Computations of Aerodynamic Performance Databases Using Output-Based Refinement

NASA Technical Reports Server (NTRS)

Nemec, Marian; Aftosmis, Michael J.

2009-01-01

Objectives: Handle complex geometry problems; Control discretization errors via solution-adaptive mesh refinement; Focus on aerodynamic databases of parametric and optimization studies: 1. Accuracy: satisfy prescribed error bounds 2. Robustness and speed: may require over 105 mesh generations 3. Automation: avoid user supervision Obtain "expert meshes" independent of user skill; and Run every case adaptively in production settings.

Solutions for medical databases optimal exploitation.

PubMed

Branescu, I; Purcarea, V L; Dobrescu, R

2014-03-15

The paper discusses the methods to apply OLAP techniques for multidimensional databases that leverage the existing, performance-enhancing technique, known as practical pre-aggregation, by making this technique relevant to a much wider range of medical applications, as a logistic support to the data warehousing techniques. The transformations have practically low computational complexity and they may be implemented using standard relational database technology. The paper also describes how to integrate the transformed hierarchies in current OLAP systems, transparently to the user and proposes a flexible, "multimodel" federated system for extending OLAP querying to external object databases.

A service-oriented data access control model

NASA Astrophysics Data System (ADS)

Meng, Wei; Li, Fengmin; Pan, Juchen; Song, Song; Bian, Jiali

2017-01-01

The development of mobile computing, cloud computing and distributed computing meets the growing individual service needs. Facing with complex application system, it's an urgent problem to ensure real-time, dynamic, and fine-grained data access control. By analyzing common data access control models, on the basis of mandatory access control model, the paper proposes a service-oriented access control model. By regarding system services as subject and data of databases as object, the model defines access levels and access identification of subject and object, and ensures system services securely to access databases.

Spatial Databases

DTIC Science & Technology

2007-09-19

extended object relations such as boundary, interior, open, closed , within, connected, and overlaps, which are invariant under elastic deformation...is required in a geo-spatial semantic web is challenging because the defining properties of geographic entities are very closely related to space. In...Objects under Primitive will be open (i.e., they will not contain their boundary points) and the objects under Complex will be closed . In addition to

Prevention of data duplication for high throughput sequencing repositories

PubMed Central

Gabdank, Idan; Chan, Esther T; Davidson, Jean M; Hilton, Jason A; Davis, Carrie A; Baymuradov, Ulugbek K; Narayanan, Aditi; Onate, Kathrina C; Graham, Keenan; Miyasato, Stuart R; Dreszer, Timothy R; Strattan, J Seth; Jolanki, Otto; Tanaka, Forrest Y; Hitz, Benjamin C

2018-01-01

Abstract Prevention of unintended duplication is one of the ongoing challenges many databases have to address. Working with high-throughput sequencing data, the complexity of that challenge increases with the complexity of the definition of a duplicate. In a computational data model, a data object represents a real entity like a reagent or a biosample. This representation is similar to how a card represents a book in a paper library catalog. Duplicated data objects not only waste storage, they can mislead users into assuming the model represents more than the single entity. Even if it is clear that two objects represent a single entity, data duplication opens the door to potential inconsistencies between the objects since the content of the duplicated objects can be updated independently, allowing divergence of the metadata associated with the objects. Analogously to a situation in which a catalog in a paper library would contain by mistake two cards for a single copy of a book. If these cards are listing simultaneously two different individuals as current book borrowers, it would be difficult to determine which borrower (out of the two listed) actually has the book. Unfortunately, in a large database with multiple submitters, unintended duplication is to be expected. In this article, we present three principal guidelines the Encyclopedia of DNA Elements (ENCODE) Portal follows in order to prevent unintended duplication of both actual files and data objects: definition of identifiable data objects (I), object uniqueness validation (II) and de-duplication mechanism (III). In addition to explaining our modus operandi, we elaborate on the methods used for identification of sequencing data files. Comparison of the approach taken by the ENCODE Portal vs other widely used biological data repositories is provided. Database URL: https://www.encodeproject.org/ PMID:29688363

A survey of commercial object-oriented database management systems

NASA Technical Reports Server (NTRS)

Atkins, John

1992-01-01

The object-oriented data model is the culmination of over thirty years of database research. Initially, database research focused on the need to provide information in a consistent and efficient manner to the business community. Early data models such as the hierarchical model and the network model met the goal of consistent and efficient access to data and were substantial improvements over simple file mechanisms for storing and accessing data. However, these models required highly skilled programmers to provide access to the data. Consequently, in the early 70's E.F. Codd, an IBM research computer scientists, proposed a new data model based on the simple mathematical notion of the relation. This model is known as the Relational Model. In the relational model, data is represented in flat tables (or relations) which have no physical or internal links between them. The simplicity of this model fostered the development of powerful but relatively simple query languages that now made data directly accessible to the general database user. Except for large, multi-user database systems, a database professional was in general no longer necessary. Database professionals found that traditional data in the form of character data, dates, and numeric data were easily represented and managed via the relational model. Commercial relational database management systems proliferated and performance of relational databases improved dramatically. However, there was a growing community of potential database users whose needs were not met by the relational model. These users needed to store data with data types not available in the relational model and who required a far richer modelling environment than that provided by the relational model. Indeed, the complexity of the objects to be represented in the model mandated a new approach to database technology. The Object-Oriented Model was the result.

Benefits of an Object-oriented Database Representation for Controlled Medical Terminologies

PubMed Central

Gu, Huanying; Halper, Michael; Geller, James; Perl, Yehoshua

1999-01-01

Objective: Controlled medical terminologies (CMTs) have been recognized as important tools in a variety of medical informatics applications, ranging from patient-record systems to decision-support systems. Controlled medical terminologies are typically organized in semantic network structures consisting of tens to hundreds of thousands of concepts. This overwhelming size and complexity can be a serious barrier to their maintenance and widespread utilization. The authors propose the use of object-oriented databases to address the problems posed by the extensive scope and high complexity of most CMTs for maintenance personnel and general users alike. Design: The authors present a methodology that allows an existing CMT, modeled as a semantic network, to be represented as an equivalent object-oriented database. Such a representation is called an object-oriented health care terminology repository (OOHTR). Results: The major benefit of an OOHTR is its schema, which provides an important layer of structural abstraction. Using the high-level view of a CMT afforded by the schema, one can gain insight into the CMT's overarching organization and begin to better comprehend it. The authors' methodology is applied to the Medical Entities Dictionary (MED), a large CMT developed at Columbia-Presbyterian Medical Center. Examples of how the OOHTR schema facilitated updating, correcting, and improving the design of the MED are presented. Conclusion: The OOHTR schema can serve as an important abstraction mechanism for enhancing comprehension of a large CMT, and thus promotes its usability. PMID:10428002

Information Network Model Query Processing

NASA Astrophysics Data System (ADS)

Song, Xiaopu

Information Networking Model (INM) [31] is a novel database model for real world objects and relationships management. It naturally and directly supports various kinds of static and dynamic relationships between objects. In INM, objects are networked through various natural and complex relationships. INM Query Language (INM-QL) [30] is designed to explore such information network, retrieve information about schema, instance, their attributes, relationships, and context-dependent information, and process query results in the user specified form. INM database management system has been implemented using Berkeley DB, and it supports INM-QL. This thesis is mainly focused on the implementation of the subsystem that is able to effectively and efficiently process INM-QL. The subsystem provides a lexical and syntactical analyzer of INM-QL, and it is able to choose appropriate evaluation strategies and index mechanism to process queries in INM-QL without the user's intervention. It also uses intermediate result structure to hold intermediate query result and other helping structures to reduce complexity of query processing.

Solutions for medical databases optimal exploitation

PubMed Central

Branescu, I; Purcarea, VL; Dobrescu, R

2014-01-01

The paper discusses the methods to apply OLAP techniques for multidimensional databases that leverage the existing, performance-enhancing technique, known as practical pre-aggregation, by making this technique relevant to a much wider range of medical applications, as a logistic support to the data warehousing techniques. The transformations have practically low computational complexity and they may be implemented using standard relational database technology. The paper also describes how to integrate the transformed hierarchies in current OLAP systems, transparently to the user and proposes a flexible, “multimodel" federated system for extending OLAP querying to external object databases. PMID:24653769

The portable UNIX programming system (PUPS) and CANTOR: a computational environment for dynamical representation and analysis of complex neurobiological data.

PubMed

O'Neill, M A; Hilgetag, C C

2001-08-29

Many problems in analytical biology, such as the classification of organisms, the modelling of macromolecules, or the structural analysis of metabolic or neural networks, involve complex relational data. Here, we describe a software environment, the portable UNIX programming system (PUPS), which has been developed to allow efficient computational representation and analysis of such data. The system can also be used as a general development tool for database and classification applications. As the complexity of analytical biology problems may lead to computation times of several days or weeks even on powerful computer hardware, the PUPS environment gives support for persistent computations by providing mechanisms for dynamic interaction and homeostatic protection of processes. Biological objects and their interrelations are also represented in a homeostatic way in PUPS. Object relationships are maintained and updated by the objects themselves, thus providing a flexible, scalable and current data representation. Based on the PUPS environment, we have developed an optimization package, CANTOR, which can be applied to a wide range of relational data and which has been employed in different analyses of neuroanatomical connectivity. The CANTOR package makes use of the PUPS system features by modifying candidate arrangements of objects within the system's database. This restructuring is carried out via optimization algorithms that are based on user-defined cost functions, thus providing flexible and powerful tools for the structural analysis of the database content. The use of stochastic optimization also enables the CANTOR system to deal effectively with incomplete and inconsistent data. Prototypical forms of PUPS and CANTOR have been coded and used successfully in the analysis of anatomical and functional mammalian brain connectivity, involving complex and inconsistent experimental data. In addition, PUPS has been used for solving multivariate engineering optimization problems and to implement the digital identification system (DAISY), a system for the automated classification of biological objects. PUPS is implemented in ANSI-C under the POSIX.1 standard and is to a great extent architecture- and operating-system independent. The software is supported by systems libraries that allow multi-threading (the concurrent processing of several database operations), as well as the distribution of the dynamic data objects and library operations over clusters of computers. These attributes make the system easily scalable, and in principle allow the representation and analysis of arbitrarily large sets of relational data. PUPS and CANTOR are freely distributed (http://www.pups.org.uk) as open-source software under the GNU license agreement.

The portable UNIX programming system (PUPS) and CANTOR: a computational environment for dynamical representation and analysis of complex neurobiological data.

PubMed Central

O'Neill, M A; Hilgetag, C C

2001-01-01

Many problems in analytical biology, such as the classification of organisms, the modelling of macromolecules, or the structural analysis of metabolic or neural networks, involve complex relational data. Here, we describe a software environment, the portable UNIX programming system (PUPS), which has been developed to allow efficient computational representation and analysis of such data. The system can also be used as a general development tool for database and classification applications. As the complexity of analytical biology problems may lead to computation times of several days or weeks even on powerful computer hardware, the PUPS environment gives support for persistent computations by providing mechanisms for dynamic interaction and homeostatic protection of processes. Biological objects and their interrelations are also represented in a homeostatic way in PUPS. Object relationships are maintained and updated by the objects themselves, thus providing a flexible, scalable and current data representation. Based on the PUPS environment, we have developed an optimization package, CANTOR, which can be applied to a wide range of relational data and which has been employed in different analyses of neuroanatomical connectivity. The CANTOR package makes use of the PUPS system features by modifying candidate arrangements of objects within the system's database. This restructuring is carried out via optimization algorithms that are based on user-defined cost functions, thus providing flexible and powerful tools for the structural analysis of the database content. The use of stochastic optimization also enables the CANTOR system to deal effectively with incomplete and inconsistent data. Prototypical forms of PUPS and CANTOR have been coded and used successfully in the analysis of anatomical and functional mammalian brain connectivity, involving complex and inconsistent experimental data. In addition, PUPS has been used for solving multivariate engineering optimization problems and to implement the digital identification system (DAISY), a system for the automated classification of biological objects. PUPS is implemented in ANSI-C under the POSIX.1 standard and is to a great extent architecture- and operating-system independent. The software is supported by systems libraries that allow multi-threading (the concurrent processing of several database operations), as well as the distribution of the dynamic data objects and library operations over clusters of computers. These attributes make the system easily scalable, and in principle allow the representation and analysis of arbitrarily large sets of relational data. PUPS and CANTOR are freely distributed (http://www.pups.org.uk) as open-source software under the GNU license agreement. PMID:11545702

Strabo: An App and Database for Structural Geology and Tectonics Data

NASA Astrophysics Data System (ADS)

Newman, J.; Williams, R. T.; Tikoff, B.; Walker, J. D.; Good, J.; Michels, Z. D.; Ash, J.

2016-12-01

Strabo is a data system designed to facilitate digital storage and sharing of structural geology and tectonics data. The data system allows researchers to store and share field and laboratory data as well as construct new multi-disciplinary data sets. Strabo is built on graph database technology, as opposed to a relational database, which provides the flexibility to define relationships between objects of any type. This framework allows observations to be linked in a complex and hierarchical manner that is not possible in traditional database topologies. Thus, the advantage of the Strabo data structure is the ability of graph databases to link objects in both numerous and complex ways, in a manner that more accurately reflects the realities of the collecting and organizing of geological data sets. The data system is accessible via a mobile interface (iOS and Android devices) that allows these data to be stored, visualized, and shared during primary collection in the field or the laboratory. The Strabo Data System is underlain by the concept of a "Spot," which we define as any observation that characterizes a specific area. This can be anything from a strike and dip measurement of bedding to cross-cutting relationships between faults in complex dissected terrains. Each of these spots can then contain other Spots and/or measurements (e.g., lithology, slickenlines, displacement magnitude.) Hence, the Spot concept is applicable to all relationships and observation sets. Strabo is therefore capable of quantifying and digitally storing large spatial variations and complex geometries of naturally deformed rocks within hierarchically related maps and images. These approaches provide an observational fidelity comparable to a traditional field book, but with the added benefits of digital data storage, processing, and ease of sharing. This approach allows Strabo to integrate seamlessly into the workflow of most geologists. Future efforts will focus on extending Strabo to other sub-disciplines as well as developing a desktop system for the enhanced collection and organization of microstructural data.

Comprehensive coverage of cardiovascular disease data in the disease portals at the Rat Genome Database.

PubMed

Wang, Shur-Jen; Laulederkind, Stanley J F; Hayman, G Thomas; Petri, Victoria; Smith, Jennifer R; Tutaj, Marek; Nigam, Rajni; Dwinell, Melinda R; Shimoyama, Mary

2016-08-01

Cardiovascular diseases are complex diseases caused by a combination of genetic and environmental factors. To facilitate progress in complex disease research, the Rat Genome Database (RGD) provides the community with a disease portal where genome objects and biological data related to cardiovascular diseases are systematically organized. The purpose of this study is to present biocuration at RGD, including disease, genetic, and pathway data. The RGD curation team uses controlled vocabularies/ontologies to organize data curated from the published literature or imported from disease and pathway databases. These organized annotations are associated with genes, strains, and quantitative trait loci (QTLs), thus linking functional annotations to genome objects. Screen shots from the web pages are used to demonstrate the organization of annotations at RGD. The human cardiovascular disease genes identified by annotations were grouped according to data sources and their annotation profiles were compared by in-house tools and other enrichment tools available to the public. The analysis results show that the imported cardiovascular disease genes from ClinVar and OMIM are functionally different from the RGD manually curated genes in terms of pathway and Gene Ontology annotations. The inclusion of disease genes from other databases enriches the collection of disease genes not only in quantity but also in quality. Copyright © 2016 the American Physiological Society.

Reuseable Objects Software Environment (ROSE): Introduction to Air Force Software Reuse Workshop

NASA Technical Reports Server (NTRS)

Cottrell, William L.

1994-01-01

The Reusable Objects Software Environment (ROSE) is a common, consistent, consolidated implementation of software functionality using modern object oriented software engineering including designed-in reuse and adaptable requirements. ROSE is designed to minimize abstraction and reduce complexity. A planning model for the reverse engineering of selected objects through object oriented analysis is depicted. Dynamic and functional modeling are used to develop a system design, the object design, the language, and a database management system. The return on investment for a ROSE pilot program and timelines are charted.

Rotation And Scale Invariant Object Recognition Using A Distributed Associative Memory

NASA Astrophysics Data System (ADS)

Wechsler, Harry; Zimmerman, George Lee

1988-04-01

This paper describes an approach to 2-dimensional object recognition. Complex-log conformal mapping is combined with a distributed associative memory to create a system which recognizes objects regardless of changes in rotation or scale. Recalled information from the memorized database is used to classify an object, reconstruct the memorized version of the object, and estimate the magnitude of changes in scale or rotation. The system response is resistant to moderate amounts of noise and occlusion. Several experiments, using real, gray scale images, are presented to show the feasibility of our approach.

Organization of Heterogeneous Scientific Data Using the EAV/CR Representation

PubMed Central

Nadkarni, Prakash M.; Marenco, Luis; Chen, Roland; Skoufos, Emmanouil; Shepherd, Gordon; Miller, Perry

1999-01-01

Entity-attribute-value (EAV) representation is a means of organizing highly heterogeneous data using a relatively simple physical database schema. EAV representation is widely used in the medical domain, most notably in the storage of data related to clinical patient records. Its potential strengths suggest its use in other biomedical areas, in particular research databases whose schemas are complex as well as constantly changing to reflect evolving knowledge in rapidly advancing scientific domains. When deployed for such purposes, the basic EAV representation needs to be augmented significantly to handle the modeling of complex objects (classes) as well as to manage interobject relationships. The authors refer to their modification of the basic EAV paradigm as EAV/CR (EAV with classes and relationships). They describe EAV/CR representation with examples from two biomedical databases that use it. PMID:10579606

Remembering complex objects in visual working memory: do capacity limits restrict objects or features?

PubMed

Hardman, Kyle O; Cowan, Nelson

2015-03-01

Visual working memory stores stimuli from our environment as representations that can be accessed by high-level control processes. This study addresses a longstanding debate in the literature about whether storage limits in visual working memory include a limit to the complexity of discrete items. We examined the issue with a number of change-detection experiments that used complex stimuli that possessed multiple features per stimulus item. We manipulated the number of relevant features of the stimulus objects in order to vary feature load. In all of our experiments, we found that increased feature load led to a reduction in change-detection accuracy. However, we found that feature load alone could not account for the results but that a consideration of the number of relevant objects was also required. This study supports capacity limits for both feature and object storage in visual working memory. PsycINFO Database Record (c) 2015 APA, all rights reserved.

Cardiological database management system as a mediator to clinical decision support.

PubMed

Pappas, C; Mavromatis, A; Maglaveras, N; Tsikotis, A; Pangalos, G; Ambrosiadou, V

1996-03-01

An object-oriented medical database management system is presented for a typical cardiologic center, facilitating epidemiological trials. Object-oriented analysis and design were used for the system design, offering advantages for the integrity and extendibility of medical information systems. The system was developed using object-oriented design and programming methodology, the C++ language and the Borland Paradox Relational Data Base Management System on an MS-Windows NT environment. Particular attention was paid to system compatibility, portability, the ease of use, and the suitable design of the patient record so as to support the decisions of medical personnel in cardiovascular centers. The system was designed to accept complex, heterogeneous, distributed data in various formats and from different kinds of examinations such as Holter, Doppler and electrocardiography.

ExxonMobil Refining and Supply Company, Baton Rouge Complex - Order Denying Petition for Object to Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Petition for the Administrator to Object to Title V Operating Permit for Fort Smallwood Complex Brandon Shores and H.A. Wagner Generating Stations

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Thai Norms for Name, Image, and Category Agreement, Object Familiarity, Visual Complexity, Manipulability, and Age of Acquisition for 480 Color Photographic Objects

ERIC Educational Resources Information Center

Clarke, A. J. Benjamin; Ludington, Jason D.

2018-01-01

Normative databases containing psycholinguistic variables are commonly used to aid stimulus selection for investigations into language and other cognitive processes. Norms exist for many languages, but not for Thai. The aim of the present research, therefore, was to obtain Thai normative data for the BOSS, a set of 480 high resolution color…

C++, objected-oriented programming, and astronomical data models

NASA Technical Reports Server (NTRS)

Farris, A.

1992-01-01

Contemporary astronomy is characterized by increasingly complex instruments and observational techniques, higher data collection rates, and large data archives, placing severe stress on software analysis systems. The object-oriented paradigm represents a significant new approach to software design and implementation that holds great promise for dealing with this increased complexity. The basic concepts of this approach will be characterized in contrast to more traditional procedure-oriented approaches. The fundamental features of objected-oriented programming will be discussed from a C++ programming language perspective, using examples familiar to astronomers. This discussion will focus on objects, classes and their relevance to the data type system; the principle of information hiding; and the use of inheritance to implement generalization/specialization relationships. Drawing on the object-oriented approach, features of a new database model to support astronomical data analysis will be presented.

Object technology: A white paper

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

Jordan, S.R.; Arrowood, L.F.; Cain, W.D.

1992-05-11

Object-Oriented Technology (OOT), although not a new paradigm, has recently been prominently featured in the trade press and even general business publications. Indeed, the promises of object technology are alluring: the ability to handle complex design and engineering information through the full manufacturing production life cycle or to manipulate multimedia information, and the ability to improve programmer productivity in creating and maintaining high quality software. Groups at a number of the DOE facilities have been exploring the use of object technology for engineering, business, and other applications. In this white paper, the technology is explored thoroughly and compared with previousmore » means of developing software and storing databases of information. Several specific projects within the DOE Complex are described, and the state of the commercial marketplace is indicated.« less

[Technical improvement of cohort constitution in administrative health databases: Providing a tool for integration and standardization of data applicable in the French National Health Insurance Database (SNIIRAM)].

PubMed

Ferdynus, C; Huiart, L

2016-09-01

Administrative health databases such as the French National Heath Insurance Database - SNIIRAM - are a major tool to answer numerous public health research questions. However the use of such data requires complex and time-consuming data management. Our objective was to develop and make available a tool to optimize cohort constitution within administrative health databases. We developed a process to extract, transform and load (ETL) data from various heterogeneous sources in a standardized data warehouse. This data warehouse is architected as a star schema corresponding to an i2b2 star schema model. We then evaluated the performance of this ETL using data from a pharmacoepidemiology research project conducted in the SNIIRAM database. The ETL we developed comprises a set of functionalities for creating SAS scripts. Data can be integrated into a standardized data warehouse. As part of the performance assessment of this ETL, we achieved integration of a dataset from the SNIIRAM comprising more than 900 million lines in less than three hours using a desktop computer. This enables patient selection from the standardized data warehouse within seconds of the request. The ETL described in this paper provides a tool which is effective and compatible with all administrative health databases, without requiring complex database servers. This tool should simplify cohort constitution in health databases; the standardization of warehouse data facilitates collaborative work between research teams. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

SNAPPI-DB: a database and API of Structures, iNterfaces and Alignments for Protein–Protein Interactions

PubMed Central

Jefferson, Emily R.; Walsh, Thomas P.; Roberts, Timothy J.; Barton, Geoffrey J.

2007-01-01

SNAPPI-DB, a high performance database of Structures, iNterfaces and Alignments of Protein–Protein Interactions, and its associated Java Application Programming Interface (API) is described. SNAPPI-DB contains structural data, down to the level of atom co-ordinates, for each structure in the Protein Data Bank (PDB) together with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary Structures (PQS) and secondary structure information. Domain–domain interactions are stored for multiple domain definitions and are classified by their Superfamily/Family pair and interaction interface. Each set of classified domain–domain interactions has an associated multiple structure alignment for each partner. The API facilitates data access via PDB entries, domains and domain–domain interactions. Rapid development, fast database access and the ability to perform advanced queries without the requirement for complex SQL statements are provided via an object oriented database and the Java Data Objects (JDO) API. SNAPPI-DB contains many features which are not available in other databases of structural protein–protein interactions. It has been applied in three studies on the properties of protein–protein interactions and is currently being employed to train a protein–protein interaction predictor and a functional residue predictor. The database, API and manual are available for download at: . PMID:17202171

Aggregated Indexing of Biomedical Time Series Data

PubMed Central

Woodbridge, Jonathan; Mortazavi, Bobak; Sarrafzadeh, Majid; Bui, Alex A.T.

2016-01-01

Remote and wearable medical sensing has the potential to create very large and high dimensional datasets. Medical time series databases must be able to efficiently store, index, and mine these datasets to enable medical professionals to effectively analyze data collected from their patients. Conventional high dimensional indexing methods are a two stage process. First, a superset of the true matches is efficiently extracted from the database. Second, supersets are pruned by comparing each of their objects to the query object and rejecting any objects falling outside a predetermined radius. This pruning stage heavily dominates the computational complexity of most conventional search algorithms. Therefore, indexing algorithms can be significantly improved by reducing the amount of pruning. This paper presents an online algorithm to aggregate biomedical times series data to significantly reduce the search space (index size) without compromising the quality of search results. This algorithm is built on the observation that biomedical time series signals are composed of cyclical and often similar patterns. This algorithm takes in a stream of segments and groups them to highly concentrated collections. Locality Sensitive Hashing (LSH) is used to reduce the overall complexity of the algorithm, allowing it to run online. The output of this aggregation is used to populate an index. The proposed algorithm yields logarithmic growth of the index (with respect to the total number of objects) while keeping sensitivity and specificity simultaneously above 98%. Both memory and runtime complexities of time series search are improved when using aggregated indexes. In addition, data mining tasks, such as clustering, exhibit runtimes that are orders of magnitudes faster when run on aggregated indexes. PMID:27617298

Sequence modelling and an extensible data model for genomic database

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

Li, Peter Wei-Der

1992-01-01

The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS's do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data modelmore » that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the Extensible Object Model'', to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.« less

Sequence modelling and an extensible data model for genomic database

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

Li, Peter Wei-Der

1992-01-01

The Human Genome Project (HGP) plans to sequence the human genome by the beginning of the next century. It will generate DNA sequences of more than 10 billion bases and complex marker sequences (maps) of more than 100 million markers. All of these information will be stored in database management systems (DBMSs). However, existing data models do not have the abstraction mechanism for modelling sequences and existing DBMS`s do not have operations for complex sequences. This work addresses the problem of sequence modelling in the context of the HGP and the more general problem of an extensible object data modelmore » that can incorporate the sequence model as well as existing and future data constructs and operators. First, we proposed a general sequence model that is application and implementation independent. This model is used to capture the sequence information found in the HGP at the conceptual level. In addition, abstract and biological sequence operators are defined for manipulating the modelled sequences. Second, we combined many features of semantic and object oriented data models into an extensible framework, which we called the ``Extensible Object Model``, to address the need of a modelling framework for incorporating the sequence data model with other types of data constructs and operators. This framework is based on the conceptual separation between constructors and constraints. We then used this modelling framework to integrate the constructs for the conceptual sequence model. The Extensible Object Model is also defined with a graphical representation, which is useful as a tool for database designers. Finally, we defined a query language to support this model and implement the query processor to demonstrate the feasibility of the extensible framework and the usefulness of the conceptual sequence model.« less

Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases

PubMed Central

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2018-01-01

This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query Language)) standardized electronic health record (EHR) medical information database systems (DBMS). It uses a set of three doubling-sized databases, i.e. databases storing 5000, 10,000 and 20,000 realistic standardized EHR extracts, in three different database management systems (DBMS): relational MySQL object-relational mapping (ORM), document-based NoSQL MongoDB, and native extensible markup language (XML) NoSQL eXist. The average response times to six complexity-increasing queries were computed, and the results showed a linear behavior in the NoSQL cases. In the NoSQL field, MongoDB presents a much flatter linear slope than eXist. NoSQL systems may also be more appropriate to maintain standardized medical information systems due to the special nature of the updating policies of medical information, which should not affect the consistency and efficiency of the data stored in NoSQL databases. One limitation of this protocol is the lack of direct results of improved relational systems such as archetype relational mapping (ARM) with the same data. However, the interpolation of doubling-size database results to those presented in the literature and other published results suggests that NoSQL systems might be more appropriate in many specific scenarios and problems to be solved. For example, NoSQL may be appropriate for document-based tasks such as EHR extracts used in clinical practice, or edition and visualization, or situations where the aim is not only to query medical information, but also to restore the EHR in exactly its original form. PMID:29608174

Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2018-03-19

This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query Language)) standardized electronic health record (EHR) medical information database systems (DBMS). It uses a set of three doubling-sized databases, i.e. databases storing 5000, 10,000 and 20,000 realistic standardized EHR extracts, in three different database management systems (DBMS): relational MySQL object-relational mapping (ORM), document-based NoSQL MongoDB, and native extensible markup language (XML) NoSQL eXist. The average response times to six complexity-increasing queries were computed, and the results showed a linear behavior in the NoSQL cases. In the NoSQL field, MongoDB presents a much flatter linear slope than eXist. NoSQL systems may also be more appropriate to maintain standardized medical information systems due to the special nature of the updating policies of medical information, which should not affect the consistency and efficiency of the data stored in NoSQL databases. One limitation of this protocol is the lack of direct results of improved relational systems such as archetype relational mapping (ARM) with the same data. However, the interpolation of doubling-size database results to those presented in the literature and other published results suggests that NoSQL systems might be more appropriate in many specific scenarios and problems to be solved. For example, NoSQL may be appropriate for document-based tasks such as EHR extracts used in clinical practice, or edition and visualization, or situations where the aim is not only to query medical information, but also to restore the EHR in exactly its original form.

Generation of large scale urban environments to support advanced sensor and seeker simulation

NASA Astrophysics Data System (ADS)

Giuliani, Joseph; Hershey, Daniel; McKeown, David, Jr.; Willis, Carla; Van, Tan

2009-05-01

One of the key aspects for the design of a next generation weapon system is the need to operate in cluttered and complex urban environments. Simulation systems rely on accurate representation of these environments and require automated software tools to construct the underlying 3D geometry and associated spectral and material properties that are then formatted for various objective seeker simulation systems. Under an Air Force Small Business Innovative Research (SBIR) contract, we have developed an automated process to generate 3D urban environments with user defined properties. These environments can be composed from a wide variety of source materials, including vector source data, pre-existing 3D models, and digital elevation models, and rapidly organized into a geo-specific visual simulation database. This intermediate representation can be easily inspected in the visible spectrum for content and organization and interactively queried for accuracy. Once the database contains the required contents, it can then be exported into specific synthetic scene generation runtime formats, preserving the relationship between geometry and material properties. To date an exporter for the Irma simulation system developed and maintained by AFRL/Eglin has been created and a second exporter to Real Time Composite Hardbody and Missile Plume (CHAMP) simulation system for real-time use is currently being developed. This process supports significantly more complex target environments than previous approaches to database generation. In this paper we describe the capabilities for content creation for advanced seeker processing algorithms simulation and sensor stimulation, including the overall database compilation process and sample databases produced and exported for the Irma runtime system. We also discuss the addition of object dynamics and viewer dynamics within the visual simulation into the Irma runtime environment.

The development of a dynamic software for the user interaction from the geographic information system environment with the database of the calibration site of the satellite remote electro-optic sensors

NASA Astrophysics Data System (ADS)

Zyelyk, Ya. I.; Semeniv, O. V.

2015-12-01

The state of the problem of the post-launch calibration of the satellite electro-optic remote sensors and its solutions in Ukraine is analyzed. The database is improved and dynamic services for user interaction with database from the environment of open geographical information system Quantum GIS for information support of calibration activities are created. A dynamic application under QGIS is developed, implementing these services in the direction of the possibility of data entering, editing and extraction from the database, using the technology of object-oriented programming and of modern complex program design patterns. The functional and algorithmic support of this dynamic software and its interface are developed.

The IRMIS object model and services API.

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

Saunders, C.; Dohan, D. A.; Arnold, N. D.

2005-01-01

The relational model developed for the Integrated Relational Model of Installed Systems (IRMIS) toolkit has been successfully used to capture the Advanced Photon Source (APS) control system software (EPICS process variables and their definitions). The relational tables are populated by a crawler script that parses each Input/Output Controller (IOC) start-up file when an IOC reboot is detected. User interaction is provided by a Java Swing application that acts as a desktop for viewing the process variable information. Mapping between the display objects and the relational tables was carried out with the Hibernate Object Relational Modeling (ORM) framework. Work is wellmore » underway at the APS to extend the relational modeling to include control system hardware. For this work, due in part to the complex user interaction required, the primary application development environment has shifted from the relational database view to the object oriented (Java) perspective. With this approach, the business logic is executed in Java rather than in SQL stored procedures. This paper describes the object model used to represent control system software, hardware, and interconnects in IRMIS. We also describe the services API used to encapsulate the required behaviors for creating and maintaining the complex data. In addition to the core schema and object model, many important concepts in IRMIS are captured by the services API. IRMIS is an ambitious collaborative effort for defining and developing a relational database and associated applications to comprehensively document the large and complex EPICS-based control systems of today's accelerators. The documentation effort includes process variables, control system hardware, and interconnections. The approach could also be used to document all components of the accelerator, including mechanical, vacuum, power supplies, etc. One key aspect of IRMIS is that it is a documentation framework, not a design and development tool. We do not generate EPICS control system configurations from IRMIS, and hence do not impose any additional requirements on EPICS developers.« less

It's all connected: Pathways in visual object recognition and early noun learning.

PubMed

Smith, Linda B

2013-11-01

A developmental pathway may be defined as the route, or chain of events, through which a new structure or function forms. For many human behaviors, including object name learning and visual object recognition, these pathways are often complex and multicausal and include unexpected dependencies. This article presents three principles of development that suggest the value of a developmental psychology that explicitly seeks to trace these pathways and uses empirical evidence on developmental dependencies among motor development, action on objects, visual object recognition, and object name learning in 12- to 24-month-old infants to make the case. The article concludes with a consideration of the theoretical implications of this approach. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

The Clinical Aspects of Mirror Therapy in Rehabilitation: A Systematic Review of the Literature

ERIC Educational Resources Information Center

Rothgangel, Andreas Stefan; Braun, Susy M.; Beurskens, Anna J.; Seitz, Rudiger J.; Wade, Derick T.

2011-01-01

The objective of this study was to evaluate the clinical aspects of mirror therapy (MT) interventions after stroke, phantom limb pain and complex regional pain syndrome. A systematic literature search of the Cochrane Database of controlled trials, PubMed/MEDLINE, CINAHL, EMBASE, PsycINFO, PEDro, RehabTrials and Rehadat, was made by two…

Distributed query plan generation using multiobjective genetic algorithm.

PubMed

Panicker, Shina; Kumar, T V Vijay

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability.

Distributed Query Plan Generation Using Multiobjective Genetic Algorithm

PubMed Central

Panicker, Shina; Vijay Kumar, T. V.

2014-01-01

A distributed query processing strategy, which is a key performance determinant in accessing distributed databases, aims to minimize the total query processing cost. One way to achieve this is by generating efficient distributed query plans that involve fewer sites for processing a query. In the case of distributed relational databases, the number of possible query plans increases exponentially with respect to the number of relations accessed by the query and the number of sites where these relations reside. Consequently, computing optimal distributed query plans becomes a complex problem. This distributed query plan generation (DQPG) problem has already been addressed using single objective genetic algorithm, where the objective is to minimize the total query processing cost comprising the local processing cost (LPC) and the site-to-site communication cost (CC). In this paper, this DQPG problem is formulated and solved as a biobjective optimization problem with the two objectives being minimize total LPC and minimize total CC. These objectives are simultaneously optimized using a multiobjective genetic algorithm NSGA-II. Experimental comparison of the proposed NSGA-II based DQPG algorithm with the single objective genetic algorithm shows that the former performs comparatively better and converges quickly towards optimal solutions for an observed crossover and mutation probability. PMID:24963513

A SYSTEMATIC SEARCH FOR THE SPECTRA WITH FEATURES OF CRYSTALLINE SILICATES IN THE SPITZER IRS ENHANCED PRODUCTS

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

Chen, Rui; Luo, Ali; Liu, Jiaming

2016-06-01

The crystalline silicate features are mainly reflected in infrared bands. The Spitzer Infrared Spectrograph (IRS) collected numerous spectra of various objects and provided a big database to investigate crystalline silicates in a wide range of astronomical environments. We apply the manifold ranking algorithm to perform a systematic search for the spectra with crystalline silicate features in the Spitzer IRS Enhanced Products available. In total, 868 spectra of 790 sources are found to show the features of crystalline silicates. These objects are cross-matched with the SIMBAD database as well as with the Large Sky Area Multi-object Fiber Spectroscopic Telescope (LAMOST)/DR2. Themore » average spectrum of young stellar objects shows a variety of features dominated either by forsterite or enstatite or neither, while the average spectrum of evolved objects consistently present dominant features of forsterite in AGB, OH/IR, post-AGB, and planetary nebulae. They are identified optically as early-type stars, evolved stars, galaxies and so on. In addition, the strength of spectral features in typical silicate complexes is calculated. The results are available through CDS for the astronomical community to further study crystalline silicates.« less

An assembly process model based on object-oriented hierarchical time Petri Nets

NASA Astrophysics Data System (ADS)

Wang, Jiapeng; Liu, Shaoli; Liu, Jianhua; Du, Zenghui

2017-04-01

In order to improve the versatility, accuracy and integrity of the assembly process model of complex products, an assembly process model based on object-oriented hierarchical time Petri Nets is presented. A complete assembly process information model including assembly resources, assembly inspection, time, structure and flexible parts is established, and this model describes the static and dynamic data involved in the assembly process. Through the analysis of three-dimensional assembly process information, the assembly information is hierarchically divided from the whole, the local to the details and the subnet model of different levels of object-oriented Petri Nets is established. The communication problem between Petri subnets is solved by using message database, and it reduces the complexity of system modeling effectively. Finally, the modeling process is presented, and a five layer Petri Nets model is established based on the hoisting process of the engine compartment of a wheeled armored vehicle.

Security Event Recognition for Visual Surveillance

NASA Astrophysics Data System (ADS)

Liao, W.; Yang, C.; Yang, M. Ying; Rosenhahn, B.

2017-05-01

With rapidly increasing deployment of surveillance cameras, the reliable methods for automatically analyzing the surveillance video and recognizing special events are demanded by different practical applications. This paper proposes a novel effective framework for security event analysis in surveillance videos. First, convolutional neural network (CNN) framework is used to detect objects of interest in the given videos. Second, the owners of the objects are recognized and monitored in real-time as well. If anyone moves any object, this person will be verified whether he/she is its owner. If not, this event will be further analyzed and distinguished between two different scenes: moving the object away or stealing it. To validate the proposed approach, a new video dataset consisting of various scenarios is constructed for more complex tasks. For comparison purpose, the experiments are also carried out on the benchmark databases related to the task on abandoned luggage detection. The experimental results show that the proposed approach outperforms the state-of-the-art methods and effective in recognizing complex security events.

Identification and characterization of low-mass stars and brown dwarfs using Virtual Observatory tools.

NASA Astrophysics Data System (ADS)

Aberasturi, M.; Solano, E.; Martín, E.

2015-05-01

Low-mass stars and brown dwarfs (with spectral types M, L, T and Y) are the most common objects in the Milky Way. A complete census of these objects is necessary to understand the theories about their complex structure and formation processes. In order to increase the number of known objects in the Solar neighborhood (d<30 pc), we have made use of the Virtual Observatory which allows an efficient handling of the huge amount of information available in astronomical databases. We also used the WFC3 installed in the Hubble Space Telescope to look for T5+ dwarfs binaries.

Aerodynamic Optimization of Rocket Control Surface Geometry Using Cartesian Methods and CAD Geometry

NASA Technical Reports Server (NTRS)

Nelson, Andrea; Aftosmis, Michael J.; Nemec, Marian; Pulliam, Thomas H.

2004-01-01

Aerodynamic design is an iterative process involving geometry manipulation and complex computational analysis subject to physical constraints and aerodynamic objectives. A design cycle consists of first establishing the performance of a baseline design, which is usually created with low-fidelity engineering tools, and then progressively optimizing the design to maximize its performance. Optimization techniques have evolved from relying exclusively on designer intuition and insight in traditional trial and error methods, to sophisticated local and global search methods. Recent attempts at automating the search through a large design space with formal optimization methods include both database driven and direct evaluation schemes. Databases are being used in conjunction with surrogate and neural network models as a basis on which to run optimization algorithms. Optimization algorithms are also being driven by the direct evaluation of objectives and constraints using high-fidelity simulations. Surrogate methods use data points obtained from simulations, and possibly gradients evaluated at the data points, to create mathematical approximations of a database. Neural network models work in a similar fashion, using a number of high-fidelity database calculations as training iterations to create a database model. Optimal designs are obtained by coupling an optimization algorithm to the database model. Evaluation of the current best design then gives either a new local optima and/or increases the fidelity of the approximation model for the next iteration. Surrogate methods have also been developed that iterate on the selection of data points to decrease the uncertainty of the approximation model prior to searching for an optimal design. The database approximation models for each of these cases, however, become computationally expensive with increase in dimensionality. Thus the method of using optimization algorithms to search a database model becomes problematic as the number of design variables is increased.

Object Recognition and Localization: The Role of Tactile Sensors

PubMed Central

Aggarwal, Achint; Kirchner, Frank

2014-01-01

Tactile sensors, because of their intrinsic insensitivity to lighting conditions and water turbidity, provide promising opportunities for augmenting the capabilities of vision sensors in applications involving object recognition and localization. This paper presents two approaches for haptic object recognition and localization for ground and underwater environments. The first approach called Batch Ransac and Iterative Closest Point augmented Particle Filter (BRICPPF) is based on an innovative combination of particle filters, Iterative-Closest-Point algorithm, and a feature-based Random Sampling and Consensus (RANSAC) algorithm for database matching. It can handle a large database of 3D-objects of complex shapes and performs a complete six-degree-of-freedom localization of static objects. The algorithms are validated by experimentation in ground and underwater environments using real hardware. To our knowledge this is the first instance of haptic object recognition and localization in underwater environments. The second approach is biologically inspired, and provides a close integration between exploration and recognition. An edge following exploration strategy is developed that receives feedback from the current state of recognition. A recognition by parts approach is developed which uses the BRICPPF for object sub-part recognition. Object exploration is either directed to explore a part until it is successfully recognized, or is directed towards new parts to endorse the current recognition belief. This approach is validated by simulation experiments. PMID:24553087

Open Geoscience Database

NASA Astrophysics Data System (ADS)

Bashev, A.

2012-04-01

Currently there is an enormous amount of various geoscience databases. Unfortunately the only users of the majority of the databases are their elaborators. There are several reasons for that: incompaitability, specificity of tasks and objects and so on. However the main obstacles for wide usage of geoscience databases are complexity for elaborators and complication for users. The complexity of architecture leads to high costs that block the public access. The complication prevents users from understanding when and how to use the database. Only databases, associated with GoogleMaps don't have these drawbacks, but they could be hardly named "geoscience" Nevertheless, open and simple geoscience database is necessary at least for educational purposes (see our abstract for ESSI20/EOS12). We developed a database and web interface to work with them and now it is accessible at maps.sch192.ru. In this database a result is a value of a parameter (no matter which) in a station with a certain position, associated with metadata: the date when the result was obtained; the type of a station (lake, soil etc); the contributor that sent the result. Each contributor has its own profile, that allows to estimate the reliability of the data. The results can be represented on GoogleMaps space image as a point in a certain position, coloured according to the value of the parameter. There are default colour scales and each registered user can create the own scale. The results can be also extracted in *.csv file. For both types of representation one could select the data by date, object type, parameter type, area and contributor. The data are uploaded in *.csv format: Name of the station; Lattitude(dd.dddddd); Longitude(ddd.dddddd); Station type; Parameter type; Parameter value; Date(yyyy-mm-dd). The contributor is recognised while entering. This is the minimal set of features that is required to connect a value of a parameter with a position and see the results. All the complicated data treatment could be conducted in other programs after extraction the filtered data into *.csv file. It makes the database understandable for non-experts. The database employs open data format (*.csv) and wide spread tools: PHP as the program language, MySQL as database management system, JavaScript for interaction with GoogleMaps and JQueryUI for create user interface. The database is multilingual: there are association tables, which connect with elements of the database. In total the development required about 150 hours. The database still has several problems. The main problem is the reliability of the data. Actually it needs an expert system for estimation the reliability, but the elaboration of such a system would take more resources than the database itself. The second problem is the problem of stream selection - how to select the stations that are connected with each other (for example, belong to one water stream) and indicate their sequence. Currently the interface is English and Russian. However it can be easily translated to your language. But some problems we decided. For example problem "the problem of the same station" (sometimes the distance between stations is smaller, than the error of position): when you adding new station to the database our application automatically find station near this place. Also we decided problem of object and parameter type (how to regard "EC" and "electrical conductivity" as the same parameter). This problem has been solved using "associative tables". If you would like to see the interface on your language, just contact us. We should send you the list of terms and phrases for translation on your language. The main advantage of the database is that it is totally open: everybody can see, extract the data from the database and use them for non-commercial purposes with no charge. Registered users can contribute to the database without getting paid. We hope, that it will be widely used first of all for education purposes, but professional scientists could use it also.

Broad attention to multiple individual objects may facilitate change detection with complex auditory scenes.

PubMed

Irsik, Vanessa C; Vanden Bosch der Nederlanden, Christina M; Snyder, Joel S

2016-11-01

Attention and other processing constraints limit the perception of objects in complex scenes, which has been studied extensively in the visual sense. We used a change deafness paradigm to examine how attention to particular objects helps and hurts the ability to notice changes within complex auditory scenes. In a counterbalanced design, we examined how cueing attention to particular objects affected performance in an auditory change-detection task through the use of valid or invalid cues and trials without cues (Experiment 1). We further examined how successful encoding predicted change-detection performance using an object-encoding task and we addressed whether performing the object-encoding task along with the change-detection task affected performance overall (Experiment 2). Participants had more error for invalid compared to valid and uncued trials, but this effect was reduced in Experiment 2 compared to Experiment 1. When the object-encoding task was present, listeners who completed the uncued condition first had less overall error than those who completed the cued condition first. All participants showed less change deafness when they successfully encoded change-relevant compared to irrelevant objects during valid and uncued trials. However, only participants who completed the uncued condition first also showed this effect during invalid cue trials, suggesting a broader scope of attention. These findings provide converging evidence that attention to change-relevant objects is crucial for successful detection of acoustic changes and that encouraging broad attention to multiple objects is the best way to reduce change deafness. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

[Review of digital ground object spectral library].

PubMed

Zhou, Xiao-Hu; Zhou, Ding-Wu

2009-06-01

A higher spectral resolution is the main direction of developing remote sensing technology, and it is quite important to set up the digital ground object reflectance spectral database library, one of fundamental research fields in remote sensing application. Remote sensing application has been increasingly relying on ground object spectral characteristics, and quantitative analysis has been developed to a new stage. The present article summarized and systematically introduced the research status quo and development trend of digital ground object reflectance spectral libraries at home and in the world in recent years. Introducing the spectral libraries has been established, including desertification spectral database library, plants spectral database library, geological spectral database library, soil spectral database library, minerals spectral database library, cloud spectral database library, snow spectral database library, the atmosphere spectral database library, rocks spectral database library, water spectral database library, meteorites spectral database library, moon rock spectral database library, and man-made materials spectral database library, mixture spectral database library, volatile compounds spectral database library, and liquids spectral database library. In the process of establishing spectral database libraries, there have been some problems, such as the lack of uniform national spectral database standard and uniform standards for the ground object features as well as the comparability between different databases. In addition, data sharing mechanism can not be carried out, etc. This article also put forward some suggestions on those problems.

A resource oriented webs service for environmental modeling

NASA Astrophysics Data System (ADS)

Ferencik, Ioan

2013-04-01

Environmental modeling is a largely adopted practice in the study of natural phenomena. Environmental models can be difficult to build and use and thus sharing them within the community is an important aspect. The most common approach to share a model is to expose it as a web service. In practice the interaction with this web service is cumbersome due to lack of standardized contract and the complexity of the model being exposed. In this work we investigate the use of a resource oriented approach in exposing environmental models as web services. We view a model as a layered resource build atop the object concept from Object Oriented Programming, augmented with persistence capabilities provided by an embedded object database to keep track of its state and implementing the four basic principles of resource oriented architectures: addressability, statelessness, representation and uniform interface. For implementation we use exclusively open source software: Django framework, dyBase object oriented database and Python programming language. We developed a generic framework of resources structured into a hierarchy of types and consequently extended this typology with recurses specific to the domain of environmental modeling. To test our web service we used cURL, a robust command-line based web client.

French database of children and adolescents with Prader-Willi syndrome

PubMed Central

Molinas, Catherine; Cazals, Laurent; Diene, Gwenaelle; Glattard, Melanie; Arnaud, Catherine; Tauber, Maithe

2008-01-01

Background Prader-Willi syndrome (PWS) is a rare multisystem genetic disease leading to severe complications mainly related to obesity. We strongly lack information on the natural history of this complex disease and on what factors are involved in its evolution and its outcome. One of the objectives of the French reference centre for Prader-Willi syndrome set-up in 2004 was to set-up a database in order to make the inventory of Prader-Willi syndrome cases and initiate a national cohort study in the area covered by the centre. Description the database includes medical data of children and adolescents with Prader-Willi syndrome, details about their management, socio-demographic data on their families, psychological data and quality of life of the parents. The tools and organisation used to ensure data collection and data quality in respect of good clinical practice procedures are discussed, and main characteristics of our Prader-Willi population at inclusion are presented. Conclusion this database covering all the aspects of PWS clinical, psychological and social profiles, including familial psychological and quality of life will be a powerful tool for retrospective studies concerning this complex and multi factorial disease and could be a basis for the design of future prospective multicentric studies. The complete database and the Stata.do files are available to any researcher wishing to use them for non-commercial purposes and can be provided upon request to the corresponding author. PMID:18831731

An advanced web query interface for biological databases

PubMed Central

Latendresse, Mario; Karp, Peter D.

2010-01-01

Although most web-based biological databases (DBs) offer some type of web-based form to allow users to author DB queries, these query forms are quite restricted in the complexity of DB queries that they can formulate. They can typically query only one DB, and can query only a single type of object at a time (e.g. genes) with no possible interaction between the objects—that is, in SQL parlance, no joins are allowed between DB objects. Writing precise queries against biological DBs is usually left to a programmer skillful enough in complex DB query languages like SQL. We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough to be used by biologists. It supports queries containing multiple conditions, and connecting multiple object types without using the join concept, which is unintuitive to biologists. This interactive web interface is called the Structured Advanced Query Page (SAQP). Users interactively build up a wide range of query constructs. Interactive documentation within the SAQP describes the schema of the queried DBs. The SAQP is based on BioVelo, a query language based on list comprehension. The SAQP is part of the Pathway Tools software and is available as part of several bioinformatics web sites powered by Pathway Tools, including the BioCyc.org site that contains more than 500 Pathway/Genome DBs. PMID:20624715

The Planetary Virtual Observatory and Laboratory (PVOL) and its integration into the Virtual European Solar and Planetary Access (VESPA)

NASA Astrophysics Data System (ADS)

Hueso, R.; Juaristi, J.; Legarreta, J.; Sánchez-Lavega, A.; Rojas, J. F.; Erard, S.; Cecconi, B.; Le Sidaner, Pierre

2018-01-01

Since 2003 the Planetary Virtual Observatory and Laboratory (PVOL) has been storing and serving publicly through its web site a large database of amateur observations of the Giant Planets (Hueso et al., 2010a). These images are used for scientific research of the atmospheric dynamics and cloud structure on these planets and constitute a powerful resource to address time variable phenomena in their atmospheres. Advances over the last decade in observation techniques, and a wider recognition by professional astronomers of the quality of amateur observations, have resulted in the need to upgrade this database. We here present major advances in the PVOL database, which has evolved into a full virtual planetary observatory encompassing also observations of Mercury, Venus, Mars, the Moon and the Galilean satellites. Besides the new objects, the images can be tagged and the database allows simple and complex searches over the data. The new web service: PVOL2 is available online in http://pvol2.ehu.eus/.

The Biomolecular Interaction Network Database and related tools 2005 update

PubMed Central

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

2005-01-01

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

A standardized set of 3-D objects for virtual reality research and applications.

PubMed

Peeters, David

2018-06-01

The use of immersive virtual reality as a research tool is rapidly increasing in numerous scientific disciplines. By combining ecological validity with strict experimental control, immersive virtual reality provides the potential to develop and test scientific theories in rich environments that closely resemble everyday settings. This article introduces the first standardized database of colored three-dimensional (3-D) objects that can be used in virtual reality and augmented reality research and applications. The 147 objects have been normed for name agreement, image agreement, familiarity, visual complexity, and corresponding lexical characteristics of the modal object names. The availability of standardized 3-D objects for virtual reality research is important, because reaching valid theoretical conclusions hinges critically on the use of well-controlled experimental stimuli. Sharing standardized 3-D objects across different virtual reality labs will allow for science to move forward more quickly.

