preparation of mature primary mouse megakaryocytes using serial analysis of gene expression in view of the increasing importance of mutant mouse models in establishing protein function in platelets. This approach identified all of the major classes of platelet transmembrane receptors, including multitransmembrane proteins. Strikingly 17 of the 25 most megakaryocyte-specific genes (relative to 30 other serial analysis of gene expression libraries) were transmembrane proteins, illustrating the unique nature of the megakaryocyte/platelet surface. The list of novel plasma membrane proteins identified using proteomics includes the immunoglobulin superfamily member G6b, which undergoes extensive alternate splicing. Specific antibodies were used to demonstrate expression of the G6b-B isoform, which contains an immunoreceptor tyrosine-based inhibition motif. G6b-B undergoes tyrosine phosphorylation and association with the SH2 domain-containing phosphatase

  12. The Ribosomal Database Project.

    PubMed

    Maidak, B L; Larsen, N; McCaughey, M J; Overbeek, R; Olsen, G J; Fogel, K; Blandy, J; Woese, C R

    1994-09-01

    The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services, and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server/rdp.life.uiuc.edu) and gopher (rdpgopher.life.uiuc.edu). The electronic mail server also provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for chimeric nature of newly sequenced rRNAs, and automated alignment.

  13. Introduction to the MAUDE database.

    PubMed

    Gurtcheff, Shawn E

    2008-03-01

    The Manufacturer and User Facility Device Experience (MAUDE) database represents a reporting system mandated by the Food and Drug Administration for postmarket surveillance. MAUDE has been made into a searchable online database that includes all reported events in which medical devices may have malfunctioned or caused a death or serious injury. For the clinician considering the use of a new medical device, searching the MAUDE database is useful to search for complications not yet reported in the medical literature.

  14. ARTI Refrigerant Database

    SciTech Connect

    Calm, J.M.

    1992-04-30

    The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on R-32, R-123, R-124, R- 125, R-134a, R-141b, R142b, R-143a, R-152a, R-290 (propane), R-717 (ammonia), ethers, and others as well as azeotropic and zeotropic blends of these fluids. It addresses polyalkylene glycol (PAG), ester, and other lubricants. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits.

  15. National Ambient Radiation Database

    SciTech Connect

    Dziuban, J.; Sears, R.

    2003-02-25

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

  16. Mouse genome database 2016

    PubMed Central

    Bult, Carol J.; Eppig, Janan T.; Blake, Judith A.; Kadin, James A.; Richardson, Joel E.

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data. PMID:26578600

  17. 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.

  18. Shuttle Hypervelocity Impact Database

    NASA Technical Reports Server (NTRS)

    Hyde, James L.; Christiansen, Eric L.; Lear, Dana M.

    2011-01-01

    With three missions outstanding, the Shuttle Hypervelocity Impact Database has nearly 3000 entries. The data is divided into tables for crew module windows, payload bay door radiators and thermal protection system regions, with window impacts compromising just over half the records. In general, the database provides dimensions of hypervelocity impact damage, a component level location (i.e., window number or radiator panel number) and the orbiter mission when the impact occurred. Additional detail on the type of particle that produced the damage site is provided when sampling data and definitive analysis results are available. Details and insights on the contents of the database including examples of descriptive statistics will be provided. Post flight impact damage inspection and sampling techniques that were employed during the different observation campaigns will also be discussed. Potential enhancements to the database structure and availability of the data for other researchers will be addressed in the Future Work section. A related database of returned surfaces from the International Space Station will also be introduced.

  19. Shuttle Hypervelocity Impact Database

    NASA Technical Reports Server (NTRS)

    Hyde, James I.; Christiansen, Eric I.; Lear, Dana M.

    2011-01-01

    With three flights remaining on the manifest, the shuttle impact hypervelocity database has over 2800 entries. The data is currently divided into tables for crew module windows, payload bay door radiators and thermal protection system regions, with window impacts compromising just over half the records. In general, the database provides dimensions of hypervelocity impact damage, a component level location (i.e., window number or radiator panel number) and the orbiter mission when the impact occurred. Additional detail on the type of particle that produced the damage site is provided when sampling data and definitive analysis results are available. The paper will provide details and insights on the contents of the database including examples of descriptive statistics using the impact data. A discussion of post flight impact damage inspection and sampling techniques that were employed during the different observation campaigns will be presented. Future work to be discussed will be possible enhancements to the database structure and availability of the data for other researchers. A related database of ISS returned surfaces that are under development will also be introduced.

  20. Shuttle Hypervelocity Impact Database

    NASA Technical Reports Server (NTRS)

    Hyde, James L.; Christiansen, Eric L.; Lear, Dana M.

    2011-01-01

    With three missions outstanding, the Shuttle Hypervelocity Impact Database has nearly 3000 entries. The data is divided into tables for crew module windows, payload bay door radiators and thermal protection system regions, with window impacts compromising just over half the records. In general, the database provides dimensions of hypervelocity impact damage, a component level location (i.e., window number or radiator panel number) and the orbiter mission when the impact occurred. Additional detail on the type of particle that produced the damage site is provided when sampling data and definitive analysis results are available. Details and insights on the contents of the database including examples of descriptive statistics will be provided. Post flight impact damage inspection and sampling techniques that were employed during the different observation campaigns will also be discussed. Potential enhancements to the database structure and availability of the data for other researchers will be addressed in the Future Work section. A related database of returned surfaces from the International Space Station will also be introduced.

  1. ADANS database specification

    SciTech Connect

    1997-01-16

    The purpose of the Air Mobility Command (AMC) Deployment Analysis System (ADANS) Database Specification (DS) is to describe the database organization and storage allocation and to provide the detailed data model of the physical design and information necessary for the construction of the parts of the database (e.g., tables, indexes, rules, defaults). The DS includes entity relationship diagrams, table and field definitions, reports on other database objects, and a description of the ADANS data dictionary. ADANS is the automated system used by Headquarters AMC and the Tanker Airlift Control Center (TACC) for airlift planning and scheduling of peacetime and contingency operations as well as for deliberate planning. ADANS also supports planning and scheduling of Air Refueling Events by the TACC and the unit-level tanker schedulers. ADANS receives input in the form of movement requirements and air refueling requests. It provides a suite of tools for planners to manipulate these requirements/requests against mobility assets and to develop, analyze, and distribute schedules. Analysis tools are provided for assessing the products of the scheduling subsystems, and editing capabilities support the refinement of schedules. A reporting capability provides formatted screen, print, and/or file outputs of various standard reports. An interface subsystem handles message traffic to and from external systems. The database is an integral part of the functionality summarized above.

  2. The Chandra Bibliography Database

    NASA Astrophysics Data System (ADS)

    Rots, A. H.; Winkelman, S. L.; Paltani, S.; Blecksmith, S. E.; Bright, J. D.

    2004-07-01

    Early in the mission, the Chandra Data Archive started the development of a bibliography database, tracking publications in refereed journals and on-line conference proceedings that are based on Chandra observations, allowing our users to link directly to articles in the ADS from our archive, and to link to the relevant data in the archive from the ADS entries. Subsequently, we have been working closely with the ADS and other data centers, in the context of the ADEC-ITWG, on standardizing the literature-data linking. We have also extended our bibliography database to include all Chandra-related articles and we are also keeping track of the number of citations of each paper. Obviously, in addition to providing valuable services to our users, this database allows us to extract a wide variety of statistical information. The project comprises five components: the bibliography database-proper, a maintenance database, an interactive maintenance tool, a user browsing interface, and a web services component for exchanging information with the ADS. All of these elements are nearly mission-independent and we intend make the package as a whole available for use by other data centers. The capabilities thus provided represent support for an essential component of the Virtual Observatory.

