A Standard-Driven Data Dictionary for Data Harmonization of Heterogeneous Datasets in Urban Geological Information Systems

NASA Astrophysics Data System (ADS)

Liu, G.; Wu, C.; Li, X.; Song, P.

2013-12-01

The 3D urban geological information system has been a major part of the national urban geological survey project of China Geological Survey in recent years. Large amount of multi-source and multi-subject data are to be stored in the urban geological databases. There are various models and vocabularies drafted and applied by industrial companies in urban geological data. The issues such as duplicate and ambiguous definition of terms and different coding structure increase the difficulty of information sharing and data integration. To solve this problem, we proposed a national standard-driven information classification and coding method to effectively store and integrate urban geological data, and we applied the data dictionary technology to achieve structural and standard data storage. The overall purpose of this work is to set up a common data platform to provide information sharing service. Research progresses are as follows: (1) A unified classification and coding method for multi-source data based on national standards. Underlying national standards include GB 9649-88 for geology and GB/T 13923-2006 for geography. Current industrial models are compared with national standards to build a mapping table. The attributes of various urban geological data entity models are reduced to several categories according to their application phases and domains. Then a logical data model is set up as a standard format to design data file structures for a relational database. (2) A multi-level data dictionary for data standardization constraint. Three levels of data dictionary are designed: model data dictionary is used to manage system database files and enhance maintenance of the whole database system; attribute dictionary organizes fields used in database tables; term and code dictionary is applied to provide a standard for urban information system by adopting appropriate classification and coding methods; comprehensive data dictionary manages system operation and security. (3) An extension to system data management function based on data dictionary. Data item constraint input function is making use of the standard term and code dictionary to get standard input result. Attribute dictionary organizes all the fields of an urban geological information database to ensure the consistency of term use for fields. Model dictionary is used to generate a database operation interface automatically with standard semantic content via term and code dictionary. The above method and technology have been applied to the construction of Fuzhou Urban Geological Information System, South-East China with satisfactory results.

Data Auditor: Analyzing Data Quality Using Pattern Tableaux

NASA Astrophysics Data System (ADS)

Srivastava, Divesh

Monitoring databases maintain configuration and measurement tables about computer systems, such as networks and computing clusters, and serve important business functions, such as troubleshooting customer problems, analyzing equipment failures, planning system upgrades, etc. These databases are prone to many data quality issues: configuration tables may be incorrect due to data entry errors, while measurement tables may be affected by incorrect, missing, duplicate and delayed polls. We describe Data Auditor, a tool for analyzing data quality and exploring data semantics of monitoring databases. Given a user-supplied constraint, such as a boolean predicate expected to be satisfied by every tuple, a functional dependency, or an inclusion dependency, Data Auditor computes "pattern tableaux", which are concise summaries of subsets of the data that satisfy or fail the constraint. We discuss the architecture of Data Auditor, including the supported types of constraints and the tableau generation mechanism. We also show the utility of our approach on an operational network monitoring database.

EOSCUBE: A Constraint Database System for High-Level Specification and Efficient Generation of EOSDIS Products. Phase 1; Proof-of-Concept

NASA Technical Reports Server (NTRS)

Brodsky, Alexander; Segal, Victor E.

1999-01-01

The EOSCUBE constraint database system is designed to be a software productivity tool for high-level specification and efficient generation of EOSDIS and other scientific products. These products are typically derived from large volumes of multidimensional data which are collected via a range of scientific instruments.

Design and Implementation of a Threaded Search Engine for Tour Recommendation Systems

NASA Astrophysics Data System (ADS)

Lee, Junghoon; Park, Gyung-Leen; Ko, Jin-Hee; Shin, In-Hye; Kang, Mikyung

This paper implements a threaded scan engine for the O(n!) search space and measures its performance, aiming at providing a responsive tour recommendation and scheduling service. As a preliminary step of integrating POI ontology, mobile object database, and personalization profile for the development of new vehicular telematics services, this implementation can give a useful guideline to design a challenging and computation-intensive vehicular telematics service. The implemented engine allocates the subtree to the respective threads and makes them run concurrently exploiting the primitives provided by the operating system and the underlying multiprocessor architecture. It also makes it easy to add a variety of constraints, for example, the search tree is pruned if the cost of partial allocation already exceeds the current best. The performance measurement result shows that the service can run even in the low-power telematics device when the number of destinations does not exceed 15, with an appropriate constraint processing.

X-48B Phase 1 Flight Maneuver Database and ICP Airspace Constraint Analysis

NASA Technical Reports Server (NTRS)

Fast, Peter Alan

2010-01-01

The work preformed during the Summer 2010 by Peter Fast. The main tasks assigned were to update and improve the X-48 Flight Maneuver Database and conduct an Airspace Constraint Analysis for the Remotely Operated Aircraft Area used to flight test Unmanned Arial Vehicles. The final task was to develop and demonstrate a working knowledge of flight control theory.

Integration of gene normalization stages and co-reference resolution using a Markov logic network.

PubMed

Dai, Hong-Jie; Chang, Yen-Ching; Tsai, Richard Tzong-Han; Hsu, Wen-Lian

2011-09-15

Gene normalization (GN) is the task of normalizing a textual gene mention to a unique gene database ID. Traditional top performing GN systems usually need to consider several constraints to make decisions in the normalization process, including filtering out false positives, or disambiguating an ambiguous gene mention, to improve system performance. However, these constraints are usually executed in several separate stages and cannot use each other's input/output interactively. In this article, we propose a novel approach that employs a Markov logic network (MLN) to model the constraints used in the GN task. Firstly, we show how various constraints can be formulated and combined in an MLN. Secondly, we are the first to apply the two main concepts of co-reference resolution-discourse salience in centering theory and transitivity-to GN models. Furthermore, to make our results more relevant to developers of information extraction applications, we adopt the instance-based precision/recall/F-measure (PRF) in addition to the article-wide PRF to assess system performance. Experimental results show that our system outperforms baseline and state-of-the-art systems under two evaluation schemes. Through further analysis, we have found several unexplored challenges in the GN task. hongjie@iis.sinica.edu.tw Supplementary data are available at Bioinformatics online.

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.

Expediting topology data gathering for the TOPDB database.

PubMed

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

2015-01-01

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

JAMSTEC DARWIN Database Assimilates GANSEKI and COEDO

NASA Astrophysics Data System (ADS)

Tomiyama, T.; Toyoda, Y.; Horikawa, H.; Sasaki, T.; Fukuda, K.; Hase, H.; Saito, H.

2017-12-01

Introduction: Japan Agency for Marine-Earth Science and Technology (JAMSTEC) archives data and samples obtained by JAMSTEC research vessels and submersibles. As a common property of the human society, JAMSTEC archive is open for public users with scientific/educational purposes [1]. For publicizing its data and samples online, JAMSTEC is operating NUUNKUI data sites [2], a group of several databases for various data and sample types. For years, data and metadata of JAMSTEC rock samples, sediment core samples and cruise/dive observation were publicized through databases named GANSEKI, COEDO, and DARWIN, respectively. However, because they had different user interfaces and data structures, these services were somewhat confusing for unfamiliar users. Maintenance costs of multiple hardware and software were also problematic for performing sustainable services and continuous improvements. Database Integration: In 2017, GANSEKI, COEDO and DARWIN were integrated into DARWIN+ [3]. The update also included implementation of map-search function as a substitute of closed portal site. Major functions of previous systems were incorporated into the new system; users can perform the complex search, by thumbnail browsing, map area, keyword filtering, and metadata constraints. As for data handling, the new system is more flexible, allowing the entry of variety of additional data types. Data Management: After the DARWIN major update, JAMSTEC data & sample team has been dealing with minor issues of individual sample data/metadata which sometimes need manual modification to be transferred to the new system. Some new data sets, such as onboard sample photos and surface close-up photos of rock samples, are getting available online. Geochemical data of sediment core samples will supposedly be added in the near future. Reference: [1] http://www.jamstec.go.jp/e/database/data_policy.html [2] http://www.godac.jamstec.go.jp/jmedia/portal/e/ [3] http://www.godac.jamstec.go.jp/darwin/e/

Use of information on disease diagnoses from databases for animal health economic, welfare and food safety purposes: strengths and limitations of recordings.

PubMed

Houe, Hans; Gardner, Ian Andrew; Nielsen, Liza Rosenbaum

2011-01-01

Many animal health, welfare and food safety databases include data on clinical and test-based disease diagnoses. However, the circumstances and constraints for establishing the diagnoses vary considerably among databases. Therefore results based on different databases are difficult to compare and compilation of data in order to perform meta-analysis is almost impossible. Nevertheless, diagnostic information collected either routinely or in research projects is valuable in cross comparisons between databases, but there is a need for improved transparency and documentation of the data and the performance characteristics of tests used to establish diagnoses. The objective of this paper is to outline the circumstances and constraints for recording of disease diagnoses in different types of databases, and to discuss these in the context of disease diagnoses when using them for additional purposes, including research. Finally some limitations and recommendations for use of data and for recording of diagnostic information in the future are given. It is concluded that many research questions have such a specific objective that investigators need to collect their own data. However, there are also examples, where a minimal amount of extra information or continued validation could make sufficient improvement of secondary data to be used for other purposes. Regardless, researchers should always carefully evaluate the opportunities and constraints when they decide to use secondary data. If the data in the existing databases are not sufficiently valid, researchers may have to collect their own data, but improved recording of diagnostic data may improve the usefulness of secondary diagnostic data in the future.

Virasoro constraints and polynomial recursion for the linear Hodge integrals

NASA Astrophysics Data System (ADS)

Guo, Shuai; Wang, Gehao

2017-04-01

The Hodge tau-function is a generating function for the linear Hodge integrals. It is also a tau-function of the KP hierarchy. In this paper, we first present the Virasoro constraints for the Hodge tau-function in the explicit form of the Virasoro equations. The expression of our Virasoro constraints is simply a linear combination of the Virasoro operators, where the coefficients are restored from a power series for the Lambert W function. Then, using this result, we deduce a simple version of the Virasoro constraints for the linear Hodge partition function, where the coefficients are restored from the Gamma function. Finally, we establish the equivalence relation between the Virasoro constraints and polynomial recursion formula for the linear Hodge integrals.

Recent development in low-constraint fracture toughness testing for structural integrity assessment of pipelines

NASA Astrophysics Data System (ADS)

Kang, Jidong; Gianetto, James A.; Tyson, William R.

2018-03-01

Fracture toughness measurement is an integral part of structural integrity assessment of pipelines. Traditionally, a single-edge-notched bend (SE(B)) specimen with a deep crack is recommended in many existing pipeline structural integrity assessment procedures. Such a test provides high constraint and therefore conservative fracture toughness results. However, for girth welds in service, defects are usually subjected to primarily tensile loading where the constraint is usually much lower than in the three-point bend case. Moreover, there is increasing use of strain-based design of pipelines that allows applied strains above yield. Low-constraint toughness tests represent more realistic loading conditions for girth weld defects, and the corresponding increased toughness can minimize unnecessary conservatism in assessments. In this review, we present recent developments in low-constraint fracture toughness testing, specifically using single-edgenotched tension specimens, SENT or SE(T). We focus our review on the test procedure development and automation, round-robin test results and some common concerns such as the effect of crack tip, crack size monitoring techniques, and testing at low temperatures. Examples are also given of the integration of fracture toughness data from SE(T) tests into structural integrity assessment.

Projected Regression Methods for Inverting Fredholm Integrals: Formalism and Application to Analytical Continuation

NASA Astrophysics Data System (ADS)

Arsenault, Louis-Francois; Neuberg, Richard; Hannah, Lauren A.; Millis, Andrew J.

We present a machine learning-based statistical regression approach to the inversion of Fredholm integrals of the first kind by studying an important example for the quantum materials community, the analytical continuation problem of quantum many-body physics. It involves reconstructing the frequency dependence of physical excitation spectra from data obtained at specific points in the complex frequency plane. The approach provides a natural regularization in cases where the inverse of the Fredholm kernel is ill-conditioned and yields robust error metrics. The stability of the forward problem permits the construction of a large database of input-output pairs. Machine learning methods applied to this database generate approximate solutions which are projected onto the subspace of functions satisfying relevant constraints. We show that for low input noise the method performs as well or better than Maximum Entropy (MaxEnt) under standard error metrics, and is substantially more robust to noise. We expect the methodology to be similarly effective for any problem involving a formally ill-conditioned inversion, provided that the forward problem can be efficiently solved. AJM was supported by the Office of Science of the U.S. Department of Energy under Subcontract No. 3F-3138 and LFA by the Columbia Univeristy IDS-ROADS project, UR009033-05 which also provided part support to RN and LH.

A Discussion of Issues in Integrity Constraint Monitoring

NASA Technical Reports Server (NTRS)

Fernandez, Francisco G.; Gates, Ann Q.; Cooke, Daniel E.

1998-01-01

In the development of large-scale software systems, analysts, designers, and programmers identify properties of data objects in the system. The ability to check those assertions during runtime is desirable as a means of verifying the integrity of the program. Typically, programmers ensure the satisfaction of such properties through the use of some form of manually embedded assertion check. The disadvantage to this approach is that these assertions become entangled within the program code. The goal of the research is to develop an integrity constraint monitoring mechanism whereby a repository of software system properties (called integrity constraints) are automatically inserted into the program by the mechanism to check for incorrect program behaviors. Such a mechanism would overcome many of the deficiencies of manually embedded assertion checks. This paper gives an overview of the preliminary work performed toward this goal. The manual instrumentation of constraint checking on a series of test programs is discussed, This review then is used as the basis for a discussion of issues to be considered in developing an automated integrity constraint monitor.