Feasibility of Population Health Analytics and Data Visualization for Decision Support in the Infectious Diseases Domain

PubMed Central

Del Fiol, Guilherme; Butler, Jorie; Livnat, Yarden; Mayer, Jeanmarie; Samore, Matthew; Jones, Makoto; Weir, Charlene

2016-01-01

Summary Objective Big data or population-based information has the potential to reduce uncertainty in medicine by informing clinicians about individual patient care. The objectives of this study were: 1) to explore the feasibility of extracting and displaying population-based information from an actual clinical population’s database records, 2) to explore specific design features for improving population display, 3) to explore perceptions of population information displays, and 4) to explore the impact of population information display on cognitive outcomes. Methods We used the Veteran’s Affairs (VA) database to identify similar complex patients based on a similar complex patient case. Study outcomes measures were 1) preferences for population information display 2) time looking at the population display, 3) time to read the chart, and 4) appropriateness of plans with pre- and post-presentation of population data. Finally, we redesigned the population information display based on our findings from this study. Results The qualitative data analysis for preferences of population information display resulted in four themes: 1) trusting the big/population data can be an issue, 2) embedded analytics is necessary to explore patient similarities, 3) need for tools to control the view (overview, zoom and filter), and 4) different presentations of the population display can be beneficial to improve the display. We found that appropriateness of plans was at 60% for both groups (t9=-1.9; p=0.08), and overall time looking at the population information display was 2.3 minutes versus 3.6 minutes with experts processing information faster than non-experts (t8= -2.3, p=0.04). Conclusion A population database has great potential for reducing complexity and uncertainty in medicine to improve clinical care. The preferences identified for the population information display will guide future health information technology system designers for better and more intuitive display. PMID:27437065

A rudimentary database for three-dimensional objects using structural representation

NASA Technical Reports Server (NTRS)

Sowers, James P.

1987-01-01

A database which enables users to store and share the description of three-dimensional objects in a research environment is presented. The main objective of the design is to make it a compact structure that holds sufficient information to reconstruct the object. The database design is based on an object representation scheme which is information preserving, reasonably efficient, and yet economical in terms of the storage requirement. The determination of the needed data for the reconstruction process is guided by the belief that it is faster to do simple computations to generate needed data/information for construction than to retrieve everything from memory. Some recent techniques of three-dimensional representation that influenced the design of the database are discussed. The schema for the database and the structural definition used to define an object are given. The user manual for the software developed to create and maintain the contents of the database is included.

Web-based Electronic Sharing and RE-allocation of Assets

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

Leverett, Dave; Miller, Robert A.; Berlin, Gary J.

2002-09-09

The Electronic Asses Sharing Program is a web-based application that provides the capability for complex-wide sharing and reallocation of assets that are excess, under utilized, or un-utilized. through a web-based fron-end and supporting has database with a search engine, users can search for assets that they need, search for assets needed by others, enter assets they need, and enter assets they have available for reallocation. In addition, entire listings of available assets and needed assets can be viewed. The application is written in Java, the hash database and search engine are in Object-oriented Java Database Management (OJDBM). The application willmore » be hosted on an SRS-managed server outside the Firewall and access will be controlled via a protected realm. An example of the application can be viewed at the followinig (temporary) URL: http://idgdev.srs.gov/servlet/srs.weshare.WeShare« less

Paradise: A Parallel Information System for EOSDIS

NASA Technical Reports Server (NTRS)

DeWitt, David

1996-01-01

The Paradise project was begun-in 1993 in order to explore the application of the parallel and object-oriented database system technology developed as a part of the Gamma, Exodus. and Shore projects to the design and development of a scaleable, geo-spatial database system for storing both massive spatial and satellite image data sets. Paradise is based on an object-relational data model. In addition to the standard attribute types such as integers, floats, strings and time, Paradise also provides a set of and multimedia data types, designed to facilitate the storage and querying of complex spatial and multimedia data sets. An individual tuple can contain any combination of this rich set of data types. For example, in the EOSDIS context, a tuple might mix terrain and map data for an area along with the latest satellite weather photo of the area. The use of a geo-spatial metaphor simplifies the task of fusing disparate forms of data from multiple data sources including text, image, map, and video data sets.

Randomized Approaches for Nearest Neighbor Search in Metric Space When Computing the Pairwise Distance Is Extremely Expensive

NASA Astrophysics Data System (ADS)

Wang, Lusheng; Yang, Yong; Lin, Guohui

Finding the closest object for a query in a database is a classical problem in computer science. For some modern biological applications, computing the similarity between two objects might be very time consuming. For example, it takes a long time to compute the edit distance between two whole chromosomes and the alignment cost of two 3D protein structures. In this paper, we study the nearest neighbor search problem in metric space, where the pair-wise distance between two objects in the database is known and we want to minimize the number of distances computed on-line between the query and objects in the database in order to find the closest object. We have designed two randomized approaches for indexing metric space databases, where objects are purely described by their distances with each other. Analysis and experiments show that our approaches only need to compute O(logn) objects in order to find the closest object, where n is the total number of objects in the database.

Study of Temporal Effects on Subjective Video Quality of Experience.

PubMed

Bampis, Christos George; Zhi Li; Moorthy, Anush Krishna; Katsavounidis, Ioannis; Aaron, Anne; Bovik, Alan Conrad

2017-11-01

HTTP adaptive streaming is being increasingly deployed by network content providers, such as Netflix and YouTube. By dividing video content into data chunks encoded at different bitrates, a client is able to request the appropriate bitrate for the segment to be played next based on the estimated network conditions. However, this can introduce a number of impairments, including compression artifacts and rebuffering events, which can severely impact an end-user's quality of experience (QoE). We have recently created a new video quality database, which simulates a typical video streaming application, using long video sequences and interesting Netflix content. Going beyond previous efforts, the new database contains highly diverse and contemporary content, and it includes the subjective opinions of a sizable number of human subjects regarding the effects on QoE of both rebuffering and compression distortions. We observed that rebuffering is always obvious and unpleasant to subjects, while bitrate changes may be less obvious due to content-related dependencies. Transient bitrate drops were preferable over rebuffering only on low complexity video content, while consistently low bitrates were poorly tolerated. We evaluated different objective video quality assessment algorithms on our database and found that objective video quality models are unreliable for QoE prediction on videos suffering from both rebuffering events and bitrate changes. This implies the need for more general QoE models that take into account objective quality models, rebuffering-aware information, and memory. The publicly available video content as well as metadata for all of the videos in the new database can be found at http://live.ece.utexas.edu/research/LIVE_NFLXStudy/nflx_index.html.

An Evaluation of Database Solutions to Spatial Object Association

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

Kumar, V S; Kurc, T; Saltz, J

2008-06-24

Object association is a common problem encountered in many applications. Spatial object association, also referred to as crossmatch of spatial datasets, is the problem of identifying and comparing objects in two datasets based on their positions in a common spatial coordinate system--one of the datasets may correspond to a catalog of objects observed over time in a multi-dimensional domain; the other dataset may consist of objects observed in a snapshot of the domain at a time point. The use of database management systems to the solve the object association problem provides portability across different platforms and also greater flexibility. Increasingmore » dataset sizes in today's applications, however, have made object association a data/compute-intensive problem that requires targeted optimizations for efficient execution. In this work, we investigate how database-based crossmatch algorithms can be deployed on different database system architectures and evaluate the deployments to understand the impact of architectural choices on crossmatch performance and associated trade-offs. We investigate the execution of two crossmatch algorithms on (1) a parallel database system with active disk style processing capabilities, (2) a high-throughput network database (MySQL Cluster), and (3) shared-nothing databases with replication. We have conducted our study in the context of a large-scale astronomy application with real use-case scenarios.« less

We should ban the OPCAB approach in CABG, just as we should ban jetliners and bicycles, or maybe not!

PubMed Central

2016-01-01

Implementing a new technical process demands a complex preparation. In cardiac surgery this complex preparation is often reduced to visiting a surgeon who is familiar with a technique. The science of learning has identified that several steps are needed towards a successful implementation. The first step is the creation of a complete conceptual approach; this demands the deposit in writing of the actions and reactions of every involved party in this new approach. By definition a successful implementation starts with the creation of a group of involved individuals willing to collaborate towards a new goal. Then every teachable component, described in this concept, needs to be worked out in simulation training, from the smallest manual step to complete scenario training for complex situations. Finally, optimal organisational learning needs to have an existing database of the previous situation, a clear goal and objective and a new database where every new approach is restudied versus the previous one, using appropriate methods of corrections for variability. A complete implementation will always be more successful versus a partial one, due to the habit in partial implementation to return to the previous routines. PMID:27942400

Effective Use of Java Data Objects in Developing Database Applications; Advantages and Disadvantages

DTIC Science & Technology

2004-06-01

DATA OBJECTS IN DEVELOPING DATABASE APPLICATIONS. ADVANTAGES AND DISADVANTAGES Paschalis Zilidis June 2004 Thesis Advisor: Thomas...Objects in Developing Database Applications. Advantages and Disadvantages 6. AUTHOR(S) Paschalis ZILIDIS 5. FUNDING NUMBERS 7. PERFORMING...database for the backend datastore. The major disadvantage of this approach is the well-known “impedance mismatch” in which some form of mapping is

Idea and implementation studies of populating TOPO250 component with the data from TOPO10 - generalization of geographic information in the BDG database. (Polish Title: Koncepcja i studium implementacji procesu zasilania komponentu TOPO250 danymi TOPO10 - generalizacja informacji geograficznej w bazie danych BDG )

NASA Astrophysics Data System (ADS)

Olszewski, R.; Pillich-Kolipińska, A.; Fiedukowicz, A.

2013-12-01

Implementation of INSPIRE Directive in Poland requires not only legal transposition but also development of a number of technological solutions. The one of such tasks, associated with creation of Spatial Information Infrastructure in Poland, is developing a complex model of georeference database. Significant funding for GBDOT project enables development of the national basic topographical database as a multiresolution database (MRDB). Effective implementation of this type of database requires developing procedures for generalization of geographic information (generalization of digital landscape model - DLM), which, treating TOPO10 component as the only source for creation of TOPO250 component, will allow keeping conceptual and classification consistency between those database elements. To carry out this task, the implementation of the system's concept (prepared previously for Head Office of Geodesy and Cartography) is required. Such system is going to execute the generalization process using constrained-based modeling and allows to keep topological relationships between the objects as well as between the object classes. Full implementation of the designed generalization system requires running comprehensive tests which would help with its calibration and parameterization of the generalization procedures (related to the character of generalized area). Parameterization of this process will allow determining the criteria of specific objects selection, simplification algorithms as well as the operation order. Tests with the usage of differentiated, related to the character of the area, generalization process parameters become nowadays the priority issue. Parameters are delivered to the system in the form of XML files, which, with the help of dedicated tool, are generated from the spreadsheet files (XLS) filled in by user. Using XLS file makes entering and modifying the parameters easier. Among the other elements defined by the external parametric files there are: criteria of object selection, metric parameters of generalization algorithms (e.g. simplification or aggregation) and the operations' sequence. Testing on the trial areas of diverse character will allow developing the rules of generalization process' realization, its parameterization with the proposed tool within the multiresolution reference database. The authors have attempted to develop a generalization process' parameterization for a number of different trial areas. The generalization of the results will contribute to the development of a holistic system of generalized reference data stored in the national geodetic and cartographic resources.

Adverse drug events with hyperkalaemia during inpatient stays: evaluation of an automated method for retrospective detection in hospital databases

PubMed Central

2014-01-01

Background Adverse drug reactions and adverse drug events (ADEs) are major public health issues. Many different prospective tools for the automated detection of ADEs in hospital databases have been developed and evaluated. The objective of the present study was to evaluate an automated method for the retrospective detection of ADEs with hyperkalaemia during inpatient stays. Methods We used a set of complex detection rules to take account of the patient’s clinical and biological context and the chronological relationship between the causes and the expected outcome. The dataset consisted of 3,444 inpatient stays in a French general hospital. An automated review was performed for all data and the results were compared with those of an expert chart review. The complex detection rules’ analytical quality was evaluated for ADEs. Results In terms of recall, 89.5% of ADEs with hyperkalaemia “with or without an abnormal symptom” were automatically identified (including all three serious ADEs). In terms of precision, 63.7% of the automatically identified ADEs with hyperkalaemia were true ADEs. Conclusions The use of context-sensitive rules appears to improve the automated detection of ADEs with hyperkalaemia. This type of tool may have an important role in pharmacoepidemiology via the routine analysis of large inter-hospital databases. PMID:25212108

Adverse drug events with hyperkalaemia during inpatient stays: evaluation of an automated method for retrospective detection in hospital databases.

PubMed

Ficheur, Grégoire; Chazard, Emmanuel; Beuscart, Jean-Baptiste; Merlin, Béatrice; Luyckx, Michel; Beuscart, Régis

2014-09-12

Adverse drug reactions and adverse drug events (ADEs) are major public health issues. Many different prospective tools for the automated detection of ADEs in hospital databases have been developed and evaluated. The objective of the present study was to evaluate an automated method for the retrospective detection of ADEs with hyperkalaemia during inpatient stays. We used a set of complex detection rules to take account of the patient's clinical and biological context and the chronological relationship between the causes and the expected outcome. The dataset consisted of 3,444 inpatient stays in a French general hospital. An automated review was performed for all data and the results were compared with those of an expert chart review. The complex detection rules' analytical quality was evaluated for ADEs. In terms of recall, 89.5% of ADEs with hyperkalaemia "with or without an abnormal symptom" were automatically identified (including all three serious ADEs). In terms of precision, 63.7% of the automatically identified ADEs with hyperkalaemia were true ADEs. The use of context-sensitive rules appears to improve the automated detection of ADEs with hyperkalaemia. This type of tool may have an important role in pharmacoepidemiology via the routine analysis of large inter-hospital databases.

Cavitation, Flow Structure and Turbulence in the Tip Region of a Rotor Blade

NASA Technical Reports Server (NTRS)

Wu, H.; Miorini, R.; Soranna, F.; Katz, J.; Michael, T.; Jessup, S.

2010-01-01

Objectives: Measure the flow structure and turbulence within a Naval, axial waterjet pump. Create a database for benchmarking and validation of parallel computational efforts. Address flow and turbulence modeling issues that are unique to this complex environment. Measure and model flow phenomena affecting cavitation within the pump and its effect on pump performance. This presentation focuses on cavitation phenomena and associated flow structure in the tip region of a rotor blade.

Knowledge Transfer on Complex Social Interventions in Public Health: A Scoping Study

PubMed Central

Dagenais, Christian; Malo, Marie; Robert, Émilie; Ouimet, Mathieu; Berthelette, Diane; Ridde, Valéry

2013-01-01

Objectives Scientific knowledge can help develop interventions that improve public health. The objectives of this review are (1) to describe the status of research on knowledge transfer strategies in the field of complex social interventions in public health and (2) to identify priorities for future research in this field. Method A scoping study is an exploratory study. After searching databases of bibliographic references and specialized periodicals, we summarized the relevant studies using a predetermined assessment framework. In-depth analysis focused on the following items: types of knowledge transfer strategies, fields of public health, types of publics, types of utilization, and types of research specifications. Results From the 1,374 references identified, we selected 26 studies. The strategies targeted mostly administrators of organizations and practitioners. The articles generally dealt with instrumental utilization and most often used qualitative methods. In general, the bias risk for the studies is high. Conclusion Researchers need to consider the methodological challenges in this field of research in order to improve assessment of more complex knowledge transfer strategies (when they exist), not just diffusion/dissemination strategies and conceptual and persuasive utilization. PMID:24324593

Evaluating a NoSQL Alternative for Chilean Virtual Observatory Services

NASA Astrophysics Data System (ADS)

Antognini, J.; Araya, M.; Solar, M.; Valenzuela, C.; Lira, F.

2015-09-01

Currently, the standards and protocols for data access in the Virtual Observatory architecture (DAL) are generally implemented with relational databases based on SQL. In particular, the Astronomical Data Query Language (ADQL), language used by IVOA to represent queries to VO services, was created to satisfy the different data access protocols, such as Simple Cone Search. ADQL is based in SQL92, and has extra functionality implemented using PgSphere. An emergent alternative to SQL are the so called NoSQL databases, which can be classified in several categories such as Column, Document, Key-Value, Graph, Object, etc.; each one recommended for different scenarios. Within their notable characteristics we can find: schema-free, easy replication support, simple API, Big Data, etc. The Chilean Virtual Observatory (ChiVO) is developing a functional prototype based on the IVOA architecture, with the following relevant factors: Performance, Scalability, Flexibility, Complexity, and Functionality. Currently, it's very difficult to compare these factors, due to a lack of alternatives. The objective of this paper is to compare NoSQL alternatives with SQL through the implementation of a Web API REST that satisfies ChiVO's needs: a SESAME-style name resolver for the data from ALMA. Therefore, we propose a test scenario by configuring a NoSQL database with data from different sources and evaluating the feasibility of creating a Simple Cone Search service and its performance. This comparison will allow to pave the way for the application of Big Data databases in the Virtual Observatory.

GIS-project: geodynamic globe for global monitoring of geological processes

NASA Astrophysics Data System (ADS)

Ryakhovsky, V.; Rundquist, D.; Gatinsky, Yu.; Chesalova, E.

2003-04-01

A multilayer geodynamic globe at the scale 1:10,000,000 was created at the end of the nineties in the GIS Center of the Vernadsky Museum. A special soft-and-hardware complex was elaborated for its visualization with a set of multitarget object directed databases. The globe includes separate thematic covers represented by digital sets of spatial geological, geochemical, and geophysical information (maps, schemes, profiles, stratigraphic columns, arranged databases etc.). At present the largest databases included in the globe program are connected with petrochemical and isotopic data on magmatic rocks of the World Ocean and with the large and supperlarge mineral deposits. Software by the Environmental Scientific Research Institute (ESRI), USA as well as ArcScan vectrorizator were used for covers digitizing and database adaptation (ARC/INFO 7.0, 8.0). All layers of the geoinformational project were obtained by scanning of separate objects and their transfer to the real geographic co-ordinates of an equiintermediate conic projection. Then the covers were projected on plane degree-system geographic co-ordinates. Some attributive databases were formed for each thematic layer, and in the last stage all covers were combined into the single information system. Separate digital covers represent mathematical descriptions of geological objects and relations between them, such as Earth's altimetry, active fault systems, seismicity etc. Some grounds of the cartographic generalization were taken into consideration in time of covers compilation with projection and co-ordinate systems precisely answered a given scale. The globe allows us to carry out in the interactive regime the formation of coordinated with each other object-oriented databases and thematic covers directly connected with them. They can be spread for all the Earth and the near-Earth space, and for the most well known parts of divergent and convergent boundaries of the lithosphere plates. Such covers and time series reflect in diagram form a total combination and dynamics of data on the geological structure, geophysical fields, seismicity, geomagnetism, composition of rock complexes, and metalloge-ny of different areas on the Earth's surface. They give us possibility to scale, detail, and develop 3D spatial visualization. Information filling the covers could be replenished as in the existing so in newly formed databases with new data. The integrated analyses of the data allows us more precisely to define our ideas on regularities in development of lithosphere and mantle unhomogeneities using some original technologies. It also enables us to work out 3D digital models for geodynamic development of tectonic zones in convergent and divergent plate boundaries with the purpose of integrated monitoring of mineral resources and establishing correlation between seismicity, magmatic activity, and metallogeny in time-spatial co-ordinates. The created multifold geoinformation system gives a chance to execute an integral analyses of geoinformation flows in the interactive regime and, in particular, to establish some regularities in the time-spatial distribution and dynamics of main structural units in the lithosphere, as well as illuminate the connection between stages of their development and epochs of large and supperlarge mineral deposit formation. Now we try to use the system for prediction of large oil and gas concentration in the main sedimentary basins. The work was supported by RFBR, (grants 93-07-14680, 96-07-89499, 99-07-90030, 00-15-98535, 02-07-90140) and MTC.

The BDNYC database of low-mass stars, brown dwarfs, and planetary mass companions

NASA Astrophysics Data System (ADS)

Cruz, Kelle; Rodriguez, David; Filippazzo, Joseph; Gonzales, Eileen; Faherty, Jacqueline K.; Rice, Emily; BDNYC

2018-01-01

We present a web-interface to a database of low-mass stars, brown dwarfs, and planetary mass companions. Users can send SELECT SQL queries to the database, perform searches by coordinates or name, check the database inventory on specified objects, and even plot spectra interactively. The initial version of this database contains information for 198 objects and version 2 will contain over 1000 objects. The database currently includes photometric data from 2MASS, WISE, and Spitzer and version 2 will include a significant portion of the publicly available optical and NIR spectra for brown dwarfs. The database is maintained and curated by the BDNYC research group and we welcome contributions from other researchers via GitHub.

Mining moving object trajectories in location-based services for spatio-temporal database update

NASA Astrophysics Data System (ADS)

Guo, Danhuai; Cui, Weihong

2008-10-01

Advances in wireless transmission and mobile technology applied to LBS (Location-based Services) flood us with amounts of moving objects data. Vast amounts of gathered data from position sensors of mobile phones, PDAs, or vehicles hide interesting and valuable knowledge and describe the behavior of moving objects. The correlation between temporal moving patterns of moving objects and geo-feature spatio-temporal attribute was ignored, and the value of spatio-temporal trajectory data was not fully exploited too. Urban expanding or frequent town plan change bring about a large amount of outdated or imprecise data in spatial database of LBS, and they cannot be updated timely and efficiently by manual processing. In this paper we introduce a data mining approach to movement pattern extraction of moving objects, build a model to describe the relationship between movement patterns of LBS mobile objects and their environment, and put up with a spatio-temporal database update strategy in LBS database based on trajectories spatiotemporal mining. Experimental evaluation reveals excellent performance of the proposed model and strategy. Our original contribution include formulation of model of interaction between trajectory and its environment, design of spatio-temporal database update strategy based on moving objects data mining, and the experimental application of spatio-temporal database update by mining moving objects trajectories.

Utilizing OODB schema modeling for vocabulary management.

PubMed Central

Gu, H.; Cimino, J. J.; Halper, M.; Geller, J.; Perl, Y.

1996-01-01

Comprehension of complex controlled vocabularies is often difficult. We present a method, facilitated by an object-oriented database, for depicting such a vocabulary (the Medical Entities Dictionary (MED) from the Columbia-Presbyterian Medical Center) in a schematic way which uses a sparse inheritance network of area classes. The resulting Object Oriented Health Vocabulary repository (OOHVR) allows visualization of the 43,000 MED concepts as 90 area classes. This view has provided valuable information to those responsible with maintaining the MED. As a result, the MED organization has been improved and some previously-unrecognized errors and inconsistencies have been removed. We believe that this schematic approach allows improved comprehension of the gestalt of large controlled medical vocabulary. PMID:8947671

Science information systems: Archive, access, and retrieval

NASA Technical Reports Server (NTRS)

Campbell, William J.

1991-01-01

The objective of this research is to develop technology for the automated characterization and interactive retrieval and visualization of very large, complex scientific data sets. Technologies will be developed for the following specific areas: (1) rapidly archiving data sets; (2) automatically characterizing and labeling data in near real-time; (3) providing users with the ability to browse contents of databases efficiently and effectively; (4) providing users with the ability to access and retrieve system independent data sets electronically; and (5) automatically alerting scientists to anomalies detected in data.

Analysis of Rhythms in Experimental Signals

NASA Astrophysics Data System (ADS)

Desherevskii, A. V.; Zhuravlev, V. I.; Nikolsky, A. N.; Sidorin, A. Ya.

2017-12-01

We compare algorithms designed to extract quasiperiodic components of a signal and estimate the amplitude, phase, stability, and other characteristics of a rhythm in a sliding window in the presence of data gaps. Each algorithm relies on its own rhythm model; therefore, it is necessary to use different algorithms depending on the research objectives. The described set of algorithms and methods is implemented in the WinABD software package, which includes a time-series database management system, a powerful research complex, and an interactive data-visualization environment.

An Efficient Method for the Retrieval of Objects by Topological Relations in Spatial Database Systems.

ERIC Educational Resources Information Center

Lin, P. L.; Tan, W. H.

2003-01-01

Presents a new method to improve the performance of query processing in a spatial database. Experiments demonstrated that performance of database systems can be improved because both the number of objects accessed and number of objects requiring detailed inspection are much less than those in the previous approach. (AEF)

Object recognition for autonomous robot utilizing distributed knowledge database

NASA Astrophysics Data System (ADS)

Takatori, Jiro; Suzuki, Kenji; Hartono, Pitoyo; Hashimoto, Shuji

2003-10-01

In this paper we present a novel method of object recognition utilizing a remote knowledge database for an autonomous robot. The developed robot has three robot arms with different sensors; two CCD cameras and haptic sensors. It can see, touch and move the target object from different directions. Referring to remote knowledge database of geometry and material, the robot observes and handles the objects to understand them including their physical characteristics.

Use of Graph Database for the Integration of Heterogeneous Biological Data.

PubMed

Yoon, Byoung-Ha; Kim, Seon-Kyu; Kim, Seon-Young

2017-03-01

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.

Use of Graph Database for the Integration of Heterogeneous Biological Data

PubMed Central

Yoon, Byoung-Ha; Kim, Seon-Kyu

2017-01-01

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data. PMID:28416946

OWLing Clinical Data Repositories With the Ontology Web Language

PubMed Central

Pastor, Xavier; Lozano, Esther

2014-01-01

Background The health sciences are based upon information. Clinical information is usually stored and managed by physicians with precarious tools, such as spreadsheets. The biomedical domain is more complex than other domains that have adopted information and communication technologies as pervasive business tools. Moreover, medicine continuously changes its corpus of knowledge because of new discoveries and the rearrangements in the relationships among concepts. This scenario makes it especially difficult to offer good tools to answer the professional needs of researchers and constitutes a barrier that needs innovation to discover useful solutions. Objective The objective was to design and implement a framework for the development of clinical data repositories, capable of facing the continuous change in the biomedicine domain and minimizing the technical knowledge required from final users. Methods We combined knowledge management tools and methodologies with relational technology. We present an ontology-based approach that is flexible and efficient for dealing with complexity and change, integrated with a solid relational storage and a Web graphical user interface. Results Onto Clinical Research Forms (OntoCRF) is a framework for the definition, modeling, and instantiation of data repositories. It does not need any database design or programming. All required information to define a new project is explicitly stated in ontologies. Moreover, the user interface is built automatically on the fly as Web pages, whereas data are stored in a generic repository. This allows for immediate deployment and population of the database as well as instant online availability of any modification. Conclusions OntoCRF is a complete framework to build data repositories with a solid relational storage. Driven by ontologies, OntoCRF is more flexible and efficient to deal with complexity and change than traditional systems and does not require very skilled technical people facilitating the engineering of clinical software systems. PMID:25599697

Focusing attention on objects of interest using multiple matched filters.

PubMed

Stough, T M; Brodley, C E

2001-01-01

In order to be of use to scientists, large image databases need to be analyzed to create a catalog of the objects of interest. One approach is to apply a multiple tiered search algorithm that uses reduction techniques of increasing computational complexity to select the desired objects from the database. The first tier of this type of algorithm, often called a focus of attention (FOA) algorithm, selects candidate regions from the image data and passes them to the next tier of the algorithm. In this paper we present a new approach to FOA that employs multiple matched filters (MMF), one for each object prototype, to detect the regions of interest. The MMFs are formed using k-means clustering on a set of image patches identified by domain experts as positive examples of objects of interest. An innovation of the approach is to radically reduce the dimensionality of the feature space, used by the k-means algorithm, by taking block averages (spoiling) the sample image patches. The process of spoiling is analyzed and its applicability to other domains is discussed. The combination of the output of the MMFs is achieved through the projection of the detections back into an empty image and then thresholding. This research was motivated by the need to detect small volcanos in the Magellan probe data from Venus. An empirical evaluation of the approach illustrates that a combination of the MMF plus the average filter results in a higher likelihood of 100% detection of the objects of interest at a lower false positive rate than a single matched filter alone.

Geometric database maintenance using CCTV cameras and overlay graphics

NASA Astrophysics Data System (ADS)

Oxenberg, Sheldon C.; Landell, B. Patrick; Kan, Edwin

1988-01-01

An interactive graphics system using closed circuit television (CCTV) cameras for remote verification and maintenance of a geometric world model database has been demonstrated in GE's telerobotics testbed. The database provides geometric models and locations of objects viewed by CCTV cameras and manipulated by telerobots. To update the database, an operator uses the interactive graphics system to superimpose a wireframe line drawing of an object with known dimensions on a live video scene containing that object. The methodology used is multipoint positioning to easily superimpose a wireframe graphic on the CCTV image of an object in the work scene. An enhanced version of GE's interactive graphics system will provide the object designation function for the operator control station of the Jet Propulsion Laboratory's telerobot demonstration system.

Quantum Private Queries

NASA Astrophysics Data System (ADS)

Giovannetti, Vittorio; Lloyd, Seth; Maccone, Lorenzo

2008-06-01

We propose a cheat sensitive quantum protocol to perform a private search on a classical database which is efficient in terms of communication complexity. It allows a user to retrieve an item from the database provider without revealing which item he or she retrieved: if the provider tries to obtain information on the query, the person querying the database can find it out. The protocol ensures also perfect data privacy of the database: the information that the user can retrieve in a single query is bounded and does not depend on the size of the database. With respect to the known (quantum and classical) strategies for private information retrieval, our protocol displays an exponential reduction in communication complexity and in running-time computational complexity.

Differentiating Obstructive from Central and Complex Sleep Apnea Using an Automated Electrocardiogram-Based Method

PubMed Central

Thomas, Robert Joseph; Mietus, Joseph E.; Peng, Chung-Kang; Gilmartin, Geoffrey; Daly, Robert W.; Goldberger, Ary L.; Gottlieb, Daniel J.

2007-01-01

Study Objectives: Complex sleep apnea is defined as sleep disordered breathing secondary to simultaneous upper airway obstruction and respiratory control dysfunction. The objective of this study was to assess the utility of an electrocardiogram (ECG)-based cardiopulmonary coupling technique to distinguish obstructive from central or complex sleep apnea. Design: Analysis of archived polysomnographic datasets. Setting: A laboratory for computational signal analysis. Interventions: None. Measurements and Results: The PhysioNet Sleep Apnea Database, consisting of 70 polysomnograms including single-lead ECG signals of approximately 8 hours duration, was used to train an ECG-based measure of autonomic and respiratory interactions (cardiopulmonary coupling) to detect periods of apnea and hypopnea, based on the presence of elevated low-frequency coupling (e-LFC). In the PhysioNet BIDMC Congestive Heart Failure Database (ECGs of 15 subjects), a pattern of “narrow spectral band” e-LFC was especially common. The algorithm was then applied to the Sleep Heart Health Study–I dataset, to select the 15 records with the highest amounts of broad and narrow spectral band e-LFC. The latter spectral characteristic seemed to detect not only periods of central apnea, but also obstructive hypopneas with a periodic breathing pattern. Applying the algorithm to 77 sleep laboratory split-night studies showed that the presence of narrow band e-LFC predicted an increased sensitivity to induction of central apneas by positive airway pressure. Conclusions: ECG-based spectral analysis allows automated, operator-independent characterization of probable interactions between respiratory dyscontrol and upper airway anatomical obstruction. The clinical utility of spectrographic phenotyping, especially in predicting failure of positive airway pressure therapy, remains to be more thoroughly tested. Citation: Thomas RJ; Mietus JE; Peng CK; Gilmartin G; Daly RW; Goldberger AL; Gottlieb DJ. Differentiating obstructive from central and complex sleep apnea using an automated electrocardiogram-based method. SLEEP 2007;30(12):1756-1769. PMID:18246985

The Footprint Database and Web Services of the Herschel Space Observatory

NASA Astrophysics Data System (ADS)

Dobos, László; Varga-Verebélyi, Erika; Verdugo, Eva; Teyssier, David; Exter, Katrina; Valtchanov, Ivan; Budavári, Tamás; Kiss, Csaba

2016-10-01

Data from the Herschel Space Observatory is freely available to the public but no uniformly processed catalogue of the observations has been published so far. To date, the Herschel Science Archive does not contain the exact sky coverage (footprint) of individual observations and supports search for measurements based on bounding circles only. Drawing on previous experience in implementing footprint databases, we built the Herschel Footprint Database and Web Services for the Herschel Space Observatory to provide efficient search capabilities for typical astronomical queries. The database was designed with the following main goals in mind: (a) provide a unified data model for meta-data of all instruments and observational modes, (b) quickly find observations covering a selected object and its neighbourhood, (c) quickly find every observation in a larger area of the sky, (d) allow for finding solar system objects crossing observation fields. As a first step, we developed a unified data model of observations of all three Herschel instruments for all pointing and instrument modes. Then, using telescope pointing information and observational meta-data, we compiled a database of footprints. As opposed to methods using pixellation of the sphere, we represent sky coverage in an exact geometric form allowing for precise area calculations. For easier handling of Herschel observation footprints with rather complex shapes, two algorithms were implemented to reduce the outline. Furthermore, a new visualisation tool to plot footprints with various spherical projections was developed. Indexing of the footprints using Hierarchical Triangular Mesh makes it possible to quickly find observations based on sky coverage, time and meta-data. The database is accessible via a web site http://herschel.vo.elte.hu and also as a set of REST web service functions, which makes it readily usable from programming environments such as Python or IDL. The web service allows downloading footprint data in various formats including Virtual Observatory standards.

Impact of data base structure in a successful in vitro-in vivo correlation for pharmaceutical products.

PubMed

Roudier, B; Davit, B; Schütz, H; Cardot, J-M

2015-01-01

The in vitro-in vivo correlation (IVIVC) (Food and Drug Administration 1997) aims to predict performances in vivo of a pharmaceutical formulation based on its in vitro characteristics. It is a complex process that (i) incorporates in a gradual and incremental way a large amount of information and (ii) requires information from different properties (formulation, analytical, clinical) and associated dedicated treatments (statistics, modeling, simulation). These results in many studies that are initiated and integrated into the specifications (quality target product profile, QTPP). This latter defines the appropriate experimental designs (quality by design, QbD) (Food and Drug Administration 2011, 2012) whose main objectives are determination (i) of key factors of development and manufacturing (critical process parameters, CPPs) and (ii) of critical points of physicochemical nature relating to active ingredients (API) and critical quality attribute (CQA) which may have implications in terms of efficiency, safety, and inoffensiveness for the patient, due to their non-inclusion. These processes generate a very large amount of data that is necessary to structure. In this context, the storage of information in a database (DB) and the management of this database (database management system, DBMS) become an important issue for the management of projects and IVIVC and more generally for development of new pharmaceutical forms. This article describes the implementation of a prototype object-oriented database (OODB) considered as a tool, which is helpful for decision taking, responding in a structured and consistent way to the issues of project management of IVIVC (including bioequivalence and bioavailability) (Food and Drug Administration 2003) necessary for the implementation of QTPP.

Animal Detection in Natural Images: Effects of Color and Image Database

PubMed Central

Zhu, Weina; Drewes, Jan; Gegenfurtner, Karl R.

2013-01-01

The visual system has a remarkable ability to extract categorical information from complex natural scenes. In order to elucidate the role of low-level image features for the recognition of objects in natural scenes, we recorded saccadic eye movements and event-related potentials (ERPs) in two experiments, in which human subjects had to detect animals in previously unseen natural images. We used a new natural image database (ANID) that is free of some of the potential artifacts that have plagued the widely used COREL images. Color and grayscale images picked from the ANID and COREL databases were used. In all experiments, color images induced a greater N1 EEG component at earlier time points than grayscale images. We suggest that this influence of color in animal detection may be masked by later processes when measuring reation times. The ERP results of go/nogo and forced choice tasks were similar to those reported earlier. The non-animal stimuli induced bigger N1 than animal stimuli both in the COREL and ANID databases. This result indicates ultra-fast processing of animal images is possible irrespective of the particular database. With the ANID images, the difference between color and grayscale images is more pronounced than with the COREL images. The earlier use of the COREL images might have led to an underestimation of the contribution of color. Therefore, we conclude that the ANID image database is better suited for the investigation of the processing of natural scenes than other databases commonly used. PMID:24130744

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

PubMed

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

2015-01-01

The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

A method to implement fine-grained access control for personal health records through standard relational database queries.

PubMed

Sujansky, Walter V; Faus, Sam A; Stone, Ethan; Brennan, Patricia Flatley

2010-10-01

Online personal health records (PHRs) enable patients to access, manage, and share certain of their own health information electronically. This capability creates the need for precise access-controls mechanisms that restrict the sharing of data to that intended by the patient. The authors describe the design and implementation of an access-control mechanism for PHR repositories that is modeled on the eXtensible Access Control Markup Language (XACML) standard, but intended to reduce the cognitive and computational complexity of XACML. The authors implemented the mechanism entirely in a relational database system using ANSI-standard SQL statements. Based on a set of access-control rules encoded as relational table rows, the mechanism determines via a single SQL query whether a user who accesses patient data from a specific application is authorized to perform a requested operation on a specified data object. Testing of this query on a moderately large database has demonstrated execution times consistently below 100ms. The authors include the details of the implementation, including algorithms, examples, and a test database as Supplementary materials. Copyright © 2010 Elsevier Inc. All rights reserved.

Building MapObjects attribute field in cadastral database based on the method of Jackson system development

NASA Astrophysics Data System (ADS)

Chen, Zhu-an; Zhang, Li-ting; Liu, Lu

2009-10-01

ESRI's GIS components MapObjects are applied in many cadastral information system because of its miniaturization and flexibility. Some cadastral information was saved in cadastral database directly by MapObjects's Shape file format in this cadastral information system. However, MapObjects didn't provide the function of building attribute field for map layer's attribute data file in cadastral database and user cann't save the result of analysis. This present paper designed and realized the function of building attribute field in MapObjects based on the method of Jackson's system development.

Curating and Preserving the Big Canopy Database System: an Active Curation Approach using SEAD

NASA Astrophysics Data System (ADS)

Myers, J.; Cushing, J. B.; Lynn, P.; Weiner, N.; Ovchinnikova, A.; Nadkarni, N.; McIntosh, A.

2015-12-01

Modern research is increasingly dependent upon highly heterogeneous data and on the associated cyberinfrastructure developed to organize, analyze, and visualize that data. However, due to the complexity and custom nature of such combined data-software systems, it can be very challenging to curate and preserve them for the long term at reasonable cost and in a way that retains their scientific value. In this presentation, we describe how this challenge was met in preserving the Big Canopy Database (CanopyDB) system using an agile approach and leveraging the Sustainable Environment - Actionable Data (SEAD) DataNet project's hosted data services. The CanopyDB system was developed over more than a decade at Evergreen State College to address the needs of forest canopy researchers. It is an early yet sophisticated exemplar of the type of system that has become common in biological research and science in general, including multiple relational databases for different experiments, a custom database generation tool used to create them, an image repository, and desktop and web tools to access, analyze, and visualize this data. SEAD provides secure project spaces with a semantic content abstraction (typed content with arbitrary RDF metadata statements and relationships to other content), combined with a standards-based curation and publication pipeline resulting in packaged research objects with Digital Object Identifiers. Using SEAD, our cross-project team was able to incrementally ingest CanopyDB components (images, datasets, software source code, documentation, executables, and virtualized services) and to iteratively define and extend the metadata and relationships needed to document them. We believe that both the process, and the richness of the resultant standards-based (OAI-ORE) preservation object, hold lessons for the development of best-practice solutions for preserving scientific data in association with the tools and services needed to derive value from it.

BNDB - the Biochemical Network Database.

PubMed

Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter

2007-10-02

Technological advances in high-throughput techniques and efficient data acquisition methods have resulted in a massive amount of life science data. The data is stored in numerous databases that have been established over the last decades and are essential resources for scientists nowadays. However, the diversity of the databases and the underlying data models make it difficult to combine this information for solving complex problems in systems biology. Currently, researchers typically have to browse several, often highly focused, databases to obtain the required information. Hence, there is a pressing need for more efficient systems for integrating, analyzing, and interpreting these data. The standardization and virtual consolidation of the databases is a major challenge resulting in a unified access to a variety of data sources. We present the Biochemical Network Database (BNDB), a powerful relational database platform, allowing a complete semantic integration of an extensive collection of external databases. BNDB is built upon a comprehensive and extensible object model called BioCore, which is powerful enough to model most known biochemical processes and at the same time easily extensible to be adapted to new biological concepts. Besides a web interface for the search and curation of the data, a Java-based viewer (BiNA) provides a powerful platform-independent visualization and navigation of the data. BiNA uses sophisticated graph layout algorithms for an interactive visualization and navigation of BNDB. BNDB allows a simple, unified access to a variety of external data sources. Its tight integration with the biochemical network library BN++ offers the possibility for import, integration, analysis, and visualization of the data. BNDB is freely accessible at http://www.bndb.org.

Regulatory administrative databases in FDA's Center for Biologics Evaluation and Research: convergence toward a unified database.

PubMed

Smith, Jeffrey K

2013-04-01

Regulatory administrative database systems within the Food and Drug Administration's (FDA) Center for Biologics Evaluation and Research (CBER) are essential to supporting its core mission, as a regulatory agency. Such systems are used within FDA to manage information and processes surrounding the processing, review, and tracking of investigational and marketed product submissions. This is an area of increasing interest in the pharmaceutical industry and has been a topic at trade association conferences (Buckley 2012). Such databases in CBER are complex, not for the type or relevance of the data to any particular scientific discipline but because of the variety of regulatory submission types and processes the systems support using the data. Commonalities among different data domains of CBER's regulatory administrative databases are discussed. These commonalities have evolved enough to constitute real database convergence and provide a valuable asset for business process intelligence. Balancing review workload across staff, exploring areas of risk in review capacity, process improvement, and presenting a clear and comprehensive landscape of review obligations are just some of the opportunities of such intelligence. This convergence has been occurring in the presence of usual forces that tend to drive information technology (IT) systems development toward separate stovepipes and data silos. CBER has achieved a significant level of convergence through a gradual process, using a clear goal, agreed upon development practices, and transparency of database objects, rather than through a single, discrete project or IT vendor solution. This approach offers a path forward for FDA systems toward a unified database.

EMEN2: An Object Oriented Database and Electronic Lab Notebook

PubMed Central

Rees, Ian; Langley, Ed; Chiu, Wah; Ludtke, Steven J.

2013-01-01

Transmission electron microscopy and associated methods such as single particle analysis, 2-D crystallography, helical reconstruction and tomography, are highly data-intensive experimental sciences, which also have substantial variability in experimental technique. Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving. We present EMEN2, an easy to use object-oriented database with a highly flexible infrastructure originally targeted for transmission electron microscopy and tomography, which has been extended to be adaptable for use in virtually any experimental science. It is a pure object-oriented database designed for easy adoption in diverse laboratory environments, and does not require professional database administration. It includes a full featured, dynamic web interface in addition to APIs for programmatic access. EMEN2 installations currently support roughly 800 scientists worldwide with over 1/2 million experimental records and over 20 TB of experimental data. The software is freely available with complete source. PMID:23360752

Imprecision and Uncertainty in the UFO Database Model.

ERIC Educational Resources Information Center

Van Gyseghem, Nancy; De Caluwe, Rita

1998-01-01

Discusses how imprecision and uncertainty are dealt with in the UFO (Uncertainty and Fuzziness in an Object-oriented) database model. Such information is expressed by means of possibility distributions, and modeled by means of the proposed concept of "role objects." The role objects model uncertain, tentative information about objects,…

Object-Oriented Approach to Integrating Database Semantics. Volume 4.

DTIC Science & Technology

1987-12-01

schemata for; 1. Object Classification Shema -- Entities 2. Object Structure and Relationship Schema -- Relations 3. Operation Classification and... relationships are represented in a database is non- intuitive for naive users. *It is difficult to access and combine information in multiple databases. In this...from the CURRENT-.CLASSES table. Choosing a selected item do-selects it. Choose 0 to exit. 1. STUDENTS 2. CUR~RENT-..CLASSES 3. MANAGMNT -.CLASS

Bioinformatics analysis on molecular mechanism of rheum officinale in treatment of jaundice

NASA Astrophysics Data System (ADS)

Shan, Si; Tu, Jun; Nie, Peng; Yan, Xiaojun

2017-01-01

Objective: To study the molecular mechanism of Rheum officinale in the treatment of Jaundice by building molecular networks and comparing canonical pathways. Methods: Target proteins of Rheum officinale and related genes of Jaundice were searched from Pubchem and Gene databases online respectively. Molecular networks and canonical pathways comparison analyses were performed by Ingenuity Pathway Analysis (IPA). Results: The molecular networks of Rheum officinale and Jaundice were complex and multifunctional. The 40 target proteins of Rheum officinale and 33 Homo sapiens genes of Jaundice were found in databases. There were 19 common pathways both related networks. Rheum officinale could regulate endothelial differentiation, Interleukin-1B (IL-1B) and Tumor Necrosis Factor (TNF) in these pathways. Conclusions: Rheum officinale treat Jaundice by regulating many effective nodes of Apoptotic pathway and cellular immunity related pathways.

SCEGRAM: An image database for semantic and syntactic inconsistencies in scenes.

PubMed

Öhlschläger, Sabine; Võ, Melissa Le-Hoa

2017-10-01

Our visual environment is not random, but follows compositional rules according to what objects are usually found where. Despite the growing interest in how such semantic and syntactic rules - a scene grammar - enable effective attentional guidance and object perception, no common image database containing highly-controlled object-scene modifications has been publically available. Such a database is essential in minimizing the risk that low-level features drive high-level effects of interest, which is being discussed as possible source of controversial study results. To generate the first database of this kind - SCEGRAM - we took photographs of 62 real-world indoor scenes in six consistency conditions that contain semantic and syntactic (both mild and extreme) violations as well as their combinations. Importantly, always two scenes were paired, so that an object was semantically consistent in one scene (e.g., ketchup in kitchen) and inconsistent in the other (e.g., ketchup in bathroom). Low-level salience did not differ between object-scene conditions and was generally moderate. Additionally, SCEGRAM contains consistency ratings for every object-scene condition, as well as object-absent scenes and object-only images. Finally, a cross-validation using eye-movements replicated previous results of longer dwell times for both semantic and syntactic inconsistencies compared to consistent controls. In sum, the SCEGRAM image database is the first to contain well-controlled semantic and syntactic object-scene inconsistencies that can be used in a broad range of cognitive paradigms (e.g., verbal and pictorial priming, change detection, object identification, etc.) including paradigms addressing developmental aspects of scene grammar. SCEGRAM can be retrieved for research purposes from http://www.scenegrammarlab.com/research/scegram-database/ .

The Network Configuration of an Object Relational Database Management System

NASA Technical Reports Server (NTRS)

Diaz, Philip; Harris, W. C.

2000-01-01

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

Data, knowledge and method bases in chemical sciences. Part IV. Current status in databases.

PubMed

Braibanti, Antonio; Rao, Rupenaguntla Sambasiva; Rao, Gollapalli Nagesvara; Ramam, Veluri Anantha; Rao, Sattiraju Veera Venkata Satyanarayana

2002-01-01

Computer readable databases have become an integral part of chemical research right from planning data acquisition to interpretation of the information generated. The databases available today are numerical, spectral and bibliographic. Data representation by different schemes--relational, hierarchical and objects--is demonstrated. Quality index (QI) throws light on the quality of data. The objective, prospects and impact of database activity on expert systems are discussed. The number and size of corporate databases available on international networks crossed manageable number leading to databases about their contents. Subsets of corporate or small databases have been developed by groups of chemists. The features and role of knowledge-based or intelligent databases are described.

Algorithm for detection the QRS complexes based on support vector machine

NASA Astrophysics Data System (ADS)

Van, G. V.; Podmasteryev, K. V.

2017-11-01

The efficiency of computer ECG analysis depends on the accurate detection of QRS-complexes. This paper presents an algorithm for QRS complex detection based of support vector machine (SVM). The proposed algorithm is evaluated on annotated standard databases such as MIT-BIH Arrhythmia database. The QRS detector obtained a sensitivity Se = 98.32% and specificity Sp = 95.46% for MIT-BIH Arrhythmia database. This algorithm can be used as the basis for the software to diagnose electrical activity of the heart.

Gulf Arabic nouns and verbs: A standardized set of 319 object pictures and 141 action pictures, with predictors of naming latencies.

PubMed

Khwaileh, Tariq; Mustafawi, Eiman; Herbert, Ruth; Howard, David

2018-02-15

Standardized pictorial stimuli and predictors of successful picture naming are not readily available for Gulf Arabic. On the basis of data obtained from Qatari Arabic, a variety of Gulf Arabic, the present study provides norms for a set of 319 object pictures and a set of 141 action pictures. Norms were collected from healthy speakers, using a picture-naming paradigm and rating tasks. Norms for naming latencies, name agreement, visual complexity, image agreement, imageability, age of acquisition, and familiarity were established. Furthermore, the database includes other intrinsic factors, such as syllable length and phoneme length. It also includes orthographic frequency values (extracted from Aralex; Boudelaa & Marslen-Wilson, 2010). These factors were then examined for their impact on picture-naming latencies in object- and action-naming tasks. The analysis showed that the primary determinants of naming latencies in both nouns and verbs are (in descending order) image agreement, name agreement, familiarity, age of acquisition, and imageability. These results indicate no evidence that noun- and verb-naming processes in Gulf Arabic are influenced in different ways by these variables. This is the first database for Gulf Arabic, and therefore the norms collected from the present study will be of paramount importance for researchers and clinicians working with speakers of this variety of Arabic. Due to the similarity of the Arabic varieties spoken in the Gulf, these different varieties are grouped together under the label "Gulf Arabic" in the literature. The normative databases and the standardized pictures from this study can be downloaded from http://qufaculty.qu.edu.qa/tariq-khwaileh/download-center/ .

PDB-wide collection of binding data: current status of the PDBbind database.

PubMed

Liu, Zhihai; Li, Yan; Han, Li; Li, Jie; Liu, Jie; Zhao, Zhixiong; Nie, Wei; Liu, Yuchen; Wang, Renxiao

2015-02-01

Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank (PDB). It thus provides the linkage between structural information and energetic properties of biomolecular complexes, which is especially desirable for computational studies or statistical analyses. Since its first public release in 2004, the PDBbind database has been updated on an annual basis. The latest release (version 2013) provides experimental binding affinity data for 10,776 biomolecular complexes in PDB, including 8302 protein-ligand complexes and 2474 other types of complexes. In this article, we will describe the current methods used for compiling PDBbind and the updated status of this database. We will also review some typical applications of PDBbind published in the scientific literature. All contents of this database are freely accessible at the PDBbind-CN Web server at http://www.pdbbind-cn.org/. wangrx@mail.sioc.ac.cn. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Exploring the feasibility of traditional image querying tasks for industrial radiographs

NASA Astrophysics Data System (ADS)

Bray, Iliana E.; Tsai, Stephany J.; Jimenez, Edward S.

2015-08-01

Although there have been great strides in object recognition with optical images (photographs), there has been comparatively little research into object recognition for X-ray radiographs. Our exploratory work contributes to this area by creating an object recognition system designed to recognize components from a related database of radiographs. Object recognition for radiographs must be approached differently than for optical images, because radiographs have much less color-based information to distinguish objects, and they exhibit transmission overlap that alters perceived object shapes. The dataset used in this work contained more than 55,000 intermixed radiographs and photographs, all in a compressed JPEG form and with multiple ways of describing pixel information. For this work, a robust and efficient system is needed to combat problems presented by properties of the X-ray imaging modality, the large size of the given database, and the quality of the images contained in said database. We have explored various pre-processing techniques to clean the cluttered and low-quality images in the database, and we have developed our object recognition system by combining multiple object detection and feature extraction methods. We present the preliminary results of the still-evolving hybrid object recognition system.

NPIDB: Nucleic acid-Protein Interaction DataBase.

PubMed

Kirsanov, Dmitry D; Zanegina, Olga N; Aksianov, Evgeniy A; Spirin, Sergei A; Karyagina, Anna S; Alexeevski, Andrei V

2013-01-01

The Nucleic acid-Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA-protein and RNA-protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid-Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA-binding protein domains and data on conserved water molecules on the DNA-protein interface.

Case Study Analyses of the Success DC-8 Scanning Lidar Database

NASA Technical Reports Server (NTRS)

Uthe, Edward E.

2000-01-01

Under project SUCCESS (Subsonic Aircraft Contrail and Cloud Effects Special Study) funded by the Atmospheric Effects of Aviation Program, SRI International (SRI) developed an angular scanning back'scatter lidar for operation on the NASA DC-8 research aircraft and deployed the scanning lidar during the SUCCESS field campaign. The primary purpose of the lidar was to generate real-time video displays of clouds and contrails above, ahead of, and below the DC-8 as a means to help position the aircraft for optimum cloud and contrail sampling by onboard in situ sensors, and to help extend the geometrical domain of the in situ sampling records. A large, relatively complex lidar database was collected and several data examples were processed to illustrate the value of the lidar data for interpreting the other data records collected during SUCCESS. These data examples were used to develop a journal publication for the special SUCCESS Geophysical Research Letters issue (reprint presented as Appendix A). The data examples justified data analyses of a larger part of the DC-8 lidar database and is the objective of the current study.

Reliability database development for use with an object-oriented fault tree evaluation program

NASA Technical Reports Server (NTRS)

Heger, A. Sharif; Harringtton, Robert J.; Koen, Billy V.; Patterson-Hine, F. Ann

1989-01-01

A description is given of the development of a fault-tree analysis method using object-oriented programming. In addition, the authors discuss the programs that have been developed or are under development to connect a fault-tree analysis routine to a reliability database. To assess the performance of the routines, a relational database simulating one of the nuclear power industry databases has been constructed. For a realistic assessment of the results of this project, the use of one of existing nuclear power reliability databases is planned.

Motivational Objects in Natural Scenes (MONS): A Database of >800 Objects.