  3. [DICOM data conversion technology research for database].

    PubMed

    Wang, Shiyu; Lin, Hao

    2010-12-01

    A comprehensive medical image platform built for medical images network access, measurements and virtual surgery navigation needs the support of medical image databases. The medical image database we built contains two-dimensional images and three-dimensional models. The common databases based on DICOM storing do not meet the requirements. We use the technology of DICOM conversion to convert DICOM into BMP images and indispensable data elements, and then we use the BMP images and indispensable data elements to reconstruct the three-dimensional model. The reliability of DICOM data conversion is verified, and on this basis, a human hip joint medical image database is built. Experimental results show that this method used in building the medical image database can not only meet the requirements of database application, but also greatly reduce the amount of database storage.

  4. Manual Cardiopulmonary Resuscitation Versus CPR Including a Mechanical Chest Compression Device in Out-of-Hospital Cardiac Arrest: A Comprehensive Meta-analysis From Randomized and Observational Studies.

    PubMed

    Bonnes, Judith L; Brouwer, Marc A; Navarese, Eliano P; Verhaert, Dominique V M; Verheugt, Freek W A; Smeets, Joep L R M; de Boer, Menko-Jan

    2016-03-01

    Mechanical chest compression devices have been developed to facilitate continuous delivery of high-quality cardiopulmonary resuscitation (CPR). Despite promising hemodynamic data, evidence on clinical outcomes remains inconclusive. With the completion of 3 randomized controlled trials, we conduct a meta-analysis on the effect of in-field mechanical versus manual CPR on clinical outcomes after out-of-hospital cardiac arrest. With a systematic search (PubMed, Web of Science, EMBASE, and the Cochrane Libraries), we identified all eligible studies (randomized controlled trials and nonrandomized studies) that compared a CPR strategy including an automated mechanical chest compression device with a strategy of manual CPR only. Outcome variables were survival to hospital admission, survival to discharge, and favorable neurologic outcome. Twenty studies (n=21,363) were analyzed: 5 randomized controlled trials and 15 nonrandomized studies, pooled separately. For survival to admission, the pooled estimate of the randomized controlled trials did not indicate a difference (odds ratio 0.94; 95% confidence interval 0.84 to 1.05; P=.24) between mechanical and manual CPR. In contrast, meta-analysis of nonrandomized studies demonstrated a benefit in favor of mechanical CPR (odds ratio 1.42; 95% confidence interval 1.21 to 1.67; P<.001). No interaction was found between the endorsed CPR guidelines (2000 versus 2005) and the CPR strategy (P=.27). Survival to discharge and neurologic outcome did not differ between strategies. Although there are lower-quality, observational data that suggest that mechanical CPR used at the rescuer's discretion could improve survival to hospital admission, the cumulative high-quality randomized evidence does not support a routine strategy of mechanical CPR to improve survival or neurologic outcome. These findings are irrespective of the endorsed CPR guidelines during the study periods. Copyright © 2015 American College of Emergency Physicians

  5. The Neotoma Paleoecology Database

    NASA Astrophysics Data System (ADS)

    Grimm, E. C.; Ashworth, A. C.; Barnosky, A. D.; Betancourt, J. L.; Bills, B.; Booth, R.; Blois, J.; Charles, D. F.; Graham, R. W.; Goring, S. J.; Hausmann, S.; Smith, A. J.; Williams, J. W.; Buckland, P.

    2015-12-01

    The Neotoma Paleoecology Database (www.neotomadb.org) is a multiproxy, open-access, relational database that includes fossil data for the past 5 million years (the late Neogene and Quaternary Periods). Modern distributional data for various organisms are also being made available for calibration and paleoecological analyses. The project is a collaborative effort among individuals from more than 20 institutions worldwide, including domain scientists representing a spectrum of Pliocene-Quaternary fossil data types, as well as experts in information technology. Working groups are active for diatoms, insects, ostracodes, pollen and plant macroscopic remains, testate amoebae, rodent middens, vertebrates, age models, geochemistry and taphonomy. Groups are also active in developing online tools for data analyses and for developing modules for teaching at different levels. A key design concept of NeotomaDB is that stewards for various data types are able to remotely upload and manage data. Cooperatives for different kinds of paleo data, or from different regions, can appoint their own stewards. Over the past year, much progress has been made on development of the steward software-interface that will enable this capability. The steward interface uses web services that provide access to the database. More generally, these web services enable remote programmatic access to the database, which both desktop and web applications can use and which provide real-time access to the most current data. Use of these services can alleviate the need to download the entire database, which can be out-of-date as soon as new data are entered. In general, the Neotoma web services deliver data either from an entire table or from the results of a view. Upon request, new web services can be quickly generated. Future developments will likely expand the spatial and temporal dimensions of the database. NeotomaDB is open to receiving new datasets and stewards from the global Quaternary community

  6. DBGC: A Database of Human Gastric Cancer

    PubMed Central

    Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

    2015-01-01

    The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do PMID:26566288

  7. DFVF: database of fungal virulence factors

    PubMed Central

    Lu, Tao; Yao, Bo; Zhang, Chi

    2012-01-01

    Fungal pathogens cause various diseases for plant and animal hosts. Despite the extensive impact of fungi on human health and life, the threats posed by emerging fungal pathogens are poorly understood. Specifically, there exist few fungal virulence gene databases, which prevent effective bioinformatics studies on fungal pathogens. Therefore, we constructed a comprehensive online database of known fungal virulence factors, which collected 2058 pathogenic genes produced by 228 fungal strains from 85 genera. This database creates a pivotal platform capable of stimulating and facilitating further bench studies on fungal pathogens. Database URL: http://sysbio.unl.edu/DFVF/ PMID:23092926

  8. DBGC: A Database of Human Gastric Cancer.

    PubMed

    Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

    2015-01-01

    The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do.

  9. Environmental Sustainability - Including Land and Water Use

    EPA Science Inventory

    Assessments of environmental sustainability can be conducted in many ways with one of the most quantitative methods including Life Cycle Impact Assessment (LCIA). While historically LCIA has included a comprehensive list of impact categories including: ozone depletion, global c...

  10. Environmental Sustainability - Including Land and Water Use

    EPA Science Inventory

    Assessments of environmental sustainability can be conducted in many ways with one of the most quantitative methods including Life Cycle Impact Assessment (LCIA). While historically LCIA has included a comprehensive list of impact categories including: ozone depletion, global c...

  11. Wind turbine reliability database update.

    SciTech Connect

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

    2009-03-01

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

  12. Appendix A. Borderlands Site Database

    Treesearch

    A.C. MacWilliams

    2006-01-01

    The database includes modified components of the Arizona State Museum Site Recording System (Arizona State Museum 1993) and the New Mexico NMCRIS User?s Guide (State of New Mexico 1993). When sites contain more than one recorded component, these instances were entered separately with the result that many sites have multiple entries. Information for this database...

  13. Analysis of Landslide Hazard Impact Using the Landslide Database for Germany

    NASA Astrophysics Data System (ADS)

    Klose, M.; Damm, B.

    2014-12-01

    The Federal Republic of Germany has long been among the few European countries that lack a national landslide database. Systematic collection and inventory of landslide data still shows a comprehensive research history in Germany, but only one focused on development of databases with local or regional coverage. This has changed in recent years with the launch of a database initiative aimed at closing the data gap existing at national level. The present contribution reports on this project that is based on a landslide database which evolved over the last 15 years to a database covering large parts of Germany. A strategy of systematic retrieval, extraction, and fusion of landslide data is at the heart of the methodology, providing the basis for a database with a broad potential of application. The database offers a data pool of more than 4,200 landslide data sets with over 13,000 single data files and dates back to 12th century. All types of landslides are covered by the database, which stores not only core attributes, but also various complementary data, including data on landslide causes, impacts, and mitigation. The current database migration to PostgreSQL/PostGIS is focused on unlocking the full scientific potential of the database, while enabling data sharing and knowledge transfer via a web GIS platform. In this contribution, the goals and the research strategy of the database project are highlighted at first, with a summary of best practices in database development providing perspective. Next, the focus is on key aspects of the methodology, which is followed by the results of different case studies in the German Central Uplands. The case study results exemplify database application in analysis of vulnerability to landslides, impact statistics, and hazard or cost modeling.