Generalization of the event-based Carnevale-Hines integration scheme for integrate-and-fire models.

PubMed

van Elburg, Ronald A J; van Ooyen, Arjen

2009-07-01

An event-based integration scheme for an integrate-and-fire neuron model with exponentially decaying excitatory synaptic currents and double exponential inhibitory synaptic currents has been introduced by Carnevale and Hines. However, the integration scheme imposes nonphysiological constraints on the time constants of the synaptic currents, which hamper its general applicability. This letter addresses this problem in two ways. First, we provide physical arguments demonstrating why these constraints on the time constants can be relaxed. Second, we give a formal proof showing which constraints can be abolished. As part of our formal proof, we introduce the generalized Carnevale-Hines lemma, a new tool for comparing double exponentials as they naturally occur in many cascaded decay systems, including receptor-neurotransmitter dissociation followed by channel closing. Through repeated application of the generalized lemma, we lift most of the original constraints on the time constants. Thus, we show that the Carnevale-Hines integration scheme for the integrate-and-fire model can be employed for simulating a much wider range of neuron and synapse types than was previously thought.

Truncation Without Shape Constraints: The Latter Stages of Prosodic Acquisition.

ERIC Educational Resources Information Center

Kehoe, Margaret M.

2000-01-01

Evaluates the claim of uniform size and shape restrictions in prosodic development using a cross-sectional database of English-speaking children's multisyllabic word productions. Suggests children's increasing faithfulness to unstressed syllables can be explained by different constraint rankings that relate to edge alignment, syllable structure,…

Overview of the Turbine Based Combined Cycle Discipline

NASA Technical Reports Server (NTRS)

Thomas, Scott R.; Walker, James F.; Pittman, James L.

2009-01-01

The NASA Fundamental Aeronautics Hypersonics project is focused on technologies for combined cycle, airbreathing propulsions systems to enable reusable launch systems for access to space. Turbine Based Combined Cycle (TBCC) propulsion systems offer specific impulse (Isp) improvements over rocket-based propulsion systems in the subsonic takeoff and return mission segments and offer improved safety. The potential to realize more aircraft-like operations with expanded launch site capability and reduced system maintenance are additional benefits. The most critical TBCC enabling technologies as identified in the National Aeronautics Institute (NAI) study were: 1) mode transition from the low speed propulsion system to the high speed propulsion system, 2) high Mach turbine engine development, 3) transonic aero-propulsion performance, 4) low-Mach-number dual-mode scramjet operation, 5) innovative 3-D flowpath concepts and 6) innovative turbine based combined cycle integration. To address several of these key TBCC challenges, NASA s Hypersonics project (TBCC Discipline) initiated an experimental mode transition task that includes an analytic research endeavor to assess the state-of-the-art of propulsion system performance and design codes. This initiative includes inlet fluid and turbine performance codes and engineering-level algorithms. This effort has been focused on the Combined Cycle Engine Large-Scale Inlet Mode Transition Experiment (CCE LIMX) which is a fully integrated TBCC propulsion system with flow path sizing consistent with previous NASA and DoD proposed Hypersonic experimental flight test plans. This experiment is being tested in the NASA-GRC 10 x 10 Supersonic Wind Tunnel (SWT) Facility. The goal of this activity is to address key hypersonic combined-cycle-engine issues: (1) dual integrated inlet operability and performance issues unstart constraints, distortion constraints, bleed requirements, controls, and operability margins, (2) mode-transition constraints imposed by the turbine and the ramjet/scramjet flow paths (imposed variable geometry requirements), (3) turbine engine transients (and associated time scales) during transition, (4) high-altitude turbine engine re-light, and (5) the operating constraints of a Mach 3-7 combustor (specific to the TBCC). The model will be tested in several test phases to develop a unique TBCC database to assess and validate design and analysis tools and address operability, integration, and interaction issues for this class of advanced propulsion systems. The test article and all support equipment is complete and available at the facility. The test article installation and facility build-up in preparation for the inlet performance and operability characterization is near completion and testing is planned to commence in FY11.

Two frameworks for integrating knowledge in induction

NASA Technical Reports Server (NTRS)

Rosenbloom, Paul S.; Hirsh, Haym; Cohen, William W.; Smith, Benjamin D.

1994-01-01

The use of knowledge in inductive learning is critical for improving the quality of the concept definitions generated, reducing the number of examples required in order to learn effective concept definitions, and reducing the computation needed to find good concept definitions. Relevant knowledge may come in many forms (such as examples, descriptions, advice, and constraints) and from many sources (such as books, teachers, databases, and scientific instruments). How to extract the relevant knowledge from this plethora of possibilities, and then to integrate it together so as to appropriately affect the induction process is perhaps the key issue at this point in inductive learning. Here the focus is on the integration part of this problem; that is, how induction algorithms can, and do, utilize a range of extracted knowledge. Preliminary work on a transformational framework for defining knowledge-intensive inductive algorithms out of relatively knowledge-free algorithms is described, as is a more tentative problems-space framework that attempts to cover all induction algorithms within a single general approach. These frameworks help to organize what is known about current knowledge-intensive induction algorithms, and to point towards new algorithms.

Physical constraints on biological integral control design for homeostasis and sensory adaptation.

PubMed

Ang, Jordan; McMillen, David R

2013-01-22

Synthetic biology includes an effort to use design-based approaches to create novel controllers, biological systems aimed at regulating the output of other biological processes. The design of such controllers can be guided by results from control theory, including the strategy of integral feedback control, which is central to regulation, sensory adaptation, and long-term robustness. Realization of integral control in a synthetic network is an attractive prospect, but the nature of biochemical networks can make the implementation of even basic control structures challenging. Here we present a study of the general challenges and important constraints that will arise in efforts to engineer biological integral feedback controllers or to analyze existing natural systems. Constraints arise from the need to identify target output values that the combined process-plus-controller system can reach, and to ensure that the controller implements a good approximation of integral feedback control. These constraints depend on mild assumptions about the shape of input-output relationships in the biological components, and thus will apply to a variety of biochemical systems. We summarize our results as a set of variable constraints intended to provide guidance for the design or analysis of a working biological integral feedback controller. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Immediate effects of form-class constraints on spoken word recognition

PubMed Central

Magnuson, James S.; Tanenhaus, Michael K.; Aslin, Richard N.

2008-01-01

In many domains of cognitive processing there is strong support for bottom-up priority and delayed top-down (contextual) integration. We ask whether this applies to supra-lexical context that could potentially constrain lexical access. Previous findings of early context integration in word recognition have typically used constraints that can be linked to pair-wise conceptual relations between words. Using an artificial lexicon, we found immediate integration of syntactic expectations based on pragmatic constraints linked to syntactic categories rather than words: phonologically similar “nouns” and “adjectives” did not compete when a combination of syntactic and visual information strongly predicted form class. These results suggest that predictive context is integrated continuously, and that previous findings supporting delayed context integration stem from weak contexts rather than delayed integration. PMID:18675408

A Hybrid Constraint Representation and Reasoning Framework

NASA Technical Reports Server (NTRS)

Golden, Keith; Pang, Wan-Lin

2003-01-01

This paper introduces JNET, a novel constraint representation and reasoning framework that supports procedural constraints and constraint attachments, providing a flexible way of integrating the constraint reasoner with a run- time software environment. Attachments in JNET are constraints over arbitrary Java objects, which are defined using Java code, at runtime, with no changes to the JNET source code.

Development of a prototype commonality analysis tool for use in space programs

NASA Technical Reports Server (NTRS)

Yeager, Dorian P.

1988-01-01

A software tool to aid in performing commonality analyses, called Commonality Analysis Problem Solver (CAPS), was designed, and a prototype version (CAPS 1.0) was implemented and tested. The CAPS 1.0 runs in an MS-DOS or IBM PC-DOS environment. The CAPS is designed around a simple input language which provides a natural syntax for the description of feasibility constraints. It provides its users with the ability to load a database representing a set of design items, describe the feasibility constraints on items in that database, and do a comprehensive cost analysis to find the most economical substitution pattern.

The Quality Control Algorithms Used in the Process of Creating the NASA Kennedy Space Center Lightning Protection System Towers Meteorological Database

NASA Technical Reports Server (NTRS)

Orcutt, John M.; Brenton, James C.

2016-01-01

The methodology and the results of the quality control (QC) process of the meteorological data from the Lightning Protection System (LPS) towers located at Kennedy Space Center (KSC) launch complex 39B (LC-39B) are documented in this paper. Meteorological data are used to design a launch vehicle, determine operational constraints, and to apply defined constraints on day-of-launch (DOL). In order to properly accomplish these tasks, a representative climatological database of meteorological records is needed because the database needs to represent the climate the vehicle will encounter. Numerous meteorological measurement towers exist at KSC; however, the engineering tasks need measurements at specific heights, some of which can only be provided by a few towers. Other than the LPS towers, Tower 313 is the only tower that provides observations up to 150 m. This tower is located approximately 3.5 km from LC-39B. In addition, data need to be QC'ed to remove erroneous reports that could pollute the results of an engineering analysis, mislead the development of operational constraints, or provide a false image of the atmosphere at the tower's location.

Nonseparable exchange–correlation functional for molecules, including homogeneous catalysis involving transition metals

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

Yu, Haoyu S.; Zhang, Wenjing; Verma, Pragya

2015-01-01

The goal of this work is to develop a gradient approximation to the exchange–correlation functional of Kohn–Sham density functional theory for treating molecular problems with a special emphasis on the prediction of quantities important for homogeneous catalysis and other molecular energetics. Our training and validation of exchange–correlation functionals is organized in terms of databases and subdatabases. The key properties required for homogeneous catalysis are main group bond energies (database MGBE137), transition metal bond energies (database TMBE32), reaction barrier heights (database BH76), and molecular structures (database MS10). We also consider 26 other databases, most of which are subdatabases of a newlymore » extended broad database called Database 2015, which is presented in the present article and in its ESI. Based on the mathematical form of a nonseparable gradient approximation (NGA), as first employed in the N12 functional, we design a new functional by using Database 2015 and by adding smoothness constraints to the optimization of the functional. The resulting functional is called the gradient approximation for molecules, or GAM. The GAM functional gives better results for MGBE137, TMBE32, and BH76 than any available generalized gradient approximation (GGA) or than N12. The GAM functional also gives reasonable results for MS10 with an MUE of 0.018 Å. The GAM functional provides good results both within the training sets and outside the training sets. The convergence tests and the smooth curves of exchange–correlation enhancement factor as a function of the reduced density gradient show that the GAM functional is a smooth functional that should not lead to extra expense or instability in optimizations. NGAs, like GGAs, have the advantage over meta-GGAs and hybrid GGAs of respectively smaller grid-size requirements for integrations and lower costs for extended systems. These computational advantages combined with the relatively high accuracy for all the key properties needed for molecular catalysis make the GAM functional very promising for future applications.« less

Implications of water constraints for electricity capacity expansion in the United States

NASA Astrophysics Data System (ADS)

Liu, L.; Hejazi, M. I.; Iyer, G.; Forman, B. A.

2017-12-01

U.S. electricity generation is vulnerable to water supply since water is required for cooling. Constraints on the availability of water will therefore necessitate adaptive planning by the power generation sector. Hence, it is important to integrate restrictions in water availability in electricity capacity planning in order to better understand the economic viability of alternative capacity planning options. The study of the implications of water constraints for the U.S. power generation system is limited in terms of scale and robustness. We extend previous studies by including physical water constraints in a state-level model of the U.S. energy system embedded within a global integrated assessment model (GCAM-USA). We focus on the implications of such constraints for the U.S. electricity capacity expansion, integrating both supply and demand effects under a consistent framework. Constraints on the availability of water have two general effects across the U.S. First, water availability constraints increase the cost of electricity generation, resulting in reduced electrification of end-use sectors. Second, water availability constraints result in forced retirements of water-intensive technologies such as thermoelectric coal- and gas- fired technologies before the end of their natural lifetimes. The demand for electricity is then met by an increase in investments in less water-dependent technologies such as wind and solar photovoltaic. Our results show that the regional patterns of the above effects are heterogeneous across the U.S. In general, the impacts of water constraints on electricity capacity expansion are more pronounced in the West than in the East. This is largely because of lower water availability in the West compared to the East due to lower precipitation in the Western states. Constraints on the availability of water might also have important implications for U.S. electricity trade. For example, under severe constraints on the availability of water, some states flip from being net exporters of electricity to becoming net importers and vice versa. Our study demonstrates the impacts of water availability constraints on electricity capacity expansion in the U.S. and highlights the need to integrate such constraints into decision-making so as to better understand state-level challenges.

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes.

PubMed

Shao, Wei; Shan, Jigui; Kearney, Mary F; Wu, Xiaolin; Maldarelli, Frank; Mellors, John W; Luke, Brian; Coffin, John M; Hughes, Stephen H

2016-07-04

The NCI Retrovirus Integration Database is a MySql-based relational database created for storing and retrieving comprehensive information about retroviral integration sites, primarily, but not exclusively, HIV-1. The database is accessible to the public for submission or extraction of data originating from experiments aimed at collecting information related to retroviral integration sites including: the site of integration into the host genome, the virus family and subtype, the origin of the sample, gene exons/introns associated with integration, and proviral orientation. Information about the references from which the data were collected is also stored in the database. Tools are built into the website that can be used to map the integration sites to UCSC genome browser, to plot the integration site patterns on a chromosome, and to display provirus LTRs in their inserted genome sequence. The website is robust, user friendly, and allows users to query the database and analyze the data dynamically. https://rid.ncifcrf.gov ; or http://home.ncifcrf.gov/hivdrp/resources.htm .