PubMed

Schomaker, Judith; Rau, Elias M; Einhäuser, Wolfgang; Wittmann, Bianca C

2017-01-01

In daily life, we are surrounded by objects with pre-existing motivational associations. However, these are rarely controlled for in experiments with natural stimuli. Research on natural stimuli would therefore benefit from stimuli with well-defined motivational properties; in turn, such stimuli also open new paths in research on motivation. Here we introduce a database of Motivational Objects in Natural Scenes (MONS). The database consists of 107 scenes. Each scene contains 2 to 7 objects placed at approximately equal distance from the scene center. Each scene was photographed creating 3 versions, with one object ("critical object") being replaced to vary the overall motivational value of the scene (appetitive, aversive, and neutral), while maintaining high visual similarity between the three versions. Ratings on motivation, valence, arousal and recognizability were obtained using internet-based questionnaires. Since the main objective was to provide stimuli of well-defined motivational value, three motivation scales were used: (1) Desire to own the object; (2) Approach/Avoid; (3) Desire to interact with the object. Three sets of ratings were obtained in independent sets of observers: for all 805 objects presented on a neutral background, for 321 critical objects presented in their scene context, and for the entire scenes. On the basis of the motivational ratings, objects were subdivided into aversive, neutral, and appetitive categories. The MONS database will provide a standardized basis for future studies on motivational value under realistic conditions.

An Introduction to Database Structure and Database Machines.

ERIC Educational Resources Information Center

Detweiler, Karen

1984-01-01

Enumerates principal management objectives of database management systems (data independence, quality, security, multiuser access, central control) and criteria for comparison (response time, size, flexibility, other features). Conventional database management systems, relational databases, and database machines used for backend processing are…

Developing science gateways for drug discovery in a grid environment.

PubMed

Pérez-Sánchez, Horacio; Rezaei, Vahid; Mezhuyev, Vitaliy; Man, Duhu; Peña-García, Jorge; den-Haan, Helena; Gesing, Sandra

2016-01-01

Methods for in silico screening of large databases of molecules increasingly complement and replace experimental techniques to discover novel compounds to combat diseases. As these techniques become more complex and computationally costly we are faced with an increasing problem to provide the research community of life sciences with a convenient tool for high-throughput virtual screening on distributed computing resources. To this end, we recently integrated the biophysics-based drug-screening program FlexScreen into a service, applicable for large-scale parallel screening and reusable in the context of scientific workflows. Our implementation is based on Pipeline Pilot and Simple Object Access Protocol and provides an easy-to-use graphical user interface to construct complex workflows, which can be executed on distributed computing resources, thus accelerating the throughput by several orders of magnitude.

ControlShell: A real-time software framework

NASA Technical Reports Server (NTRS)

Schneider, Stanley A.; Chen, Vincent W.; Pardo-Castellote, Gerardo

1994-01-01

The ControlShell system is a programming environment that enables the development and implementation of complex real-time software. It includes many building tools for complex systems, such as a graphical finite state machine (FSM) tool to provide strategic control. ControlShell has a component-based design, providing interface definitions and mechanisms for building real-time code modules along with providing basic data management. Some of the system-building tools incorporated in ControlShell are a graphical data flow editor, a component data requirement editor, and a state-machine editor. It also includes a distributed data flow package, an execution configuration manager, a matrix package, and an object database and dynamic binding facility. This paper presents an overview of ControlShell's architecture and examines the functions of several of its tools.

Updating National Topographic Data Base Using Change Detection Methods

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

The FoodCast research image database (FRIDa)

PubMed Central

Foroni, Francesco; Pergola, Giulio; Argiris, Georgette; Rumiati, Raffaella I.

2013-01-01

In recent years we have witnessed an increasing interest in food processing and eating behaviors. This is probably due to several reasons. The biological relevance of food choices, the complexity of the food-rich environment in which we presently live (making food-intake regulation difficult), and the increasing health care cost due to illness associated with food (food hazards, food contamination, and aberrant food-intake). Despite the importance of the issues and the relevance of this research, comprehensive and validated databases of stimuli are rather limited, outdated, or not available for non-commercial purposes to independent researchers who aim at developing their own research program. The FoodCast Research Image Database (FRIDa) we present here includes 877 images belonging to eight different categories: natural-food (e.g., strawberry), transformed-food (e.g., french fries), rotten-food (e.g., moldy banana), natural-non-food items (e.g., pinecone), artificial food-related objects (e.g., teacup), artificial objects (e.g., guitar), animals (e.g., camel), and scenes (e.g., airport). FRIDa has been validated on a sample of healthy participants (N = 73) on standard variables (e.g., valence, familiarity, etc.) as well as on other variables specifically related to food items (e.g., perceived calorie content); it also includes data on the visual features of the stimuli (e.g., brightness, high frequency power, etc.). FRIDa is a well-controlled, flexible, validated, and freely available (http://foodcast.sissa.it/neuroscience/) tool for researchers in a wide range of academic fields and industry. PMID:23459781

Large scale database scrubbing using object oriented software components.

PubMed

Herting, R L; Barnes, M R

1998-01-01

Now that case managers, quality improvement teams, and researchers use medical databases extensively, the ability to share and disseminate such databases while maintaining patient confidentiality is paramount. A process called scrubbing addresses this problem by removing personally identifying information while keeping the integrity of the medical information intact. Scrubbing entire databases, containing multiple tables, requires that the implicit relationships between data elements in different tables of the database be maintained. To address this issue we developed DBScrub, a Java program that interfaces with any JDBC compliant database and scrubs the database while maintaining the implicit relationships within it. DBScrub uses a small number of highly configurable object-oriented software components to carry out the scrubbing. We describe the structure of these software components and how they maintain the implicit relationships within the database.

Interactive Database of Pulsar Flux Density Measurements

NASA Astrophysics Data System (ADS)

Koralewska, O.; Krzeszowski, K.; Kijak, J.; Lewandowski, W.

2012-12-01

The number of astronomical observations is steadily growing, giving rise to the need of cataloguing the obtained results. There are a lot of databases, created to store different types of data and serve a variety of purposes, e. g. databases providing basic data for astronomical objects (SIMBAD Astronomical Database), databases devoted to one type of astronomical object (ATNF Pulsar Database) or to a set of values of the specific parameter (Lorimer 1995 - database of flux density measurements for 280 pulsars on the frequencies up to 1606 MHz), etc. We found that creating an online database of pulsar flux measurements, provided with facilities for plotting diagrams and histograms, calculating mean values for a chosen set of data, filtering parameter values and adding new measurements by the registered users, could be useful in further studies on pulsar spectra.

Multilevel depth and image fusion for human activity detection.

PubMed

Ni, Bingbing; Pei, Yong; Moulin, Pierre; Yan, Shuicheng

2013-10-01

Recognizing complex human activities usually requires the detection and modeling of individual visual features and the interactions between them. Current methods only rely on the visual features extracted from 2-D images, and therefore often lead to unreliable salient visual feature detection and inaccurate modeling of the interaction context between individual features. In this paper, we show that these problems can be addressed by combining data from a conventional camera and a depth sensor (e.g., Microsoft Kinect). We propose a novel complex activity recognition and localization framework that effectively fuses information from both grayscale and depth image channels at multiple levels of the video processing pipeline. In the individual visual feature detection level, depth-based filters are applied to the detected human/object rectangles to remove false detections. In the next level of interaction modeling, 3-D spatial and temporal contexts among human subjects or objects are extracted by integrating information from both grayscale and depth images. Depth information is also utilized to distinguish different types of indoor scenes. Finally, a latent structural model is developed to integrate the information from multiple levels of video processing for an activity detection. Extensive experiments on two activity recognition benchmarks (one with depth information) and a challenging grayscale + depth human activity database that contains complex interactions between human-human, human-object, and human-surroundings demonstrate the effectiveness of the proposed multilevel grayscale + depth fusion scheme. Higher recognition and localization accuracies are obtained relative to the previous methods.

Searching and Extracting Data from the EMBL-EBI Complex Portal.

PubMed

Meldal, Birgit H M; Orchard, Sandra

2018-01-01

The Complex Portal ( www.ebi.ac.uk/complexportal ) is an encyclopedia of macromolecular complexes. Complexes are assigned unique, stable IDs, are species specific, and list all participating members with links to an appropriate reference database (UniProtKB, ChEBI, RNAcentral). Each complex is annotated extensively with its functions, properties, structure, stoichiometry, tissue expression profile, and subcellular location. Links to domain-specific databases allow the user to access additional information and enable data searching and filtering. Complexes can be saved and downloaded in PSI-MI XML, MI-JSON, and tab-delimited formats.

Environmental modeling and recognition for an autonomous land vehicle

NASA Technical Reports Server (NTRS)

Lawton, D. T.; Levitt, T. S.; Mcconnell, C. C.; Nelson, P. C.

1987-01-01

An architecture for object modeling and recognition for an autonomous land vehicle is presented. Examples of objects of interest include terrain features, fields, roads, horizon features, trees, etc. The architecture is organized around a set of data bases for generic object models and perceptual structures, temporary memory for the instantiation of object and relational hypotheses, and a long term memory for storing stable hypotheses that are affixed to the terrain representation. Multiple inference processes operate over these databases. Researchers describe these particular components: the perceptual structure database, the grouping processes that operate over this, schemas, and the long term terrain database. A processing example that matches predictions from the long term terrain model to imagery, extracts significant perceptual structures for consideration as potential landmarks, and extracts a relational structure to update the long term terrain database is given.

bpRNA: large-scale automated annotation and analysis of RNA secondary structure.

PubMed

Danaee, Padideh; Rouches, Mason; Wiley, Michelle; Deng, Dezhong; Huang, Liang; Hendrix, David

2018-05-09

While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, 'bpRNA-1m', of over 100 000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.

Construction of Database for Pulsating Variable Stars

NASA Astrophysics Data System (ADS)

Chen, B. Q.; Yang, M.; Jiang, B. W.

2011-07-01

A database for the pulsating variable stars is constructed for Chinese astronomers to study the variable stars conveniently. The database includes about 230000 variable stars in the Galactic bulge, LMC and SMC observed by the MACHO (MAssive Compact Halo Objects) and OGLE (Optical Gravitational Lensing Experiment) projects at present. The software used for the construction is LAMP, i.e., Linux+Apache+MySQL+PHP. A web page is provided to search the photometric data and the light curve in the database through the right ascension and declination of the object. More data will be incorporated into the database.

The NOAO Data Lab PHAT Photometry Database

NASA Astrophysics Data System (ADS)

Olsen, Knut; Williams, Ben; Fitzpatrick, Michael; PHAT Team

2018-01-01

We present a database containing both the combined photometric object catalog and the single epoch measurements from the Panchromatic Hubble Andromeda Treasury (PHAT). This database is hosted by the NOAO Data Lab (http://datalab.noao.edu), and as such exposes a number of data services to the PHAT photometry, including access through a Table Access Protocol (TAP) service, direct PostgreSQL queries, web-based and programmatic query interfaces, remote storage space for personal database tables and files, and a JupyterHub-based Notebook analysis environment, as well as image access through a Simple Image Access (SIA) service. We show how the Data Lab database and Jupyter Notebook environment allow for straightforward and efficient analyses of PHAT catalog data, including maps of object density, depth, and color, extraction of light curves of variable objects, and proper motion exploration.

Solving Relational Database Problems with ORDBMS in an Advanced Database Course

ERIC Educational Resources Information Center

Wang, Ming

2011-01-01

This paper introduces how to use the object-relational database management system (ORDBMS) to solve relational database (RDB) problems in an advanced database course. The purpose of the paper is to provide a guideline for database instructors who desire to incorporate the ORDB technology in their traditional database courses. The paper presents…

Multiple Object Retrieval in Image Databases Using Hierarchical Segmentation Tree

ERIC Educational Resources Information Center

Chen, Wei-Bang

2012-01-01

The purpose of this research is to develop a new visual information analysis, representation, and retrieval framework for automatic discovery of salient objects of user's interest in large-scale image databases. In particular, this dissertation describes a content-based image retrieval framework which supports multiple-object retrieval. The…

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

ERIC Educational Resources Information Center

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

1995-01-01

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

Construction of the Database for Pulsating Variable Stars

NASA Astrophysics Data System (ADS)

Chen, Bing-Qiu; Yang, Ming; Jiang, Bi-Wei

2012-01-01

A database for pulsating variable stars is constructed to favor the study of variable stars in China. The database includes about 230,000 variable stars in the Galactic bulge, LMC and SMC observed in an about 10 yr period by the MACHO(MAssive Compact Halo Objects) and OGLE(Optical Gravitational Lensing Experiment) projects. The software used for the construction is LAMP, i.e., Linux+Apache+MySQL+PHP. A web page is provided for searching the photometric data and light curves in the database through the right ascension and declination of an object. Because of the flexibility of this database, more up-to-date data of variable stars can be incorporated into the database conveniently.

A case study for a digital seabed database: Bohai Sea engineering geology database

NASA Astrophysics Data System (ADS)

Tianyun, Su; Shikui, Zhai; Baohua, Liu; Ruicai, Liang; Yanpeng, Zheng; Yong, Wang

2006-07-01

This paper discusses the designing plan of ORACLE-based Bohai Sea engineering geology database structure from requisition analysis, conceptual structure analysis, logical structure analysis, physical structure analysis and security designing. In the study, we used the object-oriented Unified Modeling Language (UML) to model the conceptual structure of the database and used the powerful function of data management which the object-oriented and relational database ORACLE provides to organize and manage the storage space and improve its security performance. By this means, the database can provide rapid and highly effective performance in data storage, maintenance and query to satisfy the application requisition of the Bohai Sea Oilfield Paradigm Area Information System.

Marshall Space Flight Center Technology Capabilities for Use in Space Situational Awareness Activities

NASA Technical Reports Server (NTRS)

Gagliano, Larry; McLeod, Todd; Hovater, Mary A.

2017-01-01

Marshall performs research, integrates information, matures technologies, and enhances science to bring together a diverse portfolio of products and services of interest for Space Situational Awareness (SSA) and Space Asset Management (SAM), all of which can be accessed through partnerships with Marshall. Integrated Space Situational Awareness and Asset Management (ISSAAM) is an initiative of NASA's Marshall Space Flight Center to improve space situational awareness and space asset management through technical innovation, collaboration, and cooperation with U.S. Government agencies and the global space community. Marshall Space Flight Center provides solutions for complex issues with in-depth capabilities, a broad range of experience, and expertise unique in the world, and all available in one convenient location. NASA has longstanding guidelines that are used to assess space objects. Specifically, Marshall Space Flight Center has the capabilities, facilities and expertise to address the challenges that space objects, such as near-Earth objects (NEO) or Orbital Debris pose. ISSAAM's three pronged approach brings together vital information and in-depth tools working simultaneously toward examining the complex problems encountered in space situational awareness. Marshall's role in managing, understanding and planning includes many projects grouped under each prong area: Database/Analyses/Visualization; Detection/Tracking/ Mitigation/Removal. These are not limited to those listed below.

Challenges and Experiences of Building Multidisciplinary Datasets across Cultures

NASA Astrophysics Data System (ADS)

Jamiyansharav, K.; Laituri, M.; Fernandez-Gimenez, M.; Fassnacht, S. R.; Venable, N. B. H.; Allegretti, A. M.; Reid, R.; Baival, B.; Jamsranjav, C.; Ulambayar, T.; Linn, S.; Angerer, J.

2017-12-01

Efficient data sharing and management are key challenges to multidisciplinary scientific research. These challenges are further complicated by adding a multicultural component. We address the construction of a complex database for social-ecological analysis in Mongolia. Funded by the National Science Foundation (NSF) Dynamics of Coupled Natural and Human (CNH) Systems, the Mongolian Rangelands and Resilience (MOR2) project focuses on the vulnerability of Mongolian pastoral systems to climate change and adaptive capacity. The MOR2 study spans over three years of fieldwork in 36 paired districts (Soum) from 18 provinces (Aimag) of Mongolia that covers steppe, mountain forest steppe, desert steppe and eastern steppe ecological zones. Our project team is composed of hydrologists, social scientists, geographers, and ecologists. The MOR2 database includes multiple ecological, social, meteorological, geospatial and hydrological datasets, as well as archives of original data and survey in multiple formats. Managing this complex database requires significant organizational skills, attention to detail and ability to communicate within collective team members from diverse disciplines and across multiple institutions in the US and Mongolia. We describe the database's rich content, organization, structure and complexity. We discuss lessons learned, best practices and recommendations for complex database management, sharing, and archiving in creating a cross-cultural and multi-disciplinary database.

Using a Semi-Realistic Database to Support a Database Course

ERIC Educational Resources Information Center

Yue, Kwok-Bun

2013-01-01

A common problem for university relational database courses is to construct effective databases for instructions and assignments. Highly simplified "toy" databases are easily available for teaching, learning, and practicing. However, they do not reflect the complexity and practical considerations that students encounter in real-world…

The Modular Modeling System (MMS): A modeling framework for water- and environmental-resources management

USGS Publications Warehouse

Leavesley, G.H.; Markstrom, S.L.; Viger, R.J.

2004-01-01

The interdisciplinary nature and increasing complexity of water- and environmental-resource problems require the use of modeling approaches that can incorporate knowledge from a broad range of scientific disciplines. The large number of distributed hydrological and ecosystem models currently available are composed of a variety of different conceptualizations of the associated processes they simulate. Assessment of the capabilities of these distributed models requires evaluation of the conceptualizations of the individual processes, and the identification of which conceptualizations are most appropriate for various combinations of criteria, such as problem objectives, data constraints, and spatial and temporal scales of application. With this knowledge, "optimal" models for specific sets of criteria can be created and applied. The U.S. Geological Survey (USGS) Modular Modeling System (MMS) is an integrated system of computer software that has been developed to provide these model development and application capabilities. MMS supports the integration of models and tools at a variety of levels of modular design. These include individual process models, tightly coupled models, loosely coupled models, and fully-integrated decision support systems. A variety of visualization and statistical tools are also provided. MMS has been coupled with the Bureau of Reclamation (BOR) object-oriented reservoir and river-system modeling framework, RiverWare, under a joint USGS-BOR program called the Watershed and River System Management Program. MMS and RiverWare are linked using a shared relational database. The resulting database-centered decision support system provides tools for evaluating and applying optimal resource-allocation and management strategies to complex, operational decisions on multipurpose reservoir systems and watersheds. Management issues being addressed include efficiency of water-resources management, environmental concerns such as meeting flow needs for endangered species, and optimizing operations within the constraints of multiple objectives such as power generation, irrigation, and water conservation. This decision support system approach is being developed, tested, and implemented in the Gunni-son, Yakima, San Juan, Rio Grande, and Truckee River basins of the western United States. Copyright ASCE 2004.

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

NASA Technical Reports Server (NTRS)

King, Roger

1996-01-01

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

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

NASA Technical Reports Server (NTRS)

King, Roger

1996-01-01

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

An Object-Relational Ifc Storage Model Based on Oracle Database

NASA Astrophysics Data System (ADS)

Li, Hang; Liu, Hua; Liu, Yong; Wang, Yuan

2016-06-01

With the building models are getting increasingly complicated, the levels of collaboration across professionals attract more attention in the architecture, engineering and construction (AEC) industry. In order to adapt the change, buildingSMART developed Industry Foundation Classes (IFC) to facilitate the interoperability between software platforms. However, IFC data are currently shared in the form of text file, which is defective. In this paper, considering the object-based inheritance hierarchy of IFC and the storage features of different database management systems (DBMS), we propose a novel object-relational storage model that uses Oracle database to store IFC data. Firstly, establish the mapping rules between data types in IFC specification and Oracle database. Secondly, design the IFC database according to the relationships among IFC entities. Thirdly, parse the IFC file and extract IFC data. And lastly, store IFC data into corresponding tables in IFC database. In experiment, three different building models are selected to demonstrate the effectiveness of our storage model. The comparison of experimental statistics proves that IFC data are lossless during data exchange.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

Motivational Objects in Natural Scenes (MONS): A Database of >800 Objects

PubMed Central

Schomaker, Judith; Rau, Elias M.; Einhäuser, Wolfgang; Wittmann, Bianca C.

2017-01-01

In daily life, we are surrounded by objects with pre-existing motivational associations. However, these are rarely controlled for in experiments with natural stimuli. Research on natural stimuli would therefore benefit from stimuli with well-defined motivational properties; in turn, such stimuli also open new paths in research on motivation. Here we introduce a database of Motivational Objects in Natural Scenes (MONS). The database consists of 107 scenes. Each scene contains 2 to 7 objects placed at approximately equal distance from the scene center. Each scene was photographed creating 3 versions, with one object (“critical object”) being replaced to vary the overall motivational value of the scene (appetitive, aversive, and neutral), while maintaining high visual similarity between the three versions. Ratings on motivation, valence, arousal and recognizability were obtained using internet-based questionnaires. Since the main objective was to provide stimuli of well-defined motivational value, three motivation scales were used: (1) Desire to own the object; (2) Approach/Avoid; (3) Desire to interact with the object. Three sets of ratings were obtained in independent sets of observers: for all 805 objects presented on a neutral background, for 321 critical objects presented in their scene context, and for the entire scenes. On the basis of the motivational ratings, objects were subdivided into aversive, neutral, and appetitive categories. The MONS database will provide a standardized basis for future studies on motivational value under realistic conditions. PMID:29033870

Evaluation of linking pavement related databases.

DOT National Transportation Integrated Search

2007-03-01

In general, the objectives of this study were to identify and solve various issues in linking pavement performance related database. The detailed objectives were: to evaluate the state-of-the-art in information technology for data integration and dat...

SQL is Dead; Long-live SQL: Relational Database Technology in Science Contexts

NASA Astrophysics Data System (ADS)

Howe, B.; Halperin, D.

2014-12-01

Relational databases are often perceived as a poor fit in science contexts: Rigid schemas, poor support for complex analytics, unpredictable performance, significant maintenance and tuning requirements --- these idiosyncrasies often make databases unattractive in science contexts characterized by heterogeneous data sources, complex analysis tasks, rapidly changing requirements, and limited IT budgets. In this talk, I'll argue that although the value proposition of typical relational database systems are weak in science, the core ideas that power relational databases have become incredibly prolific in open source science software, and are emerging as a universal abstraction for both big data and small data. In addition, I'll talk about two open source systems we are building to "jailbreak" the core technology of relational databases and adapt them for use in science. The first is SQLShare, a Database-as-a-Service system supporting collaborative data analysis and exchange by reducing database use to an Upload-Query-Share workflow with no installation, schema design, or configuration required. The second is Myria, a service that supports much larger scale data, complex analytics, and supports multiple back end systems. Finally, I'll describe some of the ways our collaborators in oceanography, astronomy, biology, fisheries science, and more are using these systems to replace script-based workflows for reasons of performance, flexibility, and convenience.

PROXiMATE: a database of mutant protein-protein complex thermodynamics and kinetics.

PubMed

Jemimah, Sherlyn; Yugandhar, K; Michael Gromiha, M

2017-09-01

We have developed PROXiMATE, a database of thermodynamic data for more than 6000 missense mutations in 174 heterodimeric protein-protein complexes, supplemented with interaction network data from STRING database, solvent accessibility, sequence, structural and functional information, experimental conditions and literature information. Additional features include complex structure visualization, search and display options, download options and a provision for users to upload their data. The database is freely available at http://www.iitm.ac.in/bioinfo/PROXiMATE/ . The website is implemented in Python, and supports recent versions of major browsers such as IE10, Firefox, Chrome and Opera. gromiha@iitm.ac.in. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Dynamic taxonomies applied to a web-based relational database for geo-hydrological risk mitigation

NASA Astrophysics Data System (ADS)

Sacco, G. M.; Nigrelli, G.; Bosio, A.; Chiarle, M.; Luino, F.

2012-02-01

In its 40 years of activity, the Research Institute for Geo-hydrological Protection of the Italian National Research Council has amassed a vast and varied collection of historical documentation on landslides, muddy-debris flows, and floods in northern Italy from 1600 to the present. Since 2008, the archive resources have been maintained through a relational database management system. The database is used for routine study and research purposes as well as for providing support during geo-hydrological emergencies, when data need to be quickly and accurately retrieved. Retrieval speed and accuracy are the main objectives of an implementation based on a dynamic taxonomies model. Dynamic taxonomies are a general knowledge management model for configuring complex, heterogeneous information bases that support exploratory searching. At each stage of the process, the user can explore or browse the database in a guided yet unconstrained way by selecting the alternatives suggested for further refining the search. Dynamic taxonomies have been successfully applied to such diverse and apparently unrelated domains as e-commerce and medical diagnosis. Here, we describe the application of dynamic taxonomies to our database and compare it to traditional relational database query methods. The dynamic taxonomy interface, essentially a point-and-click interface, is considerably faster and less error-prone than traditional form-based query interfaces that require the user to remember and type in the "right" search keywords. Finally, dynamic taxonomy users have confirmed that one of the principal benefits of this approach is the confidence of having considered all the relevant information. Dynamic taxonomies and relational databases work in synergy to provide fast and precise searching: one of the most important factors in timely response to emergencies.

Sting_RDB: a relational database of structural parameters for protein analysis with support for data warehousing and data mining.

PubMed

Oliveira, S R M; Almeida, G V; Souza, K R R; Rodrigues, D N; Kuser-Falcão, P R; Yamagishi, M E B; Santos, E H; Vieira, F D; Jardine, J G; Neshich, G

2007-10-05

An effective strategy for managing protein databases is to provide mechanisms to transform raw data into consistent, accurate and reliable information. Such mechanisms will greatly reduce operational inefficiencies and improve one's ability to better handle scientific objectives and interpret the research results. To achieve this challenging goal for the STING project, we introduce Sting_RDB, a relational database of structural parameters for protein analysis with support for data warehousing and data mining. In this article, we highlight the main features of Sting_RDB and show how a user can explore it for efficient and biologically relevant queries. Considering its importance for molecular biologists, effort has been made to advance Sting_RDB toward data quality assessment. To the best of our knowledge, Sting_RDB is one of the most comprehensive data repositories for protein analysis, now also capable of providing its users with a data quality indicator. This paper differs from our previous study in many aspects. First, we introduce Sting_RDB, a relational database with mechanisms for efficient and relevant queries using SQL. Sting_rdb evolved from the earlier, text (flat file)-based database, in which data consistency and integrity was not guaranteed. Second, we provide support for data warehousing and mining. Third, the data quality indicator was introduced. Finally and probably most importantly, complex queries that could not be posed on a text-based database, are now easily implemented. Further details are accessible at the Sting_RDB demo web page: http://www.cbi.cnptia.embrapa.br/StingRDB.

Methods and apparatus for constructing and implementing a universal extension module for processing objects in a database

NASA Technical Reports Server (NTRS)

Li, Chung-Sheng (Inventor); Smith, John R. (Inventor); Chang, Yuan-Chi (Inventor); Jhingran, Anant D. (Inventor); Padmanabhan, Sriram K. (Inventor); Hsiao, Hui-I (Inventor); Choy, David Mun-Hien (Inventor); Lin, Jy-Jine James (Inventor); Fuh, Gene Y. C. (Inventor); Williams, Robin (Inventor)

2004-01-01

Methods and apparatus for providing a multi-tier object-relational database architecture are disclosed. In one illustrative embodiment of the present invention, a multi-tier database architecture comprises an object-relational database engine as a top tier, one or more domain-specific extension modules as a bottom tier, and one or more universal extension modules as a middle tier. The individual extension modules of the bottom tier operationally connect with the one or more universal extension modules which, themselves, operationally connect with the database engine. The domain-specific extension modules preferably provide such functions as search, index, and retrieval services of images, video, audio, time series, web pages, text, XML, spatial data, etc. The domain-specific extension modules may include one or more IBM DB2 extenders, Oracle data cartridges and/or Informix datablades, although other domain-specific extension modules may be used.

Teaching Case: Adapting the Access Northwind Database to Support a Database Course

ERIC Educational Resources Information Center

Dyer, John N.; Rogers, Camille

2015-01-01

A common problem encountered when teaching database courses is that few large illustrative databases exist to support teaching and learning. Most database textbooks have small "toy" databases that are chapter objective specific, and thus do not support application over the complete domain of design, implementation and management concepts…

Saliency Detection on Light Field.

PubMed

Li, Nianyi; Ye, Jinwei; Ji, Yu; Ling, Haibin; Yu, Jingyi

2017-08-01

Existing saliency detection approaches use images as inputs and are sensitive to foreground/background similarities, complex background textures, and occlusions. We explore the problem of using light fields as input for saliency detection. Our technique is enabled by the availability of commercial plenoptic cameras that capture the light field of a scene in a single shot. We show that the unique refocusing capability of light fields provides useful focusness, depths, and objectness cues. We further develop a new saliency detection algorithm tailored for light fields. To validate our approach, we acquire a light field database of a range of indoor and outdoor scenes and generate the ground truth saliency map. Experiments show that our saliency detection scheme can robustly handle challenging scenarios such as similar foreground and background, cluttered background, complex occlusions, etc., and achieve high accuracy and robustness.

C++ and data

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

Naumann, Axel; /CERN; Canal, Philippe

2008-01-01

High performance computing with a large code base and C++ has proved to be a good combination. But when it comes to storing data, C++ is a problematic choice: it offers no support for serialization, type definitions are amazingly complex to parse, and the dependency analysis (what does object A need to be stored?) is incredibly difficult. Nevertheless, the LHC data consists of C++ objects that are serialized with help from ROOT's reflection database and interpreter CINT. The fact that we can do it on that scale, and the performance with which we do it makes this approach unique andmore » stirs interest even outside HEP. I will show how CINT collects and stores information about C++ types, what the current major challenges are (dictionary size), and what CINT and ROOT have done and plan to do about it.« less

The influence of the Bible geographic objects peculiarities on the concept of the spatiotemporal geoinformation system

NASA Astrophysics Data System (ADS)

Linsebarth, A.; Moscicka, A.

2010-01-01

The article describes the infl uence of the Bible geographic object peculiarities on the spatiotemporal geoinformation system of the Bible events. In the proposed concept of this system the special attention was concentrated to the Bible geographic objects and interrelations between the names of these objects and their location in the geospace. In the Bible, both in the Old and New Testament, there are hundreds of geographical names, but the selection of these names from the Bible text is not so easy. The same names are applied for the persons and geographic objects. The next problem which arises is the classification of the geographical object, because in several cases the same name is used for the towns, mountains, hills, valleys etc. Also very serious problem is related to the time-changes of the names. The interrelation between the object name and its location is also complicated. The geographic object of this same name is located in various places which should be properly correlated with the Bible text. Above mentioned peculiarities of Bible geographic objects infl uenced the concept of the proposed system which consists of three databases: reference, geographic object, and subject/thematic. The crucial component of this system is proper architecture of the geographic object database. In the paper very detailed description of this database is presented. The interrelation between the databases allows to the Bible readers to connect the Bible text with the geography of the terrain on which the Bible events occurred and additionally to have access to the other geographical and historical information related to the geographic objects.

ARACHNID: A prototype object-oriented database tool for distributed systems

NASA Technical Reports Server (NTRS)

Younger, Herbert; Oreilly, John; Frogner, Bjorn

1994-01-01

This paper discusses the results of a Phase 2 SBIR project sponsored by NASA and performed by MIMD Systems, Inc. A major objective of this project was to develop specific concepts for improved performance in accessing large databases. An object-oriented and distributed approach was used for the general design, while a geographical decomposition was used as a specific solution. The resulting software framework is called ARACHNID. The Faint Source Catalog developed by NASA was the initial database testbed. This is a database of many giga-bytes, where an order of magnitude improvement in query speed is being sought. This database contains faint infrared point sources obtained from telescope measurements of the sky. A geographical decomposition of this database is an attractive approach to dividing it into pieces. Each piece can then be searched on individual processors with only a weak data linkage between the processors being required. As a further demonstration of the concepts implemented in ARACHNID, a tourist information system is discussed. This version of ARACHNID is the commercial result of the project. It is a distributed, networked, database application where speed, maintenance, and reliability are important considerations. This paper focuses on the design concepts and technologies that form the basis for ARACHNID.

Analyzing forensic evidence based on density with magnetic levitation.

PubMed

Lockett, Matthew R; Mirica, Katherine A; Mace, Charles R; Blackledge, Robert D; Whitesides, George M

2013-01-01

This paper describes a method for determining the density of contact trace objects with magnetic levitation (MagLev). MagLev measurements accurately determine the density (± 0.0002 g/cm(3) ) of a diamagnetic object and are compatible with objects that are nonuniform in shape and size. The MagLev device (composed of two permanent magnets with like poles facing) and the method described provide a means of accurately determining the density of trace objects. This method is inexpensive, rapid, and verifiable and provides numerical values--independent of the specific apparatus or analyst--that correspond to the absolute density of the sample that may be entered into a searchable database. We discuss the feasibility of MagLev as a possible means of characterizing forensic-related evidence and demonstrate the ability of MagLev to (i) determine the density of samples of glitter and gunpowder, (ii) separate glitter particles of different densities, and (iii) determine the density of a glitter sample that was removed from a complex sample matrix. © 2012 American Academy of Forensic Sciences.

Design and Implementation of a Metadata-rich File System

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

Ames, S; Gokhale, M B; Maltzahn, C

2010-01-19

Despite continual improvements in the performance and reliability of large scale file systems, the management of user-defined file system metadata has changed little in the past decade. The mismatch between the size and complexity of large scale data stores and their ability to organize and query their metadata has led to a de facto standard in which raw data is stored in traditional file systems, while related, application-specific metadata is stored in relational databases. This separation of data and semantic metadata requires considerable effort to maintain consistency and can result in complex, slow, and inflexible system operation. To address thesemore » problems, we have developed the Quasar File System (QFS), a metadata-rich file system in which files, user-defined attributes, and file relationships are all first class objects. In contrast to hierarchical file systems and relational databases, QFS defines a graph data model composed of files and their relationships. QFS incorporates Quasar, an XPATH-extended query language for searching the file system. Results from our QFS prototype show the effectiveness of this approach. Compared to the de facto standard, the QFS prototype shows superior ingest performance and comparable query performance on user metadata-intensive operations and superior performance on normal file metadata operations.« less

Attentional gating models of object substitution masking.

PubMed

Põder, Endel

2013-11-01

Di Lollo, Enns, and Rensink (2000) proposed the computational model of object substitution (CMOS) to explain their experimental results with sparse visual maskers. This model supposedly is based on reentrant hypotheses testing in the visual system, and the modeled experiments are believed to demonstrate these reentrant processes in human vision. In this study, I analyze the main assumptions of this model. I argue that CMOS is a version of the attentional gating model and that its relationship with reentrant processing is rather illusory. The fit of this model to the data indicates that reentrant hypotheses testing is not necessary for the explanation of object substitution masking (OSM). Further, the original CMOS cannot predict some important aspects of the experimental data. I test 2 new models incorporating an unselective processing (divided attention) stage; these models are more consistent with data from OSM experiments. My modeling shows that the apparent complexity of OSM can be reduced to a few simple and well-known mechanisms of perception and memory. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Retrieving high-resolution images over the Internet from an anatomical image database

NASA Astrophysics Data System (ADS)

Strupp-Adams, Annette; Henderson, Earl

1999-12-01

The Visible Human Data set is an important contribution to the national collection of anatomical images. To enhance the availability of these images, the National Library of Medicine has supported the design and development of a prototype object-oriented image database which imports, stores, and distributes high resolution anatomical images in both pixel and voxel formats. One of the key database modules is its client-server Internet interface. This Web interface provides a query engine with retrieval access to high-resolution anatomical images that range in size from 100KB for browser viewable rendered images, to 1GB for anatomical structures in voxel file formats. The Web query and retrieval client-server system is composed of applet GUIs, servlets, and RMI application modules which communicate with each other to allow users to query for specific anatomical structures, and retrieve image data as well as associated anatomical images from the database. Selected images can be downloaded individually as single files via HTTP or downloaded in batch-mode over the Internet to the user's machine through an applet that uses Netscape's Object Signing mechanism. The image database uses ObjectDesign's object-oriented DBMS, ObjectStore that has a Java interface. The query and retrieval systems has been tested with a Java-CDE window system, and on the x86 architecture using Windows NT 4.0. This paper describes the Java applet client search engine that queries the database; the Java client module that enables users to view anatomical images online; the Java application server interface to the database which organizes data returned to the user, and its distribution engine that allow users to download image files individually and/or in batch-mode.

Data-driven indexing mechanism for the recognition of polyhedral objects

NASA Astrophysics Data System (ADS)

McLean, Stewart; Horan, Peter; Caelli, Terry M.

1992-02-01

This paper is concerned with the problem of searching large model databases. To date, most object recognition systems have concentrated on the problem of matching using simple searching algorithms. This is quite acceptable when the number of object models is small. However, in the future, general purpose computer vision systems will be required to recognize hundreds or perhaps thousands of objects and, in such circumstances, efficient searching algorithms will be needed. The problem of searching a large model database is one which must be addressed if future computer vision systems are to be at all effective. In this paper we present a method we call data-driven feature-indexed hypothesis generation as one solution to the problem of searching large model databases.

A self-organized learning strategy for object recognition by an embedded line of attraction

NASA Astrophysics Data System (ADS)

Seow, Ming-Jung; Alex, Ann T.; Asari, Vijayan K.

2012-04-01

For humans, a picture is worth a thousand words, but to a machine, it is just a seemingly random array of numbers. Although machines are very fast and efficient, they are vastly inferior to humans for everyday information processing. Algorithms that mimic the way the human brain computes and learns may be the solution. In this paper we present a theoretical model based on the observation that images of similar visual perceptions reside in a complex manifold in an image space. The perceived features are often highly structured and hidden in a complex set of relationships or high-dimensional abstractions. To model the pattern manifold, we present a novel learning algorithm using a recurrent neural network. The brain memorizes information using a dynamical system made of interconnected neurons. Retrieval of information is accomplished in an associative sense. It starts from an arbitrary state that might be an encoded representation of a visual image and converges to another state that is stable. The stable state is what the brain remembers. In designing a recurrent neural network, it is usually of prime importance to guarantee the convergence in the dynamics of the network. We propose to modify this picture: if the brain remembers by converging to the state representing familiar patterns, it should also diverge from such states when presented with an unknown encoded representation of a visual image belonging to a different category. That is, the identification of an instability mode is an indication that a presented pattern is far away from any stored pattern and therefore cannot be associated with current memories. These properties can be used to circumvent the plasticity-stability dilemma by using the fluctuating mode as an indicator to create new states. We capture this behavior using a novel neural architecture and learning algorithm, in which the system performs self-organization utilizing a stability mode and an instability mode for the dynamical system. Based on this observation we developed a self- organizing line attractor, which is capable of generating new lines in the feature space to learn unrecognized patterns. Experiments performed on UMIST pose database and CMU face expression variant database for face recognition have shown that the proposed nonlinear line attractor is able to successfully identify the individuals and it provided better recognition rate when compared to the state of the art face recognition techniques. Experiments on FRGC version 2 database has also provided excellent recognition rate in images captured in complex lighting environments. Experiments performed on the Japanese female face expression database and Essex Grimace database using the self organizing line attractor have also shown successful expression invariant face recognition. These results show that the proposed model is able to create nonlinear manifolds in a multidimensional feature space to distinguish complex patterns.

Deterministic object tracking using Gaussian ringlet and directional edge features

NASA Astrophysics Data System (ADS)

Krieger, Evan W.; Sidike, Paheding; Aspiras, Theus; Asari, Vijayan K.

2017-10-01

Challenges currently existing for intensity-based histogram feature tracking methods in wide area motion imagery (WAMI) data include object structural information distortions, background variations, and object scale change. These issues are caused by different pavement or ground types and from changing the sensor or altitude. All of these challenges need to be overcome in order to have a robust object tracker, while attaining a computation time appropriate for real-time processing. To achieve this, we present a novel method, Directional Ringlet Intensity Feature Transform (DRIFT), which employs Kirsch kernel filtering for edge features and a ringlet feature mapping for rotational invariance. The method also includes an automatic scale change component to obtain accurate object boundaries and improvements for lowering computation times. We evaluated the DRIFT algorithm on two challenging WAMI datasets, namely Columbus Large Image Format (CLIF) and Large Area Image Recorder (LAIR), to evaluate its robustness and efficiency. Additional evaluations on general tracking video sequences are performed using the Visual Tracker Benchmark and Visual Object Tracking 2014 databases to demonstrate the algorithms ability with additional challenges in long complex sequences including scale change. Experimental results show that the proposed approach yields competitive results compared to state-of-the-art object tracking methods on the testing datasets.

Prediction of enteric methane production, yield, and intensity in dairy cattle using an intercontinental database.

PubMed

Niu, Mutian; Kebreab, Ermias; Hristov, Alexander N; Oh, Joonpyo; Arndt, Claudia; Bannink, André; Bayat, Ali R; Brito, André F; Boland, Tommy; Casper, David; Crompton, Les A; Dijkstra, Jan; Eugène, Maguy A; Garnsworthy, Phil C; Haque, Md Najmul; Hellwing, Anne L F; Huhtanen, Pekka; Kreuzer, Michael; Kuhla, Bjoern; Lund, Peter; Madsen, Jørgen; Martin, Cécile; McClelland, Shelby C; McGee, Mark; Moate, Peter J; Muetzel, Stefan; Muñoz, Camila; O'Kiely, Padraig; Peiren, Nico; Reynolds, Christopher K; Schwarm, Angela; Shingfield, Kevin J; Storlien, Tonje M; Weisbjerg, Martin R; Yáñez-Ruiz, David R; Yu, Zhongtang

2018-02-16

Enteric methane (CH 4 ) production from cattle contributes to global greenhouse gas emissions. Measurement of enteric CH 4 is complex, expensive, and impractical at large scales; therefore, models are commonly used to predict CH 4 production. However, building robust prediction models requires extensive data from animals under different management systems worldwide. The objectives of this study were to (1) collate a global database of enteric CH 4 production from individual lactating dairy cattle; (2) determine the availability of key variables for predicting enteric CH 4 production (g/day per cow), yield [g/kg dry matter intake (DMI)], and intensity (g/kg energy corrected milk) and their respective relationships; (3) develop intercontinental and regional models and cross-validate their performance; and (4) assess the trade-off between availability of on-farm inputs and CH 4 prediction accuracy. The intercontinental database covered Europe (EU), the United States (US), and Australia (AU). A sequential approach was taken by incrementally adding key variables to develop models with increasing complexity. Methane emissions were predicted by fitting linear mixed models. Within model categories, an intercontinental model with the most available independent variables performed best with root mean square prediction error (RMSPE) as a percentage of mean observed value of 16.6%, 14.7%, and 19.8% for intercontinental, EU, and United States regions, respectively. Less complex models requiring only DMI had predictive ability comparable to complex models. Enteric CH 4 production, yield, and intensity prediction models developed on an intercontinental basis had similar performance across regions, however, intercepts and slopes were different with implications for prediction. Revised CH 4 emission conversion factors for specific regions are required to improve CH 4 production estimates in national inventories. In conclusion, information on DMI is required for good prediction, and other factors such as dietary neutral detergent fiber (NDF) concentration, improve the prediction. For enteric CH 4 yield and intensity prediction, information on milk yield and composition is required for better estimation. © 2018 John Wiley & Sons Ltd.

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex

PubMed Central

Maccari, Giuseppe; Robinson, James; Ballingall, Keith; Guethlein, Lisbeth A.; Grimholt, Unni; Kaufman, Jim; Ho, Chak-Sum; de Groot, Natasja G.; Flicek, Paul; Bontrop, Ronald E.; Hammond, John A.; Marsh, Steven G. E.

2017-01-01

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group. PMID:27899604

Toward An Unstructured Mesh Database

NASA Astrophysics Data System (ADS)

Rezaei Mahdiraji, Alireza; Baumann, Peter Peter

2014-05-01

Unstructured meshes are used in several application domains such as earth sciences (e.g., seismology), medicine, oceanography, cli- mate modeling, GIS as approximate representations of physical objects. Meshes subdivide a domain into smaller geometric elements (called cells) which are glued together by incidence relationships. The subdivision of a domain allows computational manipulation of complicated physical structures. For instance, seismologists model earthquakes using elastic wave propagation solvers on hexahedral meshes. The hexahedral con- tains several hundred millions of grid points and millions of hexahedral cells. Each vertex node in the hexahedrals stores a multitude of data fields. To run simulation on such meshes, one needs to iterate over all the cells, iterate over incident cells to a given cell, retrieve coordinates of cells, assign data values to cells, etc. Although meshes are used in many application domains, to the best of our knowledge there is no database vendor that support unstructured mesh features. Currently, the main tool for querying and manipulating unstructured meshes are mesh libraries, e.g., CGAL and GRAL. Mesh li- braries are dedicated libraries which includes mesh algorithms and can be run on mesh representations. The libraries do not scale with dataset size, do not have declarative query language, and need deep C++ knowledge for query implementations. Furthermore, due to high coupling between the implementations and input file structure, the implementations are less reusable and costly to maintain. A dedicated mesh database offers the following advantages: 1) declarative querying, 2) ease of maintenance, 3) hiding mesh storage structure from applications, and 4) transparent query optimization. To design a mesh database, the first challenge is to define a suitable generic data model for unstructured meshes. We proposed ImG-Complexes data model as a generic topological mesh data model which extends incidence graph model to multi-incidence relationships. We instrument ImG model with sets of optional and application-specific constraints which can be used to check validity of meshes for a specific class of object such as manifold, pseudo-manifold, and simplicial manifold. We conducted experiments to measure the performance of the graph database solution in processing mesh queries and compare it with GrAL mesh library and PostgreSQL database on synthetic and real mesh datasets. The experiments show that each system perform well on specific types of mesh queries, e.g., graph databases perform well on global path-intensive queries. In the future, we investigate database operations for the ImG model and design a mesh query language.

Lesion complexity drives the cost of superficial femoral artery endovascular interventions

PubMed Central

Walker, Karen L.; Nolan, Brian W.; Columbo, Jesse A.; Rzucidlo, Eva M.; Goodney, Philip P.; Walsh, Daniel B.; Atkinson, Benjamin J.; Powell, Richard J.

2017-01-01

Objective Patients who undergo endovascular treatment of superficial femoral artery (SFA) disease vary greatly in lesion complexity and treatment options. This study examined the association of lesion severity and cost of SFA stenting and to determine if procedure cost affects primary patency at 1 year. Methods A retrospective record review identified patients undergoing initial SFA stenting between January 1, 2010, and February 1, 2012. Medical records were reviewed to collect data on demographics, comorbidities, indication for the procedure, TransAtlantic Inter-Society Consensus (TASC) II severity, and primary patency. The interventional radiology database and hospital accounting database were queried to determine cost drivers of SFA stenting. Procedure supply cost included any item with a bar code used for the procedure. Associations between cost drivers and lesion characteristics were explored. Primary patency was determined using Kaplan-Meier survival curves and a log-rank test. Results During the study period, 95 patients underwent stenting in 98 extremities; of these, 61% of SFA stents were performed for claudication, with 80% of lesions classified as TASC II A or B. Primary patency at 1 year was 79% for the entire cohort. The mean total cost per case was $10,333. Increased procedure supply cost was associated with adjunct device use, the number of stents, and TASC II severity. Despite higher costs of treating more complex lesions, primary patency at 1 year was similar at 80% for high-cost (supply cost >$4000) vs 78% for low-cost (supply cost <$4000) interventions. Conclusions SFA lesion complexity, as defined by TASC II severity, drives the cost of endovascular interventions but does not appear to disadvantage patency at 1 year. Reimbursement agencies should consider incorporating disease severity into reimbursement algorithms for lower extremity endovascular interventions. PMID:26206581

Investigating multi-objective fluence and beam orientation IMRT optimization

NASA Astrophysics Data System (ADS)

Potrebko, Peter S.; Fiege, Jason; Biagioli, Matthew; Poleszczuk, Jan

2017-07-01

Radiation Oncology treatment planning requires compromises to be made between clinical objectives that are invariably in conflict. It would be beneficial to have a ‘bird’s-eye-view’ perspective of the full spectrum of treatment plans that represent the possible trade-offs between delivering the intended dose to the planning target volume (PTV) while optimally sparing the organs-at-risk (OARs). In this work, the authors demonstrate Pareto-aware radiotherapy evolutionary treatment optimization (PARETO), a multi-objective tool featuring such bird’s-eye-view functionality, which optimizes fluence patterns and beam angles for intensity-modulated radiation therapy (IMRT) treatment planning. The problem of IMRT treatment plan optimization is managed as a combined monolithic problem, where all beam fluence and angle parameters are treated equally during the optimization. To achieve this, PARETO is built around a powerful multi-objective evolutionary algorithm, called Ferret, which simultaneously optimizes multiple fitness functions that encode the attributes of the desired dose distribution for the PTV and OARs. The graphical interfaces within PARETO provide useful information such as: the convergence behavior during optimization, trade-off plots between the competing objectives, and a graphical representation of the optimal solution database allowing for the rapid exploration of treatment plan quality through the evaluation of dose-volume histograms and isodose distributions. PARETO was evaluated for two relatively complex clinical cases, a paranasal sinus and a pancreas case. The end result of each PARETO run was a database of optimal (non-dominated) treatment plans that demonstrated trade-offs between the OAR and PTV fitness functions, which were all equally good in the Pareto-optimal sense (where no one objective can be improved without worsening at least one other). Ferret was able to produce high quality solutions even though a large number of parameters, such as beam fluence and beam angles, were included in the optimization.

The HARPS-N archive through a Cassandra, NoSQL database suite?

NASA Astrophysics Data System (ADS)

Molinari, Emilio; Guerra, Jose; Harutyunyan, Avet; Lodi, Marcello; Martin, Adrian

2016-07-01

The TNG-INAF is developing the science archive for the WEAVE instrument. The underlying architecture of the archive is based on a non relational database, more precisely, on Apache Cassandra cluster, which uses a NoSQL technology. In order to test and validate the use of this architecture, we created a local archive which we populated with all the HARPSN spectra collected at the TNG since the instrument's start of operations in mid-2012, as well as developed tools for the analysis of this data set. The HARPS-N data set is two orders of magnitude smaller than WEAVE, but we want to demonstrate the ability to walk through a complete data set and produce scientific output, as valuable as that produced by an ordinary pipeline, though without accessing directly the FITS files. The analytics is done by Apache Solr and Spark and on a relational PostgreSQL database. As an example, we produce observables like metallicity indexes for the targets in the archive and compare the results with the ones coming from the HARPS-N regular data reduction software. The aim of this experiment is to explore the viability of a high availability cluster and distributed NoSQL database as a platform for complex scientific analytics on a large data set, which will then be ported to the WEAVE Archive System (WAS) which we are developing for the WEAVE multi object, fiber spectrograph.

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

PubMed

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

2015-01-01

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

Insertion algorithms for network model database management systems

NASA Astrophysics Data System (ADS)

Mamadolimov, Abdurashid; Khikmat, Saburov

2017-12-01

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

Integrating heterogeneous databases in clustered medic care environments using object-oriented technology

NASA Astrophysics Data System (ADS)

Thakore, Arun K.; Sauer, Frank

1994-05-01

The organization of modern medical care environments into disease-related clusters, such as a cancer center, a diabetes clinic, etc., has the side-effect of introducing multiple heterogeneous databases, often containing similar information, within the same organization. This heterogeneity fosters incompatibility and prevents the effective sharing of data amongst applications at different sites. Although integration of heterogeneous databases is now feasible, in the medical arena this is often an ad hoc process, not founded on proven database technology or formal methods. In this paper we illustrate the use of a high-level object- oriented semantic association method to model information found in different databases into an integrated conceptual global model that integrates the databases. We provide examples from the medical domain to illustrate an integration approach resulting in a consistent global view, without attacking the autonomy of the underlying databases.

Determining root correspondence between previously and newly detected objects

DOEpatents

Paglieroni, David W.; Beer, N Reginald

2014-06-17

A system that applies attribute and topology based change detection to networks of objects that were detected on previous scans of a structure, roadway, or area of interest. The attributes capture properties or characteristics of the previously detected objects, such as location, time of detection, size, elongation, orientation, etc. The topology of the network of previously detected objects is maintained in a constellation database that stores attributes of previously detected objects and implicitly captures the geometrical structure of the network. A change detection system detects change by comparing the attributes and topology of new objects detected on the latest scan to the constellation database of previously detected objects.

A spatiotemporal data model for incorporating time in geographic information systems (GEN-STGIS)

NASA Astrophysics Data System (ADS)

Narciso, Flor Eugenia

Temporal Geographic Information Systems (TGIS) is a new technology, which is being developed to work with Geographic Information Systems (GIS) that deal with geographic phenomena that change over time. The capabilities of TGIS depend on the underlying data model. However, a literature review of current spatiotemporal GIS data models has shown that they are not adequate for managing time when representing temporal data. In addition, the majority of these data models have been designed to support the requirements of specific-purpose applications. In an effort to resolve this problem, the related literature has been explored. A comparative investigation of the current spatiotemporal GIS data models has been made to identify their characteristics, advantages and disadvantages, similarities and differences, and to determine why they do not work adequately. A new object-oriented General-purpose Spatiotemporal GIS (GEN-STGIS) data model is proposed here. This model provides better representation, storage and management of data related to geographic phenomena that change over time and overcomes some of the problems detected in the reviewed data models. The proposed data model has four key benefits. First, it provides the capabilities of a standard vector-based GIS embedded in the 2-D Euclidean space. Second, it includes the two temporal dimensions, valid time and transaction time, supported by temporal databases. Third, it inherits, from the object oriented approach, the flexibility, modularity and ability to handle the complexities introduced by spatial and temporal dimensions. Fourth, it improves the geographic query capabilities of current TGIS with the introduction of the concept of bounding box while providing temporal and spatiotemporal query capabilities. The data model is then evaluated in order to assess its strengths and weaknesses as a spatiotemporal GIS data model, and to determine how well the model satisfies the requirements imposed by TGIS applications. The practicality of the data model is demonstrated by the creation of a TGIS example and the partial implementation of the model using the POET Java software for developing the object-oriented database. the object-oriented database.