  14. Development of a national, dynamic reservoir-sedimentation database

    USGS Publications Warehouse

    Gray, J.R.; Bernard, J.M.; Stewart, D.W.; McFaul, E.J.; Laurent, K.W.; Schwarz, G.E.; Stinson, J.T.; Jonas, M.M.; Randle, T.J.; Webb, J.W.

    2010-01-01

    The importance of dependable, long-term water supplies, coupled with the need to quantify rates of capacity loss of the Nation’s re servoirs due to sediment deposition, were the most compelling reasons for developing the REServoir- SEDimentation survey information (RESSED) database and website. Created under the auspices of the Advisory Committee on Water Information’s Subcommittee on Sedimenta ion by the U.S. Geological Survey and the Natural Resources Conservation Service, the RESSED database is the most comprehensive compilation of data from reservoir bathymetric and dry-basin surveys in the United States. As of March 2010, the database, which contains data compiled on the 1950s vintage Soil Conservation Service’s Form SCS-34 data sheets, contained results from 6,616 surveys on 1,823 reservoirs in the United States and two surveys on one reservoir in Puerto Rico. The data span the period 1755–1997, with 95 percent of the surveys performed from 1930–1990. The reservoir surface areas range from sub-hectare-scale farm ponds to 658 km2 Lake Powell. The data in the RESSED database can be useful for a number of purposes, including calculating changes in reservoir-storage characteristics, quantifying sediment budgets, and estimating erosion rates in a reservoir’s watershed. The March 2010 version of the RESSED database has a number of deficiencies, including a cryptic and out-of-date database architecture; some geospatial inaccuracies (although most have been corrected); other data errors; an inability to store all data in a readily retrievable manner; and an inability to store all data types that currently exist. Perhaps most importantly, the March 2010 version of RESSED database provides no publically available means to submit new data and corrections to existing data. To address these and other deficiencies, the Subcommittee on Sedimentation, through the U.S. Geological Survey and the U.S. Army Corps of Engineers, began a collaborative project in

  15. PlantCAZyme: a database for plant carbohydrate-active enzymes

    PubMed Central

    Ekstrom, Alexander; Taujale, Rahil; McGinn, Nathan; Yin, Yanbin

    2014-01-01

    PlantCAZyme is a database built upon dbCAN (database for automated carbohydrate active enzyme annotation), aiming to provide pre-computed sequence and annotation data of carbohydrate active enzymes (CAZymes) to plant carbohydrate and bioenergy research communities. The current version contains data of 43 790 CAZymes of 159 protein families from 35 plants (including angiosperms, gymnosperms, lycophyte and bryophyte mosses) and chlorophyte algae with fully sequenced genomes. Useful features of the database include: (i) a BLAST server and a HMMER server that allow users to search against our pre-computed sequence data for annotation purpose, (ii) a download page to allow batch downloading data of a specific CAZyme family or species and (iii) protein browse pages to provide an easy access to the most comprehensive sequence and annotation data. Database URL: http://cys.bios.niu.edu/plantcazyme/ PMID:25125445

  16. Danish Gynecological Cancer Database

    PubMed Central

    Sørensen, Sarah Mejer; Bjørn, Signe Frahm; Jochumsen, Kirsten Marie; Jensen, Pernille Tine; Thranov, Ingrid Regitze; Hare-Bruun, Helle; Seibæk, Lene; Høgdall, Claus

    2016-01-01

    Aim of database The Danish Gynecological Cancer Database (DGCD) is a nationwide clinical cancer database and its aim is to monitor the treatment quality of Danish gynecological cancer patients, and to generate data for scientific purposes. DGCD also records detailed data on the diagnostic measures for gynecological cancer. Study population DGCD was initiated January 1, 2005, and includes all patients treated at Danish hospitals for cancer of the ovaries, peritoneum, fallopian tubes, cervix, vulva, vagina, and uterus, including rare histological types. Main variables DGCD data are organized within separate data forms as follows: clinical data, surgery, pathology, pre- and postoperative care, complications, follow-up visits, and final quality check. DGCD is linked with additional data from the Danish “Pathology Registry”, the “National Patient Registry”, and the “Cause of Death Registry” using the unique Danish personal identification number (CPR number). Descriptive data Data from DGCD and registers are available online in the Statistical Analysis Software portal. The DGCD forms cover almost all possible clinical variables used to describe gynecological cancer courses. The only limitation is the registration of oncological treatment data, which is incomplete for a large number of patients. Conclusion The very complete collection of available data from more registries form one of the unique strengths of DGCD compared to many other clinical databases, and provides unique possibilities for validation and completeness of data. The success of the DGCD is illustrated through annual reports, high coverage, and several peer-reviewed DGCD-based publications. PMID:27822089

  17. RNA STRAND: the RNA secondary structure and statistical analysis database.

    PubMed

    Andronescu, Mirela; Bereg, Vera; Hoos, Holger H; Condon, Anne

    2008-08-13

    The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. In this paper we describe RNA STRAND - the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

  18. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

    PubMed Central

    Andronescu, Mirela; Bereg, Vera; Hoos, Holger H; Condon, Anne

    2008-01-01

    Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at . PMID:18700982

  19. The Danish Melanoma Database

    PubMed Central

    Hölmich, Lisbet Rosenkrantz; Klausen, Siri; Spaun, Eva; Schmidt, Grethe; Gad, Dorte; Svane, Inge Marie; Schmidt, Henrik; Lorentzen, Henrik Frank; Ibfelt, Else Helene

    2016-01-01

    Aim of database The aim of the database is to monitor and improve the treatment and survival of melanoma patients. Study population All Danish patients with cutaneous melanoma and in situ melanomas must be registered in the Danish Melanoma Database (DMD). In 2014, 2,525 patients with invasive melanoma and 780 with in situ tumors were registered. The coverage is currently 93% compared with the Danish Pathology Register. Main variables The main variables include demographic, clinical, and pathological characteristics, including Breslow’s tumor thickness, ± ulceration, mitoses, and tumor–node–metastasis stage. Information about the date of diagnosis, treatment, type of surgery, including safety margins, results of lymphoscintigraphy in patients for whom this was indicated (tumors > T1a), results of sentinel node biopsy, pathological evaluation hereof, and follow-up information, including recurrence, nature, and treatment hereof is registered. In case of death, the cause and date are included. Currently, all data are entered manually; however, data catchment from the existing registries is planned to be included shortly. Descriptive data The DMD is an old research database, but new as a clinical quality register. The coverage is high, and the performance in the five Danish regions is quite similar due to strong adherence to guidelines provided by the Danish Melanoma Group. The list of monitored indicators is constantly expanding, and annual quality reports are issued. Several important scientific studies are based on DMD data. Conclusion DMD holds unique detailed information about tumor characteristics, the surgical treatment, and follow-up of Danish melanoma patients. Registration and monitoring is currently expanding to encompass even more clinical parameters to benefit both patient treatment and research. PMID:27822097

  20. Database of recent tsunami deposits

    USGS Publications Warehouse

    Peters, Robert; Jaffe, Bruce E.