Integrating ergonomics knowledge into business-driven design projects: The shaping of resource constraints in engineering consultancy.

PubMed

Hall-Andersen, Lene Bjerg; Neumann, Patrick; Broberg, Ole

2016-10-17

The integration of ergonomics knowledge into engineering projects leads to both healthier and more efficient workplaces. There is a lack of knowledge about integrating ergonomic knowledge into the design practice in engineering consultancies. This study explores how organizational resources can pose constraints for the integration of ergonomics knowledge into engineering design projects in a business-driven setting, and how ergonomists cope with these resource constraints. An exploratory case study in an engineering consultancy was conducted. A total of 27 participants were interviewed. Data were collected applying semi-structured interviews, observations, and documentary studies. Interviews were transcribed, coded, and categorized into themes. From the analysis five overall themes emerged as major constituents of resource constraints: 1) maximizing project revenue, 2) payment for ergonomics services, 3) value of ergonomic services, 4) role of the client, and 5) coping strategies to overcome resource constraints. We hypothesize that resource constraints were shaped due to sub-optimization of costs in design projects. The economical contribution of ergonomics measures was not evaluated in the entire life cycle of a designed workplace. Coping strategies included teaming up with engineering designers in the sales process or creating an alliance with ergonomists in the client organization.

Rate-gyro-integral constraint for ambiguity resolution in GNSS attitude determination applications.

PubMed

Zhu, Jiancheng; Li, Tao; Wang, Jinling; Hu, Xiaoping; Wu, Meiping

2013-06-21

In the field of Global Navigation Satellite System (GNSS) attitude determination, the constraints usually play a critical role in resolving the unknown ambiguities quickly and correctly. Many constraints such as the baseline length, the geometry of multi-baselines and the horizontal attitude angles have been used extensively to improve the performance of ambiguity resolution. In the GNSS/Inertial Navigation System (INS) integrated attitude determination systems using low grade Inertial Measurement Unit (IMU), the initial heading parameters of the vehicle are usually worked out by the GNSS subsystem instead of by the IMU sensors independently. However, when a rotation occurs, the angle at which vehicle has turned within a short time span can be measured accurately by the IMU. This measurement will be treated as a constraint, namely the rate-gyro-integral constraint, which can aid the GNSS ambiguity resolution. We will use this constraint to filter the candidates in the ambiguity search stage. The ambiguity search space shrinks significantly with this constraint imposed during the rotation, thus it is helpful to speeding up the initialization of attitude parameters under dynamic circumstances. This paper will only study the applications of this new constraint to land vehicles. The impacts of measurement errors on the effect of this new constraint will be assessed for different grades of IMU and current average precision level of GNSS receivers. Simulations and experiments in urban areas have demonstrated the validity and efficacy of the new constraint in aiding GNSS attitude determinations.

An Integrated Optimization Design Method Based on Surrogate Modeling Applied to Diverging Duct Design

NASA Astrophysics Data System (ADS)

Hanan, Lu; Qiushi, Li; Shaobin, Li

2016-12-01

This paper presents an integrated optimization design method in which uniform design, response surface methodology and genetic algorithm are used in combination. In detail, uniform design is used to select the experimental sampling points in the experimental domain and the system performance is evaluated by means of computational fluid dynamics to construct a database. After that, response surface methodology is employed to generate a surrogate mathematical model relating the optimization objective and the design variables. Subsequently, genetic algorithm is adopted and applied to the surrogate model to acquire the optimal solution in the case of satisfying some constraints. The method has been applied to the optimization design of an axisymmetric diverging duct, dealing with three design variables including one qualitative variable and two quantitative variables. The method of modeling and optimization design performs well in improving the duct aerodynamic performance and can be also applied to wider fields of mechanical design and seen as a useful tool for engineering designers, by reducing the design time and computation consumption.

Utilizing ORACLE tools within Unix

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

Ferguson, R.

1995-07-01

Large databases, by their very nature, often serve as repositories of data which may be needed by other systems. The transmission of this data to other systems has in the past involved several layers of human intervention. The Integrated Cargo Data Base (ICDB) developed by Martin Marietta Energy Systems for the Military Traffic Management Command as part of the Worldwide Port System provides data integration and worldwide tracking of cargo that passes through common-user ocean cargo ports. One of the key functions of ICDB is data distribution of a variety of data files to a number of other systems. Developmentmore » of automated data distribution procedures had to deal with the following constraints: (1) variable generation time for data files, (2) use of only current data for data files, (3) use of a minimum number of select statements, (4) creation of unique data files for multiple recipients, (5) automatic transmission of data files to recipients, and (6) avoidance of extensive and long-term data storage.« less

Application of genetic algorithm in integrated setup planning and operation sequencing

NASA Astrophysics Data System (ADS)

Kafashi, Sajad; Shakeri, Mohsen

2011-01-01

Process planning is an essential component for linking design and manufacturing process. Setup planning and operation sequencing is two main tasks in process planning. Many researches solved these two problems separately. Considering the fact that the two functions are complementary, it is necessary to integrate them more tightly so that performance of a manufacturing system can be improved economically and competitively. This paper present a generative system and genetic algorithm (GA) approach to process plan the given part. The proposed approach and optimization methodology analyses the TAD (tool approach direction), tolerance relation between features and feature precedence relations to generate all possible setups and operations using workshop resource database. Based on these technological constraints the GA algorithm approach, which adopts the feature-based representation, optimizes the setup plan and sequence of operations using cost indices. Case study show that the developed system can generate satisfactory results in optimizing the setup planning and operation sequencing simultaneously in feasible condition.

Integrated Analysis of Airport Capacity and Environmental Constraints

NASA Technical Reports Server (NTRS)

Hasan, Shahab; Long, Dou; Hart, George; Eckhause, Jeremy; Hemm, Robert; Busick, Andrew; Graham, Michael; Thompson, Terry; Murphy, Charles; Poage, James

2010-01-01

LMI conducted an integrated analysis of airport capacity and environmental constraints. identifying and ranking the key factors limiting achievement of NextGen capacity goals. The primary metric used was projected throughput, which was estimated for the years 2015 and 2025 based on the unconstrained demand forecast from the Federal Aviation Administration, and planned improvements including those proposed in the NextGen plan. A set of 310 critical airports was identified.. collectively accounting for more than 99 percent of domestic air traffic volume; a one-off analytical approach was used to isolate the constraint being assessed. The study considered three capacity constraints (runway.. taxiway, and gate) and three environmental constraints (fuel, NO(x) emissions, and noise). For the ten busiest airports, runway and noise are the primary and secondary constraints in both 2015 and 2025. For the OEP 35 airports and overall for the remaining airports, the most binding constraint is noise. Six of the 10 busiest airports, will face runway constraints in 2025, and 95 will face gate constraints. Nearly every airport will be subject to constraints due to emissions and NOx. Runway and taxi constraints are more concentrated in the large airports: environmental constraints are present at almost every airport regardless of size.

Balancing Your Database Network Licenses against Your Budget.

ERIC Educational Resources Information Center

Bauer, Benjamin F.

1995-01-01

Discussion of choosing database access to satisfy users and budgetary constraints highlights a method to make educated estimates of simultaneous usage levels. Topics include pricing; advances in networks and CD-ROM technology; and two networking scenarios, one in an academic library and one in a corporate research facility. (LRW)

Ontology based heterogeneous materials database integration and semantic query

NASA Astrophysics Data System (ADS)

Zhao, Shuai; Qian, Quan

2017-10-01

Materials digital data, high throughput experiments and high throughput computations are regarded as three key pillars of materials genome initiatives. With the fast growth of materials data, the integration and sharing of data is very urgent, that has gradually become a hot topic of materials informatics. Due to the lack of semantic description, it is difficult to integrate data deeply in semantic level when adopting the conventional heterogeneous database integration approaches such as federal database or data warehouse. In this paper, a semantic integration method is proposed to create the semantic ontology by extracting the database schema semi-automatically. Other heterogeneous databases are integrated to the ontology by means of relational algebra and the rooted graph. Based on integrated ontology, semantic query can be done using SPARQL. During the experiments, two world famous First Principle Computational databases, OQMD and Materials Project are used as the integration targets, which show the availability and effectiveness of our method.

An Integrated Constraint Programming Approach to Scheduling Sports Leagues with Divisional and Round-robin Tournaments

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

Carlsson, Mats; Johansson, Mikael; Larson, Jeffrey

Previous approaches for scheduling a league with round-robin and divisional tournaments involved decomposing the problem into easier subproblems. This approach, used to schedule the top Swedish handball league Elitserien, reduces the problem complexity but can result in suboptimal schedules. This paper presents an integrated constraint programming model that allows to perform the scheduling in a single step. Particular attention is given to identifying implied and symmetry-breaking constraints that reduce the computational complexity significantly. The experimental evaluation of the integrated approach takes considerably less computational effort than the previous approach.

Functional integration of automated system databases by means of artificial intelligence

NASA Astrophysics Data System (ADS)

Dubovoi, Volodymyr M.; Nikitenko, Olena D.; Kalimoldayev, Maksat; Kotyra, Andrzej; Gromaszek, Konrad; Iskakova, Aigul

2017-08-01

The paper presents approaches for functional integration of automated system databases by means of artificial intelligence. The peculiarities of turning to account the database in the systems with the usage of a fuzzy implementation of functions were analyzed. Requirements for the normalization of such databases were defined. The question of data equivalence in conditions of uncertainty and collisions in the presence of the databases functional integration is considered and the model to reveal their possible occurrence is devised. The paper also presents evaluation method of standardization of integrated database normalization.

TransAtlasDB: an integrated database connecting expression data, metadata and variants

PubMed Central

Adetunji, Modupeore O; Lamont, Susan J; Schmidt, Carl J

2018-01-01

Abstract High-throughput transcriptome sequencing (RNAseq) is the universally applied method for target-free transcript identification and gene expression quantification, generating huge amounts of data. The constraint of accessing such data and interpreting results can be a major impediment in postulating suitable hypothesis, thus an innovative storage solution that addresses these limitations, such as hard disk storage requirements, efficiency and reproducibility are paramount. By offering a uniform data storage and retrieval mechanism, various data can be compared and easily investigated. We present a sophisticated system, TransAtlasDB, which incorporates a hybrid architecture of both relational and NoSQL databases for fast and efficient data storage, processing and querying of large datasets from transcript expression analysis with corresponding metadata, as well as gene-associated variants (such as SNPs) and their predicted gene effects. TransAtlasDB provides the data model of accurate storage of the large amount of data derived from RNAseq analysis and also methods of interacting with the database, either via the command-line data management workflows, written in Perl, with useful functionalities that simplifies the complexity of data storage and possibly manipulation of the massive amounts of data generated from RNAseq analysis or through the web interface. The database application is currently modeled to handle analyses data from agricultural species, and will be expanded to include more species groups. Overall TransAtlasDB aims to serve as an accessible repository for the large complex results data files derived from RNAseq gene expression profiling and variant analysis. Database URL: https://modupeore.github.io/TransAtlasDB/ PMID:29688361

Highlights from a Mach 4 Experimental Demonstration of Inlet Mode Transition for Turbine-Based Combined Cycle Hypersonic Propulsion

NASA Technical Reports Server (NTRS)

Foster, Lancert E.; Saunders, John D., Jr.; Sanders, Bobby W.; Weir, Lois J.

2012-01-01

NASA is focused on technologies for combined cycle, air-breathing propulsion systems to enable reusable launch systems for access to space. Turbine Based Combined Cycle (TBCC) propulsion systems offer specific impulse (Isp) improvements over rocket-based propulsion systems in the subsonic takeoff and return mission segments along with improved safety. Among the most critical TBCC enabling technologies are: 1) mode transition from the low speed propulsion system to the high speed propulsion system, 2) high Mach turbine engine development and 3) innovative turbine based combined cycle integration. To address these challenges, NASA initiated an experimental mode transition task including analytical methods to assess the state-of-the-art of propulsion system performance and design codes. One effort has been the Combined-Cycle Engine Large Scale Inlet Mode Transition Experiment (CCE-LIMX) which is a fully integrated TBCC propulsion system with flowpath sizing consistent with previous NASA and DoD proposed Hypersonic experimental flight test plans. This experiment was tested in the NASA GRC 10 by 10-Foot Supersonic Wind Tunnel (SWT) Facility. The goal of this activity is to address key hypersonic combined-cycle engine issues including: (1) dual integrated inlet operability and performance issues-unstart constraints, distortion constraints, bleed requirements, and controls, (2) mode-transition sequence elements caused by switching between the turbine and the ramjet/scramjet flowpaths (imposed variable geometry requirements), and (3) turbine engine transients (and associated time scales) during transition. Testing of the initial inlet and dynamic characterization phases were completed and smooth mode transition was demonstrated. A database focused on a Mach 4 transition speed with limited off-design elements was developed and will serve to guide future TBCC system studies and to validate higher level analyses.

SAADA: Astronomical Databases Made Easier

NASA Astrophysics Data System (ADS)

Michel, L.; Nguyen, H. N.; Motch, C.