Simple Logic for Big Problems: An Inside Look at Relational Databases.

ERIC Educational Resources Information Center

Seba, Douglas B.; Smith, Pat

1982-01-01

Discusses database design concept termed "normalization" (process replacing associations between data with associations in two-dimensional tabular form) which results in formation of relational databases (they are to computers what dictionaries are to spoken languages). Applications of the database in serials control and complex systems…

Using semantic data modeling techniques to organize an object-oriented database for extending the mass storage model

NASA Technical Reports Server (NTRS)

Campbell, William J.; Short, Nicholas M., Jr.; Roelofs, Larry H.; Dorfman, Erik

1991-01-01

A methodology for optimizing organization of data obtained by NASA earth and space missions is discussed. The methodology uses a concept based on semantic data modeling techniques implemented in a hierarchical storage model. The modeling is used to organize objects in mass storage devices, relational database systems, and object-oriented databases. The semantic data modeling at the metadata record level is examined, including the simulation of a knowledge base and semantic metadata storage issues. The semantic data model hierarchy and its application for efficient data storage is addressed, as is the mapping of the application structure to the mass storage.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

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

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

Architectural Implications for Spatial Object Association Algorithms*

PubMed Central

Kumar, Vijay S.; Kurc, Tahsin; Saltz, Joel; Abdulla, Ghaleb; Kohn, Scott R.; Matarazzo, Celeste

2013-01-01

Spatial object association, also referred to as crossmatch of spatial datasets, is the problem of identifying and comparing objects in two or more datasets based on their positions in a common spatial coordinate system. In this work, we evaluate two crossmatch algorithms that are used for astronomical sky surveys, on the following database system architecture configurations: (1) Netezza Performance Server®, a parallel database system with active disk style processing capabilities, (2) MySQL Cluster, a high-throughput network database system, and (3) a hybrid configuration consisting of a collection of independent database system instances with data replication support. Our evaluation provides insights about how architectural characteristics of these systems affect the performance of the spatial crossmatch algorithms. We conducted our study using real use-case scenarios borrowed from a large-scale astronomy application known as the Large Synoptic Survey Telescope (LSST). PMID:25692244

Determining object orientation with a hierarchical database of binary synthetic discriminant function filters

NASA Technical Reports Server (NTRS)

Reid, Max B.; Ma, Paul W.; Downie, John D.

1990-01-01

An optical correlation-based system is demonstrated which recognizes an object and determines its angular orientation by traversing a hierarchical data base of binary filters. The data-base architecture is made possible by the development of binary synthetic discriminant function filters.

Automatic QRS complex detection using two-level convolutional neural network.

PubMed

Xiang, Yande; Lin, Zhitao; Meng, Jianyi

2018-01-29

The QRS complex is the most noticeable feature in the electrocardiogram (ECG) signal, therefore, its detection is critical for ECG signal analysis. The existing detection methods largely depend on hand-crafted manual features and parameters, which may introduce significant computational complexity, especially in the transform domains. In addition, fixed features and parameters are not suitable for detecting various kinds of QRS complexes under different circumstances. In this study, based on 1-D convolutional neural network (CNN), an accurate method for QRS complex detection is proposed. The CNN consists of object-level and part-level CNNs for extracting different grained ECG morphological features automatically. All the extracted morphological features are used by multi-layer perceptron (MLP) for QRS complex detection. Additionally, a simple ECG signal preprocessing technique which only contains difference operation in temporal domain is adopted. Based on the MIT-BIH arrhythmia (MIT-BIH-AR) database, the proposed detection method achieves overall sensitivity Sen = 99.77%, positive predictivity rate PPR = 99.91%, and detection error rate DER = 0.32%. In addition, the performance variation is performed according to different signal-to-noise ratio (SNR) values. An automatic QRS detection method using two-level 1-D CNN and simple signal preprocessing technique is proposed for QRS complex detection. Compared with the state-of-the-art QRS complex detection approaches, experimental results show that the proposed method acquires comparable accuracy.

Accessing and distributing EMBL data using CORBA (common object request broker architecture).

PubMed

Wang, L; Rodriguez-Tomé, P; Redaschi, N; McNeil, P; Robinson, A; Lijnzaad, P

2000-01-01

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems.

Accessing and distributing EMBL data using CORBA (common object request broker architecture)

PubMed Central

Wang, Lichun; Rodriguez-Tomé, Patricia; Redaschi, Nicole; McNeil, Phil; Robinson, Alan; Lijnzaad, Philip

2000-01-01

Background: The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences and related information traditionally made available in flat-file format. Queries through tools such as SRS (Sequence Retrieval System) also return data in flat-file format. Flat files have a number of shortcomings, however, and the resources therefore currently lack a flexible environment to meet individual researchers' needs. The Object Management Group's common object request broker architecture (CORBA) is an industry standard that provides platform-independent programming interfaces and models for portable distributed object-oriented computing applications. Its independence from programming languages, computing platforms and network protocols makes it attractive for developing new applications for querying and distributing biological data. Results: A CORBA infrastructure developed by EMBL-EBI provides an efficient means of accessing and distributing EMBL data. The EMBL object model is defined such that it provides a basis for specifying interfaces in interface definition language (IDL) and thus for developing the CORBA servers. The mapping from the object model to the relational schema in the underlying Oracle database uses the facilities provided by PersistenceTM, an object/relational tool. The techniques of developing loaders and 'live object caching' with persistent objects achieve a smart live object cache where objects are created on demand. The objects are managed by an evictor pattern mechanism. Conclusions: The CORBA interfaces to the EMBL database address some of the problems of traditional flat-file formats and provide an efficient means for accessing and distributing EMBL data. CORBA also provides a flexible environment for users to develop their applications by building clients to our CORBA servers, which can be integrated into existing systems. PMID:11178259

Ukrainian Database and Atlas of Light Curves of Artificial Space Objects

NASA Astrophysics Data System (ADS)

Koshkin, N.; Savanevich, V.; Pohorelov, A.; Shakun, L.; Zhukov, V.; Korobeynikova, E.; Strakhova, S.; Moskalenko, S.; Kashuba, V.; Krasnoshchokov, A.

This paper describes the Ukrainian database of long-term photometric observations of resident space objects (RSO). For the purpose of using this database for the outer space monitoring and space situational awareness (SSA) the open internet resource has been developed. The paper shows examples of using the Atlas of light curves of RSO's for analyzing the state of rotation around the center of mass of several active and non-functioning satellites in orbit.

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

DTIC Science & Technology

2017-01-01

CII-B 2800 Powder Mill Road Adelphi, MD 20783-1138 8. PERFORMING ORGANIZATION REPORT NUMBER ARL-TR-7921 9. SPONSORING/MONITORING AGENCY NAME(S...server database, structured query language, information objects, instructions, maintenance , cursor on target events, unattended ground sensors...unlimited. iii Contents List of Figures iv 1. Introduction 1 2. Computer and Software Development Tools Requirements 1 3. Database Maintenance 2 3.1

Information system of mineral deposits in Slovenia

NASA Astrophysics Data System (ADS)

Hribernik, K.; Rokavec, D.; Šinigioj, J.; Šolar, S.

2010-03-01

At the Geologic Survey of Slovenia the need for complex overview and control of the deposits of available non-metallic mineral raw materials and of their exploitations became urgent. In the framework of the Geologic Information System we established the Database of non-metallic mineral deposits comprising all important data of deposits and concessionars. Relational database is built with program package MS Access, but in year 2008 we plan to transfer it on SQL server. In the evidence there is 272 deposits and 200 concessionars. The mineral resources information system of Slovenia, which was started back in 2002, consists of two integrated parts, mentioned relational database of mineral deposits, which relates information in tabular way so that rules of relational algebra can be applied, and geographic information system (GIS), which relates spatial information of deposits. . The complex relationships between objects and the concepts of normalized data structures, lead to the practical informative and useful data model, transparent to the user and to better decision-making by allowing future scenarios to be developed and inspected. Computerized storage, and display system is as already said, developed and managed under the support of Geological Survey of Slovenia, which conducts research on the occurrence, quality, quantity, and availability of mineral resources in order to help the Nation make informed decisions using earth-science information. Information about deposit is stored in records in approximately hundred data fields. A numeric record number uniquely identifies each site. The data fields are grouped under principal categories. Each record comprise elementary data of deposit (name, type, location, prospect, rock), administrative data (concessionar, number of decree in official paper, object of decree, number of contract and its duration) and data of mineral resource produced amount and size of exploration area). The data can also be searched, sorted and printed using any of these fields. New records are being added annually, and existing records updated or upgraded. Relational database is connected with scanned exploration/exploitation areas of deposits, defined on the base of digital ortofoto. Register of those areas is indispensable because of spatial planning and spatial municipal and regional strategy development. Database is also part of internet application for quick search and review of data and part of web page of mineral resources of Slovenia. The technology chosen for internet application is ESRI's ArcIMS Internet Map Server. ArcIMS allows users to readily and easily display, analyze, and interpret spatial data from desktop using a Web browser connected to the Internet. We believe that there is an opportunity for cooperation within this activity. We can offer a single location where users can come to browse relatively simply for geoscience-related digital data sets.

Chemical and mineralogical data and processing methods management system prototype with application to study of the North Caucasus Blybsky Metamorphic Complexes metamorphism PT-condition

NASA Astrophysics Data System (ADS)

Ivanov, Stanislav; Kamzolkin, Vladimir; Konilov, Aleksandr; Aleshin, Igor

2014-05-01

There are many various methods of assessing the conditions of rocks formation based on determining the composition of the constituent minerals. Our objective was to create a universal tool for processing mineral's chemical analysis results and solving geothermobarometry problems by creating a database of existing sensors and providing a user-friendly standard interface. Similar computer assisted tools are based upon large collection of sensors (geothermometers and geobarometers) are known, for example, the project TPF (Konilov A.N., 1999) - text-based sensor collection tool written in PASCAL. The application contained more than 350 different sensors and has been used widely in petrochemical studies (see A.N. Konilov , A.A. Grafchikov, V.I. Fonarev 2010 for review). Our prototype uses the TPF project concept and is designed with modern application development techniques, which allows better flexibility. Main components of the designed system are 3 connected datasets: sensors collection (geothermometers, geobarometers, oxygen geobarometers, etc.), petrochemical data and modeling results. All data is maintained by special management and visualization tools and resides in sql database. System utilities allow user to import and export data in various file formats, edit records and plot graphs. Sensors database contains up to date collections of known methods. New sensors may be added by user. Measured database should be filled in by researcher. User friendly interface allows access to all available data and sensors, automates routine work, reduces the risk of common user mistakes and simplifies information exchange between research groups. We use prototype to evaluate peak pressure during the formation of garnet-amphibolite apoeclogites, gneisses and schists Blybsky metamorphic complex of the Front Range of the Northern Caucasus. In particular, our estimation of formation pressure range (18 ± 4 kbar) agrees on independent research results. The reported study was partially supported by RFBR, research project No. 14-05-00615.

Physical Science Informatics: Providing Open Science Access to Microheater Array Boiling Experiment Data

NASA Technical Reports Server (NTRS)

McQuillen, John; Green, Robert D.; Henrie, Ben; Miller, Teresa; Chiaramonte, Fran

2014-01-01

The Physical Science Informatics (PSI) system is the next step in this an effort to make NASA sponsored flight data available to the scientific and engineering community, along with the general public. The experimental data, from six overall disciplines, Combustion Science, Fluid Physics, Complex Fluids, Fundamental Physics, and Materials Science, will present some unique challenges. Besides data in textual or numerical format, large portions of both the raw and analyzed data for many of these experiments are digital images and video, requiring large data storage requirements. In addition, the accessible data will include experiment design and engineering data (including applicable drawings), any analytical or numerical models, publications, reports, and patents, and any commercial products developed as a result of the research. This objective of paper includes the following: Present the preliminary layout (Figure 2) of MABE data within the PSI database. Obtain feedback on the layout. Present the procedure to obtain access to this database.

A high performance, ad-hoc, fuzzy query processing system for relational databases

NASA Technical Reports Server (NTRS)

Mansfield, William H., Jr.; Fleischman, Robert M.

1992-01-01

Database queries involving imprecise or fuzzy predicates are currently an evolving area of academic and industrial research. Such queries place severe stress on the indexing and I/O subsystems of conventional database environments since they involve the search of large numbers of records. The Datacycle architecture and research prototype is a database environment that uses filtering technology to perform an efficient, exhaustive search of an entire database. It has recently been modified to include fuzzy predicates in its query processing. The approach obviates the need for complex index structures, provides unlimited query throughput, permits the use of ad-hoc fuzzy membership functions, and provides a deterministic response time largely independent of query complexity and load. This paper describes the Datacycle prototype implementation of fuzzy queries and some recent performance results.

HOWDY: an integrated database system for human genome research

PubMed Central

Hirakawa, Mika

2002-01-01

HOWDY is an integrated database system for accessing and analyzing human genomic information (http://www-alis.tokyo.jst.go.jp/HOWDY/). HOWDY stores information about relationships between genetic objects and the data extracted from a number of databases. HOWDY consists of an Internet accessible user interface that allows thorough searching of the human genomic databases using the gene symbols and their aliases. It also permits flexible editing of the sequence data. The database can be searched using simple words and the search can be restricted to a specific cytogenetic location. Linear maps displaying markers and genes on contig sequences are available, from which an object can be chosen. Any search starting point identifies all the information matching the query. HOWDY provides a convenient search environment of human genomic data for scientists unsure which database is most appropriate for their search. PMID:11752279

Ioss IO Subsystem

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

Sjaardema, Gregory; Bauer, David; Erik, & Illescas

2017-01-06

The Ioss is a database-independent package for providing an object-oriented, abstract interface to IO capabilities for a finite element application; and concrete database interfaces which provided input and/or output to exodusII, xdmf, generated, and heartbeat database formats. The Ioss provides an object-oriented C++-based IO interface for a finite element application code. The application code can perform all IO operations through the Ioss interface which is typically at a higher abstraction level than the concrete database formats. The Ioss then performs the needed operations to translate the finite element data to the specific format required by the concrete database implementations. Themore » Ioss currently supports interfaces to exodusII, xdmf, generated, and heartbeat formats, but additional formats can be easily added.« less

On-line database of voltammetric data of immobilized particles for identifying pigments and minerals in archaeometry, conservation and restoration (ELCHER database).

PubMed

Doménech-Carbó, Antonio; Doménech-Carbó, María Teresa; Valle-Algarra, Francisco Manuel; Gimeno-Adelantado, José Vicente; Osete-Cortina, Laura; Bosch-Reig, Francisco

2016-07-13

A web-based database of voltammograms is presented for characterizing artists' pigments and corrosion products of ceramic, stone and metal objects by means of the voltammetry of immobilized particles methodology. Description of the website and the database is provided. Voltammograms are, in most cases, accompanied by scanning electron microphotographs, X-ray spectra, infrared spectra acquired in attenuated total reflectance Fourier transform infrared spectroscopy mode (ATR-FTIR) and diffuse reflectance spectra in the UV-Vis-region. For illustrating the usefulness of the database two case studies involving identification of pigments and a case study describing deterioration of an archaeological metallic object are presented. Copyright © 2016 Elsevier B.V. All rights reserved.

[Systematization of nursing care: viewing care as interactive, complementary and multi-professional].

PubMed

do Nascimento, Keyla Cristiane; Backes, Dirce Stein; Koerich, Magda Santos; Erdmann, Alacoque Lorenzini

2008-12-01

This study is the result of an extended project, named: The systematization of nursing care in the perspective of complex thinking. The objective of this qualitative study is to better comprehend the meaning of the systematization of nursing care among healthcare professionals. The Data-Based Theory was used as a methodological reference. Data were collected by interviewing three sample groups, in a total of fifteen healthcare professionals. Data codification and analysis led us to the central theme: Viewing the Systematization of Nursing Care (SNC) as an Interactive and Complex Phenomenon. This theme is complemented by two phenomena. In this article, we discuss the phenomenon: Verifying the necessity of on interactive, complementary, and multi-professional process. The Systematization of Nursing Care is part of a process that has been developing over time by nurses committed to improve the care given to the patient, since they view the necessity for interactive, complementary, and multi-professional care.

Towards the Architecture of an Instructional Multimedia Database.

ERIC Educational Resources Information Center

Verhagen, Plin W.; Bestebreurtje, R.

1994-01-01

Discussion of multimedia databases in education focuses on the development of an adaptable database in The Netherlands that uses optical storage media to hold the audiovisual components. Highlights include types of applications; types of users; accessibility; adaptation; an object-oriented approach; levels of the database architecture; and…

SM-TF: A structural database of small molecule-transcription factor complexes.

PubMed

Xu, Xianjin; Ma, Zhiwei; Sun, Hongmin; Zou, Xiaoqin

2016-06-30

Transcription factors (TFs) are the proteins involved in the transcription process, ensuring the correct expression of specific genes. Numerous diseases arise from the dysfunction of specific TFs. In fact, over 30 TFs have been identified as therapeutic targets of about 9% of the approved drugs. In this study, we created a structural database of small molecule-transcription factor (SM-TF) complexes, available online at http://zoulab.dalton.missouri.edu/SM-TF. The 3D structures of the co-bound small molecule and the corresponding binding sites on TFs are provided in the database, serving as a valuable resource to assist structure-based drug design related to TFs. Currently, the SM-TF database contains 934 entries covering 176 TFs from a variety of species. The database is further classified into several subsets by species and organisms. The entries in the SM-TF database are linked to the UniProt database and other sequence-based TF databases. Furthermore, the druggable TFs from human and the corresponding approved drugs are linked to the DrugBank. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Understanding sources of uncertainty and bias error in models of human response to low amplitude sonic booms

NASA Astrophysics Data System (ADS)

Collmar, M.; Cook, B. G.; Cowart, R.; Freund, D.; Gavin, J.

2015-10-01

A pool of 240 subjects was exposed to a library of waveforms consisting of example signatures of low boom aircraft. The signature library included intentional variations in both loudness and spectral content, and were auralized using the Gulfstream SASS-II sonic boom simulator. Post-processing was used to quantify the impacts of test design decisions on the "quality" of the resultant database. Specific lessons learned from this study include insight regarding potential for bias error due to variations in loudness or peak over-pressure, sources of uncertainty and their relative importance on objective measurements and robustness of individual metrics to wide variations in spectral content. Results provide clear guidance for design of future large scale community surveys, where one must optimize the complex tradeoffs between the size of the surveyed population, spatial footprint of those participants, and the fidelity/density of objective measurements.

BioInt: an integrative biological object-oriented application framework and interpreter.

PubMed

Desai, Sanket; Burra, Prasad

2015-01-01

BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

Conditioning 3D object-based models to dense well data

NASA Astrophysics Data System (ADS)

Wang, Yimin C.; Pyrcz, Michael J.; Catuneanu, Octavian; Boisvert, Jeff B.

2018-06-01

Object-based stochastic simulation models are used to generate categorical variable models with a realistic representation of complicated reservoir heterogeneity. A limitation of object-based modeling is the difficulty of conditioning to dense data. One method to achieve data conditioning is to apply optimization techniques. Optimization algorithms can utilize an objective function measuring the conditioning level of each object while also considering the geological realism of the object. Here, an objective function is optimized with implicit filtering which considers constraints on object parameters. Thousands of objects conditioned to data are generated and stored in a database. A set of objects are selected with linear integer programming to generate the final realization and honor all well data, proportions and other desirable geological features. Although any parameterizable object can be considered, objects from fluvial reservoirs are used to illustrate the ability to simultaneously condition multiple types of geologic features. Channels, levees, crevasse splays and oxbow lakes are parameterized based on location, path, orientation and profile shapes. Functions mimicking natural river sinuosity are used for the centerline model. Channel stacking pattern constraints are also included to enhance the geological realism of object interactions. Spatial layout correlations between different types of objects are modeled. Three case studies demonstrate the flexibility of the proposed optimization-simulation method. These examples include multiple channels with high sinuosity, as well as fragmented channels affected by limited preservation. In all cases the proposed method reproduces input parameters for the object geometries and matches the dense well constraints. The proposed methodology expands the applicability of object-based simulation to complex and heterogeneous geological environments with dense sampling.

Attribute and topology based change detection in a constellation of previously detected objects

DOEpatents

Paglieroni, David W.; Beer, Reginald N.

2016-01-19

A system that applies attribute and topology based change detection to networks of objects that were detected on previous scans of a structure, roadway, or area of interest. The attributes capture properties or characteristics of the previously detected objects, such as location, time of detection, size, elongation, orientation, etc. The topology of the network of previously detected objects is maintained in a constellation database that stores attributes of previously detected objects and implicitly captures the geometrical structure of the network. A change detection system detects change by comparing the attributes and topology of new objects detected on the latest scan to the constellation database of previously detected objects.

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex.

PubMed

Maccari, Giuseppe; Robinson, James; Ballingall, Keith; Guethlein, Lisbeth A; Grimholt, Unni; Kaufman, Jim; Ho, Chak-Sum; de Groot, Natasja G; Flicek, Paul; Bontrop, Ronald E; Hammond, John A; Marsh, Steven G E

2017-01-04

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Research on keyword retrieval method of HBase database based on index structure

NASA Astrophysics Data System (ADS)

Gong, Pijin; Lv, Congmin; Gong, Yongsheng; Ma, Haozhi; Sun, Yang; Wang, Lu

2017-10-01

With the rapid development of manned spaceflight engineering, the scientific experimental data in space application system is increasing rapidly. How to efficiently query the specific data in the mass data volume has become a problem. In this paper, a method of retrieving the object data based on the object attribute as the keyword is proposed. The HBase database is used to store the object data and object attributes, and the secondary index is constructed. The research shows that this method is a good way to retrieve specified data based on object attributes.

Emission Database for Global Atmospheric Research (EDGAR).

ERIC Educational Resources Information Center

Olivier, J. G. J.; And Others

1994-01-01

Presents the objective and methodology chosen for the construction of a global emissions source database called EDGAR and the structural design of the database system. The database estimates on a regional and grid basis, 1990 annual emissions of greenhouse gases, and of ozone depleting compounds from all known sources. (LZ)

VAS: A Vision Advisor System combining agents and object-oriented databases

NASA Technical Reports Server (NTRS)

Eilbert, James L.; Lim, William; Mendelsohn, Jay; Braun, Ron; Yearwood, Michael

1994-01-01

A model-based approach to identifying and finding the orientation of non-overlapping parts on a tray has been developed. The part models contain both exact and fuzzy descriptions of part features, and are stored in an object-oriented database. Full identification of the parts involves several interacting tasks each of which is handled by a distinct agent. Using fuzzy information stored in the model allowed part features that were essentially at the noise level to be extracted and used for identification. This was done by focusing attention on the portion of the part where the feature must be found if the current hypothesis of the part ID is correct. In going from one set of parts to another the only thing that needs to be changed is the database of part models. This work is part of an effort in developing a Vision Advisor System (VAS) that combines agents and objected-oriented databases.

Architectural Implications for Spatial Object Association Algorithms

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

Kumar, V S; Kurc, T; Saltz, J

2009-01-29

Spatial object association, also referred to as cross-match of spatial datasets, is the problem of identifying and comparing objects in two or more datasets based on their positions in a common spatial coordinate system. In this work, we evaluate two crossmatch algorithms that are used for astronomical sky surveys, on the following database system architecture configurations: (1) Netezza Performance Server R, a parallel database system with active disk style processing capabilities, (2) MySQL Cluster, a high-throughput network database system, and (3) a hybrid configuration consisting of a collection of independent database system instances with data replication support. Our evaluation providesmore » insights about how architectural characteristics of these systems affect the performance of the spatial crossmatch algorithms. We conducted our study using real use-case scenarios borrowed from a large-scale astronomy application known as the Large Synoptic Survey Telescope (LSST).« less

Image Engine: an object-oriented multimedia database for storing, retrieving and sharing medical images and text.

PubMed Central

Lowe, H. J.

1993-01-01

This paper describes Image Engine, an object-oriented, microcomputer-based, multimedia database designed to facilitate the storage and retrieval of digitized biomedical still images, video, and text using inexpensive desktop computers. The current prototype runs on Apple Macintosh computers and allows network database access via peer to peer file sharing protocols. Image Engine supports both free text and controlled vocabulary indexing of multimedia objects. The latter is implemented using the TView thesaurus model developed by the author. The current prototype of Image Engine uses the National Library of Medicine's Medical Subject Headings (MeSH) vocabulary (with UMLS Meta-1 extensions) as its indexing thesaurus. PMID:8130596

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PubMed

Honsa, Erin; Fricke, Thomas; Stephens, Alex J; Ko, Danny; Kong, Fanrong; Gilbert, Gwendolyn L; Huygens, Flavia; Giffard, Philip M

2008-08-19

Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes. It was found that a SNP set derived from the MLST database on the basis of maximization of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates. A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms

PubMed Central

Honsa, Erin; Fricke, Thomas; Stephens, Alex J; Ko, Danny; Kong, Fanrong; Gilbert, Gwendolyn L; Huygens, Flavia; Giffard, Philip M

2008-01-01

Background Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes. Results It was found that a SNP set derived from the MLST database on the basis of maximisation of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates. Conclusion A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required. PMID:18710585

Prototyping Visual Database Interface by Object-Oriented Language

DTIC Science & Technology

1988-06-01

approach is to use object-oriented programming. Object-oriented languages are characterized by three criteria [Ref. 4:p. 1.2.1]: - encapsulation of...made it a sub-class of our DMWindow.Cls, which is discussed later in this chapter. This extension to the application had to be intergrated with our... abnormal behaviors similar to Korth’s discussion of pitfalls in relational database designing. Even extensions like GEM [Ref. 8] that are powerful and

Delayed Instantiation Bulk Operations for Management of Distributed, Object-Based Storage Systems

DTIC Science & Technology

2009-08-01

source and destination object sets, while they have attribute pages to indicate that history . Fourth, we allow for operations to occur on any objects...client dialogue to the PostgreSQL database where server-side functions implement the service logic for the requests. The translation is done...to satisfy client requests, and performs delayed instantiation bulk operations. It is built around a PostgreSQL database with tables for storing

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

DOT National Transportation Integrated Search

1999-10-01

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

The Brazilian Portuguese Lexicon: An Instrument for Psycholinguistic Research

PubMed Central

Estivalet, Gustavo L.; Meunier, Fanny

2015-01-01

In this article, we present the Brazilian Portuguese Lexicon, a new word-based corpus for psycholinguistic and computational linguistic research in Brazilian Portuguese. We describe the corpus development, the specific characteristics on the internet site and database for user access. We also perform distributional analyses of the corpus and comparisons to other current databases. Our main objective was to provide a large, reliable, and useful word-based corpus with a dynamic, easy-to-use, and intuitive interface with free internet access for word and word-criteria searches. We used the Núcleo Interinstitucional de Linguística Computacional’s corpus as the basic data source and developed the Brazilian Portuguese Lexicon by deriving and adding metalinguistic and psycholinguistic information about Brazilian Portuguese words. We obtained a final corpus with more than 30 million word tokens, 215 thousand word types and 25 categories of information about each word. This corpus was made available on the internet via a free-access site with two search engines: a simple search and a complex search. The simple engine basically searches for a list of words, while the complex engine accepts all types of criteria in the corpus categories. The output result presents all entries found in the corpus with the criteria specified in the input search and can be downloaded as a.csv file. We created a module in the results that delivers basic statistics about each search. The Brazilian Portuguese Lexicon also provides a pseudoword engine and specific tools for linguistic and statistical analysis. Therefore, the Brazilian Portuguese Lexicon is a convenient instrument for stimulus search, selection, control, and manipulation in psycholinguistic experiments, as also it is a powerful database for computational linguistics research and language modeling related to lexicon distribution, functioning, and behavior. PMID:26630138

The Brazilian Portuguese Lexicon: An Instrument for Psycholinguistic Research.

PubMed

Estivalet, Gustavo L; Meunier, Fanny

2015-01-01

In this article, we present the Brazilian Portuguese Lexicon, a new word-based corpus for psycholinguistic and computational linguistic research in Brazilian Portuguese. We describe the corpus development, the specific characteristics on the internet site and database for user access. We also perform distributional analyses of the corpus and comparisons to other current databases. Our main objective was to provide a large, reliable, and useful word-based corpus with a dynamic, easy-to-use, and intuitive interface with free internet access for word and word-criteria searches. We used the Núcleo Interinstitucional de Linguística Computacional's corpus as the basic data source and developed the Brazilian Portuguese Lexicon by deriving and adding metalinguistic and psycholinguistic information about Brazilian Portuguese words. We obtained a final corpus with more than 30 million word tokens, 215 thousand word types and 25 categories of information about each word. This corpus was made available on the internet via a free-access site with two search engines: a simple search and a complex search. The simple engine basically searches for a list of words, while the complex engine accepts all types of criteria in the corpus categories. The output result presents all entries found in the corpus with the criteria specified in the input search and can be downloaded as a.csv file. We created a module in the results that delivers basic statistics about each search. The Brazilian Portuguese Lexicon also provides a pseudoword engine and specific tools for linguistic and statistical analysis. Therefore, the Brazilian Portuguese Lexicon is a convenient instrument for stimulus search, selection, control, and manipulation in psycholinguistic experiments, as also it is a powerful database for computational linguistics research and language modeling related to lexicon distribution, functioning, and behavior.

Space Object Radiometric Modeling for Hardbody Optical Signature Database Generation

DTIC Science & Technology

2009-09-01

Introduction This presentation summarizes recent activity in monitoring spacecraft health status using passive remote optical nonimaging ...Approved for public release; distribution is unlimited. Space Object Radiometric Modeling for Hardbody Optical Signature Database Generation...It is beneficial to the observer/analyst to understand the fundamental optical signature variability associated with these detection and

Navigation integrity monitoring and obstacle detection for enhanced-vision systems

NASA Astrophysics Data System (ADS)

Korn, Bernd; Doehler, Hans-Ullrich; Hecker, Peter

2001-08-01

Typically, Enhanced Vision (EV) systems consist of two main parts, sensor vision and synthetic vision. Synthetic vision usually generates a virtual out-the-window view using databases and accurate navigation data, e. g. provided by differential GPS (DGPS). The reliability of the synthetic vision highly depends on both, the accuracy of the used database and the integrity of the navigation data. But especially in GPS based systems, the integrity of the navigation can't be guaranteed. Furthermore, only objects that are stored in the database can be displayed to the pilot. Consequently, unexpected obstacles are invisible and this might cause severe problems. Therefore, additional information has to be extracted from sensor data to overcome these problems. In particular, the sensor data analysis has to identify obstacles and has to monitor the integrity of databases and navigation. Furthermore, if a lack of integrity arises, navigation data, e.g. the relative position of runway and aircraft, has to be extracted directly from the sensor data. The main contribution of this paper is about the realization of these three sensor data analysis tasks within our EV system, which uses the HiVision 35 GHz MMW radar of EADS, Ulm as the primary EV sensor. For the integrity monitoring, objects extracted from radar images are registered with both database objects and objects (e. g. other aircrafts) transmitted via data link. This results in a classification into known and unknown radar image objects and consequently, in a validation of the integrity of database and navigation. Furthermore, special runway structures are searched for in the radar image where they should appear. The outcome of this runway check contributes to the integrity analysis, too. Concurrent to this investigation a radar image based navigation is performed without using neither precision navigation nor detailed database information to determine the aircraft's position relative to the runway. The performance of our approach is demonstrated with real data acquired during extensive flight tests to several airports in Northern Germany.

Structural analysis of the coordination of dinitrogen to transition metal complexes.

PubMed

Peigné, Benjamin; Aullón, Gabriel

2015-06-01

Transition-metal complexes show a wide variety of coordination modes for the nitrogen molecule. A structural database study has been undertaken for dinitrogen complexes, and geometrical parameters around the L(n)M-N2 unit are retrieved from the Cambridge Structural Database. These data were classified in families of compounds, according to metal properties, to determine the degree of lengthening for the dinitrogen bonding. The importance of the nature of the metal center, such as coordination number and electronic configuration, is reported. Our study reveals poor activation by coordination of dinitrogen in mononuclear complexes, always having end-on coordination. However, partial weakening of nitrogen-nitrogen bonding is found for end-on binuclear complexes, whereas side-on complexes can be completely activated.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

PubMed

Lepoivre, Cyrille; Bergon, Aurélie; Lopez, Fabrice; Perumal, Narayanan B; Nguyen, Catherine; Imbert, Jean; Puthier, Denis

2012-01-31

Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information and is a productive avenue in generating new hypotheses. The second objective of InteractomeBrowser is to fill the gap between interaction databases and dynamic modeling. It is thus compatible with the network analysis software Cytoscape and with the Gene Interaction Network simulation software (GINsim). We provide examples underlying the benefits of this visualization tool for large gene set analysis related to thymocyte differentiation. The InteractomeBrowser plugin is a powerful tool to get quick access to a knowledge database that includes both predicted and validated molecular interactions. InteractomeBrowser is available through the TranscriptomeBrowser framework and can be found at: http://tagc.univ-mrs.fr/tbrowser/. Our database is updated on a regular basis.

What’s New in Addiction Prevention in Young People: A Literature Review of the Last Years of Research

PubMed Central

Kempf, Cédric; Llorca, Pierre-Michel; Pizon, Frank; Brousse, Georges; Flaudias, Valentin

2017-01-01

Rationale: Addiction prevention is a major public health problem, particularly concerning young people. Despite the consensus that primary prevention is essential, the evaluation of its impact is questioned. Objective: The objective of this paper is to assess the latest knowledge of addiction prevention programs for young people. Method: Review a collection of research articles using a keyword-based search on three databases: Pubmed, Eric, and PsycInfo. The research was carried out using three groups of keywords and the eligibility study was completed using two criteria: articles published between 2010 and 2017, and articles in refereed journals. Results: Of a total of 13,720 articles in the three databases, 32 studies were included in the review and listed in a grid with five themes: authors, type of population, total population, addictive behavior, and results. Four categories were created based on the objective of the studies: the evaluation of prevention strategies, the study of risk factors for consumption, the prevalence study and other subjects studied. The analysis of the corpus was used to establish a list of risk factors to be taken into consideration in future interventions and research. A list of key elements for performing effective interventions and future research is also proposed. Conclusion: The understanding of the prevention strategies implementation process is discussed as a central element for future research, which will combine stakeholders and researchers. The complexity of the situations and the multifactorial aspects of addiction prevention in young people require a multidisciplinary approach involving the various stakeholders and researchers. PMID:28729846

The ATLAS conditions database architecture for the Muon spectrometer

NASA Astrophysics Data System (ADS)

Verducci, Monica; ATLAS Muon Collaboration

2010-04-01

The Muon System, facing the challenge requirement of the conditions data storage, has extensively started to use the conditions database project 'COOL' as the basis for all its conditions data storage both at CERN and throughout the worldwide collaboration as decided by the ATLAS Collaboration. The management of the Muon COOL conditions database will be one of the most challenging applications for Muon System, both in terms of data volumes and rates, but also in terms of the variety of data stored. The Muon conditions database is responsible for almost all of the 'non event' data and detector quality flags storage needed for debugging of the detector operations and for performing reconstruction and analysis. The COOL database allows database applications to be written independently of the underlying database technology and ensures long term compatibility with the entire ATLAS Software. COOL implements an interval of validity database, i.e. objects stored or referenced in COOL have an associated start and end time between which they are valid, the data is stored in folders, which are themselves arranged in a hierarchical structure of folder sets. The structure is simple and mainly optimized to store and retrieve object(s) associated with a particular time. In this work, an overview of the entire Muon conditions database architecture is given, including the different sources of the data and the storage model used. In addiction the software interfaces used to access to the conditions data are described, more emphasis is given to the Offline Reconstruction framework ATHENA and the services developed to provide the conditions data to the reconstruction.

Visualization and manipulating the image of a formal data structure (FDS)-based database

NASA Astrophysics Data System (ADS)

Verdiesen, Franc; de Hoop, Sylvia; Molenaar, Martien

1994-08-01

A vector map is a terrain representation with a vector-structured geometry. Molenaar formulated an object-oriented formal data structure for 3D single valued vector maps. This FDS is implemented in a database (Oracle). In this study we describe a methodology for visualizing a FDS-based database and manipulating the image. A data set retrieved by querying the database is converted into an import file for a drawing application. An objective of this study is that an end-user can alter and add terrain objects in the image. The drawing application creates an export file, that is compared with the import file. Differences between these files result in updating the database which involves checks on consistency. In this study Autocad is used for visualizing and manipulating the image of the data set. A computer program has been written for the data exchange and conversion between Oracle and Autocad. The data structure of the FDS is compared to the data structure of Autocad and the data of the FDS is converted into the structure of Autocad equal to the FDS.

Image correlation method for DNA sequence alignment.

PubMed

Curilem Saldías, Millaray; Villarroel Sassarini, Felipe; Muñoz Poblete, Carlos; Vargas Vásquez, Asticio; Maureira Butler, Iván

2012-01-01

The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs) and 100 scenes represented by 100 x 100 images each (in total, one million base pair database) were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%), specificity (98.99%) and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

CB Database: A change blindness database for objects in natural indoor scenes.

PubMed

Sareen, Preeti; Ehinger, Krista A; Wolfe, Jeremy M

2016-12-01

Change blindness has been a topic of interest in cognitive sciences for decades. Change detection experiments are frequently used for studying various research topics such as attention and perception. However, creating change detection stimuli is tedious and there is no open repository of such stimuli using natural scenes. We introduce the Change Blindness (CB) Database with object changes in 130 colored images of natural indoor scenes. The size and eccentricity are provided for all the changes as well as reaction time data from a baseline experiment. In addition, we have two specialized satellite databases that are subsets of the 130 images. In one set, changes are seen in rooms or in mirrors in those rooms (Mirror Change Database). In the other, changes occur in a room or out a window (Window Change Database). Both the sets have controlled background, change size, and eccentricity. The CB Database is intended to provide researchers with a stimulus set of natural scenes with defined stimulus parameters that can be used for a wide range of experiments. The CB Database can be found at http://search.bwh.harvard.edu/new/CBDatabase.html .

Developing Database Files for Student Use.

ERIC Educational Resources Information Center

Warner, Michael

1988-01-01

Presents guidelines for creating student database files that supplement classroom teaching. Highlights include determining educational objectives, planning the database with computer specialists and subject area specialists, data entry, and creating student worksheets. Specific examples concerning elements of the periodic table and…

Point pattern match-based change detection in a constellation of previously detected objects

DOEpatents

Paglieroni, David W.

2016-06-07

A method and system is provided that applies attribute- and topology-based change detection to objects that were detected on previous scans of a medium. The attributes capture properties or characteristics of the previously detected objects, such as location, time of detection, detection strength, size, elongation, orientation, etc. The locations define a three-dimensional network topology forming a constellation of previously detected objects. The change detection system stores attributes of the previously detected objects in a constellation database. The change detection system detects changes by comparing the attributes and topological consistency of newly detected objects encountered during a new scan of the medium to previously detected objects in the constellation database. The change detection system may receive the attributes of the newly detected objects as the objects are detected by an object detection system in real time.

Database Technology Activities and Assessment for Defense Modeling and Simulation Office (DMSO) (August 1991-November 1992). A Documented Briefing

DTIC Science & Technology

1994-01-01

databases and identifying new data entities, data elements, and relationships . - Standard data naming conventions, schema, and definition processes...management system. The use of such a tool could offer: (1) structured support for representation of objects and their relationships to each other (and...their relationships to related multimedia objects such as an engineering drawing of the tank object or a satellite image that contains the installation

Knowledge transfer on complex social interventions in public health: a scoping study.

PubMed

Dagenais, Christian; Malo, Marie; Robert, Émilie; Ouimet, Mathieu; Berthelette, Diane; Ridde, Valéry

2013-01-01

Scientific knowledge can help develop interventions that improve public health. The objectives of this review are (1) to describe the status of research on knowledge transfer strategies in the field of complex social interventions in public health and (2) to identify priorities for future research in this field. A scoping study is an exploratory study. After searching databases of bibliographic references and specialized periodicals, we summarized the relevant studies using a predetermined assessment framework. In-depth analysis focused on the following items: types of knowledge transfer strategies, fields of public health, types of publics, types of utilization, and types of research specifications. From the 1,374 references identified, we selected 26 studies. The strategies targeted mostly administrators of organizations and practitioners. The articles generally dealt with instrumental utilization and most often used qualitative methods. In general, the bias risk for the studies is high. Researchers need to consider the methodological challenges in this field of research in order to improve assessment of more complex knowledge transfer strategies (when they exist), not just diffusion/dissemination strategies and conceptual and persuasive utilization.

CORUM: the comprehensive resource of mammalian protein complexes

PubMed Central

Ruepp, Andreas; Brauner, Barbara; Dunger-Kaltenbach, Irmtraud; Frishman, Goar; Montrone, Corinna; Stransky, Michael; Waegele, Brigitte; Schmidt, Thorsten; Doudieu, Octave Noubibou; Stümpflen, Volker; Mewes, H. Werner

2008-01-01

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes. For functional annotation, we use the FunCat catalogue that enables to organize the protein complex space into biologically meaningful subsets. The database contains more than 1750 protein complexes that are built from 2400 different genes, thus representing 12% of the protein-coding genes in human. A web-based system is available to query, view and download the data. CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases. Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes. PMID:17965090

An object-oriented approach to the management of meteorological and hydrological data

NASA Technical Reports Server (NTRS)

Graves, S. J.; Williams, S. F.; Criswell, E. A.

1990-01-01

An interface to several meteorological and hydrological databases have been developed that enables researchers efficiently to access and interrelate data through a customized menu system. By extending a relational database system with object-oriented concepts, each user or group of users may have different 'views' of the data to allow user access to data in customized ways without altering the organization of the database. An application to COHMEX and WetNet, two earth science projects within NASA Marshall Space Flight Center's Earth Science and Applications Division, are described.

United States Air Force Summer Research Program -- 1993. Volume 4. Rome Laboratory

DTIC Science & Technology

1993-12-01

H., eds., Object-Oriented Concepts, Databases , and Applications, Addison-Wesley, Reading, MA, 1989. [Lano9l] Lano, K., "Z++, An Object-Orientated...1433 46.92 60 TCP janus.rl.af.mil mensa.rl.af.mil 1433 2611 The Target Filter Manager responds to requests for data and accesses the target database . A...2.5 2- 1.5- 28 -3 -2 -10 12 3 AZIMUTH (OE(3) Figure 12. Contour plot of antenna pattern, QC2 algorithm 5-32 UPDATING PROBABILISTIC DATABASES Michael A

Exudate detection in color retinal images for mass screening of diabetic retinopathy.

PubMed

Zhang, Xiwei; Thibault, Guillaume; Decencière, Etienne; Marcotegui, Beatriz; Laÿ, Bruno; Danno, Ronan; Cazuguel, Guy; Quellec, Gwénolé; Lamard, Mathieu; Massin, Pascale; Chabouis, Agnès; Victor, Zeynep; Erginay, Ali

2014-10-01

The automatic detection of exudates in color eye fundus images is an important task in applications such as diabetic retinopathy screening. The presented work has been undertaken in the framework of the TeleOphta project, whose main objective is to automatically detect normal exams in a tele-ophthalmology network, thus reducing the burden on the readers. A new clinical database, e-ophtha EX, containing precisely manually contoured exudates, is introduced. As opposed to previously available databases, e-ophtha EX is very heterogeneous. It contains images gathered within the OPHDIAT telemedicine network for diabetic retinopathy screening. Image definition, quality, as well as patients condition or the retinograph used for the acquisition, for example, are subject to important changes between different examinations. The proposed exudate detection method has been designed for this complex situation. We propose new preprocessing methods, which perform not only normalization and denoising tasks, but also detect reflections and artifacts in the image. A new candidates segmentation method, based on mathematical morphology, is proposed. These candidates are characterized using classical features, but also novel contextual features. Finally, a random forest algorithm is used to detect the exudates among the candidates. The method has been validated on the e-ophtha EX database, obtaining an AUC of 0.95. It has been also validated on other databases, obtaining an AUC between 0.93 and 0.95, outperforming state-of-the-art methods. Copyright © 2014 Elsevier B.V. All rights reserved.

Architecture Knowledge for Evaluating Scalable Databases

DTIC Science & Technology

2015-01-16

problems, arising from the proliferation of new data models and distributed technologies for building scalable, available data stores . Architects must...longer are relational databases the de facto standard for building data repositories. Highly distributed, scalable “ NoSQL ” databases [11] have emerged...This is especially challenging at the data storage layer. The multitude of competing NoSQL database technologies creates a complex and rapidly

Object-oriented parsing of biological databases with Python.

PubMed

Ramu, C; Gemünd, C; Gibson, T J

2000-07-01

While database activities in the biological area are increasing rapidly, rather little is done in the area of parsing them in a simple and object-oriented way. We present here an elegant, simple yet powerful way of parsing biological flat-file databases. We have taken EMBL, SWISSPROT and GENBANK as examples. EMBL and SWISS-PROT do not differ much in the format structure. GENBANK has a very different format structure than EMBL and SWISS-PROT. Extracting the desired fields in an entry (for example a sub-sequence with an associated feature) for later analysis is a constant need in the biological sequence-analysis community: this is illustrated with tools to make new splice-site databases. The interface to the parser is abstract in the sense that the access to all the databases is independent from their different formats, since parsing instructions are hidden.

Using Object Storage Technology vs Vendor Neutral Archives for an Image Data Repository Infrastructure.

PubMed

Bialecki, Brian; Park, James; Tilkin, Mike

2016-08-01

The intent of this project was to use object storage and its database, which has the ability to add custom extensible metadata to an imaging object being stored within the system, to harness the power of its search capabilities, and to close the technology gap that healthcare faces. This creates a non-disruptive tool that can be used natively by both legacy systems and the healthcare systems of today which leverage more advanced storage technologies. The base infrastructure can be populated alongside current workflows without any interruption to the delivery of services. In certain use cases, this technology can be seen as a true alternative to the VNA (Vendor Neutral Archive) systems implemented by healthcare today. The scalability, security, and ability to process complex objects makes this more than just storage for image data and a commodity to be consumed by PACS (Picture Archiving and Communication System) and workstations. Object storage is a smart technology that can be leveraged to create vendor independence, standards compliance, and a data repository that can be mined for truly relevant content by adding additional context to search capabilities. This functionality can lead to efficiencies in workflow and a wealth of minable data to improve outcomes into the future.

Low-complexity R-peak detection in ECG signals: a preliminary step towards ambulatory fetal monitoring.

PubMed

Rooijakkers, Michiel; Rabotti, Chiara; Bennebroek, Martijn; van Meerbergen, Jef; Mischi, Massimo

2011-01-01

Non-invasive fetal health monitoring during pregnancy has become increasingly important. Recent advances in signal processing technology have enabled fetal monitoring during pregnancy, using abdominal ECG recordings. Ubiquitous ambulatory monitoring for continuous fetal health measurement is however still unfeasible due to the computational complexity of noise robust solutions. In this paper an ECG R-peak detection algorithm for ambulatory R-peak detection is proposed, as part of a fetal ECG detection algorithm. The proposed algorithm is optimized to reduce computational complexity, while increasing the R-peak detection quality compared to existing R-peak detection schemes. Validation of the algorithm is performed on two manually annotated datasets, the MIT/BIH Arrhythmia database and an in-house abdominal database. Both R-peak detection quality and computational complexity are compared to state-of-the-art algorithms as described in the literature. With a detection error rate of 0.22% and 0.12% on the MIT/BIH Arrhythmia and in-house databases, respectively, the quality of the proposed algorithm is comparable to the best state-of-the-art algorithms, at a reduced computational complexity.

The Master Lens Database and The Orphan Lenses Project

NASA Astrophysics Data System (ADS)

Moustakas, Leonidas

2012-10-01

Strong gravitational lenses are uniquely suited for the study of dark matter structure and substructure within massive halos of many scales, act as gravitational telescopes for distant faint objects, and can give powerful and competitive cosmological constraints. While hundreds of strong lenses are known to date, spanning five orders of magnitude in mass scale, thousands will be identified this decade. To fully exploit the power of these objects presently, and in the near future, we are creating the Master Lens Database. This is a clearinghouse of all known strong lens systems, with a sophisticated and modern database of uniformly measured and derived observational and lens-model derived quantities, using archival Hubble data across several instruments. This Database enables new science that can be done with a comprehensive sample of strong lenses. The operational goal of this proposal is to develop the process and the code to semi-automatically stage Hubble data of each system, create appropriate masks of the lensing objects and lensing features, and derive gravitational lens models, to provide a uniform and fairly comprehensive information set that is ingested into the Database. The scientific goal for this team is to use the properties of the ensemble of lenses to make a new study of the internal structure of lensing galaxies, and to identify new objects that show evidence of strong substructure lensing, for follow-up study. All data, scripts, masks, model setup files, and derived parameters, will be public, and free. The Database will be accessible online and through a sophisticated smartphone application, which will also be free.

HIV Structural Database

National Institute of Standards and Technology Data Gateway

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

Challenges in Database Design with Microsoft Access

ERIC Educational Resources Information Center

Letkowski, Jerzy

2014-01-01

Design, development and explorations of databases are popular topics covered in introductory courses taught at business schools. Microsoft Access is the most popular software used in those courses. Despite quite high complexity of Access, it is considered to be one of the most friendly database programs for beginners. A typical Access textbook…

Thematic video indexing to support video database retrieval and query processing

NASA Astrophysics Data System (ADS)

Khoja, Shakeel A.; Hall, Wendy

1999-08-01

This paper presents a novel video database system, which caters for complex and long videos, such as documentaries, educational videos, etc. As compared to relatively structured format videos like CNN news or commercial advertisements, this database system has the capacity to work with long and unstructured videos.

Spatial and symbolic queries for 3D image data

NASA Astrophysics Data System (ADS)

Benson, Daniel C.; Zick, Gregory L.

1992-04-01

We present a query system for an object-oriented biomedical imaging database containing 3-D anatomical structures and their corresponding 2-D images. The graphical interface facilitates the formation of spatial queries, nonspatial or symbolic queries, and combined spatial/symbolic queries. A query editor is used for the creation and manipulation of 3-D query objects as volumes, surfaces, lines, and points. Symbolic predicates are formulated through a combination of text fields and multiple choice selections. Query results, which may include images, image contents, composite objects, graphics, and alphanumeric data, are displayed in multiple views. Objects returned by the query may be selected directly within the views for further inspection or modification, or for use as query objects in subsequent queries. Our image database query system provides visual feedback and manipulation of spatial query objects, multiple views of volume data, and the ability to combine spatial and symbolic queries. The system allows for incremental enhancement of existing objects and the addition of new objects and spatial relationships. The query system is designed for databases containing symbolic and spatial data. This paper discuses its application to data acquired in biomedical 3- D image reconstruction, but it is applicable to other areas such as CAD/CAM, geographical information systems, and computer vision.

Quest for a universal density functional: the accuracy of density functionals across a broad spectrum of databases in chemistry and physics.

PubMed

Peverati, Roberto; Truhlar, Donald G

2014-03-13

Kohn-Sham density functional theory is in principle an exact formulation of quantum mechanical electronic structure theory, but in practice we have to rely on approximate exchange-correlation (xc) functionals. The objective of our work has been to design an xc functional with broad accuracy across as wide an expanse of chemistry and physics as possible, leading--as a long-range goal--to a functional with good accuracy for all problems, i.e. a universal functional. To guide our path towards that goal and to measure our progress, we have developed-building on earlier work of our group-a set of databases of reference data for a variety of energetic and structural properties in chemistry and physics. These databases include energies of molecular processes, such as atomization, complexation, proton addition and ionization; they also include molecular geometries and solid-state lattice constants, chemical reaction barrier heights, and cohesive energies and band gaps of solids. For this paper, we gather many of these databases into four comprehensive databases, two with 384 energetic data for chemistry and solid-state physics and another two with 68 structural data for chemistry and solid-state physics, and we test two wave function methods and 77 density functionals (12 Minnesota meta functionals and 65 others) in a consistent way across this same broad set of data. We especially highlight the Minnesota density functionals, but the results have broader implications in that one may see the successes and failures of many kinds of density functionals when they are all applied to the same data. Therefore, the results provide a status report on the quest for a universal functional.