    2010-01-01

    This report describes a database of sedimentary characteristics of tsunami deposits derived from published accounts of tsunami deposit investigations conducted shortly after the occurrence of a tsunami. The database contains 228 entries, each entry containing data from up to 71 categories. It includes data from 51 publications covering 15 tsunamis distributed between 16 countries. The database encompasses a wide range of depositional settings including tropical islands, beaches, coastal plains, river banks, agricultural fields, and urban environments. It includes data from both local tsunamis and teletsunamis. The data are valuable for interpreting prehistorical, historical, and modern tsunami deposits, and for the development of criteria to identify tsunami deposits in the geologic record.

  1. SITE COMPREHENSIVE LISTING (CERCLIS) - Contaminants at CERCLIS (Superfund) Sites

    EPA Pesticide Factsheets

    Contaminants at Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Sites - The CERCLIS 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 ).

  2. Information Literacy Skills: Comparing and Evaluating Databases

    ERIC Educational Resources Information Center

    Grismore, Brian A.

    2012-01-01

    The purpose of this database comparison is to express the importance of teaching information literacy skills and to apply those skills to commonly used Internet-based research tools. This paper includes a comparison and evaluation of three databases (ProQuest, ERIC, and Google Scholar). It includes strengths and weaknesses of each database based…

  3. ARTI refrigerant database

    SciTech Connect

    Calm, J.M.

    1998-08-01

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

  4. Comprehensive Trail Making Test

    ERIC Educational Resources Information Center

    Gray, Rebecca

    2006-01-01

    The Comprehensive Trail Making Test (CTMT) is designed to be used in neuropsychological assessment for the purposes of detecting effects of brain defects and deficits and in tracking progress in rehabilitation. More specific purposes include the detection of frontal lobe deficits, problems with psychomotor speed, visual search and sequencing,…

  5. Cinnarizine: Comprehensive Profile.

    PubMed

    Haress, Nadia G

    2015-01-01

    Cinnarizine is a piperazine derivative with antihistaminic, antiserotonergic, antidopaminergic, and calcium channel-blocking activities. A comprehensive profile was performed on cinnarizine including its description and the different methods of analysis. The 1H NMR and 13C one- and two-dimensional NMR methods were used. In addition, infrared and mass spectral analyses were performed which all confirmed the structure of cinnarizine.

  6. Reading Comprehension in Mathematics.

    ERIC Educational Resources Information Center

    Fuentes, Peter

    1998-01-01

    Argues that mathematics instruction is dependent not just on numbers and their manipulation, but on language, literacy, and comprehension. Uses original examples of mathematical texts to map out a rationale for the teaching of reading in math, and includes a range of practical suggestions for the math teacher that support the "spiraling" of…

  7. Designing a Comprehensive Curriculum

    ERIC Educational Resources Information Center

    Faulkner, T. L.

    1970-01-01

    A comprehensive rural "agribusiness industry" curriculum might include: (1) The World of Work (Grade 7 or 8), (2) Vocational Orientation (Grade 9), (3) Basic Agriculture and Industry (Grade 10), (4) Specialized Agribusiness Industry (Grade 11), and (5) Advanced Agribusiness Industry (Grade 12). (DM)

  8. Comprehensive Trail Making Test

    ERIC Educational Resources Information Center

    Gray, Rebecca

    2006-01-01

    The Comprehensive Trail Making Test (CTMT) is designed to be used in neuropsychological assessment for the purposes of detecting effects of brain defects and deficits and in tracking progress in rehabilitation. More specific purposes include the detection of frontal lobe deficits, problems with psychomotor speed, visual search and sequencing,…

  9. Math Sense: Comprehensive Review.

    ERIC Educational Resources Information Center

    Hoyt, Cathy Fillmore

    This book features a comprehensive review of the Math Sense series and is designed to help students gain the range of math skills they need to succeed in life, work, and on standardized tests; overcome math anxiety; discover math as interesting and purposeful; and develop good number sense. Topics covered in this book include whole numbers;…

  10. ePlantLIBRA: A composition and biological activity database for bioactive compounds in plant food supplements.

    PubMed

    Plumb, J; Lyons, J; Nørby, K; Thomas, M; Nørby, E; Poms, R; Bucchini, L; Restani, P; Kiely, M; Finglas, P

    2016-02-15

    The newly developed ePlantLIBRA database is a comprehensive and searchable database, with up-to-date coherent and validated scientific information on plant food supplement (PFS) bioactive compounds, with putative health benefits as well as adverse effects, and contaminants and residues. It is the only web-based database available compiling peer reviewed publications and case studies on PFS. A user-friendly, efficient and flexible interface has been developed for searching, extracting, and exporting the data, including links to the original references. Data from over 570 publications have been quality evaluated and entered covering 70 PFS or their botanical ingredients.

  11. ARTI Refrigerant Database

    SciTech Connect

    Calm, J.M.

    1992-11-09

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

  12. Open TG-GATEs: a large-scale toxicogenomics database.

    PubMed

    Igarashi, Yoshinobu; Nakatsu, Noriyuki; Yamashita, Tomoya; Ono, Atsushi; Ohno, Yasuo; Urushidani, Tetsuro; Yamada, Hiroshi

    2015-01-01

    Toxicogenomics focuses on assessing the safety of compounds using gene expression profiles. Gene expression signatures from large toxicogenomics databases are expected to perform better than small databases in identifying biomarkers for the prediction and evaluation of drug safety based on a compound's toxicological mechanisms in animal target organs. Over the past 10 years, the Japanese Toxicogenomics Project consortium (TGP) has been developing a large-scale toxicogenomics database consisting of data from 170 compounds (mostly drugs) with the aim of improving and enhancing drug safety assessment. Most of the data generated by the project (e.g. gene expression, pathology, lot number) are freely available to the public via Open TG-GATEs (Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System). Here, we provide a comprehensive overview of the database, including both gene expression data and metadata, with a description of experimental conditions and procedures used to generate the database. Open TG-GATEs is available from http://toxico.nibio.go.jp/english/index.html.

  13. Centre for Reviews and Dissemination databases: value, content, and developments.

    PubMed

    Booth, Alison M; Wright, Kath E; Outhwaite, Helen

    2010-10-01

    The Centre for Reviews and Dissemination (CRD) funded through the United Kingdom National Institute for Health Research undertakes systematic reviews evaluating the research evidence on health and public health questions of national and international importance. CRD is involved in methods research and produces internationally accepted guidelines for undertaking systematic reviews. A core product of the Centre are the CRD databases; a key resource for health professionals, policy makers, and researchers around the world. Research evidence evaluating the effects and cost-effectiveness of healthcare interventions is growing year on year, and can be difficult and time consuming to identify and appraise. The databases assist decision makers by systematically identifying and critically describing systematic reviews and economic evaluations, appraising their quality and highlighting their relative strengths and weaknesses; and providing a comprehensive listing of ongoing and published health technology assessments. This article briefly outlines the processes behind each of the three databases, gives details of the records, the information they contain and the value added by CRD. An overview of the new public interface for the CRD databases to be launched later this year is given. Improvements and innovations to supplement existing functions are listed, including enhanced and new search options, the addition of quick links to relevant material from within individual records, an integrated PubMed search and the ability to select personal preferences. CRD's databases provide free access to an important knowledge base and are used widely to underpin evidence informed healthcare decisions in the United Kingdom and internationally.

  14. High Performance Buildings Database

    DOE Data Explorer

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

  15. The Exoplanet Orbit Database

    NASA Astrophysics Data System (ADS)

    Wright, J. T.; Fakhouri, O.; Marcy, G. W.; Han, E.; Feng, Y.; Johnson, John Asher; Howard, A. W.; Fischer, D. A.; Valenti, J. A.; Anderson, J.; Piskunov, N.