2005-12-01

Many astronomers wish to share datasets with their community but have not enough manpower to develop databases having the functionalities required for high-level scientific applications. The SAADA project aims at automatizing the creation and deployment process of such databases. A generic but scientifically relevant data model has been designed which allows one to build databases by providing only a limited number of product mapping rules. Databases created by SAADA rely on a relational database supporting JDBC and covered by a Java layer including a lot of generated code. Such databases can simultaneously host spectra, images, source lists and plots. Data are grouped in user defined collections whose content can be seen as one unique set per data type even if their formats differ. Datasets can be correlated one with each other using qualified links. These links help, for example, to handle the nature of a cross-identification (e.g., a distance or a likelihood) or to describe their scientific content (e.g., by associating a spectrum to a catalog entry). The SAADA query engine is based on a language well suited to the data model which can handle constraints on linked data, in addition to classical astronomical queries. These constraints can be applied on the linked objects (number, class and attributes) and/or on the link qualifier values. Databases created by SAADA are accessed through a rich WEB interface or a Java API. We are currently developing an inter-operability module implanting VO protocols.

Design of Integrated Database on Mobile Information System: A Study of Yogyakarta Smart City App

NASA Astrophysics Data System (ADS)

Nurnawati, E. K.; Ermawati, E.

2018-02-01

An integration database is a database which acts as the data store for multiple applications and thus integrates data across these applications (in contrast to an Application Database). An integration database needs a schema that takes all its client applications into account. The benefit of the schema that sharing data among applications does not require an extra layer of integration services on the applications. Any changes to data made in a single application are made available to all applications at the time of database commit - thus keeping the applications’ data use better synchronized. This study aims to design and build an integrated database that can be used by various applications in a mobile device based system platforms with the based on smart city system. The built-in database can be used by various applications, whether used together or separately. The design and development of the database are emphasized on the flexibility, security, and completeness of attributes that can be used together by various applications to be built. The method used in this study is to choice of the appropriate database logical structure (patterns of data) and to build the relational-database models (Design Databases). Test the resulting design with some prototype apps and analyze system performance with test data. The integrated database can be utilized both of the admin and the user in an integral and comprehensive platform. This system can help admin, manager, and operator in managing the application easily and efficiently. This Android-based app is built based on a dynamic clientserver where data is extracted from an external database MySQL. So if there is a change of data in the database, then the data on Android applications will also change. This Android app assists users in searching of Yogyakarta (as smart city) related information, especially in culture, government, hotels, and transportation.

Finite-dimensional Liouville integrable Hamiltonian systems generated from Lax pairs of a bi-Hamiltonian soliton hierarchy by symmetry constraints

NASA Astrophysics Data System (ADS)

Manukure, Solomon

2018-04-01

We construct finite-dimensional Hamiltonian systems by means of symmetry constraints from the Lax pairs and adjoint Lax pairs of a bi-Hamiltonian hierarchy of soliton equations associated with the 3-dimensional special linear Lie algebra, and discuss the Liouville integrability of these systems based on the existence of sufficiently many integrals of motion.

Open groups of constraints. Integrating arbitrary involutions

NASA Astrophysics Data System (ADS)

Batalin, Igor; Marnelius, Robert

1998-11-01

A new type of quantum master equation is presented which is expressed in terms of a recently introduced quantum antibracket. The equation involves only two operators: an extended nilpotent BFV-BRST charge and an extended ghost charge. It is proposed to determine the generalized quantum Maurer-Cartan equations for arbitrary open groups. These groups are the integration of constraints in arbitrary involutions. The only condition for this is that the constraint operators may be embedded in an odd nilpotent operator, the BFV-BRST charge. The proposal is verified at the quasigroup level. The integration formulas are also used to construct a generating operator for quantum antibrackets of operators in arbitrary involutions.

Evidence-Based Systematic Review: Effects of Intensity of Treatment and Constraint-Induced Language Therapy for Individuals with Stroke-Induced Aphasia

ERIC Educational Resources Information Center

Cherney, Leora R.; Patterson, Janet P.; Raymer, Anastasia; Frymark, Tobi; Schooling, Tracy

2008-01-01

Purpose: This systematic review summarizes evidence for intensity of treatment and constraint-induced language therapy (CILT) on measures of language impairment and communication activity/participation in individuals with stroke-induced aphasia. Method: A systematic search of the aphasia literature using 15 electronic databases (e.g., PubMed,…

Nurses' barriers to learning: an integrative review.

PubMed

Santos, Marion C

2012-07-01

This integrative review of the literature describes nurses' barriers to learning. Five major themes emerged: time constraints, financial constraints, workplace culture, access/relevance, and competency in accessing electronic evidence-based practice literature. The nurse educator must address these barriers for the staff to achieve learning and competency.

Distribution Grid Integration Unit Cost Database | Solar Research | NREL

Science.gov Websites

Unit Cost Database Distribution Grid Integration Unit Cost Database NREL's Distribution Grid Integration Unit Cost Database contains unit cost information for different components that may be used to associated with PV. It includes information from the California utility unit cost guides on traditional

Integration of a Portfolio-based Approach to Evaluate Aerospace R and D Problem Formulation Into a Parametric Synthesis Tool

NASA Astrophysics Data System (ADS)

Oza, Amit R.

The focus of this study is to improve R&D effectiveness towards aerospace and defense planning in the early stages of the product development lifecycle. Emphasis is on: correct formulation of a decision problem, with special attention to account for data relationships between the individual design problem and the system capability required to size the aircraft, understanding of the meaning of the acquisition strategy objective and subjective data requirements that are required to arrive at a balanced analysis and/or "correct" mix of technology projects, understanding the meaning of the outputs that can be created from the technology analysis, and methods the researcher can use at effectively support decisions at the acquisition and conceptual design levels through utilization of a research and development portfolio strategy. The primary objectives of this study are to: (1) determine what strategy should be used to initialize conceptual design parametric sizing processes during requirements analysis for the materiel solution analysis stage of the product development lifecycle when utilizing data already constructed in the latter phase when working with a generic database management system synthesis tool integration architecture for aircraft design , and (2) assess how these new data relationships can contribute for innovative decision-making when solving acquisition hardware/technology portfolio problems. As such, an automated composable problem formulation system is developed to consider data interactions for the system architecture that manages acquisition pre-design concept refinement portfolio management, and conceptual design parametric sizing requirements. The research includes a way to: • Formalize the data storage and implement the data relationship structure with a system architecture automated through a database management system. • Allow for composable modeling, in terms of level of hardware abstraction, for the product model, mission model, and operational constraint model data blocks in the pre-design stages. • Allow the product model, mission model, and operational constraint model to be cross referenced with a generic aircraft synthesis capability to identify disciplinary analysis methods and processes. • Allow for matching, comparison, and balancing of the aircraft hardware portfolio to the associated developmental and technology risk metrics. • Allow for visualization technology portfolio decision space. The problem formulation architecture is finally implemented and verified for a generic hypersonic vehicle research demonstrator where a portfolio of technology hardware are measured for developmental and technology risks, prioritized by the researcher risk constraints, and the data generated delivered to a novel aircraft synthesis tool to confirm vehicle feasibility.

Dual deep modeling: multi-level modeling with dual potencies and its formalization in F-Logic.

PubMed

Neumayr, Bernd; Schuetz, Christoph G; Jeusfeld, Manfred A; Schrefl, Michael

2018-01-01

An enterprise database contains a global, integrated, and consistent representation of a company's data. Multi-level modeling facilitates the definition and maintenance of such an integrated conceptual data model in a dynamic environment of changing data requirements of diverse applications. Multi-level models transcend the traditional separation of class and object with clabjects as the central modeling primitive, which allows for a more flexible and natural representation of many real-world use cases. In deep instantiation, the number of instantiation levels of a clabject or property is indicated by a single potency. Dual deep modeling (DDM) differentiates between source potency and target potency of a property or association and supports the flexible instantiation and refinement of the property by statements connecting clabjects at different modeling levels. DDM comes with multiple generalization of clabjects, subsetting/specialization of properties, and multi-level cardinality constraints. Examples are presented using a UML-style notation for DDM together with UML class and object diagrams for the representation of two-level user views derived from the multi-level model. Syntax and semantics of DDM are formalized and implemented in F-Logic, supporting the modeler with integrity checks and rich query facilities.

The Development and Implementation of Outdoor-Based Secondary School Integrated Programs

ERIC Educational Resources Information Center

Comishin, Kelly; Dyment, Janet E.; Potter, Tom G.; Russell, Constance L.

2004-01-01

Four teachers share the challenges they faced when creating and running outdoor-focused secondary school integrated programs in British Columbia, Canada. The five most common challenges were funding constraints, insufficient support from administrators and colleagues, time constraints, liability and risk management, and inadequate skills and…

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.

Including Overweight or Obese Students in Physical Education: A Social Ecological Constraint Model

ERIC Educational Resources Information Center

Li, Weidong; Rukavina, Paul

2012-01-01

In this review, we propose a social ecological constraint model to study inclusion of overweight or obese students in physical education by integrating key concepts and assumptions from ecological constraint theory in motor development and social ecological models in health promotion and behavior. The social ecological constraint model proposes…

Capacity Model and Constraints Analysis for Integrated Remote Wireless Sensor and Satellite Network in Emergency Scenarios

PubMed Central

Zhang, Wei; Zhang, Gengxin; Dong, Feihong; Xie, Zhidong; Bian, Dongming

2015-01-01

This article investigates the capacity problem of an integrated remote wireless sensor and satellite network (IWSSN) in emergency scenarios. We formulate a general model to evaluate the remote sensor and satellite network capacity. Compared to most existing works for ground networks, the proposed model is time varying and space oriented. To capture the characteristics of a practical network, we sift through major capacity-impacting constraints and analyze the influence of these constraints. Specifically, we combine the geometric satellite orbit model and satellite tool kit (STK) engineering software to quantify the trends of the capacity constraints. Our objective in analyzing these trends is to provide insights and design guidelines for optimizing the integrated remote wireless sensor and satellite network schedules. Simulation results validate the theoretical analysis of capacity trends and show the optimization opportunities of the IWSSN. PMID:26593919

Capacity Model and Constraints Analysis for Integrated Remote Wireless Sensor and Satellite Network in Emergency Scenarios.

PubMed

Zhang, Wei; Zhang, Gengxin; Dong, Feihong; Xie, Zhidong; Bian, Dongming

2015-11-17

This article investigates the capacity problem of an integrated remote wireless sensor and satellite network (IWSSN) in emergency scenarios. We formulate a general model to evaluate the remote sensor and satellite network capacity. Compared to most existing works for ground networks, the proposed model is time varying and space oriented. To capture the characteristics of a practical network, we sift through major capacity-impacting constraints and analyze the influence of these constraints. Specifically, we combine the geometric satellite orbit model and satellite tool kit (STK) engineering software to quantify the trends of the capacity constraints. Our objective in analyzing these trends is to provide insights and design guidelines for optimizing the integrated remote wireless sensor and satellite network schedules. Simulation results validate the theoretical analysis of capacity trends and show the optimization opportunities of the IWSSN.

Symbol recognition via statistical integration of pixel-level constraint histograms: a new descriptor.

PubMed

Yang, Su

2005-02-01

A new descriptor for symbol recognition is proposed. 1) A histogram is constructed for every pixel to figure out the distribution of the constraints among the other pixels. 2) All the histograms are statistically integrated to form a feature vector with fixed dimension. The robustness and invariance were experimentally confirmed.

[A web-based integrated clinical database for laryngeal cancer].

PubMed

E, Qimin; Liu, Jialin; Li, Yong; Liang, Chuanyu

2014-08-01

To establish an integrated database for laryngeal cancer, and to provide an information platform for laryngeal cancer in clinical and fundamental researches. This database also meet the needs of clinical and scientific use. Under the guidance of clinical expert, we have constructed a web-based integrated clinical database for laryngeal carcinoma on the basis of clinical data standards, Apache+PHP+MySQL technology, laryngeal cancer specialist characteristics and tumor genetic information. A Web-based integrated clinical database for laryngeal carcinoma had been developed. This database had a user-friendly interface and the data could be entered and queried conveniently. In addition, this system utilized the clinical data standards and exchanged information with existing electronic medical records system to avoid the Information Silo. Furthermore, the forms of database was integrated with laryngeal cancer specialist characteristics and tumor genetic information. The Web-based integrated clinical database for laryngeal carcinoma has comprehensive specialist information, strong expandability, high feasibility of technique and conforms to the clinical characteristics of laryngeal cancer specialties. Using the clinical data standards and structured handling clinical data, the database can be able to meet the needs of scientific research better and facilitate information exchange, and the information collected and input about the tumor sufferers are very informative. In addition, the user can utilize the Internet to realize the convenient, swift visit and manipulation on the database.

A Meta-Analysis of the Relationship between Social Constraints and Distress in Cancer Patients

PubMed Central

Adams, Rebecca N.; Winger, Joseph G.; Mosher, Catherine E.