A Model of Object-Identities and Values

DTIC Science & Technology

1990-02-23

integrity constraints in its construct, which provides the natural integration of the logical database model and the object-oriented database model. 20...portions are integrated by a simple commutative diagram of modeling functions. The formalism includes the expression of integrity constraints in its ...38 .5.2.2 The (Concept Model and Its Semantics .. .. .. .. ... .... ... .. 40 5.2.3 Two K%.inds of Predicates

A Web-based Tool for SDSS and 2MASS Database Searches

NASA Astrophysics Data System (ADS)

Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

A Unified Satellite-Observation Polar Stratospheric Cloud (PSC) Database for Long-Term Climate-Change Studies

NASA Technical Reports Server (NTRS)

Fromm, Michael; Pitts, Michael; Alfred, Jerome

2000-01-01

This report summarizes the project team's activity and accomplishments during the period 12 February, 1999 - 12 February, 2000. The primary objective of this project was to create and test a generic algorithm for detecting polar stratospheric clouds (PSC), an algorithm that would permit creation of a unified, long term PSC database from a variety of solar occultation instruments that measure aerosol extinction near 1000 nm The second objective was to make a database of PSC observations and certain relevant related datasets. In this report we describe the algorithm, the data we are making available, and user access options. The remainder of this document provides the details of the algorithm and the database offering.

Representing metabolic pathway information: an object-oriented approach.

PubMed

Ellis, L B; Speedie, S M; McLeish, R

1998-01-01

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) is a website providing information and dynamic links for microbial metabolic pathways, enzyme reactions, and their substrates and products. The Compound, Organism, Reaction and Enzyme (CORE) object-oriented database management system was developed to contain and serve this information. CORE was developed using Java, an object-oriented programming language, and PSE persistent object classes from Object Design, Inc. CORE dynamically generates descriptive web pages for reactions, compounds and enzymes, and reconstructs ad hoc pathway maps starting from any UM-BBD reaction. CORE code is available from the authors upon request. CORE is accessible through the UM-BBD at: http://www. labmed.umn.edu/umbbd/index.html.

Incorporating Auditory Models in Speech/Audio Applications

NASA Astrophysics Data System (ADS)

Krishnamoorthi, Harish

2011-12-01

Following the success in incorporating perceptual models in audio coding algorithms, their application in other speech/audio processing systems is expanding. In general, all perceptual speech/audio processing algorithms involve minimization of an objective function that directly/indirectly incorporates properties of human perception. This dissertation primarily investigates the problems associated with directly embedding an auditory model in the objective function formulation and proposes possible solutions to overcome high complexity issues for use in real-time speech/audio algorithms. Specific problems addressed in this dissertation include: 1) the development of approximate but computationally efficient auditory model implementations that are consistent with the principles of psychoacoustics, 2) the development of a mapping scheme that allows synthesizing a time/frequency domain representation from its equivalent auditory model output. The first problem is aimed at addressing the high computational complexity involved in solving perceptual objective functions that require repeated application of auditory model for evaluation of different candidate solutions. In this dissertation, a frequency pruning and a detector pruning algorithm is developed that efficiently implements the various auditory model stages. The performance of the pruned model is compared to that of the original auditory model for different types of test signals in the SQAM database. Experimental results indicate only a 4-7% relative error in loudness while attaining up to 80-90 % reduction in computational complexity. Similarly, a hybrid algorithm is developed specifically for use with sinusoidal signals and employs the proposed auditory pattern combining technique together with a look-up table to store representative auditory patterns. The second problem obtains an estimate of the auditory representation that minimizes a perceptual objective function and transforms the auditory pattern back to its equivalent time/frequency representation. This avoids the repeated application of auditory model stages to test different candidate time/frequency vectors in minimizing perceptual objective functions. In this dissertation, a constrained mapping scheme is developed by linearizing certain auditory model stages that ensures obtaining a time/frequency mapping corresponding to the estimated auditory representation. This paradigm was successfully incorporated in a perceptual speech enhancement algorithm and a sinusoidal component selection task.

Chemical databases evaluated by order theoretical tools.

PubMed

Voigt, Kristina; Brüggemann, Rainer; Pudenz, Stefan

2004-10-01

Data on environmental chemicals are urgently needed to comply with the future chemicals policy in the European Union. The availability of data on parameters and chemicals can be evaluated by chemometrical and environmetrical methods. Different mathematical and statistical methods are taken into account in this paper. The emphasis is set on a new, discrete mathematical method called METEOR (method of evaluation by order theory). Application of the Hasse diagram technique (HDT) of the complete data-matrix comprising 12 objects (databases) x 27 attributes (parameters + chemicals) reveals that ECOTOX (ECO), environmental fate database (EFD) and extoxnet (EXT)--also called multi-database databases--are best. Most single databases which are specialised are found in a minimal position in the Hasse diagram; these are biocatalysis/biodegradation database (BID), pesticide database (PES) and UmweltInfo (UMW). The aggregation of environmental parameters and chemicals (equal weight) leads to a slimmer data-matrix on the attribute side. However, no significant differences are found in the "best" and "worst" objects. The whole approach indicates a rather bad situation in terms of the availability of data on existing chemicals and hence an alarming signal concerning the new and existing chemicals policies of the EEC.

Partitioning medical image databases for content-based queries on a Grid.

PubMed

Montagnat, J; Breton, V; E Magnin, I

2005-01-01

In this paper we study the impact of executing a medical image database query application on the grid. For lowering the total computation time, the image database is partitioned into subsets to be processed on different grid nodes. A theoretical model of the application complexity and estimates of the grid execution overhead are used to efficiently partition the database. We show results demonstrating that smart partitioning of the database can lead to significant improvements in terms of total computation time. Grids are promising for content-based image retrieval in medical databases.

The Chandra Source Catalog: Storage and Interfaces

NASA Astrophysics Data System (ADS)

van Stone, David; Harbo, Peter N.; Tibbetts, Michael S.; Zografou, Panagoula; Evans, Ian N.; Primini, Francis A.; Glotfelty, Kenny J.; Anderson, Craig S.; Bonaventura, Nina R.; Chen, Judy C.; Davis, John E.; Doe, Stephen M.; Evans, Janet D.; Fabbiano, Giuseppina; Galle, Elizabeth C.; Gibbs, Danny G., II; Grier, John D.; Hain, Roger; Hall, Diane M.; He, Xiang Qun (Helen); Houck, John C.; Karovska, Margarita; Kashyap, Vinay L.; Lauer, Jennifer; McCollough, Michael L.; McDowell, Jonathan C.; Miller, Joseph B.; Mitschang, Arik W.; Morgan, Douglas L.; Mossman, Amy E.; Nichols, Joy S.; Nowak, Michael A.; Plummer, David A.; Refsdal, Brian L.; Rots, Arnold H.; Siemiginowska, Aneta L.; Sundheim, Beth A.; Winkelman, Sherry L.

2009-09-01

The Chandra Source Catalog (CSC) is part of the Chandra Data Archive (CDA) at the Chandra X-ray Center. The catalog contains source properties and associated data objects such as images, spectra, and lightcurves. The source properties are stored in relational databases and the data objects are stored in files with their metadata stored in databases. The CDA supports different versions of the catalog: multiple fixed release versions and a live database version. There are several interfaces to the catalog: CSCview, a graphical interface for building and submitting queries and for retrieving data objects; a command-line interface for property and source searches using ADQL; and VO-compliant services discoverable though the VO registry. This poster describes the structure of the catalog and provides an overview of the interfaces.

Asynchronous Data Retrieval from an Object-Oriented Database

NASA Astrophysics Data System (ADS)

Gilbert, Jonathan P.; Bic, Lubomir

We present an object-oriented semantic database model which, similar to other object-oriented systems, combines the virtues of four concepts: the functional data model, a property inheritance hierarchy, abstract data types and message-driven computation. The main emphasis is on the last of these four concepts. We describe generic procedures that permit queries to be processed in a purely message-driven manner. A database is represented as a network of nodes and directed arcs, in which each node is a logical processing element, capable of communicating with other nodes by exchanging messages. This eliminates the need for shared memory and for centralized control during query processing. Hence, the model is suitable for implementation on a multiprocessor computer architecture, consisting of large numbers of loosely coupled processing elements.

The Vocational Guidance Research Database: A Scientometric Approach

ERIC Educational Resources Information Center

Flores-Buils, Raquel; Gil-Beltran, Jose Manuel; Caballer-Miedes, Antonio; Martinez-Martinez, Miguel Angel

2012-01-01

The scientometric study of scientific output through publications in specialized journals cannot be undertaken exclusively with the databases available today. For this reason, the objective of this article is to introduce the "Base de Datos de Investigacion en Orientacion Vocacional" [Vocational Guidance Research Database], based on the…

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces.

PubMed

Ezra Tsur, Elishai

2017-01-01

Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.

OWLing Clinical Data Repositories With the Ontology Web Language.

PubMed

Lozano-Rubí, Raimundo; Pastor, Xavier; Lozano, Esther

2014-08-01

The health sciences are based upon information. Clinical information is usually stored and managed by physicians with precarious tools, such as spreadsheets. The biomedical domain is more complex than other domains that have adopted information and communication technologies as pervasive business tools. Moreover, medicine continuously changes its corpus of knowledge because of new discoveries and the rearrangements in the relationships among concepts. This scenario makes it especially difficult to offer good tools to answer the professional needs of researchers and constitutes a barrier that needs innovation to discover useful solutions. The objective was to design and implement a framework for the development of clinical data repositories, capable of facing the continuous change in the biomedicine domain and minimizing the technical knowledge required from final users. We combined knowledge management tools and methodologies with relational technology. We present an ontology-based approach that is flexible and efficient for dealing with complexity and change, integrated with a solid relational storage and a Web graphical user interface. Onto Clinical Research Forms (OntoCRF) is a framework for the definition, modeling, and instantiation of data repositories. It does not need any database design or programming. All required information to define a new project is explicitly stated in ontologies. Moreover, the user interface is built automatically on the fly as Web pages, whereas data are stored in a generic repository. This allows for immediate deployment and population of the database as well as instant online availability of any modification. OntoCRF is a complete framework to build data repositories with a solid relational storage. Driven by ontologies, OntoCRF is more flexible and efficient to deal with complexity and change than traditional systems and does not require very skilled technical people facilitating the engineering of clinical software systems.

G-Hash: Towards Fast Kernel-based Similarity Search in Large Graph Databases.

PubMed

Wang, Xiaohong; Smalter, Aaron; Huan, Jun; Lushington, Gerald H

2009-01-01

Structured data including sets, sequences, trees and graphs, pose significant challenges to fundamental aspects of data management such as efficient storage, indexing, and similarity search. With the fast accumulation of graph databases, similarity search in graph databases has emerged as an important research topic. Graph similarity search has applications in a wide range of domains including cheminformatics, bioinformatics, sensor network management, social network management, and XML documents, among others.Most of the current graph indexing methods focus on subgraph query processing, i.e. determining the set of database graphs that contains the query graph and hence do not directly support similarity search. In data mining and machine learning, various graph kernel functions have been designed to capture the intrinsic similarity of graphs. Though successful in constructing accurate predictive and classification models for supervised learning, graph kernel functions have (i) high computational complexity and (ii) non-trivial difficulty to be indexed in a graph database.Our objective is to bridge graph kernel function and similarity search in graph databases by proposing (i) a novel kernel-based similarity measurement and (ii) an efficient indexing structure for graph data management. Our method of similarity measurement builds upon local features extracted from each node and their neighboring nodes in graphs. A hash table is utilized to support efficient storage and fast search of the extracted local features. Using the hash table, a graph kernel function is defined to capture the intrinsic similarity of graphs and for fast similarity query processing. We have implemented our method, which we have named G-hash, and have demonstrated its utility on large chemical graph databases. Our results show that the G-hash method achieves state-of-the-art performance for k-nearest neighbor (k-NN) classification. Most importantly, the new similarity measurement and the index structure is scalable to large database with smaller indexing size, faster indexing construction time, and faster query processing time as compared to state-of-the-art indexing methods such as C-tree, gIndex, and GraphGrep.

Derivation of Pitzer Interaction Parameters for an Aqueous Species Pair of Sodium and Iron(II)-Citrate Complex

NASA Astrophysics Data System (ADS)

Jang, J. H.; Nemer, M.

2015-12-01

The U.S. DOE Waste Isolation Pilot Plant (WIPP) is a deep underground repository for the permanent disposal of transuranic (TRU) radioactive waste. The WIPP is located in the Permian Delaware Basin near Carlsbad, New Mexico, U.S.A. The TRU waste includes, but is not limited to, iron-based alloys and the complexing agent, citric acid. Iron is also present from the steel used in the waste containers. The objective of this analysis is to derive the Pitzer activity coefficients for the pair of Na+ and FeCit- complex to expand current WIPP thermodynamic database. An aqueous model for the dissolution of Fe(OH)2(s) in a Na3Cit solution was fitted to the experimentally measured solubility data. The aqueous model consists of several chemical reactions and related Pitzer interaction parameters. Specifically, Pitzer interaction parameters for the Na+ and FeCit- pair (β(0), β(1), and Cφ) plus the stability constant for species of FeCit- were fitted to the experimental data. Anoxic gloveboxes were used to keep the oxygen level low (<1 ppm) throughout the experiments due to redox sensitivity. EQ3NR, a computer program for geochemical aqueous speciation-solubility calculations, packaged in EQ3/6 v.8.0a, calculates the aqueous speciation and saturation index using an aqueous model addressed in EQ3/6's database. The saturation index indicates how far the system is from equilibrium with respect to the solid of interest. Thus, the smaller the sum of squared saturation indices that the aqueous model calculates for the given number of experiments, the more closely the model attributes equilibrium to each individual experiment with respect to the solid of interest. The calculation of aqueous speciation and saturation indices was repeated by adjusting stability constant of FeCit-, β(0), β(1), and Cφ in the database until the values are found that make the sum of squared saturation indices the smallest for the given number of experiments. Results will be presented at the time of conference.

Digital geomorphological landslide hazard mapping of the Alpago area, Italy

NASA Astrophysics Data System (ADS)

van Westen, Cees J.; Soeters, Rob; Sijmons, Koert

Large-scale geomorphological maps of mountainous areas are traditionally made using complex symbol-based legends. They can serve as excellent "geomorphological databases", from which an experienced geomorphologist can extract a large amount of information for hazard mapping. However, these maps are not designed to be used in combination with a GIS, due to their complex cartographic structure. In this paper, two methods are presented for digital geomorphological mapping at large scales using GIS and digital cartographic software. The methods are applied to an area with a complex geomorphological setting on the Borsoia catchment, located in the Alpago region, near Belluno in the Italian Alps. The GIS database set-up is presented with an overview of the data layers that have been generated and how they are interrelated. The GIS database was also converted into a paper map, using a digital cartographic package. The resulting largescale geomorphological hazard map is attached. The resulting GIS database and cartographic product can be used to analyse the hazard type and hazard degree for each polygon, and to find the reasons for the hazard classification.

Nuclear plants gain integrated information systems

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

Villavicencio-Ramirez, A.; Rodriquez-Alvarez, J.M.

1994-10-01

With the objective of simplifying the complex mesh of computing devices employed within nuclear power plants, modern technology and integration techniques are being used to form centralized (but backed up) databases and distributed processing and display networks. Benefits are immediate as a result of the integration and the use of standards. The use of a unique data acquisition and database subsystem optimizes the high costs of engineering, as this task is done only once for the life span of the system. This also contributes towards a uniform user interface and allows for graceful expansion and maintenance. This article features anmore » integrated information system, Sistema Integral de Informacion de Proceso (SIIP). The development of this system enabled the Laguna Verde Nuclear Power plant to fully use the already existing universe of signals and its related engineering during all plant conditions, namely, start up, normal operation, transient analysis, and emergency operation. Integrated systems offer many advantages over segregated systems, and this experience should benefit similar development efforts in other electric power utilities, not only for nuclear but also for other types of generating plants.« less

Developing a Deep Brain Stimulation Neuromodulation Network for Parkinson Disease, Essential Tremor, and Dystonia: Report of a Quality Improvement Project

PubMed Central

O’Suilleabhain, Padraig E.; Sanghera, Manjit; Patel, Neepa; Khemani, Pravin; Lacritz, Laura H.; Chitnis, Shilpa; Whitworth, Louis A.; Dewey, Richard B.

2016-01-01

Objective To develop a process to improve patient outcomes from deep brain stimulation (DBS) surgery for Parkinson disease (PD), essential tremor (ET), and dystonia. Methods We employed standard quality improvement methodology using the Plan-Do-Study-Act process to improve patient selection, surgical DBS lead implantation, postoperative programming, and ongoing assessment of patient outcomes. Results The result of this quality improvement process was the development of a neuromodulation network. The key aspect of this program is rigorous patient assessment of both motor and non-motor outcomes tracked longitudinally using a REDCap database. We describe how this information is used to identify problems and to initiate Plan-Do-Study-Act cycles to address them. Preliminary outcomes data is presented for the cohort of PD and ET patients who have received surgery since the creation of the neuromodulation network. Conclusions Careful outcomes tracking is essential to ensure quality in a complex therapeutic endeavor like DBS surgery for movement disorders. The REDCap database system is well suited to store outcomes data for the purpose of ongoing quality assurance monitoring. PMID:27711133

Similarity-based modeling in large-scale prediction of drug-drug interactions.

PubMed

Vilar, Santiago; Uriarte, Eugenio; Santana, Lourdes; Lorberbaum, Tal; Hripcsak, George; Friedman, Carol; Tatonetti, Nicholas P

2014-09-01

Drug-drug interactions (DDIs) are a major cause of adverse drug effects and a public health concern, as they increase hospital care expenses and reduce patients' quality of life. DDI detection is, therefore, an important objective in patient safety, one whose pursuit affects drug development and pharmacovigilance. In this article, we describe a protocol applicable on a large scale to predict novel DDIs based on similarity of drug interaction candidates to drugs involved in established DDIs. The method integrates a reference standard database of known DDIs with drug similarity information extracted from different sources, such as 2D and 3D molecular structure, interaction profile, target and side-effect similarities. The method is interpretable in that it generates drug interaction candidates that are traceable to pharmacological or clinical effects. We describe a protocol with applications in patient safety and preclinical toxicity screening. The time frame to implement this protocol is 5-7 h, with additional time potentially necessary, depending on the complexity of the reference standard DDI database and the similarity measures implemented.

Structure-Based Characterization of Multiprotein Complexes

PubMed Central

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J.

2014-01-01

Summary Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. PMID:24954616

A new experiment-independent mechanism to persistify and serve the detector geometry of ATLAS

NASA Astrophysics Data System (ADS)

Bianchi, Riccardo Maria; Boudreau, Joseph; Vukotic, Ilija

2017-10-01

The complex geometry of the whole detector of the ATLAS experiment at LHC is currently stored only in custom online databases, from which it is built on-the-fly on request. Accessing the online geometry guarantees accessing the latest version of the detector description, but requires the setup of the full ATLAS software framework “Athena”, which provides the online services and the tools to retrieve the data from the database. This operation is cumbersome and slows down the applications that need to access the geometry. Moreover, all applications that need to access the detector geometry need to be built and run on the same platform as the ATLAS framework, preventing the usage of the actual detector geometry in stand-alone applications. Here we propose a new mechanism to persistify (in software development in general, and in HEP computing in particular, persistifying means taking an object which lives in memory only - for example because it was built on-the-fly while processing the experimental data, - serializing it and storing it on disk as a persistent object) and serve the geometry of HEP experiments. The new mechanism is composed by a new file format and the modules to make use of it. The new file format allows to store the whole detector description locally in a file, and it is especially optimized to describe large complex detectors with the minimum file size, making use of shared instances and storing compressed representations of geometry transformations. Then, the detector description can be read back in, to fully restore the in-memory geometry tree. Moreover, a dedicated REST API is being designed and developed to serve the geometry in standard exchange formats like JSON, to let users and applications download specific partial geometry information. With this new geometry persistification a new generation of applications could be developed, which can use the actual detector geometry while being platform-independent and experiment-independent.

A structured interface to the object-oriented genomics unified schema for XML-formatted data.

PubMed

Clark, Terry; Jurek, Josef; Kettler, Gregory; Preuss, Daphe

2005-01-01

Data management systems are fast becoming required components in many biology laboratories as the role of computer-based information grows. Although the need for data management systems is on the rise, their inherent complexities can deter the full and routine use of their computational capabilities. The significant undertaking to implement a capable production system can be reduced in part by adapting an established data management system. In such a way, we are leveraging the Genomics Unified Schema (GUS) developed at the Computational Biology and Informatics Laboratory at the University of Pennsylvania as a foundation for managing and analysing DNA sequence data in centromere research projects around Arabidopsis thaliana and related species. Because GUS provides a core schema that includes support for genome sequences, mRNA and its expression, and annotated chromosomes, it is ideal for synthesising a variety of parameters to analyse these repetitive and highly dynamic portions of the genome. Despite this, production-strength data management frameworks are complex, requiring dedicated efforts to adapt and maintain. The work reported in this article addresses one component of such an effort, namely the pivotal task of marshalling data from various sources into GUS. In order to harness GUS for our project, and motivated by efficiency needs, we developed a structured framework for transferring data into GUS from outside sources. This technology is embodied in a GUS object-layer processor, XMLGUS. XMLGUS facilitates incorporating data into GUS by (i) formulating an XML interface that includes relational database key constraint definitions, (ii) regularising traversal through that XML, (iii) realising automatic processing of the XML with database key constraints and (iv) allowing for special processing of input data within the framework for automated processing. The application of XMLGUS to production pipeline processing for a sequencing project and inputting the Arabidopsis genome into GUS is discussed. XMLGUS is available from the Flora website (http://flora.ittc.ku.edu/).

An Experimental Investigation of Complexity in Database Query Formulation Tasks

ERIC Educational Resources Information Center

Casterella, Gretchen Irwin; Vijayasarathy, Leo

2013-01-01

Information Technology professionals and other knowledge workers rely on their ability to extract data from organizational databases to respond to business questions and support decision making. Structured query language (SQL) is the standard programming language for querying data in relational databases, and SQL skills are in high demand and are…

The Starlite Project - Prototyping Real-Time Software.

DTIC Science & Technology

1992-11-01

by ONR under contract ledge of transactions and a temporal data model. A N00014-91-J-l 102, by DOE, and by NOSC. multiversion data object is one...environment. Section 4 presents experimentations of priority-based synchronization algorithms and multiversion data objects using the prototyping environment...priority-based .yn- chronization algorithms and between a multiversion database and its corresponding single- version database, through the sensitivity

77 FR 38277 - Wind and Water Power Program

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-27

..., modeling, and database efforts. This meeting will be a technical discussion to provide those involved in... ecological survey, modeling, and database efforts in the waters off the Mid-Atlantic. The workshop aims to... models and compatible Federal and regional databases. It is not the object of this session to obtain any...

A question-answer pair (QAP) database integrated with websites to answer complex questions submitted to the Regional Medicines Information and Pharmacovigilance Centres in Norway (RELIS): a descriptive study.

PubMed

Schjøtt, Jan; Reppe, Linda A; Roland, Pål-Didrik H; Westergren, Tone

2012-01-01

To assess a question-answer pair (QAP) database integrated with websites developed for drug information centres to answer complex questions effectively. Descriptive study with comparison of two subsequent 6-year periods (1995-2000 and 2001-2006). The Regional Medicines Information and Pharmacovigilance Centres in Norway (RELIS). A randomised sample of QAPs from the RELIS database. Answer time in days compared with Mann-Whitney U test. Number of drugs involved (one, two, three or more), complexity (judgemental and/or patient-related or not) and literature search (none, simple or advanced) compared with χ(2) tests. 842 QAPs (312 from 1995 to 2000 and 530 from 2001 to 2006) were compared. The fraction of judgemental and patient-related questions increased (66%-75% and 54%-72%, respectively, p<0.01). Number of drugs and literature search (>50% advanced) was similar in the two periods, but the fraction of answers referring to the RELIS database increased (13%-31%, p<0.01). Median answer time was reduced from 2 days to 1 (p<0.01), although the fraction of complex questions increased from the first to the second period. Furthermore, the mean number of questions per employee per year increased from 66 to 89 from the first to the second period. The authors conclude that RELIS has a potential to efficiently answer complex questions. The model is of relevance for organisation of drug information centres.

Informatics in radiology: use of CouchDB for document-based storage of DICOM objects.

PubMed

Rascovsky, Simón J; Delgado, Jorge A; Sanz, Alexander; Calvo, Víctor D; Castrillón, Gabriel

2012-01-01

Picture archiving and communication systems traditionally have depended on schema-based Structured Query Language (SQL) databases for imaging data management. To optimize database size and performance, many such systems store a reduced set of Digital Imaging and Communications in Medicine (DICOM) metadata, discarding informational content that might be needed in the future. As an alternative to traditional database systems, document-based key-value stores recently have gained popularity. These systems store documents containing key-value pairs that facilitate data searches without predefined schemas. Document-based key-value stores are especially suited to archive DICOM objects because DICOM metadata are highly heterogeneous collections of tag-value pairs conveying specific information about imaging modalities, acquisition protocols, and vendor-supported postprocessing options. The authors used an open-source document-based database management system (Apache CouchDB) to create and test two such databases; CouchDB was selected for its overall ease of use, capability for managing attachments, and reliance on HTTP and Representational State Transfer standards for accessing and retrieving data. A large database was created first in which the DICOM metadata from 5880 anonymized magnetic resonance imaging studies (1,949,753 images) were loaded by using a Ruby script. To provide the usual DICOM query functionality, several predefined "views" (standard queries) were created by using JavaScript. For performance comparison, the same queries were executed in both the CouchDB database and a SQL-based DICOM archive. The capabilities of CouchDB for attachment management and database replication were separately assessed in tests of a similar, smaller database. Results showed that CouchDB allowed efficient storage and interrogation of all DICOM objects; with the use of information retrieval algorithms such as map-reduce, all the DICOM metadata stored in the large database were searchable with only a minimal increase in retrieval time over that with the traditional database management system. Results also indicated possible uses for document-based databases in data mining applications such as dose monitoring, quality assurance, and protocol optimization. RSNA, 2012

Python and computer vision

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

Doak, J. E.; Prasad, Lakshman

2002-01-01

This paper discusses the use of Python in a computer vision (CV) project. We begin by providing background information on the specific approach to CV employed by the project. This includes a brief discussion of Constrained Delaunay Triangulation (CDT), the Chordal Axis Transform (CAT), shape feature extraction and syntactic characterization, and normalization of strings representing objects. (The terms 'object' and 'blob' are used interchangeably, both referring to an entity extracted from an image.) The rest of the paper focuses on the use of Python in three critical areas: (1) interactions with a MySQL database, (2) rapid prototyping of algorithms, andmore » (3) gluing together all components of the project including existing C and C++ modules. For (l), we provide a schema definition and discuss how the various tables interact to represent objects in the database as tree structures. (2) focuses on an algorithm to create a hierarchical representation of an object, given its string representation, and an algorithm to match unknown objects against objects in a database. And finally, (3) discusses the use of Boost Python to interact with the pre-existing C and C++ code that creates the CDTs and CATS, performs shape feature extraction and syntactic characterization, and normalizes object strings. The paper concludes with a vision of the future use of Python for the CV project.« less

The Role of IMAT Solutions for Training Development at the Royal Netherlands Air Force. IMAT Follow-up Research Part 1

DTIC Science & Technology

2005-09-01

e.g. the transformation of a fragment to an instructional fragment. "* IMAT Database: A Jasmine ® database is used as central database in IMAT for the...storage of fragments. This is an object-oriented relational database. Jasmine ® was, amongst other factors, chosen for its ability to handle multimedia...to the Jasmine ® database, which is used in IMAT as central database. 3.1.1.1 Ontologies In IMAT, the proposed solution on problems with information

eMelanoBase: an online locus-specific variant database for familial melanoma.

PubMed

Fung, David C Y; Holland, Elizabeth A; Becker, Therese M; Hayward, Nicholas K; Bressac-de Paillerets, Brigitte; Mann, Graham J

2003-01-01

A proportion of melanoma-prone individuals in both familial and non-familial contexts has been shown to carry inactivating mutations in either CDKN2A or, rarely, CDK4. CDKN2A is a complex locus that encodes two unrelated proteins from alternately spliced transcripts that are read in different frames. The alpha transcript (exons 1alpha, 2, and 3) produces the p16INK4A cyclin-dependent kinase inhibitor, while the beta transcript (exons 1beta and 2) is translated as p14ARF, a stabilizing factor of p53 levels through binding to MDM2. Mutations in exon 2 can impair both polypeptides and insertions and deletions in exons 1alpha, 1beta, and 2, which can theoretically generate p16INK4A-p14ARF fusion proteins. No online database currently takes into account all the consequences of these genotypes, a situation compounded by some problematic previous annotations of CDKN2A-related sequences and descriptions of their mutations. As an initiative of the international Melanoma Genetics Consortium, we have therefore established a database of germline variants observed in all loci implicated in familial melanoma susceptibility. Such a comprehensive, publicly accessible database is an essential foundation for research on melanoma susceptibility and its clinical application. Our database serves two types of data as defined by HUGO. The core dataset includes the nucleotide variants on the genomic and transcript levels, amino acid variants, and citation. The ancillary dataset includes keyword description of events at the transcription and translation levels and epidemiological data. The application that handles users' queries was designed in the model-view-controller architecture and was implemented in Java. The object-relational database schema was deduced using functional dependency analysis. We hereby present our first functional prototype of eMelanoBase. The service is accessible via the URL www.wmi.usyd.edu.au:8080/melanoma.html. Copyright 2002 Wiley-Liss, Inc.

Improving data management and dissemination in web based information systems by semantic enrichment of descriptive data aspects

NASA Astrophysics Data System (ADS)

Gebhardt, Steffen; Wehrmann, Thilo; Klinger, Verena; Schettler, Ingo; Huth, Juliane; Künzer, Claudia; Dech, Stefan

2010-10-01

The German-Vietnamese water-related information system for the Mekong Delta (WISDOM) project supports business processes in Integrated Water Resources Management in Vietnam. Multiple disciplines bring together earth and ground based observation themes, such as environmental monitoring, water management, demographics, economy, information technology, and infrastructural systems. This paper introduces the components of the web-based WISDOM system including data, logic and presentation tier. It focuses on the data models upon which the database management system is built, including techniques for tagging or linking metadata with the stored information. The model also uses ordered groupings of spatial, thematic and temporal reference objects to semantically tag datasets to enable fast data retrieval, such as finding all data in a specific administrative unit belonging to a specific theme. A spatial database extension is employed by the PostgreSQL database. This object-oriented database was chosen over a relational database to tag spatial objects to tabular data, improving the retrieval of census and observational data at regional, provincial, and local areas. While the spatial database hinders processing raster data, a "work-around" was built into WISDOM to permit efficient management of both raster and vector data. The data model also incorporates styling aspects of the spatial datasets through styled layer descriptions (SLD) and web mapping service (WMS) layer specifications, allowing retrieval of rendered maps. Metadata elements of the spatial data are based on the ISO19115 standard. XML structured information of the SLD and metadata are stored in an XML database. The data models and the data management system are robust for managing the large quantity of spatial objects, sensor observations, census and document data. The operational WISDOM information system prototype contains modules for data management, automatic data integration, and web services for data retrieval, analysis, and distribution. The graphical user interfaces facilitate metadata cataloguing, data warehousing, web sensor data analysis and thematic mapping.

The approaches for the decision support in case natural hazards

NASA Astrophysics Data System (ADS)

Vyazilov, Evgeny; Chunyaev, Nikita

2013-04-01

In spite of using highly automated systems of measurement, collecting, storing, handling, prediction and delivery of information on the marine environment, including natural hazards, the amount of damage from natural phenomena increases. Because information on the marine environment delivered to the industrial facilities not effectively used. To such information pays little attention by individual decision-makers and not always perform preventive measures necessary for reduce and prevent damage. Automation of information support will improve the efficiency management of the marine activities. In Russia develops "The Unified system of the information about World ocean" (ESIMO, http://esimo.ru/), that integrates observation, analysis, prognostic and climate data. Necessary to create tools to automatic selection natural disasters through all integrated data; notification decision-makers about arising natural hazards - software agent; provision of information in a compact form for the decision-makers; assessment of possible damage and costs to the preventive measures; providing information on the impacts of environment on economic facilities and recommendations for decision-making; the use of maps, diagrams, tables for reporting. Tools for automatic selection designed for identification of natural phenomena based on the resources ESIMO and corresponding critical values of the indicators environment. The result of this module will be constantly updated database of critical situations of environment for each object or technological process. To operational notify and provide current information about natural hazards proposes using a software agent that is installed on the computer decision-makers, which is activated in case critical situations and provides a minimum of information. In the event of natural disaster software agent should be able to inform decision-makers about this, providing information on the current situation, and the possibility for more and detailed information about natural hazard. Software agent must be able to be configured by the user to a specific object: a specific station or a drilling rigs that region or area, regardless of the size of the object. And depending on the selected settings and parameters it needs to apply the values of critical indexes. There is a need for real-time display hydrometeorological information with compact scheme that reflects the environment indicators that affect industrial facility in the form of devices (thermometer, aneroid, footstock, speedometer, hygrometer, thermograph, barograph, rain gauge, wind vane, etc.) with the ability to display indicators exceed a critical value. This scheme is designed to provide maximum information in the shortest possible time reference that provides an intuitive interface (display by generally accepted standardized instruments). Analytical services ESIMO combined with geographic information service provides information about area or point to decision-makers of showing the dynamics of changes of parameters in the form of graphics, diagrams, maps, tables. If the data sources are updated, analytical services automatically provides the relevance of the data in the analytical views of the complex. Analytical services works with database of integrated data and used for the preparation and presentation of the consumers of the federal and regional level for the analysis of information on the World Oceans. The analytic services show a set of indicators about the situation in the World Ocean. The complex provides the processing, analysis of qualitative and quantitative characteristics (indexes) of the marine environment and maritime activities of the Russian Federation. To assess the need for preventive measures, decision-makers require information in the form of potential economic consequences of natural hazard, cost of preventive measures to prevent damage. We can use for that the economic and mathematical models. When making the decision decision-makers must understand the possible consequences of natural phenomena and rely on the advice that they receive from a decision support system. Such information about the impacts and recommendations are based on the knowledge base (rules of "if, then"), formed on the basis of experience gained in the past. This should take into account not only the critical values for each object and technological process, but also the type of information (observations, forecasting, climate, and after the phenomenon), the level of decision-making, the season of the year, the climate zone where the object is located. Within ESIMO created integrated database that containing the results of the monitoring of the marine environment. The database includes the observation, analysis, and forecasting and climate data. Operational data is updated automatically at specified intervals of a few minutes to a week, depending on the frequency of observations. Climatic data is updated as needed, for example, once a year or once every five years. Integrated database contains a set of indicators related to a specific object, and to a certain geographic area, according to the observations made and the data entered data. In addition to hydrometeorological parameters database contains socio-economic information. At present, was created the database of critical values and information about the impacts of and recommendations for the 30 natural hazards, developed the data structure and software is under development. The interaction of all components of an information support will reduce the economic damage from natural disaster on individual objects economy (ships, ports, etc.) and improve public safety through more prompt delivery of information to decision-makers and the public, besides receive more informative data (district with symptoms natural phenomena , assessment of possible damage, the impact of and recommendations).

Observational database for studies of nearby universe

NASA Astrophysics Data System (ADS)

Kaisina, E. I.; Makarov, D. I.; Karachentsev, I. D.; Kaisin, S. S.

2012-01-01

We present the description of a database of galaxies of the Local Volume (LVG), located within 10 Mpc around the Milky Way. It contains more than 800 objects. Based on an analysis of functional capabilities, we used the PostgreSQL DBMS as a management system for our LVG database. Applying semantic modelling methods, we developed a physical ER-model of the database. We describe the developed architecture of the database table structure, and the implemented web-access, available at http://www.sao.ru/lv/lvgdb.

Leveraging Cognitive Context for Object Recognition

DTIC Science & Technology

2014-06-01

learned from large image databases. We build upon this concept by exploring cognitive context, demonstrating how rich dynamic context provided by...context that people rely upon as they perceive the world. Context in ACT-R/E takes the form of associations between related concepts that are learned ...and accuracy of object recognition. Context is most often viewed as a static concept, learned from large image databases. We build upon this concept by

The Research Potential of the Electronic OED Database at the University of Waterloo: A Case Study.

ERIC Educational Resources Information Center

Berg, Donna Lee

1991-01-01

Discusses the history and structure of the online database of the second edition of the Oxford English Dictionary (OED) and the software tools developed at the University of Waterloo to manipulate the unusually complex database. Four sample searches that indicate some types of problems that might be encountered are appended. (DB)

Spatiotemporal Characteristics of QRS Complexes Enable the Diagnosis of Brugada Syndrome Regardless of the Appearance of a Type 1 ECG.

PubMed

Guillem, Maria S; Climent, Andreu M; Millet, José; Berne, Paola; Ramos, Rafael; Brugada, Josep; Brugada, Ramon

2016-05-01

The diagnosis of Brugada syndrome based on the ECG is hampered by the dynamic nature of its ECG manifestations. Brugada syndrome patients are only 25% likely to present a type 1 ECG. The objective of this study is to provide an ECG diagnostic criterion for Brugada syndrome patients that can be applied consistently even in the absence of a type 1 ECG. We recorded 67-lead body surface potential maps from 94 Brugada syndrome patients and 82 controls (including right bundle branch block patients and healthy individuals). The spatial propagation direction during the last r' wave and the slope at the end of the QRS complex were measured and compared between patients groups. Receiver-operating characteristic curves were constructed for half of the database to identify optimal cutoff values; sensitivity and specificity for these cutoff values were measured in the other half of the database. A spontaneous type 1 ECG was present in only 30% of BrS patients. An orientation in the sagittal plane < 101º during the last r' wave and a descending slope < 9.65 mV/s enables the diagnosis of the syndrome with a sensitivity of 69% and a specificity of 97% in non-type 1 Brugada syndrome patients. Spatiotemporal characteristics of surface ECG recordings can enable a robust identification of BrS even without the presence of a type 1 ECG. © 2016 Wiley Periodicals, Inc.

From Pharmacovigilance to Clinical Care Optimization.

PubMed

Celi, Leo Anthony; Moseley, Edward; Moses, Christopher; Ryan, Padhraig; Somai, Melek; Stone, David; Tang, Kai-Ou

2014-09-01

In order to ensure the continued, safe administration of pharmaceuticals, particularly those agents that have been recently introduced into the market, there is a need for improved surveillance after product release. This is particularly so because drugs are used by a variety of patients whose particular characteristics may not have been fully captured in the original market approval studies. Even well-conducted, randomized controlled trials are likely to have excluded a large proportion of individuals because of any number of issues. The digitization of medical care, which yields rich and accessible drug data amenable to analytic techniques, provides an opportunity to capture the required information via observational studies. We propose the development of an open, accessible database containing properly de-identified data, to provide the substrate for the required improvement in pharmacovigilance. A range of stakeholders could use this to identify delayed and low-frequency adverse events. Moreover, its power as a research tool could extend to the detection of complex interactions, potential novel uses, and subtle subpopulation effects. This far-reaching potential is demonstrated by our experience with the open Multi-parameter Intelligent Monitoring in Intensive Care (MIMIC) intensive care unit database. The new database could also inform the development of objective, robust clinical practice guidelines. Careful systematization and deliberate standardization of a fully digitized pharmacovigilance process is likely to save both time and resources for healthcare in general.

Web Database Development: Implications for Academic Publishing.

ERIC Educational Resources Information Center

Fernekes, Bob

This paper discusses the preliminary planning, design, and development of a pilot project to create an Internet accessible database and search tool for locating and distributing company data and scholarly work. Team members established four project objectives: (1) to develop a Web accessible database and decision tool that creates Web pages on the…

Interactive Scene Analysis Module - A sensor-database fusion system for telerobotic environments

NASA Technical Reports Server (NTRS)

Cooper, Eric G.; Vazquez, Sixto L.; Goode, Plesent W.

1992-01-01

Accomplishing a task with telerobotics typically involves a combination of operator control/supervision and a 'script' of preprogrammed commands. These commands usually assume that the location of various objects in the task space conform to some internal representation (database) of that task space. The ability to quickly and accurately verify the task environment against the internal database would improve the robustness of these preprogrammed commands. In addition, the on-line initialization and maintenance of a task space database is difficult for operators using Cartesian coordinates alone. This paper describes the Interactive Scene' Analysis Module (ISAM) developed to provide taskspace database initialization and verification utilizing 3-D graphic overlay modelling, video imaging, and laser radar based range imaging. Through the fusion of taskspace database information and image sensor data, a verifiable taskspace model is generated providing location and orientation data for objects in a task space. This paper also describes applications of the ISAM in the Intelligent Systems Research Laboratory (ISRL) at NASA Langley Research Center, and discusses its performance relative to representation accuracy and operator interface efficiency.

microRNAs Databases: Developmental Methodologies, Structural and Functional Annotations.

PubMed

Singh, Nagendra Kumar

2017-09-01

microRNA (miRNA) is an endogenous and evolutionary conserved non-coding RNA, involved in post-transcriptional process as gene repressor and mRNA cleavage through RNA-induced silencing complex (RISC) formation. In RISC, miRNA binds in complementary base pair with targeted mRNA along with Argonaut proteins complex, causes gene repression or endonucleolytic cleavage of mRNAs and results in many diseases and syndromes. After the discovery of miRNA lin-4 and let-7, subsequently large numbers of miRNAs were discovered by low-throughput and high-throughput experimental techniques along with computational process in various biological and metabolic processes. The miRNAs are important non-coding RNA for understanding the complex biological phenomena of organism because it controls the gene regulation. This paper reviews miRNA databases with structural and functional annotations developed by various researchers. These databases contain structural and functional information of animal, plant and virus miRNAs including miRNAs-associated diseases, stress resistance in plant, miRNAs take part in various biological processes, effect of miRNAs interaction on drugs and environment, effect of variance on miRNAs, miRNAs gene expression analysis, sequence of miRNAs, structure of miRNAs. This review focuses on the developmental methodology of miRNA databases such as computational tools and methods used for extraction of miRNAs annotation from different resources or through experiment. This study also discusses the efficiency of user interface design of every database along with current entry and annotations of miRNA (pathways, gene ontology, disease ontology, etc.). Here, an integrated schematic diagram of construction process for databases is also drawn along with tabular and graphical comparison of various types of entries in different databases. Aim of this paper is to present the importance of miRNAs-related resources at a single place.

State analysis requirements database for engineering complex embedded systems

NASA Technical Reports Server (NTRS)

Bennett, Matthew B.; Rasmussen, Robert D.; Ingham, Michel D.

2004-01-01

It has become clear that spacecraft system complexity is reaching a threshold where customary methods of control are no longer affordable or sufficiently reliable. At the heart of this problem are the conventional approaches to systems and software engineering based on subsystem-level functional decomposition, which fail to scale in the tangled web of interactions typically encountered in complex spacecraft designs. Furthermore, there is a fundamental gap between the requirements on software specified by systems engineers and the implementation of these requirements by software engineers. Software engineers must perform the translation of requirements into software code, hoping to accurately capture the systems engineer's understanding of the system behavior, which is not always explicitly specified. This gap opens up the possibility for misinterpretation of the systems engineer's intent, potentially leading to software errors. This problem is addressed by a systems engineering tool called the State Analysis Database, which provides a tool for capturing system and software requirements in the form of explicit models. This paper describes how requirements for complex aerospace systems can be developed using the State Analysis Database.

The research and implementation of coalfield spontaneous combustion of carbon emission WebGIS based on Silverlight and ArcGIS server

NASA Astrophysics Data System (ADS)

Zhu, Z.; Bi, J.; Wang, X.; Zhu, W.

2014-02-01

As an important sub-topic of the natural process of carbon emission data public information platform construction, coalfield spontaneous combustion of carbon emission WebGIS system has become an important study object. In connection with data features of coalfield spontaneous combustion carbon emissions (i.e. a wide range of data, which is rich and complex) and the geospatial characteristics, data is divided into attribute data and spatial data. Based on full analysis of the data, completed the detailed design of the Oracle database and stored on the Oracle database. Through Silverlight rich client technology and the expansion of WCF services, achieved the attribute data of web dynamic query, retrieval, statistical, analysis and other functions. For spatial data, we take advantage of ArcGIS Server and Silverlight-based API to invoke GIS server background published map services, GP services, Image services and other services, implemented coalfield spontaneous combustion of remote sensing image data and web map data display, data analysis, thematic map production. The study found that the Silverlight technology, based on rich client and object-oriented framework for WCF service, can efficiently constructed a WebGIS system. And then, combined with ArcGIS Silverlight API to achieve interactive query attribute data and spatial data of coalfield spontaneous emmission, can greatly improve the performance of WebGIS system. At the same time, it provided a strong guarantee for the construction of public information on China's carbon emission data.

Structure-based characterization of multiprotein complexes.

PubMed

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

2014-07-08

Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Computing Health Quality Measures Using Informatics for Integrating Biology and the Bedside

PubMed Central

Murphy, Shawn N

2013-01-01

Background The Health Quality Measures Format (HQMF) is a Health Level 7 (HL7) standard for expressing computable Clinical Quality Measures (CQMs). Creating tools to process HQMF queries in clinical databases will become increasingly important as the United States moves forward with its Health Information Technology Strategic Plan to Stages 2 and 3 of the Meaningful Use incentive program (MU2 and MU3). Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databases used as part of the Office of the National Coordinator (ONC)’s Query Health platform to move toward this goal. Objective Our goal is to integrate i2b2 with the Query Health HQMF architecture, to prepare for other HQMF use-cases (such as MU2 and MU3), and to articulate the functional overlap between i2b2 and HQMF. Therefore, we analyze the structure of HQMF, and then we apply this understanding to HQMF computation on the i2b2 clinical analytical database platform. Specifically, we develop a translator between two query languages, HQMF and i2b2, so that the i2b2 platform can compute HQMF queries. Methods We use the HQMF structure of queries for aggregate reporting, which define clinical data elements and the temporal and logical relationships between them. We use the i2b2 XML format, which allows flexible querying of a complex clinical data repository in an easy-to-understand domain-specific language. Results The translator can represent nearly any i2b2-XML query as HQMF and execute in i2b2 nearly any HQMF query expressible in i2b2-XML. This translator is part of the freely available reference implementation of the QueryHealth initiative. We analyze limitations of the conversion and find it covers many, but not all, of the complex temporal and logical operators required by quality measures. Conclusions HQMF is an expressive language for defining quality measures, and it will be important to understand and implement for CQM computation, in both meaningful use and population health. However, its current form might allow complexity that is intractable for current database systems (both in terms of implementation and computation). Our translator, which supports the subset of HQMF currently expressible in i2b2-XML, may represent the beginnings of a practical compromise. It is being pilot-tested in two Query Health demonstration projects, and it can be further expanded to balance computational tractability with the advanced features needed by measure developers. PMID:23603227

Tuberous Sclerosis Complex National Database

DTIC Science & Technology

2005-10-01

monotherapy LIAED dosage reduction ElDiscontinuation of AED LURemoval of VNS device O1Discontinuation of Ketogenic Diet U Seizure remission Surgical...34* Treatments "* VNS "* Ketogenic Diet "* AEDs W81XWH-04-1-0896 Annual Report 10/05 Tuberous Sclerosis Complex National Database App. H - Page 1 of 3 PI: Steven P...Page 20 of 29 Date last modified 7/14/05 Subject name: First, Middle, Last DOB: LiKetogenic diet LiEpilepsy surgery (if checked, complete the separate

Care coordination of multimorbidity: a scoping study

PubMed Central

Burau, Viola

2015-01-01

Background A key challenge in healthcare systems worldwide is the large number of patients who suffer from multimorbidity; despite this, most systems are organized within a single-disease framework. Objective The present study addresses two issues: the characteristics and preconditions of care coordination for patients with multimorbidity; and the factors that promote or inhibit care coordination at the levels of provider organizations and healthcare professionals. Design The analysis is based on a scoping study, which combines a systematic literature search with a qualitative thematic analysis. The search was conducted in November 2013 and included the PubMed, CINAHL, and Web of Science databases, as well as the Cochrane Library, websites of relevant organizations and a hand-search of reference lists. The analysis included studies with a wide range of designs, from industrialized countries, in English, German and the Scandinavian languages, which focused on both multimorbidity/comorbidity and coordination of integrated care. Results The analysis included 47 of the 226 identified studies. The central theme emerging was complexity. This related to both specific medical conditions of patients with multimorbidity (case complexity) and the organization of care delivery at the levels of provider organizations and healthcare professionals (care complexity). Conclusions In terms of how to approach care coordination, one approach is to reduce complexity and the other is to embrace complexity. Either way, future research must take a more explicit stance on complexity and also gain a better understanding of the role of professionals as a prerequisite for the development of new care coordination interventions. PMID:29090157

History in the gene: negotiations between molecular and organismal anthropology.

PubMed

Sommer, Marianne

2008-01-01

In the advertising discourse of human genetic database projects, of genetic ancestry tracing companies, and in popular books on anthropological genetics, what I refer to as the anthropological gene and genome appear as documents of human history, by far surpassing the written record and oral history in scope and accuracy as archives of our past. How did macromolecules become "documents of human evolutionary history"? Historically, molecular anthropology, a term introduced by Emile Zuckerkandl in 1962 to characterize the study of primate phylogeny and human evolution on the molecular level, asserted its claim to the privilege of interpretation regarding hominoid, hominid, and human phylogeny and evolution vis-à-vis other historical sciences such as evolutionary biology, physical anthropology, and paleoanthropology. This process will be discussed on the basis of three key conferences on primate classification and evolution that brought together exponents of the respective fields and that were held in approximately ten-years intervals between the early 1960s and the 1980s. I show how the anthropological gene and genome gained their status as the most fundamental, clean, and direct records of historical information, and how the prioritizing of these epistemic objects was part of a complex involving the objectivity of numbers, logic, and mathematics, the objectivity of machines and instruments, and the objectivity seen to reside in the epistemic objects themselves.

SU-D-BRB-02: Combining a Commercial Autoplanning Engine with Database Dose Predictions to Further Improve Plan Quality

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

Robertson, SP; Moore, JA; Hui, X

Purpose: Database dose predictions and a commercial autoplanning engine both improve treatment plan quality in different but complimentary ways. The combination of these planning techniques is hypothesized to further improve plan quality. Methods: Four treatment plans were generated for each of 10 head and neck (HN) and 10 prostate cancer patients, including Plan-A: traditional IMRT optimization using clinically relevant default objectives; Plan-B: traditional IMRT optimization using database dose predictions; Plan-C: autoplanning using default objectives; and Plan-D: autoplanning using database dose predictions. One optimization was used for each planning method. Dose distributions were normalized to 95% of the planning target volumemore » (prostate: 8000 cGy; HN: 7000 cGy). Objectives used in plan optimization and analysis were the larynx (25%, 50%, 90%), left and right parotid glands (50%, 85%), spinal cord (0%, 50%), rectum and bladder (0%, 20%, 50%, 80%), and left and right femoral heads (0%, 70%). Results: All objectives except larynx 25% and 50% resulted in statistically significant differences between plans (Friedman’s χ{sup 2} ≥ 11.2; p ≤ 0.011). Maximum dose to the rectum (Plans A-D: 8328, 8395, 8489, 8537 cGy) and bladder (Plans A-D: 8403, 8448, 8527, 8569 cGy) were significantly increased. All other significant differences reflected a decrease in dose. Plans B-D were significantly different from Plan-A for 3, 17, and 19 objectives, respectively. Plans C-D were also significantly different from Plan-B for 8 and 13 objectives, respectively. In one case (cord 50%), Plan-D provided significantly lower dose than plan C (p = 0.003). Conclusion: Combining database dose predictions with a commercial autoplanning engine resulted in significant plan quality differences for the greatest number of objectives. This translated to plan quality improvements in most cases, although special care may be needed for maximum dose constraints. Further evaluation is warranted in a larger cohort across HN, prostate, and other treatment sites. This work is supported by Philips Radiation Oncology Systems.« less

Expert system development for commonality analysis in space programs

NASA Technical Reports Server (NTRS)

Yeager, Dorian P.

1987-01-01

This report is a combination of foundational mathematics and software design. A mathematical model of the Commonality Analysis problem was developed and some important properties discovered. The complexity of the problem is described herein and techniques, both deterministic and heuristic, for reducing that complexity are presented. Weaknesses are pointed out in the existing software (System Commonality Analysis Tool) and several improvements are recommended. It is recommended that: (1) an expert system for guiding the design of new databases be developed; (2) a distributed knowledge base be created and maintained for the purpose of encoding the commonality relationships between design items in commonality databases; (3) a software module be produced which automatically generates commonality alternative sets from commonality databases using the knowledge associated with those databases; and (4) a more complete commonality analysis module be written which is capable of generating any type of feasible solution.

The BioImage Database Project: organizing multidimensional biological images in an object-relational database.

PubMed

Carazo, J M; Stelzer, E H

1999-01-01

The BioImage Database Project collects and structures multidimensional data sets recorded by various microscopic techniques relevant to modern life sciences. It provides, as precisely as possible, the circumstances in which the sample was prepared and the data were recorded. It grants access to the actual data and maintains links between related data sets. In order to promote the interdisciplinary approach of modern science, it offers a large set of key words, which covers essentially all aspects of microscopy. Nonspecialists can, therefore, access and retrieve significant information recorded and submitted by specialists in other areas. A key issue of the undertaking is to exploit the available technology and to provide a well-defined yet flexible structure for dealing with data. Its pivotal element is, therefore, a modern object relational database that structures the metadata and ameliorates the provision of a complete service. The BioImage database can be accessed through the Internet. Copyright 1999 Academic Press.