    2011-04-01

    We present a database of well-determined orbital parameters of exoplanets, and their host stars’ properties. This database comprises spectroscopic orbital elements measured for 427 planets orbiting 363 stars from radial velocity and transit measurements as reported in the literature. We have also compiled fundamental transit parameters, stellar parameters, and the method used for the planets discovery. This Exoplanet Orbit Database includes all planets with robust, well measured orbital parameters reported in peer-reviewed articles. The database is available in a searchable, filterable, and sortable form online through the Exoplanets Data Explorer table, and the data can be plotted and explored through the Exoplanet Data Explorer plotter. We use the Data Explorer to generate publication-ready plots, giving three examples of the signatures of exoplanet migration and dynamical evolution: We illustrate the character of the apparent correlation between mass and period in exoplanet orbits, the different selection biases between radial velocity and transit surveys, and that the multiplanet systems show a distinct semimajor-axis distribution from apparently singleton systems.

  16. The UCSC Genome Browser database: 2015 update.

    PubMed

    Rosenbloom, Kate R; Armstrong, Joel; Barber, Galt P; Casper, Jonathan; Clawson, Hiram; Diekhans, Mark; Dreszer, Timothy R; Fujita, Pauline A; Guruvadoo, Luvina; Haeussler, Maximilian; Harte, Rachel A; Heitner, Steve; Hickey, Glenn; Hinrichs, Angie S; Hubley, Robert; Karolchik, Donna; Learned, Katrina; Lee, Brian T; Li, Chin H; Miga, Karen H; Nguyen, Ngan; Paten, Benedict; Raney, Brian J; Smit, Arian F A; Speir, Matthew L; Zweig, Ann S; Haussler, David; Kuhn, Robert M; Kent, W James

    2015-01-01

    Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.

  17. The International Nucleotide Sequence Database Collaboration

    PubMed Central

    Cochrane, Guy; Karsch-Mizrachi, Ilene; Takagi, Toshihisa; Sequence Database Collaboration, International Nucleotide

    2016-01-01

    The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org) comprises three global partners committed to capturing, preserving and providing comprehensive public-domain nucleotide sequence information. The INSDC establishes standards, formats and protocols for data and metadata to make it easier for individuals and organisations to submit their nucleotide data reliably to public archives. This work enables the continuous, global exchange of information about living things. Here we present an update of the INSDC in 2015, including data growth and diversification, new standards and requirements by publishers for authors to submit their data to the public archives. The INSDC serves as a model for data sharing in the life sciences. PMID:26657633

  18. Comprehensive analysis of transport aircraft flight performance

    NASA Astrophysics Data System (ADS)

    Filippone, Antonio

    2008-04-01

    This paper reviews the state-of-the art in comprehensive performance codes for fixed-wing aircraft. The importance of system analysis in flight performance is discussed. The paper highlights the role of aerodynamics, propulsion, flight mechanics, aeroacoustics, flight operation, numerical optimisation, stochastic methods and numerical analysis. The latter discipline is used to investigate the sensitivities of the sub-systems to uncertainties in critical state parameters or functional parameters. The paper discusses critically the data used for performance analysis, and the areas where progress is required. Comprehensive analysis codes can be used for mission fuel planning, envelope exploration, competition analysis, a wide variety of environmental studies, marketing analysis, aircraft certification and conceptual aircraft design. A comprehensive program that uses the multi-disciplinary approach for transport aircraft is presented. The model includes a geometry deck, a separate engine input deck with the main parameters, a database of engine performance from an independent simulation, and an operational deck. The comprehensive code has modules for deriving the geometry from bitmap files, an aerodynamics model for all flight conditions, a flight mechanics model for flight envelopes and mission analysis, an aircraft noise model and engine emissions. The model is validated at different levels. Validation of the aerodynamic model is done against the scale models DLR-F4 and F6. A general model analysis and flight envelope exploration are shown for the Boeing B-777-300 with GE-90 turbofan engines with intermediate passenger capacity (394 passengers in 2 classes). Validation of the flight model is done by sensitivity analysis on the wetted area (or profile drag), on the specific air range, the brake-release gross weight and the aircraft noise. A variety of results is shown, including specific air range charts, take-off weight-altitude charts, payload-range performance

  19. 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.

  20. AMYPdb: A database dedicated to amyloid precursor proteins

    PubMed Central

    Pawlicki, Sandrine; Le Béchec, Antony; Delamarche, Christian

    2008-01-01

    Background Misfolding and aggregation of proteins into ordered fibrillar structures is associated with a number of severe pathologies, including Alzheimer's disease, prion diseases, and type II diabetes. The rapid accumulation of knowledge about the sequences and structures of these proteins allows using of in silico methods to investigate the molecular mechanisms of their abnormal conformational changes and assembly. However, such an approach requires the collection of accurate data, which are inconveniently dispersed among several generalist databases. Results We therefore created a free online knowledge database (AMYPdb) dedicated to amyloid precursor proteins and we have performed large scale sequence analysis of the included data. Currently, AMYPdb integrates data on 31 families, including 1,705 proteins from nearly 600 organisms. It displays links to more than 2,300 bibliographic references and 1,200 3D-structures. A Wiki system is available to insert data into the database, providing a sharing and collaboration environment. We generated and analyzed 3,621 amino acid sequence patterns, reporting highly specific patterns for each amyloid family, along with patterns likely to be involved in protein misfolding and aggregation. Conclusion AMYPdb is a comprehensive online database aiming at the centralization of bioinformatic data regarding all amyloid proteins and their precursors. Our sequence pattern discovery and analysis approach unveiled protein regions of significant interest. AMYPdb is freely accessible [1]. PMID:18544157

  1. Improving participant comprehension in the informed consent process.

    PubMed

    Cohn, Elizabeth; Larson, Elaine

    2007-01-01

    To critically analyze studies published within the past decade about participants' comprehension of informed consent in clinical research and to identify promising intervention strategies. Integrative review of literature. The Cumulative Index of Nursing and Allied Health Literature (CINAHL), PubMed, and the Cochrane Database of Systematic Reviews and Cochrane Central Register of Controlled Trials were searched. Inclusion criteria included studies (a) published between January 1, 1996 and January 1, 2007, (b) designed as descriptive or interventional studies of comprehension of informed consent for clinical research, (c) conducted in nonpsychiatric adult populations who were either patients or volunteer participants, (d) written in English, and (e) published in peer-reviewed journals. Of the 980 studies identified, 319 abstracts were screened, 154 studies were reviewed, and 23 met the inclusion criteria. Thirteen studies (57%) were descriptive, and 10 (43%) were interventional. Interventions tested included simplified written consent documents, multimedia approaches, and the use of a trained professional (consent educator) to assist in the consent process. Collectively, no single intervention strategy was consistently associated with improved comprehension. Studies also varied in regard to the definition of comprehension and the tools used to measure it. Despite increasing regulatory scrutiny, deficiencies still exist in participant comprehension of the research in which they participate, as well as differences in how comprehension is measured and assessed. No single intervention was identified as consistently successful for improving participant comprehension, and results indicated that any successful consent process should at a minimum include various communication modes and is likely to require one-to-one interaction with someone knowledgeable about the study.

  2. Database machines

    NASA Technical Reports Server (NTRS)

    Stiefel, M. L.

    1983-01-01

    The functions and performance characteristics of data base machines (DBM), including machines currently being studied in research laboratories and those currently offered on a commerical basis are discussed. The cost/benefit considerations that must be recognized in selecting a DBM are discussed, as well as the future outlook for such machines.

  3. COBE Astronomical Databases

    NASA Astrophysics Data System (ADS)

    Freedman, I.; Raugh, A. C.; Cheng, E. S.