2014-01-01

Social constraints on cancer-related disclosure have been associated with increased distress among cancer patients. The goals of this meta-analysis were: (1) to quantify the average strength of the relationships between social constraints and general and cancer-specific distress in cancer patients; and (2) to examine potential moderators of these relationships. A literature search was conducted using electronic databases, and 30 studies met inclusion criteria. Moderate, significant relationships were found between social constraints and both general distress (r=0.37; 95% CI: 0.31-0.43) and cancer-specific distress (r=0.37; 95% CI: 0.31-0.44). The relationship between social constraints and cancer-specific distress was stronger for studies of patients who, on average, had been diagnosed more recently. Relationships between social constraints and both general and cancer-specific distress did not vary by age or gender. Findings suggest that social constraints may be important to target in interventions to reduce distress in cancer patients, especially those who have been recently diagnosed. PMID:25262383

New seismogenic stress fields for southern Italy from a Bayesian approach

NASA Astrophysics Data System (ADS)

Totaro, Cristina; Orecchio, Barbara; Presti, Debora; Scolaro, Silvia; Neri, Giancarlo

2017-04-01

A new database of high-quality waveform inversion focal mechanism has been compiled for southern Italy by integrating the highest quality solutions, available from literature and catalogues, and 146 newly-computed ones. All the selected focal mechanisms are (i) coming from the Italian CMT, Regional CMT and TDMT catalogues (Pondrelli et al., PEPI 2006, PEPI 2011; http://www.ingv.it), or (ii) computed by using the Cut And Paste (CAP) method (Zhao & Helmberger, BSSA 1994; Zhu & Helmberger, BSSA 1996). Specific tests have been carried out in order to evaluate the robustness of the obtained solutions (e.g., by varying both seismic network configuration and Earth structure parameters) and to estimate uncertainties on the focal mechanism parameters. Only the resulting highest-quality solutions have been enclosed in the database, that has then been used for computation of posterior density distributions of stress tensor components by a Bayesian method (Arnold & Townend, GJI 2007). This algorithm furnishes the posterior density function of the principal components of stress tensor (maximum σ1, intermediate σ2, and minimum σ3 compressive stress, respectively) and the stress-magnitude ratio (R). Before stress computation, we applied the k-means clustering algorithm to subdivide the focal mechanism catalog on the basis of earthquake locations. This approach allows identifying the sectors to be investigated without any "a priori" constraint from faulting type distribution. The large amount of data and the application of the Bayesian algorithm allowed us to provide a more accurate local-to-regional scale stress distribution that has shed new light on the kinematics and dynamics of this very complex area, where lithospheric unit configuration and geodynamic engines are still strongly debated. The new high-quality information here furnished will then represent very useful tools and constraints for future geophysical analyses and geodynamic modeling.

Sensor Webs and Virtual Globes: Enabling Understanding of Changes in a partially Glaciated Watershed

NASA Astrophysics Data System (ADS)

Heavner, M.; Fatland, D. R.; Habermann, M.; Berner, L.; Hood, E.; Connor, C.; Galbraith, J.; Knuth, E.; O'Brien, W.

2008-12-01

The University of Alaska Southeast is currently implementing a sensor web identified as the SouthEast Alaska MOnitoring Network for Science, Telecommunications, Education, and Research (SEAMONSTER). SEAMONSTER is operating in the partially glaciated Mendenhall and Lemon Creek Watersheds, in the Juneau area, on the margins of the Juneau Icefield. These watersheds are studied for both 1. long term monitoring of changes, and 2. detection and analysis of transient events (such as glacier lake outburst floods). The heterogeneous sensors (meteorologic, dual frequency GPS, water quality, lake level, etc), power and bandwidth constraints, and competing time scales of interest require autonomous reactivity of the sensor web. They also present challenges for operational management of the sensor web. The harsh conditions on the glaciers provide additional operating constraints. The tight integration of the sensor web and virtual global enabling technology enhance the project in multiple ways. We are utilizing virtual globe infrastructures to enhance both sensor web management and data access. SEAMONSTER utilizes virtual globes for education and public outreach, sensor web management, data dissemination, and enabling collaboration. Using a PosgreSQL with GIS extensions database coupled to the Open Geospatial Consortium (OGC) Geoserver, we generate near-real-time auto-updating geobrowser files of the data in multiple OGC standard formats (e.g KML, WCS). Additionally, embedding wiki pages in this database allows the development of a geospatially aware wiki describing the projects for better public outreach and education. In this presentation we will describe how we have implemented these technologies to date, the lessons learned, and our efforts towards greater OGC standard implementation. A major focus will be on demonstrating how geobrowsers and virtual globes have made this project possible.

The 2006 Cape Canaveral Air Force Station Range Reference Atmosphere Model Validation Study and Sensitivity Analysis to the National Aeronautics and Space Administration's Space Shuttle

NASA Technical Reports Server (NTRS)

Decker, Ryan; Burns, Lee; Merry, Carl; Harrington, Brian

2008-01-01

NASA's Space Shuttle utilizes atmospheric thermodynamic properties to evaluate structural dynamics and vehicle flight performance impacts by the atmosphere during ascent. Statistical characteristics of atmospheric thermodynamic properties at Kennedy Space Center (KSC) used in Space. Shuttle Vehicle assessments are contained in the Cape Canaveral Air Force Station (CCAFS) Range Reference Atmosphere (RRA) Database. Database contains tabulations for monthly and annual means (mu), standard deviations (sigma) and skewness of wind and thermodynamic variables. Wind, Thermodynamic, Humidity and Hydrostatic parameters 1 km resolution interval from 0-30 km 2 km resolution interval 30-70 km Multiple revisions of the CCAFS RRA database have been developed since initial RRA published in 1963. 1971, 1983, 2006 Space Shuttle program utilized 1983 version for use in deriving "hot" and "cold" atmospheres, atmospheric density dispersions for use in vehicle certification analyses and selection of atmospheric thermodynamic profiles for use in vehicle ascent design and certification analyses. During STS-114 launch preparations in July 2005 atmospheric density observations between 50-80 kft exceeded density limits used for aerodynamic ascent heating constraints in vehicle certification analyses. Mission specific analyses were conducted and concluded that the density bias resulted in small changes to heating rates and integrated heat loading on the vehicle. In 2001, the Air Force Combat Climatology Center began developing an updated RRA for CCAFS.

INTAROS: Development of an integrated Arctic observation system under Horizon 2020

NASA Astrophysics Data System (ADS)

Beszczynska-Möller, Agnieszka; Sandven, Stein; Sagen, Hanne

2017-04-01

INTAROS is a research and innovation action funded under the H2020-BG-09 call for the five-year period 2016-2021. INTAROS will develop an integrated Arctic Observation System (iAOS) by extending, improving and unifying existing systems in the different regions of the Arctic. INTAROS will have a strong multidisciplinary focus, with tools for integration of data from atmosphere, ocean, cryosphere and terrestrial sciences, provided by institutions in Europe, North America and Asia. Satellite earth observation (EO) data plays an increasingly important role in such observing systems, because the amount of EO data for observing the global climate and environment grows year by year. EO data will therefore be integrated into iAOS based on existing products and databases. In situ observing systems are much more limited due to logistical constraints and cost limitations. The sparseness of in situ data is therefore the largest gap in the overall observing system. INTAROS will assess strengths and weaknesses of existing Arctic observing systems and contribute with innovative solutions to fill some of the critical gaps in the selected networks. INTAROS will develop a platform, iAOS, to search for and access data from distributed databases. The evolution into a sustainable Arctic observing system requires coordination, mobilization and cooperation between the existing European and international infrastructures (in-situ and remote, including space-based), the modeling communities and relevant stakeholder groups. INTAROS will include development of community-based observing systems, where local knowledge is merged with scientific data. Multidisciplinary data integrated under INTAROS will contribute to better understanding of interactions and coupling in the complex Arctic ice-ocean-land-atmosphere system. An integrated Arctic Observation System will enable better-informed decisions and better-documented processes within key sectors (e.g. local communities, shipping, tourism, fishing), in order to strengthen the societal and economic role of the Arctic region and support the EU strategy for the Arctic and related maritime and environmental policies. Following the SAON goal, INTAROS will support and strengthen the EU engagement in developing the sustained and coordinated pan-Arctic observing and data sharing systems.

Sleep underpins the plasticity of language production.

PubMed

Gaskell, M Gareth; Warker, Jill; Lindsay, Shane; Frost, Rebecca; Guest, James; Snowdon, Reza; Stackhouse, Abigail

2014-07-01

The constraints that govern acceptable phoneme combinations in speech perception and production have considerable plasticity. We addressed whether sleep influences the acquisition of new constraints and their integration into the speech-production system. Participants repeated sequences of syllables in which two phonemes were artificially restricted to syllable onset or syllable coda, depending on the vowel in that sequence. After 48 sequences, participants either had a 90-min nap or remained awake. Participants then repeated 96 sequences so implicit constraint learning could be examined, and then were tested for constraint generalization in a forced-choice task. The sleep group, but not the wake group, produced speech errors at test that were consistent with restrictions on the placement of phonemes in training. Furthermore, only the sleep group generalized their learning to new materials. Polysomnography data showed that implicit constraint learning was associated with slow-wave sleep. These results show that sleep facilitates the integration of new linguistic knowledge with existing production constraints. These data have relevance for systems-consolidation models of sleep. © The Author(s) 2014.

User assumptions about information retrieval systems: Ethical concerns

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

Froehlich, T.J.

Information professionals, whether designers, intermediaries, database producers or vendors, bear some responsibility for the information that they make available to users of information systems. The users of such systems may tend to make many assumptions about the information that a system provides, such as believing: that the data are comprehensive, current and accurate, that the information resources or databases have same degree of quality and consistency of indexing; that the abstracts, if they exist, correctly and adequate reflect the content of the article; that there is consistency informs of author names or journal titles or indexing within and across databases;more » that there is standardization in and across databases; that once errors are detected, they are corrected; that appropriate choices of databases or information resources are a relatively easy matter, etc. The truth is that few of these assumptions are valid in commercia or corporate or organizational databases. However, given these beliefs and assumptions by many users, often promoted by information providers, information professionals, impossible, should intervene to warn users about the limitations and constraints of the databases they are using. With the growth of the Internet and end-user products (e.g., CD-ROMs), such interventions have significantly declined. In such cases, information should be provided on start-up or through interface screens, indicating to users, the constraints and orientation of the system they are using. The principle of {open_quotes}caveat emptor{close_quotes} is naive and socially irresponsible: information professionals or systems have an obligation to provide some framework or context for the information that users are accessing.« less

[Design and establishment of modern literature database about acupuncture Deqi].

PubMed

Guo, Zheng-rong; Qian, Gui-feng; Pan, Qiu-yin; Wang, Yang; Xin, Si-yuan; Li, Jing; Hao, Jie; Hu, Ni-juan; Zhu, Jiang; Ma, Liang-xiao

2015-02-01

A search on acupuncture Deqi was conducted using four Chinese-language biomedical databases (CNKI, Wan-Fang, VIP and CBM) and PubMed database and using keywords "Deqi" or "needle sensation" "needling feeling" "needle feel" "obtaining qi", etc. Then, a "Modern Literature Database for Acupuncture Deqi" was established by employing Microsoft SQL Server 2005 Express Edition, introducing the contents, data types, information structure and logic constraint of the system table fields. From this Database, detailed inquiries about general information of clinical trials, acupuncturists' experience, ancient medical works, comprehensive literature, etc. can be obtained. The present databank lays a foundation for subsequent evaluation of literature quality about Deqi and data mining of undetected Deqi knowledge.

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.

Rice SNP-seek database update: new SNPs, indels, and queries.

PubMed

Mansueto, Locedie; Fuentes, Roven Rommel; Borja, Frances Nikki; Detras, Jeffery; Abriol-Santos, Juan Miguel; Chebotarov, Dmytro; Sanciangco, Millicent; Palis, Kevin; Copetti, Dario; Poliakov, Alexandre; Dubchak, Inna; Solovyev, Victor; Wing, Rod A; Hamilton, Ruaraidh Sackville; Mauleon, Ramil; McNally, Kenneth L; Alexandrov, Nickolai

2017-01-04

We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Stabilization of computational procedures for constrained dynamical systems

NASA Technical Reports Server (NTRS)

Park, K. C.; Chiou, J. C.

1988-01-01

A new stabilization method of treating constraints in multibody dynamical systems is presented. By tailoring a penalty form of the constraint equations, the method achieves stabilization without artificial damping and yields a companion matrix differential equation for the constraint forces; hence, the constraint forces are obtained by integrating the companion differential equation for the constraint forces in time. A principal feature of the method is that the errors committed in each constraint condition decay with its corresponding characteristic time scale associated with its constraint force. Numerical experiments indicate that the method yields a marked improvement over existing techniques.

A Hybrid Constraint Representation and Reasoning Framework

NASA Technical Reports Server (NTRS)

Golden, Keith; Pang, Wanlin

2004-01-01

In this paper, we introduce JNET, a novel constraint representation and reasoning framework that supports procedural constraints and constraint attachments, providing a flexible way of integrating the constraint system with a runtime software environment and improving its applicability. We describe how JNET is applied to a real-world problem - NASA's Earth-science data processing domain, and demonstrate how JNET can be extended, without any knowledge of how it is implemented, to meet the growing demands of real-world applications.

A Foot-Mounted Inertial Measurement Unit (IMU) Positioning Algorithm Based on Magnetic Constraint

PubMed Central

Zou, Jiaheng

2018-01-01

With the development of related applications, indoor positioning techniques have been more and more widely developed. Based on Wi-Fi, Bluetooth low energy (BLE) and geomagnetism, indoor positioning techniques often rely on the physical location of fingerprint information. The focus and difficulty of establishing the fingerprint database are in obtaining a relatively accurate physical location with as little given information as possible. This paper presents a foot-mounted inertial measurement unit (IMU) positioning algorithm under the loop closure constraint based on magnetic information. It can provide relatively reliable position information without maps and geomagnetic information and provides a relatively accurate coordinate for the collection of a fingerprint database. In the experiment, the features extracted by the multi-level Fourier transform method proposed in this paper are validated and the validity of loop closure matching is tested with a RANSAC-based method. Moreover, the loop closure detection results show that the cumulative error of the trajectory processed by the graph optimization algorithm is significantly suppressed, presenting a good accuracy. The average error of the trajectory under loop closure constraint is controlled below 2.15 m. PMID:29494542

A Foot-Mounted Inertial Measurement Unit (IMU) Positioning Algorithm Based on Magnetic Constraint.