Data-driven grasp synthesis using shape matching and task-based pruning.

PubMed

Li, Ying; Fu, Jiaxin L; Pollard, Nancy S

2007-01-01

Human grasps, especially whole-hand grasps, are difficult to animate because of the high number of degrees of freedom of the hand and the need for the hand to conform naturally to the object surface. Captured human motion data provides us with a rich source of examples of natural grasps. However, for each new object, we are faced with the problem of selecting the best grasp from the database and adapting it to that object. This paper presents a data-driven approach to grasp synthesis. We begin with a database of captured human grasps. To identify candidate grasps for a new object, we introduce a novel shape matching algorithm that matches hand shape to object shape by identifying collections of features having similar relative placements and surface normals. This step returns many grasp candidates, which are clustered and pruned by choosing the grasp best suited for the intended task. For pruning undesirable grasps, we develop an anatomically-based grasp quality measure specific to the human hand. Examples of grasp synthesis are shown for a variety of objects not present in the original database. This algorithm should be useful both as an animator tool for posing the hand and for automatic grasp synthesis in virtual environments.

Design and Implementation of an Interface Editor for the Amadeus Multi- Relational Database Front-end System

DTIC Science & Technology

1993-03-25

application of Object-Oriented Programming (OOP) and Human-Computer Interface (HCI) design principles. Knowledge gained from each topic has been incorporated...through the ap- plication of Object-Oriented Programming (OOP) and Human-Computer Interface (HCI) design principles. Knowledge gained from each topic has...programming and Human-Computer Interface (HCI) design. Knowledge gained from each is applied to the design of a Form-based interface for database data

Cyclone: java-based querying and computing with Pathway/Genome databases.

PubMed

Le Fèvre, François; Smidtas, Serge; Schächter, Vincent

2007-05-15

Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization. Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone. For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net.

Basic level scene understanding: categories, attributes and structures

PubMed Central

Xiao, Jianxiong; Hays, James; Russell, Bryan C.; Patterson, Genevieve; Ehinger, Krista A.; Torralba, Antonio; Oliva, Aude

2013-01-01

A longstanding goal of computer vision is to build a system that can automatically understand a 3D scene from a single image. This requires extracting semantic concepts and 3D information from 2D images which can depict an enormous variety of environments that comprise our visual world. This paper summarizes our recent efforts toward these goals. First, we describe the richly annotated SUN database which is a collection of annotated images spanning 908 different scene categories with object, attribute, and geometric labels for many scenes. This database allows us to systematically study the space of scenes and to establish a benchmark for scene and object recognition. We augment the categorical SUN database with 102 scene attributes for every image and explore attribute recognition. Finally, we present an integrated system to extract the 3D structure of the scene and objects depicted in an image. PMID:24009590

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

PubMed Central

2010-01-01

Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis.

PubMed

Dvornyk, Volodymyr; Long, Ji-Rong; Xiong, Dong-Hai; Liu, Peng-Yuan; Zhao, Lan-Juan; Shen, Hui; Zhang, Yuan-Yuan; Liu, Yong-Jun; Rocha-Sanchez, Sonia; Xiao, Peng; Recker, Robert R; Deng, Hong-Wen

2004-02-25

Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups.

Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis

PubMed Central

Dvornyk, Volodymyr; Long, Ji-Rong; Xiong, Dong-Hai; Liu, Peng-Yuan; Zhao, Lan-Juan; Shen, Hui; Zhang, Yuan-Yuan; Liu, Yong-Jun; Rocha-Sanchez, Sonia; Xiao, Peng; Recker, Robert R; Deng, Hong-Wen

2004-01-01

Background Public SNP databases are frequently used to choose SNPs for candidate genes in the association and linkage studies of complex disorders. However, their utility for such studies of diseases with ethnic-dependent background has never been evaluated. Results To estimate the accuracy and completeness of SNP public databases, we analyzed the allele frequencies of 41 SNPs in 10 candidate genes for obesity and/or osteoporosis in a large American-Caucasian sample (1,873 individuals from 405 nuclear families) by PCR-invader assay. We compared our results with those from the databases and other published studies. Of the 41 SNPs, 8 were monomorphic in our sample. Twelve were reported for the first time for Caucasians and the other 29 SNPs in our sample essentially confirmed the respective allele frequencies for Caucasians in the databases and previous studies. The comparison of our data with other ethnic groups showed significant differentiation between the three major world ethnic groups at some SNPs (Caucasians and Africans differed at 3 of the 18 shared SNPs, and Caucasians and Asians differed at 13 of the 22 shared SNPs). This genetic differentiation may have an important implication for studying the well-known ethnic differences in the prevalence of obesity and osteoporosis, and complex disorders in general. Conclusion A comparative analysis of the SNP data of the candidate genes obtained in the present study, as well as those retrieved from the public domain, suggests that the databases may currently have serious limitations for studying complex disorders with an ethnic-dependent background due to the incomplete and uneven representation of the candidate SNPs in the databases for the major ethnic groups. This conclusion attests to the imperative necessity of large-scale and accurate characterization of these SNPs in different ethnic groups. PMID:15113403

Trends in maar crater size and shape using the global Maar Volcano Location and Shape (MaarVLS) database

NASA Astrophysics Data System (ADS)

Graettinger, A. H.

2018-05-01

A maar crater is the top of a much larger subsurface diatreme structure produced by phreatomagmatic explosions and the size and shape of the crater reflects the growth history of that structure during an eruption. Recent experimental and geophysical research has shown that crater complexity can reflect subsurface complexity. Morphometry provides a means of characterizing a global population of maar craters in order to establish the typical size and shape of features. A global database of Quaternary maar crater planform morphometry indicates that maar craters are typically not circular and frequently have compound shapes resembling overlapping circles. Maar craters occur in volcanic fields that contain both small volume and complex volcanoes. The global perspective provided by the database shows that maars are common in many volcanic and tectonic settings producing a similar diversity of size and shape within and between volcanic fields. A few exceptional populations of maars were revealed by the database, highlighting directions of future research to improve our understanding on the geometry and spacing of subsurface explosions that produce maars. These outlying populations, such as anomalously large craters (>3000 m), chains of maars, and volcanic fields composed of mostly maar craters each represent a small portion of the database, but provide opportunities to reinvestigate fundamental questions on maar formation. Maar crater morphometry can be integrated with structural, hydrological studies to investigate lateral migration of phreatomagmatic explosion location in the subsurface. A comprehensive database of intact maar morphometry is also beneficial for the hunt for maar-diatremes on other planets.

Efficient view based 3-D object retrieval using Hidden Markov Model

NASA Astrophysics Data System (ADS)

Jain, Yogendra Kumar; Singh, Roshan Kumar

2013-12-01

Recent research effort has been dedicated to view based 3-D object retrieval, because of highly discriminative property of 3-D object and has multi view representation. The state-of-art method is highly depending on their own camera array setting for capturing views of 3-D object and use complex Zernike descriptor, HAC for representative view selection which limit their practical application and make it inefficient for retrieval. Therefore, an efficient and effective algorithm is required for 3-D Object Retrieval. In order to move toward a general framework for efficient 3-D object retrieval which is independent of camera array setting and avoidance of representative view selection, we propose an Efficient View Based 3-D Object Retrieval (EVBOR) method using Hidden Markov Model (HMM). In this framework, each object is represented by independent set of view, which means views are captured from any direction without any camera array restriction. In this, views are clustered (including query view) to generate the view cluster, which is then used to build the query model with HMM. In our proposed method, HMM is used in twofold: in the training (i.e. HMM estimate) and in the retrieval (i.e. HMM decode). The query model is trained by using these view clusters. The EVBOR query model is worked on the basis of query model combining with HMM. The proposed approach remove statically camera array setting for view capturing and can be apply for any 3-D object database to retrieve 3-D object efficiently and effectively. Experimental results demonstrate that the proposed scheme has shown better performance than existing methods. [Figure not available: see fulltext.

The volatile compound BinBase mass spectral database.

PubMed

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

2011-08-04

Volatile compounds comprise diverse chemical groups with wide-ranging sources and functions. These compounds originate from major pathways of secondary metabolism in many organisms and play essential roles in chemical ecology in both plant and animal kingdoms. In past decades, sampling methods and instrumentation for the analysis of complex volatile mixtures have improved; however, design and implementation of database tools to process and store the complex datasets have lagged behind. The volatile compound BinBase (vocBinBase) is an automated peak annotation and database system developed for the analysis of GC-TOF-MS data derived from complex volatile mixtures. The vocBinBase DB is an extension of the previously reported metabolite BinBase software developed to track and identify derivatized metabolites. The BinBase algorithm uses deconvoluted spectra and peak metadata (retention index, unique ion, spectral similarity, peak signal-to-noise ratio, and peak purity) from the Leco ChromaTOF software, and annotates peaks using a multi-tiered filtering system with stringent thresholds. The vocBinBase algorithm assigns the identity of compounds existing in the database. Volatile compound assignments are supported by the Adams mass spectral-retention index library, which contains over 2,000 plant-derived volatile compounds. Novel molecules that are not found within vocBinBase are automatically added using strict mass spectral and experimental criteria. Users obtain fully annotated data sheets with quantitative information for all volatile compounds for studies that may consist of thousands of chromatograms. The vocBinBase database may also be queried across different studies, comprising currently 1,537 unique mass spectra generated from 1.7 million deconvoluted mass spectra of 3,435 samples (18 species). Mass spectra with retention indices and volatile profiles are available as free download under the CC-BY agreement (http://vocbinbase.fiehnlab.ucdavis.edu). The BinBase database algorithms have been successfully modified to allow for tracking and identification of volatile compounds in complex mixtures. The database is capable of annotating large datasets (hundreds to thousands of samples) and is well-suited for between-study comparisons such as chemotaxonomy investigations. This novel volatile compound database tool is applicable to research fields spanning chemical ecology to human health. The BinBase source code is freely available at http://binbase.sourceforge.net/ under the LGPL 2.0 license agreement.

The volatile compound BinBase mass spectral database

PubMed Central

2011-01-01

Background Volatile compounds comprise diverse chemical groups with wide-ranging sources and functions. These compounds originate from major pathways of secondary metabolism in many organisms and play essential roles in chemical ecology in both plant and animal kingdoms. In past decades, sampling methods and instrumentation for the analysis of complex volatile mixtures have improved; however, design and implementation of database tools to process and store the complex datasets have lagged behind. Description The volatile compound BinBase (vocBinBase) is an automated peak annotation and database system developed for the analysis of GC-TOF-MS data derived from complex volatile mixtures. The vocBinBase DB is an extension of the previously reported metabolite BinBase software developed to track and identify derivatized metabolites. The BinBase algorithm uses deconvoluted spectra and peak metadata (retention index, unique ion, spectral similarity, peak signal-to-noise ratio, and peak purity) from the Leco ChromaTOF software, and annotates peaks using a multi-tiered filtering system with stringent thresholds. The vocBinBase algorithm assigns the identity of compounds existing in the database. Volatile compound assignments are supported by the Adams mass spectral-retention index library, which contains over 2,000 plant-derived volatile compounds. Novel molecules that are not found within vocBinBase are automatically added using strict mass spectral and experimental criteria. Users obtain fully annotated data sheets with quantitative information for all volatile compounds for studies that may consist of thousands of chromatograms. The vocBinBase database may also be queried across different studies, comprising currently 1,537 unique mass spectra generated from 1.7 million deconvoluted mass spectra of 3,435 samples (18 species). Mass spectra with retention indices and volatile profiles are available as free download under the CC-BY agreement (http://vocbinbase.fiehnlab.ucdavis.edu). Conclusions The BinBase database algorithms have been successfully modified to allow for tracking and identification of volatile compounds in complex mixtures. The database is capable of annotating large datasets (hundreds to thousands of samples) and is well-suited for between-study comparisons such as chemotaxonomy investigations. This novel volatile compound database tool is applicable to research fields spanning chemical ecology to human health. The BinBase source code is freely available at http://binbase.sourceforge.net/ under the LGPL 2.0 license agreement. PMID:21816034

Data structures and organisation: Special problems in scientific applications

NASA Astrophysics Data System (ADS)

Read, Brian J.

1989-12-01

In this paper we discuss and offer answers to the following questions: What, really, are the benifits of databases in physics? Are scientific databases essentially different from conventional ones? What are the drawbacks of a commercial database management system for use with scientific data? Do they outweigh the advantages? Do databases systems have adequate graphics facilities, or is a separate graphics package necessary? SQL as a standard language has deficiencies, but what are they for scientific data in particular? Indeed, is the relational model appropriate anyway? Or, should we turn to object oriented databases?

Schizophrenia, narrative, and neurocognition: The utility of life-stories in understanding social problem-solving skills.

PubMed

Moe, Aubrey M; Breitborde, Nicholas J K; Bourassa, Kyle J; Gallagher, Colin J; Shakeel, Mohammed K; Docherty, Nancy M

2018-06-01

Schizophrenia researchers have focused on phenomenological aspects of the disorder to better understand its underlying nature. In particular, development of personal narratives-that is, the complexity with which people form, organize, and articulate their "life stories"-has recently been investigated in individuals with schizophrenia. However, less is known about how aspects of narrative relate to indicators of neurocognitive and social functioning. The objective of the present study was to investigate the association of linguistic complexity of life-story narratives to measures of cognitive and social problem-solving abilities among people with schizophrenia. Thirty-two individuals with a diagnosis of schizophrenia completed a research battery consisting of clinical interviews, a life-story narrative, neurocognitive testing, and a measure assessing multiple aspects of social problem solving. Narrative interviews were assessed for linguistic complexity using computerized technology. The results indicate differential relationships of linguistic complexity and neurocognition to domains of social problem-solving skills. More specifically, although neurocognition predicted how well one could both describe and enact a solution to a social problem, linguistic complexity alone was associated with accurately recognizing that a social problem had occurred. In addition, linguistic complexity appears to be a cognitive factor that is discernible from other broader measures of neurocognition. Linguistic complexity may be more relevant in understanding earlier steps of the social problem-solving process than more traditional, broad measures of cognition, and thus is relevant in conceptualizing treatment targets. These findings also support the relevance of developing narrative-focused psychotherapies. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Etoile Project : Social Intelligent ICT-System for very large scale education in complex systems

NASA Astrophysics Data System (ADS)

Bourgine, P.; Johnson, J.

2009-04-01

The project will devise new theory and implement new ICT-based methods of delivering high-quality low-cost postgraduate education to many thousands of people in a scalable way, with the cost of each extra student being negligible (< a few Euros). The research will create an in vivo laboratory of one to ten thousand postgraduate students studying courses in complex systems. This community is chosen because it is large and interdisciplinary and there is a known requirement for courses for thousand of students across Europe. The project involves every aspect of course production and delivery. Within this the research focused on the creation of a Socially Intelligent Resource Mining system to gather large volumes of high quality educational resources from the internet; new methods to deconstruct these to produce a semantically tagged Learning Object Database; a Living Course Ecology to support the creation and maintenance of evolving course materials; systems to deliver courses; and a ‘socially intelligent assessment system'. The system will be tested on one to ten thousand postgraduate students in Europe working towards the Complex System Society's title of European PhD in Complex Systems. Étoile will have a very high impact both scientifically and socially by (i) the provision of new scalable ICT-based methods for providing very low cost scientific education, (ii) the creation of new mathematical and statistical theory for the multiscale dynamics of complex systems, (iii) the provision of a working example of adaptation and emergence in complex socio-technical systems, and (iv) making a major educational contribution to European complex systems science and its applications.

Context indexing of digital cardiac ultrasound records in PACS

NASA Astrophysics Data System (ADS)

Lobodzinski, S. Suave; Meszaros, Georg N.

1998-07-01

Recent wide adoption of the DICOM 3.0 standard by ultrasound equipment vendors created a need for practical clinical implementations of cardiac imaging study visualization, management and archiving, DICOM 3.0 defines only a logical and physical format for exchanging image data (still images, video, patient and study demographics). All DICOM compliant imaging studies must presently be archived on a 650 Mb recordable compact disk. This is a severe limitation for ultrasound applications where studies of 3 to 10 minutes long are a common practice. In addition, DICOM digital echocardiography objects require physiological signal indexing, content segmentation and characterization. Since DICOM 3.0 is an interchange standard only, it does not define how to database composite video objects. The goal of this research was therefore to address the issues of efficient storage, retrieval and management of DICOM compliant cardiac video studies in a distributed PACS environment. Our Web based implementation has the advantage of accommodating both DICOM defined entity-relation modules (equipment data, patient data, video format, etc.) in standard relational database tables and digital indexed video with its attributes in an object relational database. Object relational data model facilitates content indexing of full motion cardiac imaging studies through bi-directional hyperlink generation that tie searchable video attributes and related objects to individual video frames in the temporal domain. Benefits realized from use of bi-directionally hyperlinked data models in an object relational database include: (1) real time video indexing during image acquisition, (2) random access and frame accurate instant playback of previously recorded full motion imaging data, and (3) time savings from faster and more accurate access to data through multiple navigation mechanisms such as multidimensional queries on an index, queries on a hyperlink attribute, free search and browsing.

The BiolAD-DB system : an informatics system for clinical and genetic data.

PubMed

Nielsen, David A; Leidner, Marty; Haynes, Chad; Krauthammer, Michael; Kreek, Mary Jeanne

2007-01-01

The Biology of Addictive Diseases-Database (BiolAD-DB) system is a research bioinformatics system for archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password-protected BiolAD-DB SQL compliant server and database. BiolAD-DB tools further provide functionalities for generating customized reports and views. The BiolAD-DB system schema, client, and installation instructions are freely available at http://www.rockefeller.edu/biolad-db/.

The database design of LAMOST based on MYSQL/LINUX

NASA Astrophysics Data System (ADS)

Li, Hui-Xian, Sang, Jian; Wang, Sha; Luo, A.-Li

2006-03-01

The Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) will be set up in the coming years. A fully automated software system for reducing and analyzing the spectra has to be developed with the telescope. This database system is an important part of the software system. The requirements for the database of the LAMOST, the design of the LAMOST database system based on MYSQL/LINUX and performance tests of this system are described in this paper.

Identification of a New Isoindole-2-yl Scaffold as a Qo and Qi Dual Inhibitor of Cytochrome bc 1 Complex: Virtual Screening, Synthesis, and Biochemical Assay.

PubMed

Azizian, Homa; Bagherzadeh, Kowsar; Shahbazi, Sophia; Sharifi, Niusha; Amanlou, Massoud

2017-09-18

Respiratory chain ubiquinol-cytochrome (cyt) c oxidoreductase (cyt bc 1 or complex III) has been demonstrated as a promising target for numerous antibiotics and fungicide applications. In this study, a virtual screening of NCI diversity database was carried out in order to find novel Qo/Qi cyt bc 1 complex inhibitors. Structure-based virtual screening and molecular docking methodology were employed to further screen compounds with inhibition activity against cyt bc 1 complex after extensive reliability validation protocol with cross-docking method and identification of the best score functions. Subsequently, the application of rational filtering procedure over the target database resulted in the elucidation of a novel class of cyt bc 1 complex potent inhibitors with comparable binding energies and biological activities to those of the standard inhibitor, antimycin.

Kaizen newspaper

NASA Technical Reports Server (NTRS)

Shearer, Scott C. (Inventor); Proferes, John Nicholas (Inventor); Baker, Sr., Mitchell D. (Inventor); Reilly, Kenneth B. (Inventor); Tiwari, Vijai K. (Inventor)

2013-01-01

Systems, computer program products, and methods are disclosed for tracking an improvement event. An embodiment includes an event interface configured to receive a plurality of entries related to each of a plurality of improvement events. The plurality of entries includes a project identifier for the improvement event, a creation date, an objective, an action related to reaching the objective, and a first deadline related to the improvement event. A database interface is configured to store the plurality of entries in an event database.

A Gromov-Hausdorff Framework with Diffusion Geometry for Topologically-Robust Non-Rigid Shape Matching

DTIC Science & Technology

2009-02-01

topology changes. We used a subset of the TOSCA shape database , [10], consisting of four different objects: cat, dog, male, and female. Each of the...often encountered as acquisition imperfections when the shapes are acquired using a 3D scanner. We used a subset of the TOSCA shape database , consisting...object recognition, Point Based Graphics, Prague, 2007. 18 44. A. Spira and R. Kimmel, An efficient solution to the eikonal equation on parametric

Representation and Management of the Knowledge of Brittle Deformation in Shear Zones Using Microstructural Data From the SAFOD Core Samples

NASA Astrophysics Data System (ADS)

Babaie, H. A.; Broda, C. M.; Kumar, A.; Hadizadeh, J.

2010-12-01

Web access to data that represent knowledge acquired by investigators studying the microstructures in the core samples of the SAFOD (San Andreas Observatory at Depth) project can help scientists efficiently integrate and share knowledge, query the data, and update the knowledge base on the Web. To achieve this, we have used OWL (Web Ontology Language) to build the brittle deformation ontology for the microstructures observed in the SAFOD core samples, by explicitly formalizing the knowledge about deformational processes, geological objects undergoing deformation, and the underlying mechanical and environmental conditions in brittle shear zones. The developed Web-based ‘SAFOD Brittle Microstructure and Mechanics Knowledge base’ (SAFOD BM2KB), which instantiates this ontology and is available at http://codd.cs.gsu.edu:9999/safod/index.jsp, will host and serve data that pertains to spatial objects, such as microstructure, gouge, fault, and SEM image, acquired by the SAFOD investigators through the studies of the SAFOD core samples. Deformation in shear zones involves complex brittle and ductile processes that alter, create, and/or destroy a wide variety of one- to three-dimensional, multi-scale spatial entities such as rocks and their constituent minerals and structure. These processes occur through a series of sub-processes that happen in different time intervals, and affect the spatial objects at granular to regional scales within shear zones. The processes bring about qualitative change to the spatial entities over time intervals that start and end with events. Processes, such as mylonitization and cataclastic flow, change the spatial location, distribution, dimension, size, shape, and orientation of some objects through translation, rotation and strain. These processes may also result in newly formed entities, such as a new mineral, gouge, vein, or fault, during one or more phases of deformation. Deformation processes may also destroy entities, such as a mineral, fossil, or original structure. Laboratory investigations by the SAFOD scientists result in ever-increasing volumes of complex data related to different tectonic processes, deformed rocks, and structures. These data are often published in the tables of scientific articles or are stored in personal Excel worksheets or, in rare cases, in a network community database. It is extremely hard to integrate autonomously built databases distributed on the Web because of their heterogeneous schemas. As a closed world model, databases can only store and serve a finite set of static data that are known to be true. They cannot represent knowledge in a constantly changing, open world. In contrast, integration of scientific data and presentation of their underlying knowledge can be achieved through the use of Semantic Web technologies. These technologies are capable of handling an infinite supply of known and yet to be known facts due to their open world model. The inference rules of OWL and its underlying RDFS and RDF semantic languages allow formal and explicit specification of the theories and knowledge of a particular domain such as brittle deformation in shear zone.

Measuring Academic Performance for Healthcare Researchers with the H Index: Which Search Tool Should Be Used?

PubMed Central

Patel, Vanash M.; Ashrafian, Hutan; Almoudaris, Alex; Makanjuola, Jonathan; Bucciarelli-Ducci, Chiara; Darzi, Ara; Athanasiou, Thanos

2013-01-01

Objectives To compare H index scores for healthcare researchers returned by Google Scholar, Web of Science and Scopus databases, and to assess whether a researcher's age, country of institutional affiliation and physician status influences calculations. Subjects and Methods One hundred and ninety-five Nobel laureates in Physiology and Medicine from 1901 to 2009 were considered. Year of first and last publications, total publications and citation counts, and the H index for each laureate were calculated from each database. Cronbach's alpha statistics was used to measure the reliability of H index scores between the databases. Laureate characteristic influence on the H index was analysed using linear regression. Results There was no concordance between the databases when considering the number of publications and citations count per laureate. The H index was the most reliably calculated bibliometric across the three databases (Cronbach's alpha = 0.900). All databases returned significantly higher H index scores for younger laureates (p < 0.0001). Google Scholar and Web of Science returned significantly higher H index for physician laureates (p = 0.025 and p = 0.029, respectively). Country of institutional affiliation did not influence the H index in any database. Conclusion The H index appeared to be the most consistently calculated bibliometric between the databases for Nobel laureates in Physiology and Medicine. Researcher-specific characteristics constituted an important component of objective research assessment. The findings of this study call to question the choice of current and future academic performance databases. PMID:22964880

Guidelines for establishing and maintaining construction quality databases.

DOT National Transportation Integrated Search

2006-11-01

The main objective of this study was to develop and present guidelines for State highway agencies (SHAs) in establishing and maintaining database systems geared towards construction quality issues for asphalt and concrete paving projects. To accompli...

Advanced Traffic Management Systems (ATMS) research analysis database system

DOT National Transportation Integrated Search

2001-06-01

The ATMS Research Analysis Database Systems (ARADS) consists of a Traffic Software Data Dictionary (TSDD) and a Traffic Software Object Model (TSOM) for application to microscopic traffic simulation and signal optimization domains. The purpose of thi...

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.

Breach Risk Magnitude: A Quantitative Measure of Database Security.

PubMed

Yasnoff, William A

2016-01-01

A quantitative methodology is described that provides objective evaluation of the potential for health record system breaches. It assumes that breach risk increases with the number of potential records that could be exposed, while it decreases when more authentication steps are required for access. The breach risk magnitude (BRM) is the maximum value for any system user of the common logarithm of the number of accessible database records divided by the number of authentication steps needed to achieve such access. For a one million record relational database, the BRM varies from 5.52 to 6 depending on authentication protocols. For an alternative data architecture designed specifically to increase security by separately storing and encrypting each patient record, the BRM ranges from 1.3 to 2.6. While the BRM only provides a limited quantitative assessment of breach risk, it may be useful to objectively evaluate the security implications of alternative database organization approaches.

Building a genome database using an object-oriented approach.

PubMed

Barbasiewicz, Anna; Liu, Lin; Lang, B Franz; Burger, Gertraud

2002-01-01

GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

HLLV avionics requirements study and electronic filing system database development

NASA Technical Reports Server (NTRS)

1994-01-01

This final report provides a summary of achievements and activities performed under Contract NAS8-39215. The contract's objective was to explore a new way of delivering, storing, accessing, and archiving study products and information and to define top level system requirements for Heavy Lift Launch Vehicle (HLLV) avionics that incorporate Vehicle Health Management (VHM). This report includes technical objectives, methods, assumptions, recommendations, sample data, and issues as specified by DPD No. 772, DR-3. The report is organized into two major subsections, one specific to each of the two tasks defined in the Statement of Work: the Index Database Task and the HLLV Avionics Requirements Task. The Index Database Task resulted in the selection and modification of a commercial database software tool to contain the data developed during the HLLV Avionics Requirements Task. All summary information is addressed within each task's section.

The StarLite Project Prototyping Real-Time Software

DTIC Science & Technology

1991-10-01

multiversion data objects using the prototyping environment. Section 5 concludes the paper. 2. Message-Based Simulation When prototyping distributed...phase locking and priority-based synchronization algorithms, and between a multiversion database and its corresponding single-version database, through...its deadline, since the transaction is only aborted in the validation phase. 4.5. A Multiversion Database System To illustrate the effctivcness of the

Comparison of glaucoma diagnostic accuracy of macular ganglion cell complex thickness based on nonhighly myopic and highly myopic normative database

PubMed Central

Chen, Henry Shen-Lih; Liu, Chun-Hsiu; Lu, Da-Wen

2016-01-01

Background/Purpose: To evaluate and compare the diagnostic discriminative ability for detecting glaucoma in highly myopic eyes from a normative database of macular ganglion cell complex (mGCC) thickness based on nonhighly myopic and highly myopic normal eyes. Methods: Forty-nine eyes of 49 participants with high myopia (axial length ≥ 26.0 mm) were enrolled. Spectral-domain optical coherence tomography scans were done using RS-3000, and the mGCC thickness/significance maps within a 9-mm diameter circle were generated using built-in software. We compared the difference of sensitivity, specificity, and diagnostic accuracy between the nonhighly myopic database and the highly myopic database for differentiating the early glaucomatous eyes from the nonglaucomatous eyes. Results: This study enrolled 15 normal eyes and 34 eyes with glaucoma. The mean mGCC thickness of the glaucoma group was significantly less than that of the normal group (p < 0.001). Sensitivity was 96.3%, and the specificity was 50.0% when using the nonhighly myopic normative database. When the highly myopic normative database was used, the sensitivity was 88.9%, and the specificity was 90.0%. The false positive rate was significantly lower when using the highly myopic normative database (p < 0.05). Conclusion: The evaluations of glaucoma in eyes with high myopia using a nonhighly myopic normative database may lead to a frequent misdiagnosis. When evaluating glaucoma in high myopic eyes, the mGCC thickness determined by the long axial length high myopic normative database should be applied. PMID:29018704

The Protein-DNA Interface database

PubMed Central

2010-01-01

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 Å or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface. We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes. PMID:20482798

The Protein-DNA Interface database.

PubMed

Norambuena, Tomás; Melo, Francisco

2010-05-18

The Protein-DNA Interface database (PDIdb) is a repository containing relevant structural information of Protein-DNA complexes solved by X-ray crystallography and available at the Protein Data Bank. The database includes a simple functional classification of the protein-DNA complexes that consists of three hierarchical levels: Class, Type and Subtype. This classification has been defined and manually curated by humans based on the information gathered from several sources that include PDB, PubMed, CATH, SCOP and COPS. The current version of the database contains only structures with resolution of 2.5 A or higher, accounting for a total of 922 entries. The major aim of this database is to contribute to the understanding of the main rules that underlie the molecular recognition process between DNA and proteins. To this end, the database is focused on each specific atomic interface rather than on the separated binding partners. Therefore, each entry in this database consists of a single and independent protein-DNA interface.We hope that PDIdb will be useful to many researchers working in fields such as the prediction of transcription factor binding sites in DNA, the study of specificity determinants that mediate enzyme recognition events, engineering and design of new DNA binding proteins with distinct binding specificity and affinity, among others. Finally, due to its friendly and easy-to-use web interface, we hope that PDIdb will also serve educational and teaching purposes.

A multilocus database for the identification of Aspergillus and Penicillium species

USDA-ARS?s Scientific Manuscript database

Identification of Aspergillus and Penicillium isolates using phenotypic methods is increasingly complex and difficult but genetic tools allow recognition and description of species formerly unrecognized or cryptic. We constructed a web-based taxonomic database using BIGSdb for the identification of ...

Scale-Independent Relational Query Processing

DTIC Science & Technology

2013-10-04

source options are also available, including Postgresql, MySQL , and SQLite. These mod- ern relational databases are generally very complex software systems...and Their Application to Data Stream Management. IGI Global, 2010. [68] George Reese. Database Programming with JDBC and Java , Second Edition. Ed. by

A sharable cloud-based pancreaticoduodenectomy collaborative database for physicians: emphasis on security and clinical rule supporting.

PubMed

Yu, Hwan-Jeu; Lai, Hong-Shiee; Chen, Kuo-Hsin; Chou, Hsien-Cheng; Wu, Jin-Ming; Dorjgochoo, Sarangerel; Mendjargal, Adilsaikhan; Altangerel, Erdenebaatar; Tien, Yu-Wen; Hsueh, Chih-Wen; Lai, Feipei

2013-08-01

Pancreaticoduodenectomy (PD) is a major operation with high complication rate. Thereafter, patients may develop morbidity because of the complex reconstruction and loss of pancreatic parenchyma. A well-designed database is very important to address both the short-term and long-term outcomes after PD. The objective of this research was to build an international PD database implemented with security and clinical rule supporting functions, which made the data-sharing easier and improve the accuracy of data. The proposed system is a cloud-based application. To fulfill its requirements, the system comprises four subsystems: a data management subsystem, a clinical rule supporting subsystem, a short message notification subsystem, and an information security subsystem. After completing the surgery, the physicians input the data retrospectively, which are analyzed to study factors associated with post-PD common complications (delayed gastric emptying and pancreatic fistula) to validate the clinical value of this system. Currently, this database contains data from nearly 500 subjects. Five medical centers in Taiwan and two cancer centers in Mongolia are participating in this study. A data mining model of the decision tree analysis showed that elderly patients (>76 years) with pylorus-preserving PD (PPPD) have higher proportion of delayed gastric emptying. About the pancreatic fistula, the data mining model of the decision tree analysis revealed that cases with non-pancreaticogastrostomy (PG) reconstruction - body mass index (BMI)>29.65 or PG reconstruction - BMI>23.7 - non-classic PD have higher proportion of pancreatic fistula after PD. The proposed system allows medical staff to collect and store clinical data in a cloud, sharing the data with other physicians in a secure manner to achieve collaboration in research. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

A New Paradigm to Analyze Data Completeness of Patient Data

PubMed Central

Nasir, Ayan; Liu, Xinliang

2016-01-01

Summary Background There is a need to develop a tool that will measure data completeness of patient records using sophisticated statistical metrics. Patient data integrity is important in providing timely and appropriate care. Completeness is an important step, with an emphasis on understanding the complex relationships between data fields and their relative importance in delivering care. This tool will not only help understand where data problems are but also help uncover the underlying issues behind them. Objectives Develop a tool that can be used alongside a variety of health care database software packages to determine the completeness of individual patient records as well as aggregate patient records across health care centers and subpopulations. Methods The methodology of this project is encapsulated within the Data Completeness Analysis Package (DCAP) tool, with the major components including concept mapping, CSV parsing, and statistical analysis. Results The results from testing DCAP with Healthcare Cost and Utilization Project (HCUP) State Inpatient Database (SID) data show that this tool is successful in identifying relative data completeness at the patient, subpopulation, and database levels. These results also solidify a need for further analysis and call for hypothesis driven research to find underlying causes for data incompleteness. Conclusion DCAP examines patient records and generates statistics that can be used to determine the completeness of individual patient data as well as the general thoroughness of record keeping in a medical database. DCAP uses a component that is customized to the settings of the software package used for storing patient data as well as a Comma Separated Values (CSV) file parser to determine the appropriate measurements. DCAP itself is assessed through a proof of concept exercise using hypothetical data as well as available HCUP SID patient data. PMID:27484918

Development and application of biosorption database for the control of heavy metals in waste and wastewaters

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

Min, J.H.; Hering, J.G.

1996-11-01

The rapid removal and high sorption capacity for metals as well as the cost-effectiveness of biosorption makes it a promising alternative for remediation or treatment of metals in the aquatic environment. Depending on the type of biomass, the sorption capacity may vary significantly for different metals, and thus it is important to evaluate the sorption characteristics of biomass for optimal removal of metals from the wastewaters. The objective of developing a biosorption database was to use available literature data for preliminary evaluation of potential significance of biosorption. The database was developed by collecting biosorption data sets from the published literature,more » extracting raw data from the papers, and re-analyzing the data with a consistent model. The re-analysis was crucial in developing the database because of the inconsistency in sorption models and units used by various investigators. The raw data from the literature were obtained using a digitizer and fitted with a same isotherm model with consistent units, which enabled quantitative comparison between data sets under similar conditions from different sources by comparing the isotherm constants. Metal sorption by biomass can be influenced by various environmental conditions such as pH, temperature, the characteristics or composition of the solution, and the presence of other complexing ligands in the solution. Biosorption of a specific metal by a specific species or type of biomass under different conditions can be compared to evaluate the effect of each parameter and to assess the possibility of lumping constants for a general case. The general sorption parameters for similar types of biomass under similar conditions can be used in preliminary assessment of metal/biomass combination for the optimal removal or stabilization of heavy metals.« less

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

NASA Astrophysics Data System (ADS)

Mendela-Anzlik, Małgorzata; Borkowski, Andrzej

2017-06-01

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

Programming Wireless Handheld Devices for Applications in Teaching Astronomy

NASA Astrophysics Data System (ADS)

Budiardja, R.; Saranathan, V.; Guidry, M.

2002-12-01

Wireless technology implemented with handheld devices has attractive features because of the potential to access large amounts of data and the prospect of on-the-fly computational analysis from a device that can be carried in a shirt pocket. We shall describe applications of such technology to the general paradigm of making digital wireless connections from the field to upload information and queries to network servers, executing (potentially complex) data analysis and/or database operations on fast network computers, and returning real-time information from this analysis to the handheld device in the field. As illustration, we shall describe several client/server programs that we have written for applications in teaching introductory astronomy. For example, one program allows static and dynamic properties of astronomical objects to be accessed in a remote observation laboratory setting using a digital cell phone or PDA. Another implements interactive quizzing over a cell phone or PDA using a 700-question introductory astronomy quiz database, thus permitting students to study for astronomy quizzes in any environment in which they have a few free minutes and a digital cell phone or wireless PDA. The presentation will include hands-on demonstrations with real devices.

Monitoring, Analyzing and Assessing Radiation Belt Loss and Energization

NASA Astrophysics Data System (ADS)

Daglis, I. A.; Bourdarie, S.; Khotyaintsev, Y.; Santolik, O.; Horne, R.; Mann, I.; Turner, D.; Anastasiadis, A.; Angelopoulos, V.; Balasis, G.; Chatzichristou, E.; Cully, C.; Georgiou, M.; Glauert, S.; Grison, B.; Kolmasova, I.; Lazaro, D.; Macusova, E.; Maget, V.; Papadimitriou, C.; Ropokis, G.; Sandberg, I.; Usanova, M.

2012-09-01

We present the concept, objectives and expected impact of the MAARBLE (Monitoring, Analyzing and Assessing Radiation Belt Loss and Energization) project, which is being implemented by a consortium of seven institutions (five European, one Canadian and one US) with support from the European Community's Seventh Framework Programme. The MAARBLE project employs multi-spacecraft monitoring of the geospace environment, complemented by ground-based monitoring, in order to analyze and assess the physical mechanisms leading to radiation belt particle energization and loss. Particular attention is paid to the role of ULF/VLF waves. A database containing properties of the waves is being created and will be made available to the scientific community. Based on the wave database, a statistical model of the wave activity dependent on the level of geomagnetic activity, solar wind forcing, and magnetospheric region will be developed. Furthermore, we will incorporate multi-spacecraft particle measurements into data assimilation tools, aiming at a new understanding of the causal relationships between ULF/VLF waves and radiation belt dynamics. Data assimilation techniques have been proven to be a valuable tool in the field of radiation belts, able to guide 'the best' estimate of the state of a complex system.

Topologically Consistent Models for Efficient Big Geo-Spatio Data Distribution

NASA Astrophysics Data System (ADS)

Jahn, M. W.; Bradley, P. E.; Doori, M. Al; Breunig, M.

2017-10-01

Geo-spatio-temporal topology models are likely to become a key concept to check the consistency of 3D (spatial space) and 4D (spatial + temporal space) models for emerging GIS applications such as subsurface reservoir modelling or the simulation of energy and water supply of mega or smart cities. Furthermore, the data management for complex models consisting of big geo-spatial data is a challenge for GIS and geo-database research. General challenges, concepts, and techniques of big geo-spatial data management are presented. In this paper we introduce a sound mathematical approach for a topologically consistent geo-spatio-temporal model based on the concept of the incidence graph. We redesign DB4GeO, our service-based geo-spatio-temporal database architecture, on the way to the parallel management of massive geo-spatial data. Approaches for a new geo-spatio-temporal and object model of DB4GeO meeting the requirements of big geo-spatial data are discussed in detail. Finally, a conclusion and outlook on our future research are given on the way to support the processing of geo-analytics and -simulations in a parallel and distributed system environment.

Initial experiences with building a health care infrastructure based on Java and object-oriented database technology.

PubMed

Dionisio, J D; Sinha, U; Dai, B; Johnson, D B; Taira, R K

1999-01-01

A multi-tiered telemedicine system based on Java and object-oriented database technology has yielded a number of practical insights and experiences on their effectiveness and suitability as implementation bases for a health care infrastructure. The advantages and drawbacks to their use, as seen within the context of the telemedicine system's development, are discussed. Overall, these technologies deliver on their early promise, with a few remaining issues that are due primarily to their relative newness.

Different Success Rates and Associated Factors at Three Levels of Career Progression Among US Marine Corps Officers

DTIC Science & Technology

1993-09-01

establish a database of sufficient proportions to track Marine Corps officer career success from accession to the grade of 0-4. 12 "* To profile the...OBJECTIVES Accordingly, this study had three objectives. First, to establish a database of sufficient proportions to track Marine Corps officer career ... success from accession to the grade of 0-4. Second, to profile the successful Marine officer; that is, to determine what variables are associated with

Heterogenous database integration in a physician workstation.

PubMed

Annevelink, J; Young, C Y; Tang, P C

1991-01-01

We discuss the integration of a variety of data and information sources in a Physician Workstation (PWS), focusing on the integration of data from DHCP, the Veteran Administration's Distributed Hospital Computer Program. We designed a logically centralized, object-oriented data-schema, used by end users and applications to explore the data accessible through an object-oriented database using a declarative query language. We emphasize the use of procedural abstraction to transparently integrate a variety of information sources into the data schema.

Heterogenous database integration in a physician workstation.

PubMed Central

Annevelink, J.; Young, C. Y.; Tang, P. C.

1991-01-01

We discuss the integration of a variety of data and information sources in a Physician Workstation (PWS), focusing on the integration of data from DHCP, the Veteran Administration's Distributed Hospital Computer Program. We designed a logically centralized, object-oriented data-schema, used by end users and applications to explore the data accessible through an object-oriented database using a declarative query language. We emphasize the use of procedural abstraction to transparently integrate a variety of information sources into the data schema. PMID:1807624

Emotional Picture and Word Processing: An fMRI Study on Effects of Stimulus Complexity

PubMed Central

Schlochtermeier, Lorna H.; Kuchinke, Lars; Pehrs, Corinna; Urton, Karolina; Kappelhoff, Hermann; Jacobs, Arthur M.

2013-01-01

Neuroscientific investigations regarding aspects of emotional experiences usually focus on one stimulus modality (e.g., pictorial or verbal). Similarities and differences in the processing between the different modalities have rarely been studied directly. The comparison of verbal and pictorial emotional stimuli often reveals a processing advantage of emotional pictures in terms of larger or more pronounced emotion effects evoked by pictorial stimuli. In this study, we examined whether this picture advantage refers to general processing differences or whether it might partly be attributed to differences in visual complexity between pictures and words. We first developed a new stimulus database comprising valence and arousal ratings for more than 200 concrete objects representable in different modalities including different levels of complexity: words, phrases, pictograms, and photographs. Using fMRI we then studied the neural correlates of the processing of these emotional stimuli in a valence judgment task, in which the stimulus material was controlled for differences in emotional arousal. No superiority for the pictorial stimuli was found in terms of emotional information processing with differences between modalities being revealed mainly in perceptual processing regions. While visual complexity might partly account for previously found differences in emotional stimulus processing, the main existing processing differences are probably due to enhanced processing in modality specific perceptual regions. We would suggest that both pictures and words elicit emotional responses with no general superiority for either stimulus modality, while emotional responses to pictures are modulated by perceptual stimulus features, such as picture complexity. PMID:23409009

[The design and implementation of the web typical surface object spectral information system in arid areas based on .NET and SuperMap].

PubMed

Xia, Jun; Tashpolat, Tiyip; Zhang, Fei; Ji, Hong-jiang

2011-07-01

The characteristic of object spectrum is not only the base of the quantification analysis of remote sensing, but also the main content of the basic research of remote sensing. The typical surface object spectral database in arid areas oasis is of great significance for applied research on remote sensing in soil salinization. In the present paper, the authors took the Ugan-Kuqa River Delta Oasis as an example, unified .NET and the SuperMap platform with SQL Server database stored data, used the B/S pattern and the C# language to design and develop the typical surface object spectral information system, and established the typical surface object spectral database according to the characteristics of arid areas oasis. The system implemented the classified storage and the management of typical surface object spectral information and the related attribute data of the study areas; this system also implemented visualized two-way query between the maps and attribute data, the drawings of the surface object spectral response curves and the processing of the derivative spectral data and its drawings. In addition, the system initially possessed a simple spectral data mining and analysis capabilities, and this advantage provided an efficient, reliable and convenient data management and application platform for the Ugan-Kuqa River Delta Oasis's follow-up study in soil salinization. Finally, It's easy to maintain, convinient for secondary development and practically operating in good condition.

Towards building a team of intelligent robots

NASA Technical Reports Server (NTRS)

Varanasi, Murali R.; Mehrotra, R.

1987-01-01

Topics addressed include: collision-free motion planning of multiple robot arms; two-dimensional object recognition; and pictorial databases (storage and sharing of the representations of three-dimensional objects).

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.

Modeling Powered Aerodynamics for the Orion Launch Abort Vehicle Aerodynamic Database

NASA Technical Reports Server (NTRS)

Chan, David T.; Walker, Eric L.; Robinson, Philip E.; Wilson, Thomas M.

2011-01-01

Modeling the aerodynamics of the Orion Launch Abort Vehicle (LAV) has presented many technical challenges to the developers of the Orion aerodynamic database. During a launch abort event, the aerodynamic environment around the LAV is very complex as multiple solid rocket plumes interact with each other and the vehicle. It is further complicated by vehicle separation events such as between the LAV and the launch vehicle stack or between the launch abort tower and the crew module. The aerodynamic database for the LAV was developed mainly from wind tunnel tests involving powered jet simulations of the rocket exhaust plumes, supported by computational fluid dynamic simulations. However, limitations in both methods have made it difficult to properly capture the aerodynamics of the LAV in experimental and numerical simulations. These limitations have also influenced decisions regarding the modeling and structure of the aerodynamic database for the LAV and led to compromises and creative solutions. Two database modeling approaches are presented in this paper (incremental aerodynamics and total aerodynamics), with examples showing strengths and weaknesses of each approach. In addition, the unique problems presented to the database developers by the large data space required for modeling a launch abort event illustrate the complexities of working with multi-dimensional data.

Complexity-entropy causality plane: A useful approach for distinguishing songs

NASA Astrophysics Data System (ADS)

Ribeiro, Haroldo V.; Zunino, Luciano; Mendes, Renio S.; Lenzi, Ervin K.

2012-04-01

Nowadays we are often faced with huge databases resulting from the rapid growth of data storage technologies. This is particularly true when dealing with music databases. In this context, it is essential to have techniques and tools able to discriminate properties from these massive sets. In this work, we report on a statistical analysis of more than ten thousand songs aiming to obtain a complexity hierarchy. Our approach is based on the estimation of the permutation entropy combined with an intensive complexity measure, building up the complexity-entropy causality plane. The results obtained indicate that this representation space is very promising to discriminate songs as well as to allow a relative quantitative comparison among songs. Additionally, we believe that the here-reported method may be applied in practical situations since it is simple, robust and has a fast numerical implementation.

The Starlite Project

DTIC Science & Technology

1990-09-01

conflicts. The current prototyping tool also provides a multiversion data object control mechanism. From a series of experiments, we found that the...performance of a multiversion distributed database system is quite sensitive to the size of read-sets and write-sets of transactions. A multiversion database...510-512. (18) Son, S. H. and N. Haghighi, "Performance Evaluation of Multiversion Database Systems," Sixth IEEE International Conference on Data

Introduction to the enhanced logistics intratheater support tool (ELIST) mission application and its segments : global data segment version 8.1.0.0, database instance segment version 8.1.0.0, database fill segment version 8.1.0.0, database segment versio

DOT National Transportation Integrated Search

2002-02-26

This document, the Introduction to the Enhanced Logistics Intratheater Support Tool (ELIST) Mission Application and its Segments, satisfies the following objectives: : It identifies the mission application, known in brief as ELIST, and all seven ...

A Database Management System for Interlibrary Loan.

ERIC Educational Resources Information Center

Chang, Amy

1990-01-01

Discusses the increasing complexity of dealing with interlibrary loan requests and describes a database management system for interlibrary loans used at Texas Tech University. System functions are described, including file control, records maintenance, and report generation, and the impact on staff productivity is discussed. (CLB)

Modis, SeaWIFS, and Pathfinder funded activities

NASA Technical Reports Server (NTRS)

Evans, Robert H.

1995-01-01

MODIS (Moderate Resolution Imaging Spectrometer), SeaWIFS (Sea-viewing Wide Field Sensor), Pathfinder, and DSP (Digital Signal Processor) objectives are summarized. An overview of current progress is given for the automatic processing database, client/server status, matchup database, and DSP support.

A study of the Immune Epitope Database for some fungi species using network topological indices.

PubMed

Vázquez-Prieto, Severo; Paniagua, Esperanza; Solana, Hugo; Ubeira, Florencio M; González-Díaz, Humberto

2017-08-01

In the last years, the encryption of system structure information with different network topological indices has been a very active field of research. In the present study, we assembled for the first time a complex network using data obtained from the Immune Epitope Database for fungi species, and we then considered the general topology, the node degree distribution, and the local structure of this network. We also calculated eight node centrality measures for the observed network and compared it with three theoretical models. In view of the results obtained, we may expect that the present approach can become a valuable tool to explore the complexity of this database, as well as for the storage, manipulation, comparison, and retrieval of information contained therein.

[Concordance in the registry of dementia among the main sources of clinical information].

PubMed

Marta-Moreno, Javier; Obón-Azuara, Blanca; Gimeno-Felíu, Luis; Achkar-Tuglaman, Nesib Nicolás; Poblador-Plou, Beatriz; Calderón-Larrañaga, Amaia; Prados-Torres, Alexandra

2016-01-01

The objective of this work was to analyse the concordance in the registry of dementia among the main sources of clinical information, with the aim of determining their usefulness for epidemiological and clinical research. Descriptive study of patients assigned to the Aragon Health Service in 2010 (n=1,344,891). (i)the pharmacy billing database (n=9,392); (ii)Primary Care electronic health records (EHR) (n=9,471), and (iii)the hospital minimum basic data set (n=3,289). When studying the concordance of the databases, the group of patients with a specific treatment for dementia (i.e., acetylcholinesterase inhibitors and/or memantine) was taken as the reference. The diagnosis in Primary Care was missing for 47.3% of patients taking anti-dementia drugs. The same occurred with 38.3% of dementia patients admitted to hospital during the study year. Among patients with a diagnosis of dementia in the EHR, only half (52.3%) was under treatment for this condition. This percentage decreased to 34.4% in patients with the diagnosis registered in the hospital database. The weak concordance in the registry of the dementia diagnosis between the main health information systems makes their use and analysis more complex, and supports the need to include all available health data sources in order to gain a global picture of the epidemiological and clinical reality of this health condition. Copyright © 2015 SEGG. Publicado por Elsevier España, S.L.U. All rights reserved.

BIOSPIDA: A Relational Database Translator for NCBI.

PubMed

Hagen, Matthew S; Lee, Eva K

2010-11-13

As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time.

NRA8-21 Cycle 2 RBCC Turbopump Risk Reduction

NASA Technical Reports Server (NTRS)

Ferguson, Thomas V.; Williams, Morgan; Marcu, Bogdan

2004-01-01

This project was composed of three sub-tasks. The objective of the first task was to use the CFD code INS3D to generate both on- and off-design predictions for the consortium optimized impeller flowfield. The results of the flow simulations are given in the first section. The objective of the second task was to construct a turbomachinery testing database comprised of measurements made on several different impellers, an inducer and a diffuser. The data was in the form of static pressure measurements as well as laser velocimeter measurements of velocities and flow angles within the stated components. Several databases with this information were created for these components. The third subtask objective was two-fold: first, to validate the Enigma CFD code for pump diffuser analysis, and secondly, to perform steady and unsteady analyses on some wide flow range diffuser concepts using Enigma. The code was validated using the consortium optimized impeller database and then applied to two different concepts for wide flow diffusers.

Indexing and retrieving point and region objects

NASA Astrophysics Data System (ADS)

Ibrahim, Azzam T.; Fotouhi, Farshad A.

1996-03-01

R-tree and its variants are examples of spatial data structures for paged-secondary memory. To process a query, these structures require multiple path traversals. In this paper, we present a new image access method, SB+-tree which requires a single path traversal to process a query. Also, SB+-tree will allow commercial databases an access method for spatial objects without a major change, since most commercial databases already support B+-tree as an access method for text data. The SB+-tree can be used for zero and non-zero size data objects. Non-zero size objects are approximated by their minimum bounding rectangles (MBRs). The number of SB+-trees generated is dependent upon the number of dimensions of the approximation of the object. The structure supports efficient spatial operations such as regions-overlap, distance and direction. In this paper, we experimentally and analytically demonstrate the superiority of SB+-tree over R-tree.

COMET Multimedia modules and objects in the digital library system

NASA Astrophysics Data System (ADS)

Spangler, T. C.; Lamos, J. P.