    A project to store and convert external astronomical survey maps to the Cosmic Background Explorer (COBE) spacecraft pixelization is described. Established software is reused in order to reduce development costs. The proposed packages and systems include the Image Reduction and Analysis Facility (IRAF), Interactive Data Language Astronomy Library (IDL), the FITSIO data transfer package and the Astronomical Image Processing System (AIPS). The software structure of the astronomical databases, projected conversion schemes, quality assurance procedures and outstanding problems will be discussed.

  4. Patient comprehension of discharge instructions from the emergency department: a literature review.

    PubMed

    Alberti, Traci L; Nannini, Angela

    2013-04-01

    To examine research published from 1995 to 2010, evaluating patient comprehension of discharge instructions from emergency department (ED) or urgent care (UC) settings. Specifically, we examined: (a) the interventions utilized to provide discharge instructions, (b) the methods used to assess patient comprehension, and (c) the most effective strategies for assuring patient comprehension of ED discharge instructions. A comprehensive literature review was conducted utilizing the following databases: Cumulative Index to Nursing and Allied Health Literature (CINAHL), Health Reference Center Academic, Medline, Cochrane, and Ovid. English language peer-reviewed articles published between 1995 and 2010 were reviewed. Search terms included patient, comprehension, understanding, discharge instructions, health education, and emergency medicine. Increases in patient comprehension of ED discharge instructions are identified with alternative teaching interventions (multimedia) in comparison to traditional standardized written discharge instructions (usual care). Literature suggests clinicians seldom clarify patient comprehension in practice, though effective methods are noted in research. Future research is needed to explore innovative teaching interventions and their impact upon patient comprehension and patient outcomes. To ensure patient comprehension of discharge instructions, the simplification of discharge material is paramount. Nurse practitioners working in ED or UC settings can improve upon "usual care" by exploring more innovative teaching interventions. ©2012 The Author(s) Journal compilation ©2012 American Association of Nurse Practitioners.

  5. InterAction Database (IADB)

    Cancer.gov

    The InterAction Database includes demographic and prescription information for more than 500,000 patients in the northern and middle Netherlands and has been integrated with other systems to enhance data collection and analysis.

  6. Time to recurrence is a significant predictor of cancer-specific survival after recurrence in patients with recurrent renal cell carcinoma--results from a comprehensive multi-centre database (CORONA/SATURN-Project).

    PubMed

    Brookman-May, Sabine D; May, Matthias; Shariat, Shahrokh F; Novara, Giacomo; Zigeuner, Richard; Cindolo, Luca; De Cobelli, Ottavio; De Nunzio, Cosimo; Pahernik, Sascha; Wirth, Manfred P; Longo, Nicola; Simonato, Alchiede; Serni, Sergio; Siracusano, Salvatore; Volpe, Alessandro; Morgia, Giuseppe; Bertini, Roberto; Dalpiaz, Orietta; Stief, Christian; Ficarra, Vincenzo

    2013-11-01

    To assess the prognostic impact of time to recurrence (TTR) on cancer-specific survival (CSS) after recurrence in patients with renal cell carcinoma (RCC) undergoing radical nephrectomy or nephron-sparing surgery. To analyse differences in clinical and histopathological criteria between patients with early and late recurrence. Of 13,107 patients with RCC from an international multicentre database, 1712 patients developed recurrence in the follow-up (FU), at a median (interquartile range) of 50.1 (25-106) months. In all, 1402 patients had recurrence at ≤5 years (Group A) and 310 patients beyond this time (Group B). Differences in clinical and histopathological variables between patients with early and late recurrence were analysed. The influence of TTR and further variables on CSS after recurrence was assessed by Cox regression analysis. Male gender, advanced age, tumour diameter and stage, Fuhrman grade 3-4, lymphovascular invasion (LVI), and pN + stage were significantly more frequent in patients with early recurrence, who had a significantly reduced 3-year CSS of 30% compared with patients in Group B (41%; P = 0.001). Age, gender, tumour histology, pT stage, and continuous TTR (hazard ratio 0.99, P = 0.006; monthly interval) independently predicted CSS. By inclusion of dichotomised TTR in the multivariable model, a significant influence of this variable on CSS was present until 48 months after surgery, but not beyond this time. Advanced age, male gender, larger tumour diameters, LVI, Fuhrman grade 3-4, pN + stage, and advanced tumour stages are associated with early recurrence. Up to 4 years from surgery, a shorter TTR independently predicts a reduced CSS after recurrence. © 2013 The Authors. BJU International © 2013 BJU International.

  7. ARTI refrigerant database

    SciTech Connect

    Calm, J.M.

    1997-02-01

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

  8. The Establishment of K-CaP (the Multicenter Korean Prostate Cancer Database).

    PubMed

    Lee, Dong Hoon; Lee, Seung Hwan; Rha, Koon Ho; Choi, In Young; Lee, Ji Youl; Kim, Sae Woong; Lee, Sangchul; Hong, Sung Kyu; Byun, Seok-Soo; Jeong, In Gab; Hong, Jun Hyuk; Kim, Choung-Soo; Jeon, Hwang Gyun; Lee, Hyun Moo; Chung, Byung Ha

    2013-04-01

    The purpose of this article was to announce the establishment of the multicenter Korean Prostate Cancer Database (K-CaP) and to provide urologists with details about K-CaP's methodology. The initial participating K-CaP institutions include five medical centers in Korea. First, we registered prostate cancer patients who underwent radical prostatectomy as the basic background data. K-CaP is poised to combine these initial observational longitudinal studies with those of other eligible institutions as the database grows. All current prostate cancer patients in Korea are able to be registered into the Web-based database system and thereby have a role in several observational studies. The structure of the database for K-CaP was developed by matching it with the respective data from different studies. The operability of the K-CaP database system was verified by using the existing databases from three participating institutions. The analysis of clinicopathologic characteristics of patients with the use of the Web-based database was successfully conducted. We confirmed the accurate operation of the Web-based database system without any difficulties. We are announcing the establishment of K-CaP the first database of comprehensive observational longitudinal studies about prostate cancer in Korea. The database will be successfully maintained by sufficiently and continuously updating all patient data covering several treatments. Complete statistical results for registered prostate cancer patients are forthcoming for the basic background data to establish the database. Even though much trial and error are expected during the development process, we expect that K-CaP will eventually become one of the most powerful longitudinal observation databases.

  9. Comprehensiveness of Career Planning: The Third C--Comprehensiveness.

    ERIC Educational Resources Information Center

    Carr, James V.

    1996-01-01

    To be comprehensive, a career guidance program must acknowledge a broader meaning of career. Attributes of comprehensive programs include a structured career planning process, activities at all levels K-adult, adequate support information, a documented plan for each participant, ongoing plan revision, equity, subjective and objective assessment…

  10. ANTIMIC: a database of antimicrobial sequences

    PubMed Central

    Brahmachary, M.; Krishnan, S. P. T.; Koh, J. L. Y.; Khan, A. M.; Seah, S. H.; Tan, T. W.; Brusic, V.; Bajic, V. B.