PubMed

Wang, Yan; Li, Xin; Zou, Jiaheng

2018-03-01

With the development of related applications, indoor positioning techniques have been more and more widely developed. Based on Wi-Fi, Bluetooth low energy (BLE) and geomagnetism, indoor positioning techniques often rely on the physical location of fingerprint information. The focus and difficulty of establishing the fingerprint database are in obtaining a relatively accurate physical location with as little given information as possible. This paper presents a foot-mounted inertial measurement unit (IMU) positioning algorithm under the loop closure constraint based on magnetic information. It can provide relatively reliable position information without maps and geomagnetic information and provides a relatively accurate coordinate for the collection of a fingerprint database. In the experiment, the features extracted by the multi-level Fourier transform method proposed in this paper are validated and the validity of loop closure matching is tested with a RANSAC-based method. Moreover, the loop closure detection results show that the cumulative error of the trajectory processed by the graph optimization algorithm is significantly suppressed, presenting a good accuracy. The average error of the trajectory under loop closure constraint is controlled below 2.15 m.

Integrated Primary Care Information Database (IPCI)

Cancer.gov

The Integrated Primary Care Information Database is a longitudinal observational database that was created specifically for pharmacoepidemiological and pharmacoeconomic studies, inlcuding data from computer-based patient records supplied voluntarily by general practitioners.

Mass spectrometry-based protein identification by integrating de novo sequencing with database searching.

PubMed

Wang, Penghao; Wilson, Susan R

2013-01-01

Mass spectrometry-based protein identification is a very challenging task. The main identification approaches include de novo sequencing and database searching. Both approaches have shortcomings, so an integrative approach has been developed. The integrative approach firstly infers partial peptide sequences, known as tags, directly from tandem spectra through de novo sequencing, and then puts these sequences into a database search to see if a close peptide match can be found. However the current implementation of this integrative approach has several limitations. Firstly, simplistic de novo sequencing is applied and only very short sequence tags are used. Secondly, most integrative methods apply an algorithm similar to BLAST to search for exact sequence matches and do not accommodate sequence errors well. Thirdly, by applying these methods the integrated de novo sequencing makes a limited contribution to the scoring model which is still largely based on database searching. We have developed a new integrative protein identification method which can integrate de novo sequencing more efficiently into database searching. Evaluated on large real datasets, our method outperforms popular identification methods.

Application of a derivative-free global optimization algorithm to the derivation of a new time integration scheme for the simulation of incompressible turbulence

NASA Astrophysics Data System (ADS)

Alimohammadi, Shahrouz; Cavaglieri, Daniele; Beyhaghi, Pooriya; Bewley, Thomas R.

2016-11-01

This work applies a recently developed Derivative-free optimization algorithm to derive a new mixed implicit-explicit (IMEX) time integration scheme for Computational Fluid Dynamics (CFD) simulations. This algorithm allows imposing a specified order of accuracy for the time integration and other important stability properties in the form of nonlinear constraints within the optimization problem. In this procedure, the coefficients of the IMEX scheme should satisfy a set of constraints simultaneously. Therefore, the optimization process, at each iteration, estimates the location of the optimal coefficients using a set of global surrogates, for both the objective and constraint functions, as well as a model of the uncertainty function of these surrogates based on the concept of Delaunay triangulation. This procedure has been proven to converge to the global minimum of the constrained optimization problem provided the constraints and objective functions are twice differentiable. As a result, a new third-order, low-storage IMEX Runge-Kutta time integration scheme is obtained with remarkably fast convergence. Numerical tests are then performed leveraging the turbulent channel flow simulations to validate the theoretical order of accuracy and stability properties of the new scheme.

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

Lam, Hugo Y.K.; Marenco, Luis; Shepherd, Gordon M.; Miller, Perry L.; Cheung, Kei-Hoi

2006-01-01

Integrative neuroscience involves the integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases do not expose their schemas (database structures) and their contents to web applications/agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we describe a pilot project that illustrates how neuroscience databases can be expressed using the Web Ontology Language, which is a semantically-rich ontological language, as a common data representation language to facilitate complex cross-database queries. In this pilot project, an existing tool called “D2RQ” was used to translate two neuroscience databases (NeuronDB and CoCoDat) into OWL, and the resulting OWL ontologies were then merged. An OWL-based reasoner (Racer) was then used to provide a sophisticated query language (nRQL) to perform integrated queries across the two databases based on the merged ontology. This pilot project is one step toward exploring the use of semantic web technologies in the neurosciences. PMID:17238384

Dynamic Terrin

DTIC Science & Technology

1991-12-30

York, 1985. [ Serway 86]: Raymond Serway , Physics for Scientists and Engineers. 2nd Edition, Saunders College Publishing, Philadelphia, 1986. pp. 200... Physical Modeling System 3.4 Realtime Hydrology 3.5 Soil Dynamics and Kinematics 4. Database Issues 4.1 Goals 4.2 Object Oriented Databases 4.3 Distributed...Animation System F. Constraints and Physical Modeling G. The PM Physical Modeling System H. Realtime Hydrology I. A Simplified Model of Soil Slumping

Embedding Temporal Constraints For Coordinated Execution in Habitat Automation

NASA Technical Reports Server (NTRS)

Morris, Paul; Schwabacher, Mark; Dalal, Michael; Fry, Charles

2013-01-01

Future NASA plans call for long-duration deep space missions with human crews. Because of light-time delay and other considerations, increased autonomy will be needed. This will necessitate integration of tools in such areas as anomaly detection, diagnosis, planning, and execution. In this paper we investigate an approach that integrates planning and execution by embedding planner-derived temporal constraints in an execution procedure. To avoid the need for propagation, we convert the temporal constraints to dispatchable form. We handle some uncertainty in the durations without it affecting the execution; larger variations may cause activities to be skipped.

The use of database management systems and artificial intelligence in automating the planning of optical navigation pictures

NASA Technical Reports Server (NTRS)

Davis, Robert P.; Underwood, Ian M.

1987-01-01

The use of database management systems (DBMS) and AI to minimize human involvement in the planning of optical navigation pictures for interplanetary space probes is discussed, with application to the Galileo mission. Parameters characterizing the desirability of candidate pictures, and the program generating them, are described. How these parameters automatically build picture records in a database, and the definition of the database structure, are then discussed. The various rules, priorities, and constraints used in selecting pictures are also described. An example is provided of an expert system, written in Prolog, for automatically performing the selection process.

Optimization of the Controlled Evaluation of Closed Relational Queries

NASA Astrophysics Data System (ADS)

Biskup, Joachim; Lochner, Jan-Hendrik; Sonntag, Sebastian

For relational databases, controlled query evaluation is an effective inference control mechanism preserving confidentiality regarding a previously declared confidentiality policy. Implementations of controlled query evaluation usually lack efficiency due to costly theorem prover calls. Suitably constrained controlled query evaluation can be implemented efficiently, but is not flexible enough from the perspective of database users and security administrators. In this paper, we propose an optimized framework for controlled query evaluation in relational databases, being efficiently implementable on the one hand and relaxing the constraints of previous approaches on the other hand.

Motion Pattern Encapsulation for Data-Driven Constraint-Based Motion Editing

NASA Astrophysics Data System (ADS)

Carvalho, Schubert R.; Boulic, Ronan; Thalmann, Daniel

The growth of motion capture systems have contributed to the proliferation of human motion database, mainly because human motion is important in many applications, ranging from games entertainment and films to sports and medicine. However, the captured motions normally attend specific needs. As an effort for adapting and reusing captured human motions in new tasks and environments and improving the animator's work, we present and discuss a new data-driven constraint-based animation system for interactive human motion editing. This method offers the compelling advantage that it provides faster deformations and more natural-looking motion results compared to goal-directed constraint-based methods found in the literature.

Navigating legal constraints in clinical data warehousing: a case study in personalized medicine.

PubMed

Jefferys, Benjamin R; Nwankwo, Iheanyi; Neri, Elias; Chang, David C W; Shamardin, Lev; Hänold, Stefanie; Graf, Norbert; Forgó, Nikolaus; Coveney, Peter

2013-04-06

Personalized medicine relies in part upon comprehensive data on patient treatment and outcomes, both for analysis leading to improved models that provide the basis for enhanced treatment, and for direct use in clinical decision-making. A data warehouse is an information technology for combining and standardizing multiple databases. Data warehousing of clinical data is constrained by many legal and ethical considerations, owing to the sensitive nature of the data being stored. We describe an unconstrained clinical data warehousing architecture, some of the legal constraints that have led us to reconsider this architecture, and the legal and technical solutions to these constraints developed for the clinical data warehouse in the personalized medicine project p-medicine. We also propose some changes to the legal constraints that will further enable clinical research.

[Integrated DNA barcoding database for identifying Chinese animal medicine].

PubMed

Shi, Lin-Chun; Yao, Hui; Xie, Li-Fang; Zhu, Ying-Jie; Song, Jing-Yuan; Zhang, Hui; Chen, Shi-Lin

2014-06-01

In order to construct an integrated DNA barcoding database for identifying Chinese animal medicine, the authors and their cooperators have completed a lot of researches for identifying Chinese animal medicines using DNA barcoding technology. Sequences from GenBank have been analyzed simultaneously. Three different methods, BLAST, barcoding gap and Tree building, have been used to confirm the reliabilities of barcode records in the database. The integrated DNA barcoding database for identifying Chinese animal medicine has been constructed using three different parts: specimen, sequence and literature information. This database contained about 800 animal medicines and the adulterants and closely related species. Unknown specimens can be identified by pasting their sequence record into the window on the ID page of species identification system for traditional Chinese medicine (www. tcmbarcode. cn). The integrated DNA barcoding database for identifying Chinese animal medicine is significantly important for animal species identification, rare and endangered species conservation and sustainable utilization of animal resources.

PathCase-SB architecture and database design

PubMed Central

2011-01-01

Background Integration of metabolic pathways resources and regulatory metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation in metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks. Description PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database. Conclusions PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world. PMID:22070889

E-MSD: an integrated data resource for bioinformatics.

PubMed

Velankar, S; McNeil, P; Mittard-Runte, V; Suarez, A; Barrell, D; Apweiler, R; Henrick, K

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

Integrated Control Using the SOFFT Control Structure

NASA Technical Reports Server (NTRS)

Halyo, Nesim

1996-01-01

The need for integrated/constrained control systems has become clearer as advanced aircraft introduced new coupled subsystems such as new propulsion subsystems with thrust vectoring and new aerodynamic designs. In this study, we develop an integrated control design methodology which accomodates constraints among subsystem variables while using the Stochastic Optimal Feedforward/Feedback Control Technique (SOFFT) thus maintaining all the advantages of the SOFFT approach. The Integrated SOFFT Control methodology uses a centralized feedforward control and a constrained feedback control law. The control thus takes advantage of the known coupling among the subsystems while maintaining the identity of subsystems for validation purposes and the simplicity of the feedback law to understand the system response in complicated nonlinear scenarios. The Variable-Gain Output Feedback Control methodology (including constant gain output feedback) is extended to accommodate equality constraints. A gain computation algorithm is developed. The designer can set the cross-gains between two variables or subsystems to zero or another value and optimize the remaining gains subject to the constraint. An integrated control law is designed for a modified F-15 SMTD aircraft model with coupled airframe and propulsion subsystems using the Integrated SOFFT Control methodology to produce a set of desired flying qualities.

Enforcement of entailment constraints in distributed service-based business processes.

PubMed

Hummer, Waldemar; Gaubatz, Patrick; Strembeck, Mark; Zdun, Uwe; Dustdar, Schahram

2013-11-01

A distributed business process is executed in a distributed computing environment. The service-oriented architecture (SOA) paradigm is a popular option for the integration of software services and execution of distributed business processes. Entailment constraints, such as mutual exclusion and binding constraints, are important means to control process execution. Mutually exclusive tasks result from the division of powerful rights and responsibilities to prevent fraud and abuse. In contrast, binding constraints define that a subject who performed one task must also perform the corresponding bound task(s). We aim to provide a model-driven approach for the specification and enforcement of task-based entailment constraints in distributed service-based business processes. Based on a generic metamodel, we define a domain-specific language (DSL) that maps the different modeling-level artifacts to the implementation-level. The DSL integrates elements from role-based access control (RBAC) with the tasks that are performed in a business process. Process definitions are annotated using the DSL, and our software platform uses automated model transformations to produce executable WS-BPEL specifications which enforce the entailment constraints. We evaluate the impact of constraint enforcement on runtime performance for five selected service-based processes from existing literature. Our evaluation demonstrates that the approach correctly enforces task-based entailment constraints at runtime. The performance experiments illustrate that the runtime enforcement operates with an overhead that scales well up to the order of several ten thousand logged invocations. Using our DSL annotations, the user-defined process definition remains declarative and clean of security enforcement code. Our approach decouples the concerns of (non-technical) domain experts from technical details of entailment constraint enforcement. The developed framework integrates seamlessly with WS-BPEL and the Web services technology stack. Our prototype implementation shows the feasibility of the approach, and the evaluation points to future work and further performance optimizations.

Semiautomated head-and-neck IMRT planning using dose warping and scaling to robustly adapt plans in a knowledge database containing potentially suboptimal plans

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

Schmidt, Matthew, E-mail: matthew.schmidt@varian.com; Grzetic, Shelby; Lo, Joseph Y.