2003-12-01

Over the past ten years of developing Web- and CD-ROM-based training materials, the Cooperative Program for Operational Meteorology, Education and Training (COMET) has created a unique archive of almost 10,000 multimedia objects and some 50 web based interactive multimedia modules on various aspects of weather and weather forecasting. These objects and modules, containing illustrations, photographs, animations,video sequences, audio files, are potentially a valuable resource for university faculty and students, forecasters, emergency managers, public school educators, and other individuals and groups needing such materials for educational use. The COMET Modules are available on the COMET educational web site http://www.meted.ucar.edu, and the COMET Multimedia Database (MMDB) makes a collection of the multimedia objects available in a searchable online database for viewing and download over the Internet. Some 3200 objects are already available at the MMDB Website: http://archive.comet.ucar.edu/moria/

Automated Agatston score computation in non-ECG gated CT scans using deep learning

NASA Astrophysics Data System (ADS)

Cano-Espinosa, Carlos; González, Germán.; Washko, George R.; Cazorla, Miguel; San José Estépar, Raúl

2018-03-01

Introduction: The Agatston score is a well-established metric of cardiovascular disease related to clinical outcomes. It is computed from CT scans by a) measuring the volume and intensity of the atherosclerotic plaques and b) aggregating such information in an index. Objective: To generate a convolutional neural network that inputs a non-contrast chest CT scan and outputs the Agatston score associated with it directly, without a prior segmentation of Coronary Artery Calcifications (CAC). Materials and methods: We use a database of 5973 non-contrast non-ECG gated chest CT scans where the Agatston score has been manually computed. The heart of each scan is cropped automatically using an object detector. The database is split in 4973 cases for training and 1000 for testing. We train a 3D deep convolutional neural network to regress the Agatston score directly from the extracted hearts. Results: The proposed method yields a Pearson correlation coefficient of r = 0.93; p <= 0.0001 against manual reference standard in the 1000 test cases. It further stratifies correctly 72.6% of the cases with respect to standard risk groups. This compares to more complex state-of-the-art methods based on prior segmentations of the CACs, which achieve r = 0.94 in ECG-gated pulmonary CT. Conclusions: A convolutional neural network can regress the Agatston score from the image of the heart directly, without a prior segmentation of the CACs. This is a new and simpler paradigm in the Agatston score computation that yields similar results to the state-of-the-art literature.

Space Situational Awareness Data Processing Scalability Utilizing Google Cloud Services

NASA Astrophysics Data System (ADS)

Greenly, D.; Duncan, M.; Wysack, J.; Flores, F.

Space Situational Awareness (SSA) is a fundamental and critical component of current space operations. The term SSA encompasses the awareness, understanding and predictability of all objects in space. As the population of orbital space objects and debris increases, the number of collision avoidance maneuvers grows and prompts the need for accurate and timely process measures. The SSA mission continually evolves to near real-time assessment and analysis demanding the need for higher processing capabilities. By conventional methods, meeting these demands requires the integration of new hardware to keep pace with the growing complexity of maneuver planning algorithms. SpaceNav has implemented a highly scalable architecture that will track satellites and debris by utilizing powerful virtual machines on the Google Cloud Platform. SpaceNav algorithms for processing CDMs outpace conventional means. A robust processing environment for tracking data, collision avoidance maneuvers and various other aspects of SSA can be created and deleted on demand. Migrating SpaceNav tools and algorithms into the Google Cloud Platform will be discussed and the trials and tribulations involved. Information will be shared on how and why certain cloud products were used as well as integration techniques that were implemented. Key items to be presented are: 1.Scientific algorithms and SpaceNav tools integrated into a scalable architecture a) Maneuver Planning b) Parallel Processing c) Monte Carlo Simulations d) Optimization Algorithms e) SW Application Development/Integration into the Google Cloud Platform 2. Compute Engine Processing a) Application Engine Automated Processing b) Performance testing and Performance Scalability c) Cloud MySQL databases and Database Scalability d) Cloud Data Storage e) Redundancy and Availability

Job attitudes, job satisfaction, and job affect: A century of continuity and of change.

PubMed

Judge, Timothy A; Weiss, Howard M; Kammeyer-Mueller, John D; Hulin, Charles L

2017-03-01

Over the past 100 years, research on job attitudes has improved in the sophistication of methods and in the productive use of theory as a basis for fundamental research into questions of work psychology. Early research incorporated a diversity of methods for measuring potential predictors and outcomes of job attitudes. Over time, methods for statistically assessing these relationships became more rigorous, but the field also became narrower. In recent years, developments in theory and methodology have reinvigorated research, which now addresses a rich panoply of topics related to the daily flow of affect, the complexity of personal motives and dispositions, and the complex interplay of attitude objects and motivation in shaping behavior. Despite these apparent changes, a review of the concepts and substantive arguments that underpin this literature have remained remarkably consistent. We conclude by discussing how we expect that these major themes will be addressed in the future, emphasizing topics that have proven to be enduring guides for understanding the ways that people construe and react to their appraisals of their work. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Mobile health solutions for the aging population: A systematic narrative analysis.

PubMed

Kruse, Clemens Scott; Mileski, Michael; Moreno, Joshua

2017-05-01

Introduction The ubiquitous nature of mobile technology coupled with the acceptance of mobile health (mHealth) among the elderly offers an opportunity to augment the existing medical workforce in long-term care. The objective of this review and narrative analysis is to identify and analyse facilitators and barriers to adoption of mHealth for the elderly. Methods Studies over the last year were identified in multiple database indices, and three reviewers examined abstracts ( k = 0.82) and analysed articles for themes which were tallied in affinity diagrams to identify frequency of occurrence in the literature (n = 36). Results The three facilitators mentioned most often were independence (18%), understanding (13%), and visibility (13%). The three barriers mentioned most often were complexity (21%), limited by users (12%) and ineffective (12%). Discussion and conclusions The reviewers concluded that the work done so far illustrates that mHealth enables a perception of independence. Future research should focus on the barriers of complexity of technology and improving existing medical literacy in order to facilitate further adoption.

Mobile object retrieval in server-based image databases

NASA Astrophysics Data System (ADS)

Manger, D.; Pagel, F.; Widak, H.

2013-05-01

The increasing number of mobile phones equipped with powerful cameras leads to huge collections of user-generated images. To utilize the information of the images on site, image retrieval systems are becoming more and more popular to search for similar objects in an own image database. As the computational performance and the memory capacity of mobile devices are constantly increasing, this search can often be performed on the device itself. This is feasible, for example, if the images are represented with global image features or if the search is done using EXIF or textual metadata. However, for larger image databases, if multiple users are meant to contribute to a growing image database or if powerful content-based image retrieval methods with local features are required, a server-based image retrieval backend is needed. In this work, we present a content-based image retrieval system with a client server architecture working with local features. On the server side, the scalability to large image databases is addressed with the popular bag-of-word model with state-of-the-art extensions. The client end of the system focuses on a lightweight user interface presenting the most similar images of the database highlighting the visual information which is common with the query image. Additionally, new images can be added to the database making it a powerful and interactive tool for mobile contentbased image retrieval.

Introducing ab initio based neural networks for transition-rate prediction in kinetic Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär

2017-02-01

The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.

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

Karp, Peter D.

Pathway Tools is a systems-biology software package written by SRI International (SRI) that produces Pathway/Genome Databases (PGDBs) for organisms with a sequenced genome. Pathway Tools also provides a wide range of capabilities for analyzing predicted metabolic networks and user-generated omics data. More than 5,000 academic, industrial, and government groups have licensed Pathway Tools. This user community includes researchers at all three DOE bioenergy centers, as well as academic and industrial metabolic engineering (ME) groups. An integral part of the Pathway Tools software is MetaCyc, a large, multiorganism database of metabolic pathways and enzymes that SRI and its academic collaborators manuallymore » curate. This project included two main goals: I. Enhance the MetaCyc content of bioenergy-related enzymes and pathways. II. Develop computational tools for engineering metabolic pathways that satisfy specified design goals, in particular for bioenergy-related pathways. In part I, SRI proposed to significantly expand the coverage of bioenergy-related metabolic information in MetaCyc, followed by the generation of organism-specific PGDBs for all energy-relevant organisms sequenced at the DOE Joint Genome Institute (JGI). Part I objectives included: 1: Expand the content of MetaCyc to include bioenergy-related enzymes and pathways. 2: Enhance the Pathway Tools software to enable display of complex polymer degradation processes. 3: Create new PGDBs for the energy-related organisms sequenced by JGI, update existing PGDBs with new MetaCyc content, and make these data available to JBEI via the BioCyc website. In part II, SRI proposed to develop an efficient computational tool for the engineering of metabolic pathways. Part II objectives included: 4: Develop computational tools for generating metabolic pathways that satisfy specified design goals, enabling users to specify parameters such as starting and ending compounds, and preferred or disallowed intermediate compounds. The pathways were to be generated using metabolic reactions from a reference database (DB). 5: Develop computational tools for ranking the pathways generated in objective (4) according to their optimality. The ranking criteria include stoichiometric yield, the number and cost of additional inputs and the cofactor compounds required by the pathway, pathway length, and pathway energetics. 6: Develop tools for visualizing generated pathways to facilitate the evaluation of a large space of generated pathways.« less

Navigating spatial and temporal complexity in developing a long-term land use database for an agricultural watershed

USDA-ARS?s Scientific Manuscript database

No comprehensive protocols exist for the collection, standardization, and storage of agronomic management information into a database that preserves privacy, maintains data uncertainty, and translates everyday decisions into quantitative values. This manuscript describes the development of a databas...

Paramount Refinery, Paramount, California; Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Task-Driven Dynamic Text Summarization

ERIC Educational Resources Information Center

Workman, Terri Elizabeth

2011-01-01

The objective of this work is to examine the efficacy of natural language processing (NLP) in summarizing bibliographic text for multiple purposes. Researchers have noted the accelerating growth of bibliographic databases. Information seekers using traditional information retrieval techniques when searching large bibliographic databases are often…

Louisiana Pacific, Tomahawk, Wisconsin; Petition for Objection to Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Petition to Object to Yarnell Mining Company's Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

El Dorado Energy, LLC; Order Denying Petition for Objection to Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Petition to Object to Edwardsport Generating Station Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Enhancing SAMOS Data Access in DOMS via a Neo4j Property Graph Database.

NASA Astrophysics Data System (ADS)

Stallard, A. P.; Smith, S. R.; Elya, J. L.

2016-12-01

The Shipboard Automated Meteorological and Oceanographic System (SAMOS) initiative provides routine access to high-quality marine meteorological and near-surface oceanographic observations from research vessels. The Distributed Oceanographic Match-Up Service (DOMS) under development is a centralized service that allows researchers to easily match in situ and satellite oceanographic data from distributed sources to facilitate satellite calibration, validation, and retrieval algorithm development. The service currently uses Apache Solr as a backend search engine on each node in the distributed network. While Solr is a high-performance solution that facilitates creation and maintenance of indexed data, it is limited in the sense that its schema is fixed. The property graph model escapes this limitation by creating relationships between data objects. The authors will present the development of the SAMOS Neo4j property graph database including new search possibilities that take advantage of the property graph model, performance comparisons with Apache Solr, and a vision for graph databases as a storage tool for oceanographic data. The integration of the SAMOS Neo4j graph into DOMS will also be described. Currently, Neo4j contains spatial and temporal records from SAMOS which are modeled into a time tree and r-tree using Graph Aware and Spatial plugin tools for Neo4j. These extensions provide callable Java procedures within CYPHER (Neo4j's query language) that generate in-graph structures. Once generated, these structures can be queried using procedures from these libraries, or directly via CYPHER statements. Neo4j excels at performing relationship and path-based queries, which challenge relational-SQL databases because they require memory intensive joins due to the limitation of their design. Consider a user who wants to find records over several years, but only for specific months. If a traditional database only stores timestamps, this type of query would be complex and likely prohibitively slow. Using the time tree model, one can specify a path from the root to the data which restricts resolutions to certain timeframes (e.g., months). This query can be executed without joins, unions, or other compute-intensive operations, putting Neo4j at a computational advantage to the SQL database alternative.

An Information System for European culture collections: the way forward.

PubMed

Casaregola, Serge; Vasilenko, Alexander; Romano, Paolo; Robert, Vincent; Ozerskaya, Svetlana; Kopf, Anna; Glöckner, Frank O; Smith, David

2016-01-01

Culture collections contain indispensable information about the microorganisms preserved in their repositories, such as taxonomical descriptions, origins, physiological and biochemical characteristics, bibliographic references, etc. However, information currently accessible in databases rarely adheres to common standard protocols. The resultant heterogeneity between culture collections, in terms of both content and format, notably hampers microorganism-based research and development (R&D). The optimized exploitation of these resources thus requires standardized, and simplified, access to the associated information. To this end, and in the interest of supporting R&D in the fields of agriculture, health and biotechnology, a pan-European distributed research infrastructure, MIRRI, including over 40 public culture collections and research institutes from 19 European countries, was established. A prime objective of MIRRI is to unite and provide universal access to the fragmented, and untapped, resources, information and expertise available in European public collections of microorganisms; a key component of which is to develop a dynamic Information System. For the first time, both culture collection curators as well as their users have been consulted and their feedback, concerning the needs and requirements for collection databases and data accessibility, utilised. Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible. Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently. Moreover, complex searches are rarely possible in online databases thus limiting the extent of search queries. Curators also consider that overall harmonization-including Standard Operating Procedures, data structure, and software tools-is necessary to facilitate their work and to make high-quality data easily accessible to their users. Clearly, the needs of culture collection curators coincide with those of users on the crucial point of database interoperability. In this regard, and in order to design an appropriate Information System, important aspects on which the culture collection community should focus include: the interoperability of data sets with the ontologies to be used; setting best practice in data management, and the definition of an appropriate data standard.

Automatic image database generation from CAD for 3D object recognition

NASA Astrophysics Data System (ADS)

Sardana, Harish K.; Daemi, Mohammad F.; Ibrahim, Mohammad K.

1993-06-01

The development and evaluation of Multiple-View 3-D object recognition systems is based on a large set of model images. Due to the various advantages of using CAD, it is becoming more and more practical to use existing CAD data in computer vision systems. Current PC- level CAD systems are capable of providing physical image modelling and rendering involving positional variations in cameras, light sources etc. We have formulated a modular scheme for automatic generation of various aspects (views) of the objects in a model based 3-D object recognition system. These views are generated at desired orientations on the unit Gaussian sphere. With a suitable network file sharing system (NFS), the images can directly be stored on a database located on a file server. This paper presents the image modelling solutions using CAD in relation to multiple-view approach. Our modular scheme for data conversion and automatic image database storage for such a system is discussed. We have used this approach in 3-D polyhedron recognition. An overview of the results, advantages and limitations of using CAD data and conclusions using such as scheme are also presented.

Project Integration Architecture

NASA Technical Reports Server (NTRS)

Jones, William Henry

2008-01-01

The Project Integration Architecture (PIA) is a distributed, object-oriented, conceptual, software framework for the generation, organization, publication, integration, and consumption of all information involved in any complex technological process in a manner that is intelligible to both computers and humans. In the development of PIA, it was recognized that in order to provide a single computational environment in which all information associated with any given complex technological process could be viewed, reviewed, manipulated, and shared, it is necessary to formulate all the elements of such a process on the most fundamental level. In this formulation, any such element is regarded as being composed of any or all of three parts: input information, some transformation of that input information, and some useful output information. Another fundamental principle of PIA is the assumption that no consumer of information, whether human or computer, can be assumed to have any useful foreknowledge of an element presented to it. Consequently, a PIA-compliant computing system is required to be ready to respond to any questions, posed by the consumer, concerning the nature of the proffered element. In colloquial terms, a PIA-compliant system must be prepared to provide all the information needed to place the element in context. To satisfy this requirement, PIA extends the previously established object-oriented- programming concept of self-revelation and applies it on a grand scale. To enable pervasive use of self-revelation, PIA exploits another previously established object-oriented-programming concept - that of semantic infusion through class derivation. By means of self-revelation and semantic infusion through class derivation, a consumer of information can inquire about the contents of all information entities (e.g., databases and software) and can interact appropriately with those entities. Other key features of PIA are listed.

VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1992-01-01

One of biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental database access method, VIEWCACHE, provides such an interface for accessing distributed data sets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image data sets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate distributed database search.

HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors

National Institute of Standards and Technology Data Gateway

SRD 155 HIV Structural Database using Chem BLAST for all classes of AIDS inhibitors (Web, free access)   The HIV structural database (HIVSDB) is a comprehensive collection of the structures of HIV protease, both of unliganded enzyme and of its inhibitor complexes. It contains abstracts and crystallographic data such as inhibitor and protein coordinates for 248 data sets, of which only 141 are from the Protein Data Bank (PDB).

Direct numerical simulations of on-demand vortex generators: Mathematical formulation

NASA Technical Reports Server (NTRS)

Koumoutsakos, Petros

1994-01-01

The objective of the present research is the development and application of efficient adaptive numerical algorithms for the study, via direct numerical simulations, of active vortex generators. We are using innovative computational schemes to investigate flows past complex configurations undergoing arbitrary motions. Some of the questions we try to answer are: Can and how may we control the dynamics of the wake? What is the importance of body shape and motion in the active control of the flow? What is the effect of three-dimensionality in laboratory experiments? We are interested not only in coupling our results to ongoing, related experimental work, but furthermore to develop an extensive database relating the above mechanisms to the vortical wake structures with the long-range objective of developing feedback control mechanisms. This technology is very important to aircraft, ship, automotive, and other industries that require predictive capability for fluid mechanical problems. The results would have an impact in high angle of attack aerodynamics and help design ways to improve the efficiency of ships and submarines (maneuverability, vortex induced vibration, and noise).

Financial capacity in dementia: a systematic review.

PubMed

Sudo, Felipe Kenji; Laks, Jerson

2017-07-01

Financial capacity (FC) refers to a set of cognitively mediated abilities related to one's competency to manage propriety and income. Identifying intact from impaired FC in older persons with dementia is a growing concern in geriatric practice, but the best methods to assess this function still need to be determined. This study aims to review data on FC in dementia and on instruments used to assess this domain of capacity. Database search was performed in Medline, ISI Web of Knowledge, LILACS and PsycINFO. Studies that objectively assessed FC in dementia of any etiology were included. Of a total of 125 articles, 10 were included. Mild Alzheimer's Disease (AD) was associated with impaired complex FC abilities, namely checkbook management, bank statement management and financial judgment, but simple FC skills were preserved. Moderate AD was associated with impairment in all domains of FC. The Financial Capacity Instrument (FCI) was applied in most of the selected studies and correlated with neuropsychological and neuroimaging variables. Early dementia is associated with partially preserved FC. More validation studies using objective and evidence-based FC assessment tools, such as the FCI, are still needed.

Direct numerical simulations of on-demand vortex generators: Mathematical formulation

NASA Astrophysics Data System (ADS)

Koumoutsakos, Petros

1994-12-01

The objective of the present research is the development and application of efficient adaptive numerical algorithms for the study, via direct numerical simulations, of active vortex generators. We are using innovative computational schemes to investigate flows past complex configurations undergoing arbitrary motions. Some of the questions we try to answer are: Can and how may we control the dynamics of the wake? What is the importance of body shape and motion in the active control of the flow? What is the effect of three-dimensionality in laboratory experiments? We are interested not only in coupling our results to ongoing, related experimental work, but furthermore to develop an extensive database relating the above mechanisms to the vortical wake structures with the long-range objective of developing feedback control mechanisms. This technology is very important to aircraft, ship, automotive, and other industries that require predictive capability for fluid mechanical problems. The results would have an impact in high angle of attack aerodynamics and help design ways to improve the efficiency of ships and submarines (maneuverability, vortex induced vibration, and noise).

An alternative database approach for management of SNOMED CT and improved patient data queries.

PubMed

Campbell, W Scott; Pedersen, Jay; McClay, James C; Rao, Praveen; Bastola, Dhundy; Campbell, James R

2015-10-01

SNOMED CT is the international lingua franca of terminologies for human health. Based in Description Logics (DL), the terminology enables data queries that incorporate inferences between data elements, as well as, those relationships that are explicitly stated. However, the ontologic and polyhierarchical nature of the SNOMED CT concept model make it difficult to implement in its entirety within electronic health record systems that largely employ object oriented or relational database architectures. The result is a reduction of data richness, limitations of query capability and increased systems overhead. The hypothesis of this research was that a graph database (graph DB) architecture using SNOMED CT as the basis for the data model and subsequently modeling patient data upon the semantic core of SNOMED CT could exploit the full value of the terminology to enrich and support advanced data querying capability of patient data sets. The hypothesis was tested by instantiating a graph DB with the fully classified SNOMED CT concept model. The graph DB instance was tested for integrity by calculating the transitive closure table for the SNOMED CT hierarchy and comparing the results with transitive closure tables created using current, validated methods. The graph DB was then populated with 461,171 anonymized patient record fragments and over 2.1 million associated SNOMED CT clinical findings. Queries, including concept negation and disjunction, were then run against the graph database and an enterprise Oracle relational database (RDBMS) of the same patient data sets. The graph DB was then populated with laboratory data encoded using LOINC, as well as, medication data encoded with RxNorm and complex queries performed using LOINC, RxNorm and SNOMED CT to identify uniquely described patient populations. A graph database instance was successfully created for two international releases of SNOMED CT and two US SNOMED CT editions. Transitive closure tables and descriptive statistics generated using the graph database were identical to those using validated methods. Patient queries produced identical patient count results to the Oracle RDBMS with comparable times. Database queries involving defining attributes of SNOMED CT concepts were possible with the graph DB. The same queries could not be directly performed with the Oracle RDBMS representation of the patient data and required the creation and use of external terminology services. Further, queries of undefined depth were successful in identifying unknown relationships between patient cohorts. The results of this study supported the hypothesis that a patient database built upon and around the semantic model of SNOMED CT was possible. The model supported queries that leveraged all aspects of the SNOMED CT logical model to produce clinically relevant query results. Logical disjunction and negation queries were possible using the data model, as well as, queries that extended beyond the structural IS_A hierarchy of SNOMED CT to include queries that employed defining attribute-values of SNOMED CT concepts as search parameters. As medical terminologies, such as SNOMED CT, continue to expand, they will become more complex and model consistency will be more difficult to assure. Simultaneously, consumers of data will increasingly demand improvements to query functionality to accommodate additional granularity of clinical concepts without sacrificing speed. This new line of research provides an alternative approach to instantiating and querying patient data represented using advanced computable clinical terminologies. Copyright © 2015 Elsevier Inc. All rights reserved.

Database of amino acid-nucleotide contacts in contacts in DNA-homeodomain protein

NASA Astrophysics Data System (ADS)

Grokhlina, T. I.; Zrelov, P. V.; Ivanov, V. V.; Polozov, R. V.; Chirgadze, Yu. N.; Sivozhelezov, V. S.

2013-09-01

The analysis of amino acid-nucleotide contacts in interfaces of the protein-DNA complexes, intended to find consistencies in the protein-DNA recognition, is a complex problem that requires an analysis of the physicochemical characteristics of these contacts and the positions of the participating amino acids and nucleotides in the chains of the protein and the DNA, respectively, as well as conservatism of these contacts. Thus, those heterogeneous data should be systematized. For this purpose we have developed a database of amino acid-nucleotide contacts ANTPC (Amino acid Nucleotide Type Position Conservation) following the archetypal example of the proteins in the homeodomain family. We show that it can be used to compare and classify the interfaces of the protein-DNA complexes.

Nucleotide Sequence Database Comparison for Routine Dermatophyte Identification by Internal Transcribed Spacer 2 Genetic Region DNA Barcoding.

PubMed

Normand, A C; Packeu, A; Cassagne, C; Hendrickx, M; Ranque, S; Piarroux, R

2018-05-01

Conventional dermatophyte identification is based on morphological features. However, recent studies have proposed to use the nucleotide sequences of the rRNA internal transcribed spacer (ITS) region as an identification barcode of all fungi, including dermatophytes. Several nucleotide databases are available to compare sequences and thus identify isolates; however, these databases often contain mislabeled sequences that impair sequence-based identification. We evaluated five of these databases on a clinical isolate panel. We selected 292 clinical dermatophyte strains that were prospectively subjected to an ITS2 nucleotide sequence analysis. Sequences were analyzed against the databases, and the results were compared to clusters obtained via DNA alignment of sequence segments. The DNA tree served as the identification standard throughout the study. According to the ITS2 sequence identification, the majority of strains (255/292) belonged to the genus Trichophyton , mainly T. rubrum complex ( n = 184), T. interdigitale ( n = 40), T. tonsurans ( n = 26), and T. benhamiae ( n = 5). Other genera included Microsporum (e.g., M. canis [ n = 21], M. audouinii [ n = 10], Nannizzia gypsea [ n = 3], and Epidermophyton [ n = 3]). Species-level identification of T. rubrum complex isolates was an issue. Overall, ITS DNA sequencing is a reliable tool to identify dermatophyte species given that a comprehensive and correctly labeled database is consulted. Since many inaccurate identification results exist in the DNA databases used for this study, reference databases must be verified frequently and amended in line with the current revisions of fungal taxonomy. Before describing a new species or adding a new DNA reference to the available databases, its position in the phylogenetic tree must be verified. Copyright © 2018 American Society for Microbiology.

Aggregating todays data for tomorrows science: a geological use case

NASA Astrophysics Data System (ADS)

Glaves, H.; Kingdon, A.; Nayembil, M.; Baker, G.

2016-12-01

Geoscience data is made up of diverse and complex smaller datasets that, when aggregated together, build towards what is recognised as `big data'. The British Geological Survey (BGS), which acts as a repository for all subsurface data from the United Kingdom, has been collating these disparate small datasets that have been accumulated from the activities of a large number of geoscientists over many years. Recently this picture has been further complicated by the addition of new data sources such as near real-time sensor data, and industry or community data that is increasingly delivered via automatic donations. Many of these datasets have been aggregated in relational databases to form larger ones that are used to address a variety of issues ranging from development of national infrastructure to disaster response. These complex domain-specific SQL databases deliver effective data management using normalised subject-based database designs in a secure environment. However, the isolated subject-oriented design of these systems inhibits efficient cross-domain querying of the datasets. Additionally, the tools provided often do not enable effective data discovery as they have problems resolving the complex underlying normalised structures. Recent requirements to understand sub-surface geology in three dimensions have led BGS to develop new data systems. One such solution is PropBase which delivers a generic denormalised data structure within an RDBMS to store geological property data. Propbase facilitates rapid and standardised data discovery and access, incorporating 2D and 3D physical and chemical property data, including associated metadata. It also provides a dedicated web interface to deliver complex multiple data sets from a single database in standardised common output formats (e.g. CSV, GIS shape files) without the need for complex data conditioning. PropBase facilitates new scientific research, previously considered impractical, by enabling property data searches across multiple databases. Using the Propbase exemplar this presentation will seek to illustrate how BGS has developed systems for aggregating `small datasets' to create the `big data' necessary for the data analytics, mining, processing and visualisation needed for future geoscientific research.

A deep learning approach for fetal QRS complex detection.

PubMed

Zhong, Wei; Liao, Lijuan; Guo, Xuemei; Wang, Guoli

2018-04-20

Non-invasive foetal electrocardiography (NI-FECG) has the potential to provide more additional clinical information for detecting and diagnosing fetal diseases. We propose and demonstrate a deep learning approach for fetal QRS complex detection from raw NI-FECG signals by using a convolutional neural network (CNN) model. The main objective is to investigate whether reliable fetal QRS complex detection performance can still be obtained from features of single-channel NI-FECG signals, without canceling maternal ECG (MECG) signals. A deep learning method is proposed for recognizing fetal QRS complexes. Firstly, we collect data from set-a of the PhysioNet/computing in Cardiology Challenge database. The sample entropy method is used for signal quality assessment. Part of the bad quality signals is excluded in the further analysis. Secondly, in the proposed method, the features of raw NI-FECG signals are normalized before they are fed to a CNN classifier to perform fetal QRS complex detection. We use precision, recall, F-measure and accuracy as the evaluation metrics to assess the performance of fetal QRS complex detection. The proposed deep learning method can achieve relatively high precision (75.33%), recall (80.54%), and F-measure scores (77.85%) compared with three other well-known pattern classification methods, namely KNN, naive Bayes and SVM. the proposed deep learning method can attain reliable fetal QRS complex detection performance from the raw NI-FECG signals without canceling MECG signals. In addition, the influence of different activation functions and signal quality assessment on classification performance are evaluated, and results show that Relu outperforms the Sigmoid and Tanh on this particular task, and better classification performance is obtained with the signal quality assessment step in this study.

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

PubMed

Deutsch, Eric W; Sun, Zhi; Campbell, David S; Binz, Pierre-Alain; Farrah, Terry; Shteynberg, David; Mendoza, Luis; Omenn, Gilbert S; Moritz, Robert L

2016-11-04

The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances-a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ∼20,000 primary isoforms plus contaminants to a very large database that includes almost all nonredundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/ .

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics

PubMed Central

Deutsch, Eric W.; Sun, Zhi; Campbell, David S.; Binz, Pierre-Alain; Farrah, Terry; Shteynberg, David; Mendoza, Luis; Omenn, Gilbert S.; Moritz, Robert L.

2016-01-01

The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances – a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ~20,000 primary isoforms plus contaminants to a very large database that includes almost all non-redundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/. PMID:27577934

Verification of the databases EXFOR and ENDF

NASA Astrophysics Data System (ADS)

Berton, Gottfried; Damart, Guillaume; Cabellos, Oscar; Beauzamy, Bernard; Soppera, Nicolas; Bossant, Manuel

2017-09-01

The objective of this work is for the verification of large experimental (EXFOR) and evaluated nuclear reaction databases (JEFF, ENDF, JENDL, TENDL…). The work is applied to neutron reactions in EXFOR data, including threshold reactions, isomeric transitions, angular distributions and data in the resonance region of both isotopes and natural elements. Finally, a comparison of the resonance integrals compiled in EXFOR database with those derived from the evaluated libraries is also performed.

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 the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

Heterogeneous distributed query processing: The DAVID system

NASA Technical Reports Server (NTRS)

Jacobs, Barry E.

1985-01-01

The objective of the Distributed Access View Integrated Database (DAVID) project is the development of an easy to use computer system with which NASA scientists, engineers and administrators can uniformly access distributed heterogeneous databases. Basically, DAVID will be a database management system that sits alongside already existing database and file management systems. Its function is to enable users to access the data in other languages and file systems without having to learn the data manipulation languages. Given here is an outline of a talk on the DAVID project and several charts.

QBIC project: querying images by content, using color, texture, and shape

NASA Astrophysics Data System (ADS)

Niblack, Carlton W.; Barber, Ron; Equitz, Will; Flickner, Myron D.; Glasman, Eduardo H.; Petkovic, Dragutin; Yanker, Peter; Faloutsos, Christos; Taubin, Gabriel

1993-04-01

In the query by image content (QBIC) project we are studying methods to query large on-line image databases using the images' content as the basis of the queries. Examples of the content we use include color, texture, and shape of image objects and regions. Potential applications include medical (`Give me other images that contain a tumor with a texture like this one'), photo-journalism (`Give me images that have blue at the top and red at the bottom'), and many others in art, fashion, cataloging, retailing, and industry. Key issues include derivation and computation of attributes of images and objects that provide useful query functionality, retrieval methods based on similarity as opposed to exact match, query by image example or user drawn image, the user interfaces, query refinement and navigation, high dimensional database indexing, and automatic and semi-automatic database population. We currently have a prototype system written in X/Motif and C running on an RS/6000 that allows a variety of queries, and a test database of over 1000 images and 1000 objects populated from commercially available photo clip art images. In this paper we present the main algorithms for color texture, shape and sketch query that we use, show example query results, and discuss future directions.

Verification of road databases using multiple road models

NASA Astrophysics Data System (ADS)

Ziems, Marcel; Rottensteiner, Franz; Heipke, Christian

2017-08-01

In this paper a new approach for automatic road database verification based on remote sensing images is presented. In contrast to existing methods, the applicability of the new approach is not restricted to specific road types, context areas or geographic regions. This is achieved by combining several state-of-the-art road detection and road verification approaches that work well under different circumstances. Each one serves as an independent module representing a unique road model and a specific processing strategy. All modules provide independent solutions for the verification problem of each road object stored in the database in form of two probability distributions, the first one for the state of a database object (correct or incorrect), and a second one for the state of the underlying road model (applicable or not applicable). In accordance with the Dempster-Shafer Theory, both distributions are mapped to a new state space comprising the classes correct, incorrect and unknown. Statistical reasoning is applied to obtain the optimal state of a road object. A comparison with state-of-the-art road detection approaches using benchmark datasets shows that in general the proposed approach provides results with larger completeness. Additional experiments reveal that based on the proposed method a highly reliable semi-automatic approach for road data base verification can be designed.

Semantic mediation in the national geologic map database (US)

USGS Publications Warehouse

Percy, D.; Richard, S.; Soller, D.

2008-01-01

Controlled language is the primary challenge in merging heterogeneous databases of geologic information. Each agency or organization produces databases with different schema, and different terminology for describing the objects within. In order to make some progress toward merging these databases using current technology, we have developed software and a workflow that allows for the "manual semantic mediation" of these geologic map databases. Enthusiastic support from many state agencies (stakeholders and data stewards) has shown that the community supports this approach. Future implementations will move toward a more Artificial Intelligence-based approach, using expert-systems or knowledge-bases to process data based on the training sets we have developed manually.

The Missing Link: Context Loss in Online Databases

ERIC Educational Resources Information Center

Mi, Jia; Nesta, Frederick

2005-01-01

Full-text databases do not allow for the complexity of the interaction of the human eye and brain with printed matter. As a result, both content and context may be lost. The authors propose additional indexing fields that would maintain the content and context of print in electronic formats.

Cleaning Data Helps Clean the Air

ERIC Educational Resources Information Center

Donalds, Kelley; Liu, Xiangrong

2014-01-01

In this project, students use a real-world, complex database and experience firsthand the consequences of inadequate data modeling. The U.S. Environmental Protection Agency created the database as part of a multimillion dollar data collection effort undertaken in order to set limits on air pollutants from electric power plants. First, students…

A spatial classification and database for management, research, and policy making: The Great Lakes aquatic habitat framework

EPA Science Inventory

Managing the world’s largest and complex freshwater ecosystem, the Laurentian Great Lakes, requires a spatially hierarchical basin-wide database of ecological and socioeconomic information that are comparable across the region. To meet such a need, we developed a hierarchi...

The Efficacy of Multidimensional Constraint Keys in Database Query Performance

ERIC Educational Resources Information Center

Cardwell, Leslie K.

2012-01-01

This work is intended to introduce a database design method to resolve the two-dimensional complexities inherent in the relational data model and its resulting performance challenges through abstract multidimensional constructs. A multidimensional constraint is derived and utilized to implement an indexed Multidimensional Key (MK) to abstract a…

East Kentucky Power Cooperative Spurlock Station; Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Louisville Gas & Electric Trimble Power Station; Petition to Object to REVISED Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Premcor Refining Group, Port Arthur, Texas; Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

ConocoPhillips Wilmington Refinery, Wilmington, California; Petiton to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Tradewinds Veneer Mill, Ookala, Hawaii; Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Tradewinds Veneer Mill, Ookala, Hawaii; Petiton to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Tennessee Valley Authority, Paradise Fossil Plant; Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Thoroughbred Generating Company; Supplement to Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Cemex, Inc., Lyons, Colorado; Petition to Object (or reopen) to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Petition to Object to New United Motor Manufacturing, Inc. Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Database & information tools for transportation research management : Connecticut transportation research peer exchange report of a thematic peer exchange.

DOT National Transportation Integrated Search

2006-05-01

Specific objectives of the Peer Exchange were: : Discuss and exchange information about databases and other software : used to support the program-cycles managed by state transportation : research offices. Elements of the program cycle include: :...

Evolution of the NASA/IPAC Extragalactic Database (NED) into a Data Mining Discovery Engine

NASA Astrophysics Data System (ADS)

Mazzarella, Joseph M.; NED Team

2017-06-01

We review recent advances and ongoing work in evolving the NASA/IPAC Extragalactic Database (NED) beyond an object reference database into a data mining discovery engine. Updates to the infrastructure and data integration techniques are enabling more than a 10-fold expansion; NED will soon contain over a billion objects with their fundamental attributes fused across the spectrum via cross-identifications among the largest sky surveys (e.g., GALEX, SDSS, 2MASS, AllWISE, EMU), and over 100,000 smaller but scientifically important catalogs and journal articles. The recent discovery of super-luminous spiral galaxies exemplifies the opportunities for data mining and science discovery directly from NED's rich data synthesis. Enhancements to the user interface, including new APIs, VO protocols, and queries involving derived physical quantities, are opening new pathways for panchromatic studies of large galaxy samples. Examples are shown of graphics characterizing the content of NED, as well as initial steps in exploring the database via interactive statistical visualizations.

Final Report - Enhanced LAW Glass Property - Composition Models - Phase 1 VSL-13R2940-1, Rev. 0, dated 9/27/2013

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

Kruger, Albert A.; Muller, I.; Gilbo, K.

2013-11-13

The objectives of this work are aimed at the development of enhanced LAW propertycomposition models that expand the composition region covered by the models. The models of interest include PCT, VHT, viscosity and electrical conductivity. This is planned as a multi-year effort that will be performed in phases with the objectives listed below for the current phase.  Incorporate property- composition data from the new glasses into the database.  Assess the database and identify composition spaces in the database that need augmentation.  Develop statistically-designed composition matrices to cover the composition regions identified in the above analysis.  Preparemore » crucible melts of glass compositions from the statistically-designed composition matrix and measure the properties of interest.  Incorporate the above property-composition data into the database.  Assess existing models against the complete dataset and, as necessary, start development of new models.« less

Risk management integration into complex project organizations

NASA Technical Reports Server (NTRS)

Fisher, K.; Greanias, G.; Rose, J.; Dumas, R.

2002-01-01

This paper describes the approach used in designing and adapting the SIRTF prototype, discusses some of the lessons learned in developing the SIRTF prototype, and explains the adaptability of the risk management database to varying levels project complexity.

Cross-Matching Source Observations from the Palomar Transient Factory (PTF)

NASA Astrophysics Data System (ADS)

Laher, Russ; Grillmair, C.; Surace, J.; Monkewitz, S.; Jackson, E.

2009-01-01

Over the four-year lifetime of the PTF project, approximately 40 billion instances of astronomical-source observations will be extracted from the image data. The instances will correspond to the same astronomical objects being observed at roughly 25-50 different times, and so a very large catalog containing important object-variability information will be the chief PTF product. Organizing astronomical-source catalogs is conventionally done by dividing the catalog into declination zones and sorting by right ascension within each zone (e.g., the USNOA star catalog), in order to facilitate catalog searches. This method was reincarnated as the "zones" algorithm in a SQL-Server database implementation (Szalay et al., MSR-TR-2004-32), with corrections given by Gray et al. (MSR-TR-2006-52). The primary advantage of this implementation is that all of the work is done entirely on the database server and client/server communication is eliminated. We implemented the methods outlined in Gray et al. for a PostgreSQL database. We programmed the methods as database functions in PL/pgSQL procedural language. The cross-matching is currently based on source positions, but we intend to extend it to use both positions and positional uncertainties to form a chi-square statistic for optimal thresholding. The database design includes three main tables, plus a handful of internal tables. The Sources table stores the SExtractor source extractions taken at various times; the MergedSources table stores statistics about the astronomical objects, which are the result of cross-matching records in the Sources table; and the Merges table, which associates cross-matched primary keys in the Sources table with primary keys in the MergedSoures table. Besides judicious database indexing, we have also internally partitioned the Sources table by declination zone, in order to speed up the population of Sources records and make the database more manageable. The catalog will be accessible to the public after the proprietary period through IRSA (irsa.ipac.caltech.edu).

Logic programming to infer complex RNA expression patterns from RNA-seq data.

PubMed

Weirick, Tyler; Militello, Giuseppe; Ponomareva, Yuliya; John, David; Döring, Claudia; Dimmeler, Stefanie; Uchida, Shizuka

2018-03-01

To meet the increasing demand in the field, numerous long noncoding RNA (lncRNA) databases are available. Given many lncRNAs are specifically expressed in certain cell types and/or time-dependent manners, most lncRNA databases fall short of providing such profiles. We developed a strategy using logic programming to handle the complex organization of organs, their tissues and cell types as well as gender and developmental time points. To showcase this strategy, we introduce 'RenalDB' (http://renaldb.uni-frankfurt.de), a database providing expression profiles of RNAs in major organs focusing on kidney tissues and cells. RenalDB uses logic programming to describe complex anatomy, sample metadata and logical relationships defining expression, enrichment or specificity. We validated the content of RenalDB with biological experiments and functionally characterized two long intergenic noncoding RNAs: LOC440173 is important for cell growth or cell survival, whereas PAXIP1-AS1 is a regulator of cell death. We anticipate RenalDB will be used as a first step toward functional studies of lncRNAs in the kidney.

BIOSPIDA: A Relational Database Translator for NCBI

PubMed Central

Hagen, Matthew S.; Lee, Eva K.

2010-01-01

As the volume and availability of biological databases continue widespread growth, it has become increasingly difficult for research scientists to identify all relevant information for biological entities of interest. Details of nucleotide sequences, gene expression, molecular interactions, and three-dimensional structures are maintained across many different databases. To retrieve all necessary information requires an integrated system that can query multiple databases with minimized overhead. This paper introduces a universal parser and relational schema translator that can be utilized for all NCBI databases in Abstract Syntax Notation (ASN.1). The data models for OMIM, Entrez-Gene, Pubmed, MMDB and GenBank have been successfully converted into relational databases and all are easily linkable helping to answer complex biological questions. These tools facilitate research scientists to locally integrate databases from NCBI without significant workload or development time. PMID:21347013

The European Prader-Willi Syndrome Clinical Research Database: an aid in the investigation of a rare genetically determined neurodevelopmental disorder.

PubMed

Holland, A; Whittington, J; Cohen, O; Curfs, L; Delahaye, F; Dudley, O; Horsthemke, B; Lindgren, A-C; Nourissier, C; Sharma, N; Vogels, A

2009-06-01

Prader-Willi Syndrome (PWS) is a rare genetically determined neurodevelopmental disorder with a complex phenotype that changes with age. The rarity of the syndrome and the need to control for different variables such as genetic sub-type, age and gender limits clinical studies of sufficient size in any one country. A clinical research database has been established to structure data collection and to enable multinational investigations into the development of children and adults with PWS. As part of a joint basic science and clinical study of PWS funded through Framework 6 of the European Union (EU), an expert multidisciplinary group was established that included clinicians involved in PWS research and clinical practice, expert database software developers, and representatives from two national PWS Associations. This group identified the key issues that required resolution and the data fields necessary for a comprehensive database to support PWS research. The database consists of six 'index' entry points and branching panels and sub-panels and over 1200 data 'fields'. It is Internet-based and designed to support multi-site clinical research in PWS. An algorithm ensures that participant data are anonymous. Access to data is controlled in a manner that is compatible with EU and national laws. The database determines the assessments to be used to collect data thereby enabling the combining of data from different groups under specifically agreed conditions. The data collected at any one time will be determined by individual research groups, who retain control of the data. Over time the database will accumulate data on participants with PWS that will support future research by avoiding the need for repeat data collection of fixed data and it will also enable longitudinal studies and treatment trials. The development of the database has proved to be complex with various administrative and ethical issues to be addressed. At an early stage, it was important to clarify the exact function of the database. It was agreed that it was primarily to support grant-funded research rather than clinical practice. The most complex issues that had to be addressed were concerned with data ownership and establishing the rules for data entry, retrieval and sharing that are compatible with data protection laws, and which are likely to be acceptable to participants and their families and to individual research groups.

A web based relational database management system for filariasis control

PubMed Central

Murty, Upadhyayula Suryanarayana; Kumar, Duvvuri Venkata Rama Satya; Sriram, Kumaraswamy; Rao, Kadiri Madhusudhan; Bhattacharyulu, Chakravarthula Hayageeva Narasimha Venakata; Praveen, Bhoopathi; Krishna, Amirapu Radha

2005-01-01

The present study describes a RDBMS (relational database management system) for the effective management of Filariasis, a vector borne disease. Filariasis infects 120 million people from 83 countries. The possible re-emergence of the disease and the complexity of existing control programs warrant the development of new strategies. A database containing comprehensive data associated with filariasis finds utility in disease control. We have developed a database containing information on the socio-economic status of patients, mosquito collection procedures, mosquito dissection data, filariasis survey report and mass blood data. The database can be searched using a user friendly web interface. Availability http://www.webfil.org (login and password can be obtained from the authors) PMID:17597846

Recognition Of Complex Three Dimensional Objects Using Three Dimensional Moment Invariants

NASA Astrophysics Data System (ADS)

Sadjadi, Firooz A.

1985-01-01

A technique for the recognition of complex three dimensional objects is presented. The complex 3-D objects are represented in terms of their 3-D moment invariants, algebraic expressions that remain invariant independent of the 3-D objects' orientations and locations in the field of view. The technique of 3-D moment invariants has been used successfully for simple 3-D object recognition in the past. In this work we have extended this method for the representation of more complex objects. Two complex objects are represented digitally; their 3-D moment invariants have been calculated, and then the invariancy of these 3-D invariant moment expressions is verified by changing the orientation and the location of the objects in the field of view. The results of this study have significant impact on 3-D robotic vision, 3-D target recognition, scene analysis and artificial intelligence.

Automatic visualization of 3D geometry contained in online databases

NASA Astrophysics Data System (ADS)

Zhang, Jie; John, Nigel W.

2003-04-01

In this paper, the application of the Virtual Reality Modeling Language (VRML) for efficient database visualization is analyzed. With the help of JAVA programming, three examples of automatic visualization from a database containing 3-D Geometry are given. The first example is used to create basic geometries. The second example is used to create cylinders with a defined start point and end point. The third example is used to processs data from an old copper mine complex in Cheshire, United Kingdom. Interactive 3-D visualization of all geometric data in an online database is achieved with JSP technology.

Environmental Database For Water-Quality Data for the Penobscot River, Maine: Design Documentation and User Guide

USGS Publications Warehouse

Giffen, Sarah E.

2002-01-01

An environmental database was developed to store water-quality data collected during the 1999 U.S. Geological Survey investigation of the occurrence and distribution of dioxins, furans, and PCBs in the riverbed sediment and fish tissue in the Penobscot River in Maine. The database can be used to store a wide range of detailed information and to perform complex queries on the data it contains. The database also could be used to store data from other historical and any future environmental studies conducted on the Penobscot River and surrounding regions.

Inferring Network Controls from Topology Using the Chomp Database

DTIC Science & Technology

2015-12-03

AFRL-AFOSR-VA-TR-2016-0033 INFERRING NETWORK CONTROLS FROM TOPOLOGY USING THE CHOMP DATABASE John Harer DUKE UNIVERSITY Final Report 12/03/2015...INFERRING NETWORK CONTROLS FROM TOPOLOGY USING THE CHOMP DATABASE 5a. CONTRACT NUMBER 5b. GRANT NUMBER FA9550-10-1-0436 5c. PROGRAM ELEMENT NUMBER 6...area of Topological Data Analysis (TDA) and it’s application to dynamical systems. The role of this work in the Complex Networks program is based on

Seismic Calibration of Group 1 IMS Stations in Eastern Asia for Improved IDC Event Location

DTIC Science & Technology

2006-04-01

database has been assembled and delivered to the SMR (formerly CMR) Research and Development Support Services (RDSS) data archive. This database ...Data used in these tomographic inversions have been collected into a uniform database and delivered to the RDSS at the SMR. Extensive testing of these...complex 3-D velocity models is based on a finite difference approximation to the eikonal equation developed by Podvin and Lecomte (1 991) and

Rationale and operational plan to upgrade the U.S. gravity database

USGS Publications Warehouse

Hildenbrand, Thomas G.; Briesacher, Allen; Flanagan, Guy; Hinze, William J.; Hittelman, A.M.; Keller, Gordon R.; Kucks, R.P.; Plouff, Donald; Roest, Walter; Seeley, John; Stith, David A.; Webring, Mike

2002-01-01

A concerted effort is underway to prepare a substantially upgraded digital gravity anomaly database for the United States and to make this data set and associated usage tools available on the internet. This joint effort, spearheaded by the geophysics groups at the National Imagery and Mapping Agency (NIMA), University of Texas at El Paso (UTEP), U.S. Geological Survey (USGS), and National Oceanic and Atmospheric Administration (NOAA), is an outgrowth of the new geoscientific community initiative called Geoinformatics (www.geoinformaticsnetwork.org). This dominantly geospatial initiative reflects the realization by Earth scientists that existing information systems and techniques are inadequate to address the many complex scientific and societal issues. Currently, inadequate standardization and chaotic distribution of geoscience data, inadequate accompanying documentation, and the lack of easy-to-use access tools and computer codes for analysis are major obstacles for scientists, government agencies, and educators. An example of the type of activities envisioned, within the context of Geoinformatics, is the construction, maintenance, and growth of a public domain gravity database and development of the software tools needed to access, implement, and expand it. This product is far more than a high quality database; it is a complete data system for a specific type of geophysical measurement that includes, for example, tools to manipulate the data and tutorials to understand and properly utilize the data. On August 9, 2002, twenty-one scientists from the federal, private and academic sectors met at a workshop to discuss the rationale for upgrading both the United States and North American gravity databases (including offshore regions) and, more importantly, to begin developing an operational plan to effectively create a new gravity data system. We encourage anyone interested in contributing data or participating in this effort to contact G.R. Keller or T.G. Hildenbrand. This workshop was the first step in building a web-based data system for sharing quality gravity data and methodology, and it builds on existing collaborative efforts. This compilation effort will result in significant additions to and major refinement of the U.S. database that is currently released publicly by NOAA’s National Geophysical Data Center and will also include an additional objective to substantially upgrade the North American database, released over 15 years ago (Committee for the Gravity Anomaly Map of North America, 1987).

Databases for LDEF results

NASA Technical Reports Server (NTRS)

Bohnhoff-Hlavacek, Gail

1992-01-01

One of the objectives of the team supporting the LDEF Systems and Materials Special Investigative Groups is to develop databases of experimental findings. These databases identify the hardware flown, summarize results and conclusions, and provide a system for acknowledging investigators, tracing sources of data, and future design suggestions. To date, databases covering the optical experiments, and thermal control materials (chromic acid anodized aluminum, silverized Teflon blankets, and paints) have been developed at Boeing. We used the Filemaker Pro software, the database manager for the Macintosh computer produced by the Claris Corporation. It is a flat, text-retrievable database that provides access to the data via an intuitive user interface, without tedious programming. Though this software is available only for the Macintosh computer at this time, copies of the databases can be saved to a format that is readable on a personal computer as well. Further, the data can be exported to more powerful relational databases, capabilities, and use of the LDEF databases and describe how to get copies of the database for your own research.

Object-based modeling, identification, and labeling of medical images for content-based retrieval by querying on intervals of attribute values

NASA Astrophysics Data System (ADS)

Thies, Christian; Ostwald, Tamara; Fischer, Benedikt; Lehmann, Thomas M.

2005-04-01

The classification and measuring of objects in medical images is important in radiological diagnostics and education, especially when using large databases as knowledge resources, for instance a picture archiving and communication system (PACS). The main challenge is the modeling of medical knowledge and the diagnostic context to label the sought objects. This task is referred to as closing the semantic gap between low-level pixel information and high level application knowledge. This work describes an approach which allows labeling of a-priori unknown objects in an intuitive way. Our approach consists of four main components. At first an image is completely decomposed into all visually relevant partitions on different scales. This provides a hierarchical organized set of regions. Afterwards, for each of the obtained regions a set of descriptive features is computed. In this data structure objects are represented by regions with characteristic attributes. The actual object identification is the formulation of a query. It consists of attributes on which intervals are defined describing those regions that correspond to the sought objects. Since the objects are a-priori unknown, they are described by a medical expert by means of an intuitive graphical user interface (GUI). This GUI is the fourth component. It enables complex object definitions by browsing the data structure and examinating the attributes to formulate the query. The query is executed and if the sought objects have not been identified its parameterization is refined. By using this heuristic approach, object models for hand radiographs have been developed to extract bones from a single hand in different anatomical contexts. This demonstrates the applicability of the labeling concept. By using a rule for metacarpal bones on a series of 105 images, this type of bone could be retrieved with a precision of 0.53 % and a recall of 0.6%.

ConocoPhillips Wilmington Refinery, Wilmington, California; 2008 Petiton to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Georgia Power Company, Wansley Steam Electric Generating Plant; Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Wisconsin Public Service, Weston Generating Station; Petition to Object to Issuance of Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Thoroughbred Generating Company, Muhlenberg County, Kentucky; Order Denying Petition For Objection To Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Readiness of food composition databases and food component analysis systems for nutrigenomics

USDA-ARS?s Scientific Manuscript database

The study objective was to discuss the international implications of using nutrigenomics as the basis for individualized health promotion and chronic disease prevention and the challenges it presents to existing nutrient databases and nutrient analysis systems. Definitions and research methods of nu...

Tennessee Valley Authority, Paradise Fossil Plant; Order Responding Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Waupaca Foundry Plants 2 and 3; Order Denying Petition for Object to Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

A Method to Calculate and Analyze Residents' Evaluations by Using a Microcomputer Data-Base Management System.

ERIC Educational Resources Information Center

Mills, Myron L.

1988-01-01

A system developed for more efficient evaluation of graduate medical students' progress uses numerical scoring and a microcomputer database management system as an alternative to manual methods to produce accurate, objective, and meaningful summaries of resident evaluations. (Author/MSE)

Midwest Generation, Waukegan Generating Station; Order Partially Denying And Partially Granting Petition For Objection To Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

2001 Petition Requesting the Administrator Object to Title V Permit For Los Medanos Energy Center

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Database technology and the management of multimedia data in the Mirror project

NASA Astrophysics Data System (ADS)

de Vries, Arjen P.; Blanken, H. M.