    2004-01-01

    Antimicrobial peptides (AMPs) are important components of the innate immune system of many species. These peptides are found in eukaryotes, including mammals, amphibians, insects and plants, as well as in prokaryotes. Other than having pathogen-lytic properties, these peptides have other activities like antitumor activity, mitogen activity, or they may act as signaling molecules. Their short length, fast and efficient action against microbes and low toxicity to mammals have made them potential candidates as peptide drugs. In many cases they are effective against pathogens that are resistant to conventional antibiotics. They can serve as natural templates for the design of novel antimicrobial drugs. Although there are vast amounts of data on natural AMPs, they are not available through one central resource. We have developed a comprehensive database (ANTIMIC, http://research.i2r.a-star.edu.sg/Templar/DB/ANTIMIC/) of known and putative AMPs, which contains ∼1700 of these peptides. The database is integrated with tools to facilitate efficient extraction of data and their analysis at molecular level, as well as search for new AMPs. These tools include BLAST, PDB structure viewer and the Antimic profile module. PMID:14681487

  11. PPDB, the Plant Proteomics Database at Cornell.

    PubMed

    Sun, Qi; Zybailov, Boris; Majeran, Wojciech; Friso, Giulia; Olinares, Paul Dominic B; van Wijk, Klaas J

    2009-01-01

    The Plant Proteomics Database (PPDB; http://ppdb.tc.cornell.edu), launched in 2004, provides an integrated resource for experimentally identified proteins in Arabidopsis and maize (Zea mays). Internal BLAST alignments link maize and Arabidopsis information. Experimental identification is based on in-house mass spectrometry (MS) of cell type-specific proteomes (maize), or specific subcellular proteomes (e.g. chloroplasts, thylakoids, nucleoids) and total leaf proteome samples (maize and Arabidopsis). So far more than 5000 accessions both in maize and Arabidopsis have been identified. In addition, more than 80 published Arabidopsis proteome datasets from subcellular compartments or organs are stored in PPDB and linked to each locus. Using MS-derived information and literature, more than 1500 Arabidopsis proteins have a manually assigned subcellular location, with a strong emphasis on plastid proteins. Additional new features of PPDB include searchable posttranslational modifications and searchable experimental proteotypic peptides and spectral count information for each identified accession based on in-house experiments. Various search methods are provided to extract more than 40 data types for each accession and to extract accessions for different functional categories or curated subcellular localizations. Protein report pages for each accession provide comprehensive overviews, including predicted protein properties, with hyperlinks to the most relevant databases.

  12. World electric power plants database

    SciTech Connect

    2006-06-15

    This global database provides records for 104,000 generating units in over 220 countries. These units include installed and projected facilities, central stations and distributed plants operated by utilities, independent power companies and commercial and self-generators. Each record includes information on: geographic location and operating company; technology, fuel and boiler; generator manufacturers; steam conditions; unit capacity and age; turbine/engine; architect/engineer and constructor; and pollution control equipment. The database is issued quarterly.

  13. PMAG: Relational Database Definition

    NASA Astrophysics Data System (ADS)

    Keizer, P.; Koppers, A.; Tauxe, L.; Constable, C.; Genevey, A.; Staudigel, H.; Helly, J.

    2002-12-01

    The Scripps center for Physical and Chemical Earth References (PACER) was established to help create databases for reference data and make them available to the Earth science community. As part of these efforts PACER supports GERM, REM and PMAG and maintains multiple online databases under the http://earthref.org umbrella website. This website has been built on top of a relational database that allows for the archiving and electronic access to a great variety of data types and formats, permitting data queries using a wide range of metadata. These online databases are designed in Oracle 8.1.5 and they are maintained at the San Diego Supercomputer Center. They are directly available via http://earthref.org/databases/. A prototype of the PMAG relational database is now operational within the existing EarthRef.org framework under http://earthref.org/databases/PMAG/. As will be shown in our presentation, the PMAG design focuses around the general workflow that results in the determination of typical paleo-magnetic analyses. This ensures that individual data points can be traced between the actual analysis and the specimen, sample, site, locality and expedition it belongs to. These relations guarantee traceability of the data by distinguishing between original and derived data, where the actual (raw) measurements are performed on the specimen level, and data on the sample level and higher are then derived products in the database. These relations may also serve to recalculate site means when new data becomes available for that locality. The PMAG data records are extensively described in terms of metadata. These metadata are used when scientists search through this online database in order to view and download their needed data. They minimally include method descriptions for field sampling, laboratory techniques and statistical analyses. They also include selection criteria used during the interpretation of the data and, most importantly, critical information about the

  14. An Index to PGE-Ni-Cr Deposits and Occurrences in Selected Mineral-Occurrence Databases

    USGS Publications Warehouse

    Causey, J. Douglas; Galloway, John P.; Zientek, Michael L.

    2009-01-01

    Databases of mineral deposits and occurrences are essential to conducting assessments of undiscovered mineral resources. In the USGS's (U.S. Geological Survey) global assessment of undiscovered resources of copper, potash, and the platinum-group elements (PGE), only a few mineral deposit types will be evaluated. For example, only porphyry-copper and sediment-hosted copper deposits will be considered for the copper assessment. To support the global assessment, the USGS prepared comprehensive compilations of the occurrences of these two deposit types in order to develop grade and tonnage models and delineate permissive areas for undiscovered deposits of those types. This publication identifies previously published databases and database records that describe PGE, nickel, and chromium deposits and occurrences. Nickel and chromium were included in this overview because of the close association of PGE with nickel and chromium mineralization. Users of this database will need to refer to the original databases for detailed information about the deposits and occurrences. This information will be used to develop a current and comprehensive global database of PGE deposits and occurrences.

  15. An Alaska Soil Carbon Database

    NASA Astrophysics Data System (ADS)

    Johnson, Kristofer; Harden, Jennifer

    2009-05-01

    Database Collaborator's Meeting; Fairbanks, Alaska, 4 March 2009; Soil carbon pools in northern high-latitude regions and their response to climate changes are highly uncertain, and collaboration is required from field scientists and modelers to establish baseline data for carbon cycle studies. The Global Change Program at the U.S. Geological Survey has funded a 2-year effort to establish a soil carbon network and database for Alaska based on collaborations from numerous institutions. To initiate a community effort, a workshop for the development of an Alaska soil carbon database was held at the University of Alaska Fairbanks. The database will be a resource for spatial and biogeochemical models of Alaska ecosystems and will serve as a prototype for a nationwide community project: the National Soil Carbon Network (http://www.soilcarb.net). Studies will benefit from the combination of multiple academic and government data sets. This collaborative effort is expected to identify data gaps and uncertainties more comprehensively. Future applications of information contained in the database will identify specific vulnerabilities of soil carbon in Alaska to climate change, disturbance, and vegetation change.

  16. YCRD: Yeast Combinatorial Regulation Database

    PubMed Central

    Wu, Wei-Sheng; Hsieh, Yen-Chen; Lai, Fu-Jou

    2016-01-01

    In eukaryotes, the precise transcriptional control of gene expression is typically achieved through combinatorial regulation using cooperative transcription factors (TFs). Therefore, a database which provides regulatory associations between cooperative TFs and their target genes is helpful for biologists to study the molecular mechanisms of transcriptional regulation of gene expression. Because there is no such kind of databases in the public domain, this prompts us to construct a database, called Yeast Combinatorial Regulation Database (YCRD), which deposits 434,197 regulatory associations between 2535 cooperative TF pairs and 6243 genes. The comprehensive collection of more than 2500 cooperative TF pairs was retrieved from 17 existing algorithms in the literature. The target genes of a cooperative TF pair (e.g. TF1-TF2) are defined as the common target genes of TF1 and TF2, where a TF’s experimentally validated target genes were downloaded from YEASTRACT database. In YCRD, users can (i) search the target genes of a cooperative TF pair of interest, (ii) search the cooperative TF pairs which regulate a gene of interest and (iii) identify important cooperative TF pairs which regulate a given set of genes. We believe that YCRD will be a valuable resource for yeast biologists to study combinatorial regulation of gene expression. YCRD is available at http://cosbi.ee.ncku.edu.tw/YCRD/ or http://cosbi2.ee.ncku.edu.tw/YCRD/. PMID:27392072

  17. The AMMA database

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  18. JICST Factual Database JICST DNA Database

    NASA Astrophysics Data System (ADS)

    Shirokizawa, Yoshiko; Abe, Atsushi

    Japan Information Center of Science and Technology (JICST) has started the on-line service of DNA database in October 1988. This database is composed of EMBL Nucleotide Sequence Library and Genetic Sequence Data Bank. The authors outline the database system, data items and search commands. Examples of retrieval session are presented.