Purpose: Prior work by the authors and other groups has studied the creation of automated intensity modulated radiotherapy (IMRT) plans of equivalent quality to those in a patient database of manually created clinical plans; those database plans provided guidance on the achievable sparing to organs-at-risk (OARs). However, in certain sites, such as head-and-neck, the clinical plans may not be sufficiently optimized because of anatomical complexity and clinical time constraints. This could lead to automated plans that suboptimally exploit OAR sparing. This work investigates a novel dose warping and scaling scheme that attempts to reduce effects of suboptimal sparing in clinicalmore » database plans, thus improving the quality of semiautomated head-and-neck cancer (HNC) plans. Methods: Knowledge-based radiotherapy (KBRT) plans for each of ten “query” patients were semiautomatically generated by identifying the most similar “match” patient in a database of 103 clinical manually created patient plans. The match patient’s plans were adapted to the query case by: (1) deforming the match beam fluences to suit the query target volume and (2) warping the match primary/boost dose distribution to suit the query geometry and using the warped distribution to generate query primary/boost optimization dose-volume constraints. Item (2) included a distance scaling factor to improve query OAR dose sparing with respect to the possibly suboptimal clinical match plan. To further compensate for a component plan of the match case (primary/boost) not optimally sparing OARs, the query dose volume constraints were reduced using a dose scaling factor to be the minimum from either (a) the warped component plan (primary or boost) dose distribution or (b) the warped total plan dose distribution (primary + boost) scaled in proportion to the ratio of component prescription dose to total prescription dose. The dose-volume constraints were used to plan the query case with no human intervention to adjust constraints during plan optimization. Results: KBRT and original clinical plans were dosimetrically equivalent for parotid glands (mean/median doses), spinal cord, and brainstem (maximum doses). KBRT plans significantly reduced larynx median doses (21.5 ± 6.6 Gy to 17.9 ± 3.9 Gy), and oral cavity mean (32.3 ± 6.2 Gy to 28.9 ± 5.4 Gy) and median (28.7 ± 5.7 Gy to 23.2 ± 5.3 Gy) doses. Doses to ipsilateral parotid gland, larynx, oral cavity, and brainstem were lower or equivalent in the KBRT plans for the majority of cases. By contrast, KBRT plans generated without the dose warping and dose scaling steps were not significantly different from the clinical plans. Conclusions: Fast, semiautomatically generated HNC IMRT plans adapted from existing plans in a clinical database can be of equivalent or better quality than manually created plans. The reductions in OAR doses in the semiautomated plans, compared to the clinical plans, indicate that the proposed dose warping and scaling method shows promise in mitigating the impact of suboptimal clinical plans.« less

Effect of CT Specimen Thickness on the Mechanical Characteristics at the Crack Tip of Stress Corrosion Cracking in Ni-based Alloys

NASA Astrophysics Data System (ADS)

Yinghao, Cui; He, Xue; Lingyan, Zhao

2017-12-01

It’s important to obtain accurate stress corrosion crack(SCC) growth rate for quantitative life prediction of components in nuclear power plants. However, the engineering practice shows that the crack tip constraint effect has a great influence on the mechanical properties and crack growth rate of SCC at crack tip. To study the influence of the specimen thickness on the crack tip mechanical properties of SCC, the stress, strain and C integral at creep crack tip are analyzed under different specimens thickness. Results show that the cracked specimen is less likely to crack due to effect of crack tip constraint. When the thickness ratio B/W is larger than 0.1, the crack tip constraint is almost ineffective. Value of C integral is the largest when B/W is 0.25. Then specimen thickness has little effect on the value of C integral. The effect of specimen thickness on the value of C integral is less significant at higher thickness ratio.

New York State energy-analytic information system: first-stage implementation

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

Allentuck, J.; Carroll, O.; Fiore, L.

1979-09-01

So that energy policy by state government may be formulated within the constraints imposed by policy determined at the national level - yet reflect the diverse interests of its citizens - large quantities of data and sophisticated analytic capabilities are required. This report presents the design of an energy-information/analytic system for New York State, the data for a base year, 1976, and projections of these data. At the county level, 1976 energy-supply demand data and electric generating plant data are provided as well. Data-base management is based on System 2000. Three computerized models provide the system's basic analytic capacity. Themore » Brookhaven Energy System Network Simulator provides an integrating framework while a price-response model and a weather sensitive energy demand model furnished a short-term energy response estimation capability. The operation of these computerized models is described. 62 references, 25 figures, 39 tables.« less

Ordering actions for visibility. [distributed computing based on idea of atomic actions operating on data

NASA Technical Reports Server (NTRS)

Mckendry, M. S.

1985-01-01

The notion of 'atomic actions' has been considered in recent work on data integrity and reliability. It has been found that the standard database operations of 'read' and 'write' carry with them severe performance limitations. For this reason, systems are now being designed in which actions operate on 'objects' through operations with more-or-less arbitrary semantics. An object (i.e., an instance of an abstract data type) comprises data, a set of operations (procedures) to manipulate the data, and a set of invariants. An 'action' is a unit of work. It appears to be primitive to its surrounding environment, and 'atomic' to other actions. Attention is given to the conventional model of nested actions, ordering requirements, the maximum possible visibility (full visibility) for items which must be controlled by ordering constraints, item management paradigms, and requirements for blocking mechanisms which provide the required visibility.

SIDD: A Semantically Integrated Database towards a Global View of Human Disease

PubMed Central

Cheng, Liang; Wang, Guohua; Li, Jie; Zhang, Tianjiao; Xu, Peigang; Wang, Yadong

2013-01-01

Background A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data. Methodology To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy. Conclusions A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD. PMID:24146757

Data Integration and Mining for Synthetic Biology Design.

PubMed

Mısırlı, Göksel; Hallinan, Jennifer; Pocock, Matthew; Lord, Phillip; McLaughlin, James Alastair; Sauro, Herbert; Wipat, Anil

2016-10-21

One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.

Redundancy of constraints in the classical and quantum theories of gravitation.

NASA Technical Reports Server (NTRS)

Moncrief, V.

1972-01-01

It is shown that in Dirac's version of the quantum theory of gravitation, the Hamiltonian constraints are greatly redundant. If the Hamiltonian constraint condition is satisfied at one point on the underlying, closed three-dimensional manifold, then it is automatically satisfied at every point, provided only that the momentum constraints are everywhere satisfied. This permits one to replace the usual infinity of Hamiltonian constraints by a single condition which may be taken in the form of an integral over the manifold. Analogous theorems are given for the classical Einstein Hamilton-Jacobi equations.

Emission & Generation Resource Integrated Database (eGRID)

EPA Pesticide Factsheets

The Emissions & Generation Resource Integrated Database (eGRID) is an integrated source of data on environmental characteristics of electric power generation. Twelve federal databases are represented by eGRID, which provides air emission and resource mix information for thousands of power plants and generating companies. eGRID allows direct comparison of the environmental attributes of electricity from different plants, companies, States, or regions of the power grid.

Heterogeneous database integration in biomedicine.

PubMed

Sujansky, W

2001-08-01

The rapid expansion of biomedical knowledge, reduction in computing costs, and spread of internet access have created an ocean of electronic data. The decentralized nature of our scientific community and healthcare system, however, has resulted in a patchwork of diverse, or heterogeneous, database implementations, making access to and aggregation of data across databases very difficult. The database heterogeneity problem applies equally to clinical data describing individual patients and biological data characterizing our genome. Specifically, databases are highly heterogeneous with respect to the data models they employ, the data schemas they specify, the query languages they support, and the terminologies they recognize. Heterogeneous database systems attempt to unify disparate databases by providing uniform conceptual schemas that resolve representational heterogeneities, and by providing querying capabilities that aggregate and integrate distributed data. Research in this area has applied a variety of database and knowledge-based techniques, including semantic data modeling, ontology definition, query translation, query optimization, and terminology mapping. Existing systems have addressed heterogeneous database integration in the realms of molecular biology, hospital information systems, and application portability.

Navigating legal constraints in clinical data warehousing: a case study in personalized medicine

PubMed Central

Jefferys, Benjamin R.; Nwankwo, Iheanyi; Neri, Elias; Chang, David C. W.; Shamardin, Lev; Hänold, Stefanie; Graf, Norbert; Forgó, Nikolaus; Coveney, Peter

2013-01-01

Personalized medicine relies in part upon comprehensive data on patient treatment and outcomes, both for analysis leading to improved models that provide the basis for enhanced treatment, and for direct use in clinical decision-making. A data warehouse is an information technology for combining and standardizing multiple databases. Data warehousing of clinical data is constrained by many legal and ethical considerations, owing to the sensitive nature of the data being stored. We describe an unconstrained clinical data warehousing architecture, some of the legal constraints that have led us to reconsider this architecture, and the legal and technical solutions to these constraints developed for the clinical data warehouse in the personalized medicine project p-medicine. We also propose some changes to the legal constraints that will further enable clinical research. PMID:24427531

Programming languages for circuit design.

PubMed

Pedersen, Michael; Yordanov, Boyan

2015-01-01

This chapter provides an overview of a programming language for Genetic Engineering of Cells (GEC). A GEC program specifies a genetic circuit at a high level of abstraction through constraints on otherwise unspecified DNA parts. The GEC compiler then selects parts which satisfy the constraints from a given parts database. GEC further provides more conventional programming language constructs for abstraction, e.g., through modularity. The GEC language and compiler is available through a Web tool which also provides functionality, e.g., for simulation of designed circuits.

A dedicated database system for handling multi-level data in systems biology.

PubMed

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.

PubMed

Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming

2017-04-07

Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.

Momentum constraints as integrability conditions for the Hamiltonian constraint in general relativity.

NASA Technical Reports Server (NTRS)

Moncrief, V.; Teitelboim, C.

1972-01-01

It is shown that if the Hamiltonian constraint of general relativity is imposed as a restriction on the Hamilton principal functional in the classical theory, or on the state functional in the quantum theory, then the momentum constraints are automatically satisfied. This result holds both for closed and open spaces and it means that the full content of the theory is summarized by a single functional equation of the Tomonaga-Schwinger type.

E-MSD: an integrated data resource for bioinformatics

PubMed Central

Velankar, S.; McNeil, P.; Mittard-Runte, V.; Suarez, A.; Barrell, D.; Apweiler, R.; Henrick, K.

2005-01-01

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the ‘Structure Integration with Function, Taxonomy and Sequences (SIFTS)’ initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group. PMID:15608192

Multiconstrained gene clustering based on generalized projections

PubMed Central

2010-01-01

Background Gene clustering for annotating gene functions is one of the fundamental issues in bioinformatics. The best clustering solution is often regularized by multiple constraints such as gene expressions, Gene Ontology (GO) annotations and gene network structures. How to integrate multiple pieces of constraints for an optimal clustering solution still remains an unsolved problem. Results We propose a novel multiconstrained gene clustering (MGC) method within the generalized projection onto convex sets (POCS) framework used widely in image reconstruction. Each constraint is formulated as a corresponding set. The generalized projector iteratively projects the clustering solution onto these sets in order to find a consistent solution included in the intersection set that satisfies all constraints. Compared with previous MGC methods, POCS can integrate multiple constraints from different nature without distorting the original constraints. To evaluate the clustering solution, we also propose a new performance measure referred to as Gene Log Likelihood (GLL) that considers genes having more than one function and hence in more than one cluster. Comparative experimental results show that our POCS-based gene clustering method outperforms current state-of-the-art MGC methods. Conclusions The POCS-based MGC method can successfully combine multiple constraints from different nature for gene clustering. Also, the proposed GLL is an effective performance measure for the soft clustering solutions. PMID:20356386

Integration of an Evidence Base into a Probabilistic Risk Assessment Model. The Integrated Medical Model Database: An Organized Evidence Base for Assessing In-Flight Crew Health Risk and System Design

NASA Technical Reports Server (NTRS)

Saile, Lynn; Lopez, Vilma; Bickham, Grandin; FreiredeCarvalho, Mary; Kerstman, Eric; Byrne, Vicky; Butler, Douglas; Myers, Jerry; Walton, Marlei

2011-01-01

This slide presentation reviews the Integrated Medical Model (IMM) database, which is an organized evidence base for assessing in-flight crew health risk. The database is a relational database accessible to many people. The database quantifies the model inputs by a ranking based on the highest value of the data as Level of Evidence (LOE) and the quality of evidence (QOE) score that provides an assessment of the evidence base for each medical condition. The IMM evidence base has already been able to provide invaluable information for designers, and for other uses.

Optimizing Maintenance of Constraint-Based Database Caches

NASA Astrophysics Data System (ADS)

Klein, Joachim; Braun, Susanne

Caching data reduces user-perceived latency and often enhances availability in case of server crashes or network failures. DB caching aims at local processing of declarative queries in a DBMS-managed cache close to the application. Query evaluation must produce the same results as if done at the remote database backend, which implies that all data records needed to process such a query must be present and controlled by the cache, i. e., to achieve “predicate-specific” loading and unloading of such record sets. Hence, cache maintenance must be based on cache constraints such that “predicate completeness” of the caching units currently present can be guaranteed at any point in time. We explore how cache groups can be maintained to provide the data currently needed. Moreover, we design and optimize loading and unloading algorithms for sets of records keeping the caching units complete, before we empirically identify the costs involved in cache maintenance.

The roles of acculturative stress and social constraints on psychological distress in Hispanic/Latino and Asian immigrant college students.