1998-10-01

Multimedia digital libraries require an open distributed architecture instead of a monolithic database system. In the Mirror project, we use the Monet extensible database kernel to manage different representation of multimedia objects. To maintain independence between content, meta-data, and the creation of meta-data, we allow distribution of data and operations using CORBA. This open architecture introduces new problems for data access. From an end user's perspective, the problem is how to search the available representations to fulfill an actual information need; the conceptual gap between human perceptual processes and the meta-data is too large. From a system's perspective, several representations of the data may semantically overlap or be irrelevant. We address these problems with an iterative query process and active user participating through relevance feedback. A retrieval model based on inference networks assists the user with query formulation. The integration of this model into the database design has two advantages. First, the user can query both the logical and the content structure of multimedia objects. Second, the use of different data models in the logical and the physical database design provides data independence and allows algebraic query optimization. We illustrate query processing with a music retrieval application.

Image-based query-by-example for big databases of galaxy images

NASA Astrophysics Data System (ADS)

Shamir, Lior; Kuminski, Evan

2017-01-01

Very large astronomical databases containing millions or even billions of galaxy images have been becoming increasingly important tools in astronomy research. However, in many cases the very large size makes it more difficult to analyze these data manually, reinforcing the need for computer algorithms that can automate the data analysis process. An example of such task is the identification of galaxies of a certain morphology of interest. For instance, if a rare galaxy is identified it is reasonable to expect that more galaxies of similar morphology exist in the database, but it is virtually impossible to manually search these databases to identify such galaxies. Here we describe computer vision and pattern recognition methodology that receives a galaxy image as an input, and searches automatically a large dataset of galaxies to return a list of galaxies that are visually similar to the query galaxy. The returned list is not necessarily complete or clean, but it provides a substantial reduction of the original database into a smaller dataset, in which the frequency of objects visually similar to the query galaxy is much higher. Experimental results show that the algorithm can identify rare galaxies such as ring galaxies among datasets of 10,000 astronomical objects.

Database computing in HEP

NASA Technical Reports Server (NTRS)

Day, C. T.; Loken, S.; Macfarlane, J. F.; May, E.; Lifka, D.; Lusk, E.; Price, L. E.; Baden, A.; Grossman, R.; Qin, X.

1992-01-01

The major SSC experiments are expected to produce up to 1 Petabyte of data per year each. Once the primary reconstruction is completed by farms of inexpensive processors, I/O becomes a major factor in further analysis of the data. We believe that the application of database techniques can significantly reduce the I/O performed in these analyses. We present examples of such I/O reductions in prototypes based on relational and object-oriented databases of CDF data samples.

An Emerging Knowledge-Based Economy in China? Indicators from OECD Databases. OECD Science, Technology and Industry Working Papers, 2004/4

ERIC Educational Resources Information Center

Criscuolo, Chiara; Martin, Ralf

2004-01-01

The main objective of this Working Paper is to show a set of indicators on the knowledge-based economy for China, mainly compiled from databases within EAS, although data from databases maintained by other parts of the OECD are included as well. These indicators are put in context by comparison with data for the United States, Japan and the EU (or…

Information Security Considerations for Applications Using Apache Accumulo

DTIC Science & Technology

2014-09-01

Distributed File System INSCOM United States Army Intelligence and Security Command JPA Java Persistence API JSON JavaScript Object Notation MAC Mandatory... MySQL [13]. BigTable can process 20 petabytes per day [14]. High degree of scalability on commodity hardware. NoSQL databases do not rely on highly...manipulation in relational databases. NoSQL databases each have a unique programming interface that uses a lower level procedural language (e.g., Java

SSME environment database development

NASA Technical Reports Server (NTRS)

Reardon, John

1987-01-01

The internal environment of the Space Shuttle Main Engine (SSME) is being determined from hot firings of the prototype engines and from model tests using either air or water as the test fluid. The objectives are to develop a database system to facilitate management and analysis of test measurements and results, to enter available data into the the database, and to analyze available data to establish conventions and procedures to provide consistency in data normalization and configuration geometry references.

Issues in Big-Data Database Systems

DTIC Science & Technology

2014-06-01

Post, 18 August 2013. Berman, Jules K. (2013). Principles of Big Data: Preparing, Sharing, and Analyzing Complex Information. New York: Elsevier... Jules K. (2013). Principles of Big Data: Preparing, Sharing, and Analyzing Complex Information. New York: Elsevier. 261pp. Characterization of

The Ruby UCSC API: accessing the UCSC genome database using Ruby.

PubMed

Mishima, Hiroyuki; Aerts, Jan; Katayama, Toshiaki; Bonnal, Raoul J P; Yoshiura, Koh-ichiro

2012-09-21

The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast.The API uses the bin index-if available-when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/.

The Ruby UCSC API: accessing the UCSC genome database using Ruby

PubMed Central

2012-01-01

Background The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. Results The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast. The API uses the bin index—if available—when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Conclusions Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/. PMID:22994508

VIEWCACHE: An incremental pointer-based access method for autonomous interoperable databases

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1993-01-01

One of the biggest problems facing NASA today is to provide scientists efficient access to a large number of distributed databases. Our pointer-based incremental data base access method, VIEWCACHE, provides such an interface for accessing distributed datasets and directories. VIEWCACHE allows database browsing and search performing inter-database cross-referencing with no actual data movement between database sites. This organization and processing is especially suitable for managing Astrophysics databases which are physically distributed all over the world. Once the search is complete, the set of collected pointers pointing to the desired data are cached. VIEWCACHE includes spatial access methods for accessing image datasets, which provide much easier query formulation by referring directly to the image and very efficient search for objects contained within a two-dimensional window. We will develop and optimize a VIEWCACHE External Gateway Access to database management systems to facilitate database search.

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

Abbott, Jennifer; Sandberg, Tami

The Wind-Wildlife Impacts Literature Database (WILD), formerly known as the Avian Literature Database, was created in 1997. The goal of the database was to begin tracking the research that detailed the potential impact of wind energy development on birds. The Avian Literature Database was originally housed on a proprietary platform called Livelink ECM from Open- Text and maintained by in-house technical staff. The initial set of records was added by library staff. A vital part of the newly launched Drupal-based WILD database is the Bibliography module. Many of the resources included in the database have digital object identifiers (DOI). Themore » bibliographic information for any item that has a DOI can be imported into the database using this module. This greatly reduces the amount of manual data entry required to add records to the database. The content available in WILD is international in scope, which can be easily discerned by looking at the tags available in the browse menu.« less

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

DTIC Science & Technology

2017-06-01

relationships between objects and provides tools to quantitatively determine objects whose influence impacts other objects or the system as a whole. This... methodology identifies the most important TAMCN and provides a list of TAMCNs in order of importance. We also analyze the community and core structure of...relationships between objects and provides tools to quantitatively determine objects whose influence impacts other objects or the system as a whole. This

View generated database

NASA Technical Reports Server (NTRS)

Downward, James G.

1992-01-01

This document represents the final report for the View Generated Database (VGD) project, NAS7-1066. It documents the work done on the project up to the point at which all project work was terminated due to lack of project funds. The VGD was to provide the capability to accurately represent any real-world object or scene as a computer model. Such models include both an accurate spatial/geometric representation of surfaces of the object or scene, as well as any surface detail present on the object. Applications of such models are numerous, including acquisition and maintenance of work models for tele-autonomous systems, generation of accurate 3-D geometric/photometric models for various 3-D vision systems, and graphical models for realistic rendering of 3-D scenes via computer graphics.

An evaluation of multi-probe locality sensitive hashing for computing similarities over web-scale query logs.

PubMed

Cormode, Graham; Dasgupta, Anirban; Goyal, Amit; Lee, Chi Hoon

2018-01-01

Many modern applications of AI such as web search, mobile browsing, image processing, and natural language processing rely on finding similar items from a large database of complex objects. Due to the very large scale of data involved (e.g., users' queries from commercial search engines), computing such near or nearest neighbors is a non-trivial task, as the computational cost grows significantly with the number of items. To address this challenge, we adopt Locality Sensitive Hashing (a.k.a, LSH) methods and evaluate four variants in a distributed computing environment (specifically, Hadoop). We identify several optimizations which improve performance, suitable for deployment in very large scale settings. The experimental results demonstrate our variants of LSH achieve the robust performance with better recall compared with "vanilla" LSH, even when using the same amount of space.

Adapting the ISO 20462 softcopy ruler method for online image quality studies

NASA Astrophysics Data System (ADS)

Burns, Peter D.; Phillips, Jonathan B.; Williams, Don

2013-01-01

In this paper we address the problem of Image Quality Assessment of no reference metrics, focusing on JPEG corrupted images. In general no reference metrics are not able to measure with the same performance the distortions within their possible range and with respect to different image contents. The crosstalk between content and distortion signals influences the human perception. We here propose two strategies to improve the correlation between subjective and objective quality data. The first strategy is based on grouping the images according to their spatial complexity. The second one is based on a frequency analysis. Both the strategies are tested on two databases available in the literature. The results show an improvement in the correlations between no reference metrics and psycho-visual data, evaluated in terms of the Pearson Correlation Coefficient.

Alternatives to relational databases in precision medicine: Comparison of NoSQL approaches for big data storage using supercomputers

NASA Astrophysics Data System (ADS)

Velazquez, Enrique Israel

Improvements in medical and genomic technologies have dramatically increased the production of electronic data over the last decade. As a result, data management is rapidly becoming a major determinant, and urgent challenge, for the development of Precision Medicine. Although successful data management is achievable using Relational Database Management Systems (RDBMS), exponential data growth is a significant contributor to failure scenarios. Growing amounts of data can also be observed in other sectors, such as economics and business, which, together with the previous facts, suggests that alternate database approaches (NoSQL) may soon be required for efficient storage and management of big databases. However, this hypothesis has been difficult to test in the Precision Medicine field since alternate database architectures are complex to assess and means to integrate heterogeneous electronic health records (EHR) with dynamic genomic data are not easily available. In this dissertation, we present a novel set of experiments for identifying NoSQL database approaches that enable effective data storage and management in Precision Medicine using patients' clinical and genomic information from the cancer genome atlas (TCGA). The first experiment draws on performance and scalability from biologically meaningful queries with differing complexity and database sizes. The second experiment measures performance and scalability in database updates without schema changes. The third experiment assesses performance and scalability in database updates with schema modifications due dynamic data. We have identified two NoSQL approach, based on Cassandra and Redis, which seems to be the ideal database management systems for our precision medicine queries in terms of performance and scalability. We present NoSQL approaches and show how they can be used to manage clinical and genomic big data. Our research is relevant to the public health since we are focusing on one of the main challenges to the development of Precision Medicine and, consequently, investigating a potential solution to the progressively increasing demands on health care.

Multisensory object perception in infancy: 4-month-olds perceive a mistuned harmonic as a separate auditory and visual object

PubMed Central

A. Smith, Nicholas; A. Folland, Nicholas; Martinez, Diana M.; Trainor, Laurel J.

2017-01-01

Infants learn to use auditory and visual information to organize the sensory world into identifiable objects with particular locations. Here we use a behavioural method to examine infants' use of harmonicity cues to auditory object perception in a multisensory context. Sounds emitted by different objects sum in the air and the auditory system must figure out which parts of the complex waveform belong to different sources (auditory objects). One important cue to this source separation is that complex tones with pitch typically contain a fundamental frequency and harmonics at integer multiples of the fundamental. Consequently, adults hear a mistuned harmonic in a complex sound as a distinct auditory object (Alain et al., 2003). Previous work by our group demonstrated that 4-month-old infants are also sensitive to this cue. They behaviourally discriminate a complex tone with a mistuned harmonic from the same complex with in-tune harmonics, and show an object-related event-related potential (ERP) electrophysiological (EEG) response to the stimulus with mistuned harmonics. In the present study we use an audiovisual procedure to investigate whether infants perceive a complex tone with an 8% mistuned harmonic as emanating from two objects, rather than merely detecting the mistuned cue. We paired in-tune and mistuned complex tones with visual displays that contained either one or two bouncing balls. Four-month-old infants showed surprise at the incongruous pairings, looking longer at the display of two balls when paired with the in-tune complex and at the display of one ball when paired with the mistuned harmonic complex. We conclude that infants use harmonicity as a cue for source separation when integrating auditory and visual information in object perception. PMID:28346869

Towards the Interoperability of Web, Database, and Mass Storage Technologies for Petabyte Archives

NASA Technical Reports Server (NTRS)

Moore, Reagan; Marciano, Richard; Wan, Michael; Sherwin, Tom; Frost, Richard

1996-01-01

At the San Diego Supercomputer Center, a massive data analysis system (MDAS) is being developed to support data-intensive applications that manipulate terabyte sized data sets. The objective is to support scientific application access to data whether it is located at a Web site, stored as an object in a database, and/or storage in an archival storage system. We are developing a suite of demonstration programs which illustrate how Web, database (DBMS), and archival storage (mass storage) technologies can be integrated. An application presentation interface is being designed that integrates data access to all of these sources. We have developed a data movement interface between the Illustra object-relational database and the NSL UniTree archival storage system running in a production mode at the San Diego Supercomputer Center. With this interface, an Illustra client can transparently access data on UniTree under the control of the Illustr DBMS server. The current implementation is based on the creation of a new DBMS storage manager class, and a set of library functions that allow the manipulation and migration of data stored as Illustra 'large objects'. We have extended this interface to allow a Web client application to control data movement between its local disk, the Web server, the DBMS Illustra server, and the UniTree mass storage environment. This paper describes some of the current approaches successfully integrating these technologies. This framework is measured against a representative sample of environmental data extracted from the San Diego Ba Environmental Data Repository. Practical lessons are drawn and critical research areas are highlighted.

A Database Design and Development Case: Home Theater Video

ERIC Educational Resources Information Center

Ballenger, Robert; Pratt, Renee

2012-01-01

This case consists of a business scenario of a small video rental store, Home Theater Video, which provides background information, a description of the functional business requirements, and sample data. The case provides sufficient information to design and develop a moderately complex database to assist Home Theater Video in solving their…

Complex Adaptive Systems Based Data Integration: Theory and Applications

ERIC Educational Resources Information Center

Rohn, Eliahu

2008-01-01

Data Definition Languages (DDLs) have been created and used to represent data in programming languages and in database dictionaries. This representation includes descriptions in the form of data fields and relations in the form of a hierarchy, with the common exception of relational databases where relations are flat. Network computing created an…

MultitaskProtDB: a database of multitasking proteins.

PubMed

Hernández, Sergio; Ferragut, Gabriela; Amela, Isaac; Perez-Pons, JosepAntoni; Piñol, Jaume; Mozo-Villarias, Angel; Cedano, Juan; Querol, Enrique

2014-01-01

We have compiled MultitaskProtDB, available online at http://wallace.uab.es/multitask, to provide a repository where the many multitasking proteins found in the literature can be stored. Multitasking or moonlighting is the capability of some proteins to execute two or more biological functions. Usually, multitasking proteins are experimentally revealed by serendipity. This ability of proteins to perform multitasking functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Even so, the study of this phenomenon is complex because, among other things, there is no database of moonlighting proteins. The existence of such a tool facilitates the collection and dissemination of these important data. This work reports the database, MultitaskProtDB, which is designed as a friendly user web page containing >288 multitasking proteins with their NCBI and UniProt accession numbers, canonical and additional biological functions, monomeric/oligomeric states, PDB codes when available and bibliographic references. This database also serves to gain insight into some characteristics of multitasking proteins such as frequencies of the different pairs of functions, phylogenetic conservation and so forth.

Oglethorpe Power Company, Wansley Energy Facility; Amended Order Denying Petition for Objection to Permit in Response to Remand

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Entergy Louisiana, Little Gypsy Solid Fuel Repowering Project; Petition to Object to the Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Thematic Accuracy Assessment of the 2011 National Land Cover Database (NLCD)

EPA Science Inventory

Accuracy assessment is a standard protocol of National Land Cover Database (NLCD) mapping. Here we report agreement statistics between map and reference labels for NLCD 2011, which includes land cover for ca. 2001, ca. 2006, and ca. 2011. The two main objectives were assessment o...

New York Power Authority Pouch Terminal Power Plant, Staten Island, NY; Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Ultramar Refining, Subsidiary of Valero Energy Corporation, Wilmington, California; Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Ultramar Refining, Subsidiary of Valero Energy Corporation, Wilmington, California; Dec. 12, 2008, Petition to Object to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Kerr-McGee Gathering, LLC, Frederick Compressor Station; Order Granting Petition for Objection to Title V Operating Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Marcal Paper Mills, Inc.; Order Granting in Part and Denying in Part Petition for Object to Title V Permit

EPA Pesticide Factsheets

This document may be of assistance in applying the Title V air operating permit regulations. This document is part of the Title V Petition Database available at www2.epa.gov/title-v-operating-permits/title-v-petition-database.

Effectiveness of Motivational Interviewing Interventions for Adolescent Substance Use Behavior Change: A Meta-Analytic Review

ERIC Educational Resources Information Center

Jensen, Chad D.; Cushing, Christopher C.; Aylward, Brandon S.; Craig, James T.; Sorell, Danielle M.; Steele, Ric G.

2011-01-01

Objective: This study was designed to quantitatively evaluate the effectiveness of motivational interviewing (MI) interventions for adolescent substance use behavior change. Method: Literature searches of electronic databases were undertaken in addition to manual reference searches of identified review articles. Databases searched include…

Are nutrient databases and nutrient analysis systems ready for the International implications of nutrigenomics?

USDA-ARS?s Scientific Manuscript database

Our objective is to discuss the implications internationally of the increased focus on nutrigenomics as the underlying basis for individualized health promotion and chronic disease prevention and the challenges presented to existing nutrient database and nutrient analysis systems by these trends. De...

IPD—the Immuno Polymorphism Database

PubMed Central

Robinson, James; Halliwell, Jason A.; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G. E.

2013-01-01

The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project. PMID:23180793

Species From the Heliothinae Complex (Lepidoptera: Noctuidae) in Tucumán, Argentina, an Update of Geographical Distribution of Helicoverpa armigera

PubMed Central

Murúa, M. Gabriela; Cazado, Lucas E.; Casmuz, Augusto; Herrero, M. Inés; Villagrán, M. Elvira; Vera, Alejandro; Sosa-Gómez, Daniel R.; Gastaminza, Gerardo

2016-01-01

The Heliothinae complex in Argentina encompasses Helicoverpa gelotopoeon (Dyar), Helicoverpa zea (Boddie), Helicoverpa armigera (Hübner), and Chloridea virescens (Fabricius). In Tucumán, the native species H. gelotopoeon is one of the most voracious soybean pests and also affects cotton and chickpea, even more in soybean-chickpea succession cropping systems. Differentiation of the Heliothinae complex in the egg, larva, and pupa stages is difficult. Therefore, the observation of the adult wing pattern design and male genitalia is useful to differentiate species. The objective of this study was to identify the species of the Heliothinae complex, determine population fluctuations of the Heliothinae complex in soybean and chickpea crops using male moths collected in pheromone traps in Tucuman province, and update the geographical distribution of H. armigera in Argentina. The species found were H. gelotopoeon, H. armigera, H. zea, and C. virescens. Regardless of province, county, crop, and year, the predominant species was H. gelotopoeon. Considering the population dynamics of H. gelotopoeon and H. armigera in chickpea and soybean crops, H. gelotopoeon was the most abundant species in both crops, in all years sampled, and the differences registered were significant. On the other hand, according to the Sistema Nacional Argentino de Vigilancia y Monitoreo de Plagas (SINAVIMO) database and our collections, H. armigera was recorded in eight provinces and 20 counties of Argentina, and its larvae were found on soybean, chickpea, sunflower crops and spiny plumeless thistle (Carduus acanthoides). This is the first report of H. armigera in sunflower and spiny plumeless thistle in Argentina. PMID:27324588

Visual short-term memory capacity for simple and complex objects.

PubMed

Luria, Roy; Sessa, Paola; Gotler, Alex; Jolicoeur, Pierre; Dell'Acqua, Roberto

2010-03-01

Does the capacity of visual short-term memory (VSTM) depend on the complexity of the objects represented in memory? Although some previous findings indicated lower capacity for more complex stimuli, other results suggest that complexity effects arise during retrieval (due to errors in the comparison process with what is in memory) that is not related to storage limitations of VSTM, per se. We used ERPs to track neuronal activity specifically related to retention in VSTM by measuring the sustained posterior contralateral negativity during a change detection task (which required detecting if an item was changed between a memory and a test array). The sustained posterior contralateral negativity, during the retention interval, was larger for complex objects than for simple objects, suggesting that neurons mediating VSTM needed to work harder to maintain more complex objects. This, in turn, is consistent with the view that VSTM capacity depends on complexity.

Development and characterization of a 3D high-resolution terrain database

NASA Astrophysics Data System (ADS)

Wilkosz, Aaron; Williams, Bryan L.; Motz, Steve

2000-07-01

A top-level description of methods used to generate elements of a high resolution 3D characterization database is presented. The database elements are defined as ground plane elevation map, vegetation height elevation map, material classification map, discrete man-made object map, and temperature radiance map. The paper will cover data collection by means of aerial photography, techniques of soft photogrammetry used to derive the elevation data, and the methodology followed to generate the material classification map. The discussion will feature the development of the database elements covering Fort Greely, Alaska. The developed databases are used by the US Army Aviation and Missile Command to evaluate the performance of various missile systems.

A subjective study and an objective metric to quantify the granularity level of textures

NASA Astrophysics Data System (ADS)

Subedar, Mahesh M.; Karam, Lina J.

2015-03-01

Texture granularity is an important visual characteristic that is useful in a variety of applications, including analysis, recognition, and compression, to name a few. A texture granularity measure can be used to quantify the perceived level of texture granularity. The granularity level of the textures is influenced by the size of the texture primitives. A primitive is defined as the smallest recognizable repetitive object in the texture. If the texture has large primitives then the perceived granularity level tends to be lower as compared to a texture with smaller primitives. In this work we are presenting a texture granularity database referred as GranTEX which consists of 30 textures with varying levels of primitive sizes and granularity levels. The GranTEX database consists of both natural and man-made textures. A subjective study is conducted to measure the perceived granularity level of textures present in the GranTEX database. An objective metric that automatically measures the perceived granularity level of textures is also presented as part of this work. It is shown that the proposed granularity metric correlates well with the subjective granularity scores.

Querying and Computing with BioCyc Databases

PubMed Central

Krummenacker, Markus; Paley, Suzanne; Mueller, Lukas; Yan, Thomas; Karp, Peter D.

2006-01-01

Summary We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases: access through multiple file formats, access through Application Program Interfaces (APIs) for LISP, Perl and Java, and SQL access through the BioWarehouse relational database. Availability The Pathway Tools software and 20 BioCyc DBs in Tiers 1 and 2 are freely available to academic users; fees apply to some types of commercial use. For download instructions see http://BioCyc.org/download.shtml PMID:15961440

Application of furniture images selection based on neural network

NASA Astrophysics Data System (ADS)

Wang, Yong; Gao, Wenwen; Wang, Ying

2018-05-01

In the construction of 2 million furniture image databases, aiming at the problem of low quality of database, a combination of CNN and Metric learning algorithm is proposed, which makes it possible to quickly and accurately remove duplicate and irrelevant samples in the furniture image database. Solve problems that images screening method is complex, the accuracy is not high, time-consuming is long. Deep learning algorithm achieve excellent image matching ability in actual furniture retrieval applications after improving data quality.

Creating a VAPEPS database: A VAPEPS tutorial

NASA Technical Reports Server (NTRS)

Graves, George

1989-01-01

A procedural method is outlined for creating a Vibroacoustic Payload Environment Prediction System (VAPEPS) Database. The method of presentation employs flowcharts of sequential VAPEPS Commands used to create a VAPEPS Database. The commands are accompanied by explanatory text to the right of the command in order to minimize the need for repetitive reference to the VAPEPS user's manual. The method is demonstrated by examples of varying complexity. It is assumed that the reader has acquired a basic knowledge of the VAPEPS software program.

Information mining in remote sensing imagery

NASA Astrophysics Data System (ADS)

Li, Jiang

The volume of remotely sensed imagery continues to grow at an enormous rate due to the advances in sensor technology, and our capability for collecting and storing images has greatly outpaced our ability to analyze and retrieve information from the images. This motivates us to develop image information mining techniques, which is very much an interdisciplinary endeavor drawing upon expertise in image processing, databases, information retrieval, machine learning, and software design. This dissertation proposes and implements an extensive remote sensing image information mining (ReSIM) system prototype for mining useful information implicitly stored in remote sensing imagery. The system consists of three modules: image processing subsystem, database subsystem, and visualization and graphical user interface (GUI) subsystem. Land cover and land use (LCLU) information corresponding to spectral characteristics is identified by supervised classification based on support vector machines (SVM) with automatic model selection, while textural features that characterize spatial information are extracted using Gabor wavelet coefficients. Within LCLU categories, textural features are clustered using an optimized k-means clustering approach to acquire search efficient space. The clusters are stored in an object-oriented database (OODB) with associated images indexed in an image database (IDB). A k-nearest neighbor search is performed using a query-by-example (QBE) approach. Furthermore, an automatic parametric contour tracing algorithm and an O(n) time piecewise linear polygonal approximation (PLPA) algorithm are developed for shape information mining of interesting objects within the image. A fuzzy object-oriented database based on the fuzzy object-oriented data (FOOD) model is developed to handle the fuzziness and uncertainty. Three specific applications are presented: integrated land cover and texture pattern mining, shape information mining for change detection of lakes, and fuzzy normalized difference vegetation index (NDVI) pattern mining. The study results show the effectiveness of the proposed system prototype and the potentials for other applications in remote sensing.

Landscape features, standards, and semantics in U.S. national topographic mapping databases

USGS Publications Warehouse

Varanka, Dalia

2009-01-01

The objective of this paper is to examine the contrast between local, field-surveyed topographical representation and feature representation in digital, centralized databases and to clarify their ontological implications. The semantics of these two approaches are contrasted by examining the categorization of features by subject domains inherent to national topographic mapping. When comparing five USGS topographic mapping domain and feature lists, results indicate that multiple semantic meanings and ontology rules were applied to the initial digital database, but were lost as databases became more centralized at national scales, and common semantics were replaced by technological terms.

The LSST Data Mining Research Agenda

NASA Astrophysics Data System (ADS)

Borne, K.; Becla, J.; Davidson, I.; Szalay, A.; Tyson, J. A.

2008-12-01

We describe features of the LSST science database that are amenable to scientific data mining, object classification, outlier identification, anomaly detection, image quality assurance, and survey science validation. The data mining research agenda includes: scalability (at petabytes scales) of existing machine learning and data mining algorithms; development of grid-enabled parallel data mining algorithms; designing a robust system for brokering classifications from the LSST event pipeline (which may produce 10,000 or more event alerts per night) multi-resolution methods for exploration of petascale databases; indexing of multi-attribute multi-dimensional astronomical databases (beyond spatial indexing) for rapid querying of petabyte databases; and more.

CRAVE: a database, middleware and visualization system for phenotype ontologies.

PubMed

Gkoutos, Georgios V; Green, Eain C J; Greenaway, Simon; Blake, Andrew; Mallon, Ann-Marie; Hancock, John M

2005-04-01

A major challenge in modern biology is to link genome sequence information to organismal function. In many organisms this is being done by characterizing phenotypes resulting from mutations. Efficiently expressing phenotypic information requires combinatorial use of ontologies. However tools are not currently available to visualize combinations of ontologies. Here we describe CRAVE (Concept Relation Assay Value Explorer), a package allowing storage, active updating and visualization of multiple ontologies. CRAVE is a web-accessible JAVA application that accesses an underlying MySQL database of ontologies via a JAVA persistent middleware layer (Chameleon). This maps the database tables into discrete JAVA classes and creates memory resident, interlinked objects corresponding to the ontology data. These JAVA objects are accessed via calls through the middleware's application programming interface. CRAVE allows simultaneous display and linking of multiple ontologies and searching using Boolean and advanced searches.

An ECG storage and retrieval system embedded in client server HIS utilizing object-oriented DB.

PubMed

Wang, C; Ohe, K; Sakurai, T; Nagase, T; Kaihara, S

1996-02-01

In the University of Tokyo Hospital, the improved client server HIS has been applied to clinical practice and physicians can order prescription, laboratory examination, ECG examination and radiographic examination, etc. directly by themselves and read results of these examinations, except medical signal waves, schema and image, on UNIX workstations. Recently, we designed and developed an ECG storage and retrieval system embedded in the client server HIS utilizing object-oriented database to take the first step in dealing with digitized signal, schema and image data and show waves, graphics, and images directly to physicians by the client server HIS. The system was developed based on object-oriented analysis and design, and implemented with object-oriented database management system (OODMS) and C++ programming language. In this paper, we describe the ECG data model, functions of the storage and retrieval system, features of user interface and the result of its implementation in the HIS.

BμG@Sbase—a microbial gene expression and comparative genomic database

PubMed Central

Witney, Adam A.; Waldron, Denise E.; Brooks, Lucy A.; Tyler, Richard H.; Withers, Michael; Stoker, Neil G.; Wren, Brendan W.; Butcher, Philip D.; Hinds, Jason

2012-01-01

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future. PMID:21948792

BμG@Sbase--a microbial gene expression and comparative genomic database.

PubMed

Witney, Adam A; Waldron, Denise E; Brooks, Lucy A; Tyler, Richard H; Withers, Michael; Stoker, Neil G; Wren, Brendan W; Butcher, Philip D; Hinds, Jason

2012-01-01

The reducing cost of high-throughput functional genomic technologies is creating a deluge of high volume, complex data, placing the burden on bioinformatics resources and tool development. The Bacterial Microarray Group at St George's (BμG@S) has been at the forefront of bacterial microarray design and analysis for over a decade and while serving as a hub of a global network of microbial research groups has developed BμG@Sbase, a microbial gene expression and comparative genomic database. BμG@Sbase (http://bugs.sgul.ac.uk/bugsbase/) is a web-browsable, expertly curated, MIAME-compliant database that stores comprehensive experimental annotation and multiple raw and analysed data formats. Consistent annotation is enabled through a structured set of web forms, which guide the user through the process following a set of best practices and controlled vocabulary. The database currently contains 86 expertly curated publicly available data sets (with a further 124 not yet published) and full annotation information for 59 bacterial microarray designs. The data can be browsed and queried using an explorer-like interface; integrating intuitive tree diagrams to present complex experimental details clearly and concisely. Furthermore the modular design of the database will provide a robust platform for integrating other data types beyond microarrays into a more Systems analysis based future.

Availability and Diversity of Training Programs for Responders to International Disasters and Complex Humanitarian Emergencies

PubMed Central

Jacquet, Gabrielle A.; Obi, Chioma C.; Chang, Mary P.; Bayram, Jamil D.

2014-01-01

Introduction: Volunteers and members of relief organizations increasingly seek formal training prior to international field deployment. This paper identifies training programs for personnel responding to international disasters and complex humanitarian emergencies, and provides concise information – if available- regarding the founding organization, year established, location, cost, duration of training, participants targeted, and the content of each program. Methods: An environmental scan was conducted through a combination of a peer-reviewed literature search and an open Internet search for the training programs. Literature search engines included EMBASE, Cochrane, Scopus, PubMed, Web of Science databases using the search terms “international,” “disaster,” “complex humanitarian emergencies,” “training,” and “humanitarian response”. Both searches were conducted between January 2, 2013 and September 12, 2013. Results: 14 peer-reviewed articles mentioned or described eight training programs, while open Internet search revealed 13 additional programs. In total, twenty-one training programs were identified as currently available for responders to international disasters and CHE. Each of the programs identified has different goals and objectives, duration, expenses, targeted trainees and modules. Each of the programs identified has different goals and objectives, duration, expenses, targeted trainees and modules. Seven programs (33%) are free of charge and four programs (19%) focus on the mental aspects of disasters. The mean duration for each training program is 5 to 7 days. Fourteen of the trainings are conducted in multiple locations (66%), two in Cuba (9%) and two in Australia (9%). The cost-reported in US dollars- ranges from $100 to $2,400 with a mean cost of $480 and a median cost of $135. Most of the programs are open to the public, but some are only available by invitation only, such as the International Mobilization Preparation for Action (IMPACT) and the United Nations Humanitarian Civil-Military Coordination (UN-CMCoord) Field Course. Conclusions: A variety of training programs are available for responders to disasters and complex humanitarian emergencies. These programs vary in their objectives, audiences, modules, geographical locations, eligibility and financial cost. This paper presents an overview of available programs and serves as a resource for potential responders interested in capacity-building training prior to deployment. PMID:24987573

HEDD: Human Enhancer Disease Database

PubMed Central

Wang, Zhen; Zhang, Quanwei; Zhang, Wen; Lin, Jhih-Rong; Cai, Ying; Mitra, Joydeep

2018-01-01

Abstract Enhancers, as specialized genomic cis-regulatory elements, activate transcription of their target genes and play an important role in pathogenesis of many human complex diseases. Despite recent systematic identification of them in the human genome, currently there is an urgent need for comprehensive annotation databases of human enhancers with a focus on their disease connections. In response, we built the Human Enhancer Disease Database (HEDD) to facilitate studies of enhancers and their potential roles in human complex diseases. HEDD currently provides comprehensive genomic information for ∼2.8 million human enhancers identified by ENCODE, FANTOM5 and RoadMap with disease association scores based on enhancer–gene and gene–disease connections. It also provides Web-based analytical tools to visualize enhancer networks and score enhancers given a set of selected genes in a specific gene network. HEDD is freely accessible at http://zdzlab.einstein.yu.edu/1/hedd.php. PMID:29077884

Centre-based restricted nearest feature plane with angle classifier for face recognition

NASA Astrophysics Data System (ADS)

Tang, Linlin; Lu, Huifen; Zhao, Liang; Li, Zuohua

2017-10-01

An improved classifier based on the nearest feature plane (NFP), called the centre-based restricted nearest feature plane with the angle (RNFPA) classifier, is proposed for the face recognition problems here. The famous NFP uses the geometrical information of samples to increase the number of training samples, but it increases the computation complexity and it also has an inaccuracy problem coursed by the extended feature plane. To solve the above problems, RNFPA exploits a centre-based feature plane and utilizes a threshold of angle to restrict extended feature space. By choosing the appropriate angle threshold, RNFPA can improve the performance and decrease computation complexity. Experiments in the AT&T face database, AR face database and FERET face database are used to evaluate the proposed classifier. Compared with the original NFP classifier, the nearest feature line (NFL) classifier, the nearest neighbour (NN) classifier and some other improved NFP classifiers, the proposed one achieves competitive performance.

Ensemble gene function prediction database reveals genes important for complex I formation in Arabidopsis thaliana.

PubMed

Hansen, Bjoern Oest; Meyer, Etienne H; Ferrari, Camilla; Vaid, Neha; Movahedi, Sara; Vandepoele, Klaas; Nikoloski, Zoran; Mutwil, Marek

2018-03-01

Recent advances in gene function prediction rely on ensemble approaches that integrate results from multiple inference methods to produce superior predictions. Yet, these developments remain largely unexplored in plants. We have explored and compared two methods to integrate 10 gene co-function networks for Arabidopsis thaliana and demonstrate how the integration of these networks produces more accurate gene function predictions for a larger fraction of genes with unknown function. These predictions were used to identify genes involved in mitochondrial complex I formation, and for five of them, we confirmed the predictions experimentally. The ensemble predictions are provided as a user-friendly online database, EnsembleNet. The methods presented here demonstrate that ensemble gene function prediction is a powerful method to boost prediction performance, whereas the EnsembleNet database provides a cutting-edge community tool to guide experimentalists. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Massive parallelization of serial inference algorithms for a complex generalized linear model

PubMed Central

Suchard, Marc A.; Simpson, Shawn E.; Zorych, Ivan; Ryan, Patrick; Madigan, David

2014-01-01

Following a series of high-profile drug safety disasters in recent years, many countries are redoubling their efforts to ensure the safety of licensed medical products. Large-scale observational databases such as claims databases or electronic health record systems are attracting particular attention in this regard, but present significant methodological and computational concerns. In this paper we show how high-performance statistical computation, including graphics processing units, relatively inexpensive highly parallel computing devices, can enable complex methods in large databases. We focus on optimization and massive parallelization of cyclic coordinate descent approaches to fit a conditioned generalized linear model involving tens of millions of observations and thousands of predictors in a Bayesian context. We find orders-of-magnitude improvement in overall run-time. Coordinate descent approaches are ubiquitous in high-dimensional statistics and the algorithms we propose open up exciting new methodological possibilities with the potential to significantly improve drug safety. PMID:25328363

Quantify spatial relations to discover handwritten graphical symbols

NASA Astrophysics Data System (ADS)

Li, Jinpeng; Mouchère, Harold; Viard-Gaudin, Christian

2012-01-01

To model a handwritten graphical language, spatial relations describe how the strokes are positioned in the 2-dimensional space. Most of existing handwriting recognition systems make use of some predefined spatial relations. However, considering a complex graphical language, it is hard to express manually all the spatial relations. Another possibility would be to use a clustering technique to discover the spatial relations. In this paper, we discuss how to create a relational graph between strokes (nodes) labeled with graphemes in a graphical language. Then we vectorize spatial relations (edges) for clustering and quantization. As the targeted application, we extract the repetitive sub-graphs (graphical symbols) composed of graphemes and learned spatial relations. On two handwriting databases, a simple mathematical expression database and a complex flowchart database, the unsupervised spatial relations outperform the predefined spatial relations. In addition, we visualize the frequent patterns on two text-lines containing Chinese characters.

MM-MDS: a multidimensional scaling database with similarity ratings for 240 object categories from the Massive Memory picture database.

PubMed

Hout, Michael C; Goldinger, Stephen D; Brady, Kyle J

2014-01-01

Cognitive theories in visual attention and perception, categorization, and memory often critically rely on concepts of similarity among objects, and empirically require measures of "sameness" among their stimuli. For instance, a researcher may require similarity estimates among multiple exemplars of a target category in visual search, or targets and lures in recognition memory. Quantifying similarity, however, is challenging when everyday items are the desired stimulus set, particularly when researchers require several different pictures from the same category. In this article, we document a new multidimensional scaling database with similarity ratings for 240 categories, each containing color photographs of 16-17 exemplar objects. We collected similarity ratings using the spatial arrangement method. Reports include: the multidimensional scaling solutions for each category, up to five dimensions, stress and fit measures, coordinate locations for each stimulus, and two new classifications. For each picture, we categorized the item's prototypicality, indexed by its proximity to other items in the space. We also classified pairs of images along a continuum of similarity, by assessing the overall arrangement of each MDS space. These similarity ratings will be useful to any researcher that wishes to control the similarity of experimental stimuli according to an objective quantification of "sameness."

A flexible object-oriented software framework for developing complex multimedia simulations.

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

Sydelko, P. J.; Dolph, J. E.; Christiansen, J. H.

Decision makers involved in brownfields redevelopment and long-term stewardship must consider environmental conditions, future-use potential, site ownership, area infrastructure, funding resources, cost recovery, regulations, risk and liability management, community relations, and expected return on investment in a comprehensive and integrated fashion to achieve desired results. Successful brownfields redevelopment requires the ability to assess the impacts of redevelopment options on multiple interrelated aspects of the ecosystem, both natural and societal. Computer-based tools, such as simulation models, databases, and geographical information systems (GISs) can be used to address brownfields planning and project execution. The transparent integration of these tools into a comprehensivemore » and dynamic decision support system would greatly enhance the brownfields assessment process. Such a system needs to be able to adapt to shifting and expanding analytical requirements and contexts. The Dynamic Information Architecture System (DIAS) is a flexible, extensible, object-oriented framework for developing and maintaining complex multidisciplinary simulations of a wide variety of application domains. The modeling domain of a specific DIAS-based simulation is determined by (1) software objects that represent the real-world entities that comprise the problem space (atmosphere, watershed, human), and (2) simulation models and other data processing applications that express the dynamic behaviors of the domain entities. Models and applications used to express dynamic behaviors can be either internal or external to DIAS, including existing legacy models written in various languages (FORTRAN, C, etc.). The flexible design framework of DIAS makes the objects adjustable to the context of the problem without a great deal of recoding. The DIAS Spatial Data Set facility allows parameters to vary spatially depending on the simulation context according to any of a number of 1-D, 2-D, or 3-D topologies. DIAS is also capable of interacting with other GIS packages and can import many standard spatial data formats. DIAS simulation capabilities can also be extended by including societal process models. Models that implement societal behaviors of individuals and organizations within larger DIAS-based natural systems simulations allow for interaction and feedback among natural and societal processes. The ability to simulate the complex interplay of multimedia processes makes DIAS a promising tool for constructing applications for comprehensive community planning, including the assessment of multiple development and redevelopment scenarios.« less

Impact of Resident Involvement in Neurosurgery: An American College of Surgeons’ National Surgical Quality Improvement Program Database Analysis of 33,977 Patients

PubMed Central

Kumar, Prateek; Seicean, Sinziana; Neuhauser, Duncan; Selman, Warren R.; Bambakidis, Nicholas C.

2018-01-01

Objective There is conflicting and limited literature on the effect of intraoperative resident involvement on surgical outcomes. Our study assessed effects of resident involvement on outcomes in patients undergoing neurosurgery. Methods We identified 33,977 adult neurosurgical cases from 374 hospitals in the 2006–2012 National Surgical Quality Improvement Program, a prospectively collected national database with established reproducibility and validity. Outcomes were compared according to resident involvement before and after 1:1 matching on procedure and perioperative risk factors. Results Resident involvement was documented in 13,654 cases. We matched 10,170 resident-involved cases with 10,170 attending-alone. In the matched sample, resident involvement was associated with increased surgery duration (average, 34 minutes) and slight increases in odds for prolonged hospital stay (odds ratio, 1.2; 95% confidence interval [CI], 1.2–1.3) and complications (odds ratio, 1.2; 95% CI, 1.1–1.3) including infections (odds ratio, 1.4; 95% CI, 1.2–1.7). Increased risk for infections persisted after controlling for surgery duration (odds ratio, 1.3; 95% CI, 1.1–1.5). The majority of cases were spine surgeries, and resident involvement was not associated with morbidity or mortality for malignant tumor and aneurysm patients. Training level of residents was not associated with differences in outcomes. Conclusion Resident involvement was more common in sicker patients undergoing complex procedures, consistent with academic centers undertaking more complex cases. After controlling for patient and intraoperative characteristics, resident involvement in neurosurgical cases continued to be associated with longer surgical duration and slightly higher infection rates. Longer surgery duration did not account for differences in infection rates. PMID:29656619

Expert Search Strategies: The Information Retrieval Practices of Healthcare Information Professionals

PubMed Central

2017-01-01

Background Healthcare information professionals play a key role in closing the knowledge gap between medical research and clinical practice. Their work involves meticulous searching of literature databases using complex search strategies that can consist of hundreds of keywords, operators, and ontology terms. This process is prone to error and can lead to inefficiency and bias if performed incorrectly. Objective The aim of this study was to investigate the search behavior of healthcare information professionals, uncovering their needs, goals, and requirements for information retrieval systems. Methods A survey was distributed to healthcare information professionals via professional association email discussion lists. It investigated the search tasks they undertake, their techniques for search strategy formulation, their approaches to evaluating search results, and their preferred functionality for searching library-style databases. The popular literature search system PubMed was then evaluated to determine the extent to which their needs were met. Results The 107 respondents indicated that their information retrieval process relied on the use of complex, repeatable, and transparent search strategies. On average it took 60 minutes to formulate a search strategy, with a search task taking 4 hours and consisting of 15 strategy lines. Respondents reviewed a median of 175 results per search task, far more than they would ideally like (100). The most desired features of a search system were merging search queries and combining search results. Conclusions Healthcare information professionals routinely address some of the most challenging information retrieval problems of any profession. However, their needs are not fully supported by current literature search systems and there is demand for improved functionality, in particular regarding the development and management of search strategies. PMID:28970190

Does an English appeal court ruling increase the risks of miscarriages of justice when complex DNA profiles are searched against the national DNA database?

PubMed

Gill, P; Bleka, Ø; Egeland, T

2014-11-01

Likelihood ratio (LR) methods to interpret multi-contributor, low template, complex DNA mixtures are becoming standard practice. The next major development will be to introduce search engines based on the new methods to interrogate very large national DNA databases, such as those held by China, the USA and the UK. Here we describe a rapid method that was used to assign a LR to each individual member of database of 5 million genotypes which can be ranked in order. Previous authors have only considered database trawls in the context of binary match or non-match criteria. However, the concept of match/non-match no longer applies within the new paradigm introduced, since the distribution of resultant LRs is continuous for practical purposes. An English appeal court decision allows scientists to routinely report complex DNA profiles using nothing more than their subjective personal 'experience of casework' and 'observations' in order to apply an expression of the rarity of an evidential sample. This ruling must be considered in context of a recent high profile English case, where an individual was extracted from a database and wrongly accused of a serious crime. In this case the DNA evidence was used to negate the overwhelming exculpatory (non-DNA) evidence. Demonstrable confirmation bias, also known as the 'CSI-effect, seriously affected the investigation. The case demonstrated that in practice, databases could be used to select and prosecute an individual, simply because he ranked high in the list of possible matches. We have identified this phenomenon as a cognitive error which we term: 'the naïve investigator effect'. We take the opportunity to test the performance of database extraction strategies either by using a simple matching allele count (MAC) method or LR. The example heard by the appeal court is used as the exemplar case. It is demonstrated that the LR search-method offers substantial benefits compared to searches based on simple matching allele count (MAC) methods. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

PubMed

Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

2018-05-08

Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on docking calculations with biochemical pathways and enables users to easily and quickly assess PPI feasibilities by archiving PPI predictions. MEGADOCK-Web also promotes the discovery of new PPIs and protein functions and is freely available for use at http://www.bi.cs.titech.ac.jp/megadock-web/ .

Towards communication-efficient quantum oblivious key distribution

NASA Astrophysics Data System (ADS)

Panduranga Rao, M. V.; Jakobi, M.

2013-01-01

Symmetrically private information retrieval, a fundamental problem in the field of secure multiparty computation, is defined as follows: A database D of N bits held by Bob is queried by a user Alice who is interested in the bit Db in such a way that (1) Alice learns Db and only Db and (2) Bob does not learn anything about Alice's choice b. While solutions to this problem in the classical domain rely largely on unproven computational complexity theoretic assumptions, it is also known that perfect solutions that guarantee both database and user privacy are impossible in the quantum domain. Jakobi [Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.83.022301 83, 022301 (2011)] proposed a protocol for oblivious transfer using well-known quantum key device (QKD) techniques to establish an oblivious key to solve this problem. Their solution provided a good degree of database and user privacy (using physical principles like the impossibility of perfectly distinguishing nonorthogonal quantum states and the impossibility of superluminal communication) while being loss-resistant and implementable with commercial QKD devices (due to the use of the Scarani-Acin-Ribordy-Gisin 2004 protocol). However, their quantum oblivious key distribution (QOKD) protocol requires a communication complexity of O(NlogN). Since modern databases can be extremely large, it is important to reduce this communication as much as possible. In this paper, we first suggest a modification of their protocol wherein the number of qubits that need to be exchanged is reduced to O(N). A subsequent generalization reduces the quantum communication complexity even further in such a way that only a few hundred qubits are needed to be transferred even for very large databases.

Validation of SmartRank: A likelihood ratio software for searching national DNA databases with complex DNA profiles.

PubMed

Benschop, Corina C G; van de Merwe, Linda; de Jong, Jeroen; Vanvooren, Vanessa; Kempenaers, Morgane; Kees van der Beek, C P; Barni, Filippo; Reyes, Eusebio López; Moulin, Léa; Pene, Laurent; Haned, Hinda; Sijen, Titia

2017-07-01

Searching a national DNA database with complex and incomplete profiles usually yields very large numbers of possible matches that can present many candidate suspects to be further investigated by the forensic scientist and/or police. Current practice in most forensic laboratories consists of ordering these 'hits' based on the number of matching alleles with the searched profile. Thus, candidate profiles that share the same number of matching alleles are not differentiated and due to the lack of other ranking criteria for the candidate list it may be difficult to discern a true match from the false positives or notice that all candidates are in fact false positives. SmartRank was developed to put forward only relevant candidates and rank them accordingly. The SmartRank software computes a likelihood ratio (LR) for the searched profile and each profile in the DNA database and ranks database entries above a defined LR threshold according to the calculated LR. In this study, we examined for mixed DNA profiles of variable complexity whether the true donors are retrieved, what the number of false positives above an LR threshold is and the ranking position of the true donors. Using 343 mixed DNA profiles over 750 SmartRank searches were performed. In addition, the performance of SmartRank and CODIS were compared regarding DNA database searches and SmartRank was found complementary to CODIS. We also describe the applicable domain of SmartRank and provide guidelines. The SmartRank software is open-source and freely available. Using the best practice guidelines, SmartRank enables obtaining investigative leads in criminal cases lacking a suspect. Copyright © 2017 Elsevier B.V. All rights reserved.

System and method for authentication

DOEpatents

Duerksen, Gary L.; Miller, Seth A.

2015-12-29

Described are methods and systems for determining authenticity. For example, the method may include providing an object of authentication, capturing characteristic data from the object of authentication, deriving authentication data from the characteristic data of the object of authentication, and comparing the authentication data with an electronic database comprising reference authentication data to provide an authenticity score for the object of authentication. The reference authentication data may correspond to one or more reference objects of authentication other than the object of authentication.

RAPTOR-scan: Identifying and Tracking Objects Through Thousands of Sky Images

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

Davidoff, Sherri; Wozniak, Przemyslaw

2004-09-28

The RAPTOR-scan system mines data for optical transients associated with gamma-ray bursts and is used to create a catalog for the RAPTOR telescope system. RAPTOR-scan can detect and track individual astronomical objects across data sets containing millions of observed points.Accurately identifying a real object over many optical images (clustering the individual appearances) is necessary in order to analyze object light curves. To achieve this, RAPTOR telescope observations are sent in real time to a database. Each morning, a program based on the DBSCAN algorithm clusters the observations and labels each one with an object identifier. Once clustering is complete, themore » analysis program may be used to query the database and produce light curves, maps of the sky field, or other informative displays.Although RAPTOR-scan was designed for the RAPTOR optical telescope system, it is a general tool designed to identify objects in a collection of astronomical data and facilitate quick data analysis. RAPTOR-scan will be released as free software under the GNU General Public License.« less

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.

PubMed

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

2007-07-27

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

Pilot Aircraft Interface Objectives/Rationale

NASA Technical Reports Server (NTRS)

Shively, Jay

2010-01-01

Objective: Database and proof of concept for guidelines for GCS compliance a) Rationale: 1) Provide research test-bed to develop guidelines. 2) Modify GCS for NAS Compliance to provide proof of concept. b) Approach: 1) Assess current state of GCS technology. 2) Information Requirements Definition. 3) SME Workshop. 4) Modify an Existing GCS for NAS Compliance. 5) Define exemplar UAS (choose system to develop prototype). 6) Define Candidate Displays & Controls. 7) Evaluate/ refine in Simulations. 8) Demonstrate in flight. c) Deliverables: 1) Information Requirements Report. 2) Workshop Proceedings. 3) Technical Reports/ papers on Simulations & Flight Demo. 4) Database for guidelines.

Research on computer virus database management system

NASA Astrophysics Data System (ADS)

Qi, Guoquan

2011-12-01

The growing proliferation of computer viruses becomes the lethal threat and research focus of the security of network information. While new virus is emerging, the number of viruses is growing, virus classification increasing complex. Virus naming because of agencies' capture time differences can not be unified. Although each agency has its own virus database, the communication between each other lacks, or virus information is incomplete, or a small number of sample information. This paper introduces the current construction status of the virus database at home and abroad, analyzes how to standardize and complete description of virus characteristics, and then gives the information integrity, storage security and manageable computer virus database design scheme.

The Watershed and River Systems Management Program: Decision Support for Water- and Environmental-Resource Management

NASA Astrophysics Data System (ADS)

Leavesley, G.; Markstrom, S.; Frevert, D.; Fulp, T.; Zagona, E.; Viger, R.

2004-12-01

Increasing demands for limited fresh-water supplies, and increasing complexity of water-management issues, present the water-resource manager with the difficult task of achieving an equitable balance of water allocation among a diverse group of water users. The Watershed and River System Management Program (WARSMP) is a cooperative effort between the U.S. Geological Survey (USGS) and the Bureau of Reclamation (BOR) to develop and deploy a database-centered, decision-support system (DSS) to address these multi-objective, resource-management problems. The decision-support system couples the USGS Modular Modeling System (MMS) with the BOR RiverWare tools using a shared relational database. MMS is an integrated system of computer software that provides a research and operational framework to support the development and integration of a wide variety of hydrologic and ecosystem models, and their application to water- and ecosystem-resource management. RiverWare is an object-oriented reservoir and river-system modeling framework developed to provide tools for evaluating and applying water-allocation and management strategies. The modeling capabilities of MMS and Riverware include simulating watershed runoff, reservoir inflows, and the impacts of resource-management decisions on municipal, agricultural, and industrial water users, environmental concerns, power generation, and recreational interests. Forecasts of future climatic conditions are a key component in the application of MMS models to resource-management decisions. Forecast methods applied in MMS include a modified version of the National Weather Service's Extended Streamflow Prediction Program (ESP) and statistical downscaling from atmospheric models. The WARSMP DSS is currently operational in the Gunnison River Basin, Colorado; Yakima River Basin, Washington; Rio Grande Basin in Colorado and New Mexico; and Truckee River Basin in California and Nevada.