  19. MAGIC Database and Interfaces: An Integrated Package for Gene Discovery and Expression

    PubMed Central

    Liang, Chun; Wang, Haiming; Kolychev, Dmitri S.; Sun, Feng; Freeman, Robert; Sullivan, Robert

    2004-01-01

    The rapidly increasing rate at which biological data is being produced requires a corresponding growth in relational databases and associated tools that can help laboratories contend with that data. With this need in mind, we describe here a Modular Approach to a Genomic, Integrated and Comprehensive (MAGIC) Database. This Oracle 9i database derives from an initial focus in our laboratory on gene discovery via production and analysis of expressed sequence tags (ESTs), and subsequently on gene expression as assessed by both EST clustering and microarrays. The MAGIC Gene Discovery portion of the database focuses on information derived from DNA sequences and on its biological relevance. In addition to MAGIC SEQ-LIMS, which is designed to support activities in the laboratory, it contains several additional subschemas. The latter include MAGIC Admin for database administration, MAGIC Sequence for sequence processing as well as sequence and clone attributes, MAGIC Cluster for the results of EST clustering, MAGIC Polymorphism in support of microsatellite and single-nucleotide-polymorphism discovery, and MAGIC Annotation for electronic annotation by BLAST and BLAT. The MAGIC Microarray portion is a MIAME-compliant database with two components at present. These are MAGIC Array-LIMS, which makes possible remote entry of all information into the database, and MAGIC Array Analysis, which provides data mining and visualization. Because all aspects of interaction with the MAGIC Database are via a web browser, it is ideally suited not only for individual research laboratories but also for core facilities that serve clients at any distance. PMID:18629159

  20. DBcat: a catalog of 500 biological databases

    PubMed Central

    Discala, Claude; Benigni, Xavier; Barillot, Emmanuel; Vaysseix, Guy

    2000-01-01

    The DBcat (http://www.infobiogen.fr/services/dbcat ) is a comprehensive catalog of biological databases, maintained and curated at Infobiogen. It contains 500 databases classified by application domains. The DBcat is a structured flat-file library, that can be searched by means of an SRS server or a dedicated Web interface. The files are available for download from Infobiogen anonymous ftp server. PMID:10592168

  1. Principles for Classroom Comprehension Assessment.

    ERIC Educational Resources Information Center

    Valencia, Sheila W.; Pearson, P. David

    1988-01-01

    Principles that should guide reading comprehension assessment include acknowledging the complexity of reading, focusing on orchestrating rather than isolating skills, regarding reading as a dynamic process, developing techniques that encourage student-teacher interactions, and using a variety of reading comprehension measures. The principles are…

  2. Validated MicroRNA Target Databases: An Evaluation.

    PubMed

    Lee, Yun Ji Diana; Kim, Veronica; Muth, Dillon C; Witwer, Kenneth W

    2015-11-01

    Preclinical Research Positive findings from preclinical and clinical studies involving depletion or supplementation of microRNA (miRNA) engender optimism about miRNA-based therapeutics. However, off-target effects must be considered. Predicting these effects is complicated. Each miRNA may target many gene transcripts, and the rules governing imperfectly complementary miRNA: target interactions are incompletely understood. Several databases provide lists of the relatively small number of experimentally confirmed miRNA: target pairs. Although incomplete, this information might allow assessment of at least some of the off-target effects. We evaluated the performance of four databases of experimentally validated miRNA: target interactions (miRWalk 2.0, miRTarBase, miRecords, and TarBase 7.0) using a list of 50 alphabetically consecutive genes. We examined the provided citations to determine the degree to which each interaction was experimentally supported. To assess stability, we tested at the beginning and end of a five-month period. Results varied widely by database. Two of the databases changed significantly over the course of 5 months. Most reported evidence for miRNA: target interactions were indirect or otherwise weak, and relatively few interactions were supported by more than one publication. Some returned results appear to arise from simplistic text searches that offer no insight into the relationship of the search terms, may not even include the reported gene or miRNA, and may thus, be invalid. We conclude that validation databases provide important information, but not all information in all extant databases is up-to-date or accurate. Nevertheless, the more comprehensive validation databases may provide useful starting points for investigation of off-target effects of proposed small RNA therapies. © 2015 Wiley Periodicals, Inc.

  3. ProCarDB: a database of bacterial carotenoids.

    PubMed

    Nupur, L N U; Vats, Asheema; Dhanda, Sandeep Kumar; Raghava, Gajendra P S; Pinnaka, Anil Kumar; Kumar, Ashwani

    2016-05-26

    Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids. Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.

  4. ARTI Refrigerant Database

    SciTech Connect

    Cain, J.M.

    1993-04-30

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

  5. ARTI Refrigerant Database

    SciTech Connect

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

    1993-04-30

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

  6. Dietary Supplement Ingredient Database

    MedlinePlus

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

  7. Establishing a database of radionuclide transfer parameters for freshwater wildlife.

    PubMed

    Yankovich, T; Beresford, N A; Fesenko, S; Fesenko, J; Phaneuf, M; Dagher, E; Outola, I; Andersson, P; Thiessen, K; Ryan, J; Wood, M D; Bollhöfer, A; Barnett, C L; Copplestone, D

    2013-12-01

    Environmental assessments to evaluate potentials risks to humans and wildlife often involve modelling to predict contaminant exposure through key pathways. Such models require input of parameter values, including concentration ratios, to estimate contaminant concentrations in biota based on measurements or estimates of concentrations in environmental media, such as water. Due to the diversity of species and the range in physicochemical conditions in natural ecosystems, concentration ratios can vary by orders of magnitude, even within similar species. Therefore, to improve model input parameter values for application in aquatic systems, freshwater concentration ratios were collated or calculated from national grey literature, Russian language publications, and refereed papers. Collated data were then input into an international database that is being established by the International Atomic Energy Agency. The freshwater database enables entry of information for all radionuclides listed in ICRP (1983), in addition to the corresponding stable elements, and comprises a total of more than 16,500 concentration ratio (CRwo-water) values. Although data were available for all broad wildlife groups (with the exception of birds), data were sparse for many organism types. For example, zooplankton, crustaceans, insects and insect larvae, amphibians, and mammals, for which there were CRwo-water values for less than eight elements. Coverage was most comprehensive for fish, vascular plants, and molluscs. To our knowledge, the freshwater database that has now been established represents the most comprehensive set of CRwo-water values for freshwater species currently available for use in radiological environmental assessments.

  8. Protein Model Database

    SciTech Connect

    Fidelis, K; Adzhubej, A; Kryshtafovych, A; Daniluk, P

    2005-02-23

    The phenomenal success of the genome sequencing projects reveals the power of completeness in revolutionizing biological science. Currently it is possible to sequence entire organisms at a time, allowing for a systemic rather than fractional view of their organization and the various genome-encoded functions. There is an international plan to move towards a similar goal in the area of protein structure. This will not be achieved by experiment alone, but rather by a combination of efforts in crystallography, NMR spectroscopy, and computational modeling. Only a small fraction of structures are expected to be identified experimentally, the remainder to be modeled. Presently there is no organized infrastructure to critically evaluate and present these data to the biological community. The goal of the Protein Model Database project is to create such infrastructure, including (1) public database of theoretically derived protein structures; (2) reliable annotation of protein model quality, (3) novel structure analysis tools, and (4) access to the highest quality modeling techniques available.

  9. Windshear database for forward-looking systems certification

    NASA Technical Reports Server (NTRS)

    Switzer, G. F.; Proctor, F. H.; Hinton, D. A.; Aanstoos, J. V.

    1993-01-01

    This document contains a description of a comprehensiv