PubMed

Wong, Celia Ching Yee; Correa, Alma; Robinson, Kendall; Lu, Qian

2017-07-01

Acculturative stress has been linked to psychological distress, but few studies have explored the moderating role of social constraints on this relationship. Social constraints are the perception that social networks are unsupportive to stressor-related discussions. In the present study, the relationship between acculturative stress and psychological distress in Hispanic/Latino and Asian immigrants and the moderating role of social constraints in this relationship were examined. Participants were 306 college students (169 Hispanics/Latinos, 137 Asians; 33.9% first-generation immigrants, 66.1% second-generation immigrants) from two Texas universities. Correlation results showed that acculturative stress and social constraints were significantly associated with higher levels of psychological distress in Hispanics/Latinos and Asians. In addition, regression results indicated a significant three-way interaction effect among acculturative stress, social constraints, and racial/ethnic groups. Social constraints were found to moderate the relationship between acculturative stress and psychological distress in Asians but not in Hispanics/Latinos. Significant association between acculturative stress and psychological distress was found in Asians with higher levels of social constraints but not in Asians with lower levels of social constraints. These findings suggested that the interaction effect of acculturative stress and social constraints on psychological distress may be subject to cultural influences, and social constraints may have differential roles in Hispanics/Latinos and Asians. Potential implications on the development of culturally adaptive interventions for different racial/ethnic minority groups were discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

A Combined Solar and Geomagnetic Index for Thermospheric Climate

NASA Technical Reports Server (NTRS)

Hunt, Linda; Mlynczak, Marty

2015-01-01

Infrared radiation from nitric oxide (NO) at 5.3 Â is a primary mechanism by which the thermosphere cools to space. The SABER instrument on the NASA TIMED satellite has been measuring thermospheric cooling by NO for over 13 years. Physically, changes in NO emission are due to changes in temperature, atomic oxygen, and the NO density. These physical changes however are driven by changes in solar irradiance and changes in geomagnetic conditions. We show that the SABER time series of globally integrated infrared power (Watts) radiated by NO can be replicated accurately by a multiple linear regression fit using the F10.7, Ap, and Dst indices. This fit enables several fundamental properties of NO cooling to be determined as well as their variability with time, permitting reconstruction of the NO power time series back nearly 70 years with extant databases of these indices. The relative roles of solar ultraviolet and geomagnetic processes in determining the NO cooling are derived and shown to be solar cycle dependent. This reconstruction provides a long-term time series of an integral radiative constraint on thermospheric climate that can be used to test climate models.

Children's experiences of dialysis: a systematic review of qualitative studies.

PubMed

Tjaden, Lidwien; Tong, Allison; Henning, Paul; Groothoff, Jaap; Craig, Jonathan C

2012-05-01

To describe the experiences and perspectives of children and adolescents on dialysis. A systematic review of qualitative studies was conducted that explored the experiences of children on dialysis. Electronic databases and reference lists of relevant articles were searched to October Week 2, 2010. A total of 17 studies, which reported the experiences of 143 children receiving dialysis, were included. Five major themes were identified: loss of control (high reliance on carers, parental overprotectiveness, unrelenting dependence on a machine, impaired body integrity), restricted lifestyle (limited socialisation opportunities, academic struggle), coping strategies (hope for kidney transplant and medical advances, social support, positive determination and self-awareness, engaging in activities, denial), managing treatment (ownership, proactive involvement, adherence to fluid and diet restrictions) and feeling different (abnormal physical appearance, injustice, being a burden). Children undergoing dialysis experience impaired growth, invasive procedures, school and social constraints. They often have poor self-esteem and a pervasive sense of losing their identity, body integrity, control, independence and opportunity. Interventions are needed to equip children with the capacity to manage their health, participate in community, engage in 'permissible' recreational activities, progress in their studies, and remain vigilant in dialysis and treatment responsibilities, for improved health and treatment outcomes.

Chemical Transformation System: Cloud Based ...

EPA Pesticide Factsheets

Integrated Environmental Modeling (IEM) systems that account for the fate/transport of organics frequently require physicochemical properties as well as transformation products. A myriad of chemical property databases exist but these can be difficult to access and often do not contain the proprietary chemicals that environmental regulators must consider. We are building the Chemical Transformation System (CTS) to facilitate model parameterization and analysis. CTS integrates a number of physicochemical property calculators into the system including EPI Suite, SPARC, TEST and ChemAxon. The calculators are heterogeneous in their scientific methodologies, technology implementations and deployment stacks. CTS also includes a chemical transformation processing engine that has been loaded with reaction libraries for human biotransformation, abiotic reduction and abiotic hydrolysis. CTS implements a common interface for the disparate calculators accepting molecular identifiers (SMILES, IUPAC, CAS#, user-drawn molecule) before submission for processing. To make the system as accessible as possible and provide a consistent programmatic interface, we wrapped the calculators in a standardized RESTful Application Programming Interface (API) which makes it capable of servicing a much broader spectrum of clients without constraints to interoperability such as operating system or programming language. CTS is hosted in a shared cloud environment, the Quantitative Environmental

Definition ofthe Design Trajectory and Entry Flight Corridor for the NASA Orion Exploration Mission 1 Entry Trajectory Using an Integrated Approach and Optimization

NASA Technical Reports Server (NTRS)

McNamara, Luke W.; Braun, Robert D.

2014-01-01

One of the key design objectives of NASA's Orion Exploration Mission 1 (EM- 1) is to execute a guided entry trajectory demonstrating GN&C capability. The focus of this paper is defining the flyable entry corridor for EM-1 taking into account multiple subsystem constraints such as complex aerothermal heating constraints, aerothermal heating objectives, landing accuracy constraints, structural load limits, Human-System-Integration-Requirements, Service Module debris disposal limits and other flight test objectives. During the EM-1 Design Analysis Cycle 1 design challenges came up that made defining the flyable entry corridor for the EM-1 mission critical to mission success. This document details the optimization techniques that were explored to use with the 6-DOF ANTARES simulation to assist in defining the design entry interface state and entry corridor with respect to key flight test constraints and objectives.

Contour Tracking in Echocardiographic Sequences via Sparse Representation and Dictionary Learning

PubMed Central

Huang, Xiaojie; Dione, Donald P.; Compas, Colin B.; Papademetris, Xenophon; Lin, Ben A.; Bregasi, Alda; Sinusas, Albert J.; Staib, Lawrence H.; Duncan, James S.

2013-01-01

This paper presents a dynamical appearance model based on sparse representation and dictionary learning for tracking both endocardial and epicardial contours of the left ventricle in echocardiographic sequences. Instead of learning offline spatiotemporal priors from databases, we exploit the inherent spatiotemporal coherence of individual data to constraint cardiac contour estimation. The contour tracker is initialized with a manual tracing of the first frame. It employs multiscale sparse representation of local image appearance and learns online multiscale appearance dictionaries in a boosting framework as the image sequence is segmented frame-by-frame sequentially. The weights of multiscale appearance dictionaries are optimized automatically. Our region-based level set segmentation integrates a spectrum of complementary multilevel information including intensity, multiscale local appearance, and dynamical shape prediction. The approach is validated on twenty-six 4D canine echocardiographic images acquired from both healthy and post-infarct canines. The segmentation results agree well with expert manual tracings. The ejection fraction estimates also show good agreement with manual results. Advantages of our approach are demonstrated by comparisons with a conventional pure intensity model, a registration-based contour tracker, and a state-of-the-art database-dependent offline dynamical shape model. We also demonstrate the feasibility of clinical application by applying the method to four 4D human data sets. PMID:24292554

BioWarehouse: a bioinformatics database warehouse toolkit

PubMed Central

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David WJ; Tenenbaum, Jessica D; Karp, Peter D

2006-01-01

Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the database integration problem for bioinformatics. PMID:16556315

BioWarehouse: a bioinformatics database warehouse toolkit.

PubMed

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

2006-03-23

This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

Towards G2G: Systems of Technology Database Systems

NASA Technical Reports Server (NTRS)

Maluf, David A.; Bell, David

2005-01-01

We present an approach and methodology for developing Government-to-Government (G2G) Systems of Technology Database Systems. G2G will deliver technologies for distributed and remote integration of technology data for internal use in analysis and planning as well as for external communications. G2G enables NASA managers, engineers, operational teams and information systems to "compose" technology roadmaps and plans by selecting, combining, extending, specializing and modifying components of technology database systems. G2G will interoperate information and knowledge that is distributed across organizational entities involved that is ideal for NASA future Exploration Enterprise. Key contributions of the G2G system will include the creation of an integrated approach to sustain effective management of technology investments that supports the ability of various technology database systems to be independently managed. The integration technology will comply with emerging open standards. Applications can thus be customized for local needs while enabling an integrated management of technology approach that serves the global needs of NASA. The G2G capabilities will use NASA s breakthrough in database "composition" and integration technology, will use and advance emerging open standards, and will use commercial information technologies to enable effective System of Technology Database systems.

Building a multi-scaled geospatial temporal ecology database from disparate data sources: fostering open science and data reuse.

PubMed

Soranno, Patricia A; Bissell, Edward G; Cheruvelil, Kendra S; Christel, Samuel T; Collins, Sarah M; Fergus, C Emi; Filstrup, Christopher T; Lapierre, Jean-Francois; Lottig, Noah R; Oliver, Samantha K; Scott, Caren E; Smith, Nicole J; Stopyak, Scott; Yuan, Shuai; Bremigan, Mary Tate; Downing, John A; Gries, Corinna; Henry, Emily N; Skaff, Nick K; Stanley, Emily H; Stow, Craig A; Tan, Pang-Ning; Wagner, Tyler; Webster, Katherine E

2015-01-01

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km(2)). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

Building a multi-scaled geospatial temporal ecology database from disparate data sources: Fostering open science through data reuse

USGS Publications Warehouse

Soranno, Patricia A.; Bissell, E.G.; Cheruvelil, Kendra S.; Christel, Samuel T.; Collins, Sarah M.; Fergus, C. Emi; Filstrup, Christopher T.; Lapierre, Jean-Francois; Lotting, Noah R.; Oliver, Samantha K.; Scott, Caren E.; Smith, Nicole J.; Stopyak, Scott; Yuan, Shuai; Bremigan, Mary Tate; Downing, John A.; Gries, Corinna; Henry, Emily N.; Skaff, Nick K.; Stanley, Emily H.; Stow, Craig A.; Tan, Pang-Ning; Wagner, Tyler; Webster, Katherine E.

2015-01-01

Although there are considerable site-based data for individual or groups of ecosystems, these datasets are widely scattered, have different data formats and conventions, and often have limited accessibility. At the broader scale, national datasets exist for a large number of geospatial features of land, water, and air that are needed to fully understand variation among these ecosystems. However, such datasets originate from different sources and have different spatial and temporal resolutions. By taking an open-science perspective and by combining site-based ecosystem datasets and national geospatial datasets, science gains the ability to ask important research questions related to grand environmental challenges that operate at broad scales. Documentation of such complicated database integration efforts, through peer-reviewed papers, is recommended to foster reproducibility and future use of the integrated database. Here, we describe the major steps, challenges, and considerations in building an integrated database of lake ecosystems, called LAGOS (LAke multi-scaled GeOSpatial and temporal database), that was developed at the sub-continental study extent of 17 US states (1,800,000 km2). LAGOS includes two modules: LAGOSGEO, with geospatial data on every lake with surface area larger than 4 ha in the study extent (~50,000 lakes), including climate, atmospheric deposition, land use/cover, hydrology, geology, and topography measured across a range of spatial and temporal extents; and LAGOSLIMNO, with lake water quality data compiled from ~100 individual datasets for a subset of lakes in the study extent (~10,000 lakes). Procedures for the integration of datasets included: creating a flexible database design; authoring and integrating metadata; documenting data provenance; quantifying spatial measures of geographic data; quality-controlling integrated and derived data; and extensively documenting the database. Our procedures make a large, complex, and integrated database reproducible and extensible, allowing users to ask new research questions with the existing database or through the addition of new data. The largest challenge of this task was the heterogeneity of the data, formats, and metadata. Many steps of data integration need manual input from experts in diverse fields, requiring close collaboration.

PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data.

PubMed

Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai; Gundlach, Heidrun; Mayer, Klaus F X

2017-01-01

Plant Genome and Systems Biology (PGSB), formerly Munich Institute for Protein Sequences (MIPS) PlantsDB, is a database framework for the integration and analysis of plant genome data, developed and maintained for more than a decade now. Major components of that framework are genome databases and analysis resources focusing on individual (reference) genomes providing flexible and intuitive access to data. Another main focus is the integration of genomes from both model and crop plants to form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny). Data exchange and integrated search functionality with/over many plant genome databases is provided within the transPLANT project.

Time on your hands: Perceived duration of sensory events is biased toward concurrent actions.

PubMed

Yon, Daniel; Edey, Rosanna; Ivry, Richard B; Press, Clare

2017-02-01

Perceptual systems must rapidly generate accurate representations of the world from sensory inputs that are corrupted by internal and external noise. We can typically obtain more veridical representations by integrating information from multiple channels, but this integration can lead to biases when inputs are, in fact, not from the same source. Although a considerable amount is known about how different sources of information are combined to influence what we perceive, it is not known whether temporal features are combined. It is vital to address this question given the divergent predictions made by different models of cue combination and time perception concerning the plausibility of cross-modal temporal integration, and the implications that such integration would have for research programs in action control and social cognition. Here we present four experiments investigating the influence of movement duration on the perceived duration of an auditory tone. Participants either explicitly (Experiments 1-2) or implicitly (Experiments 3-4) produced hand movements of shorter or longer durations, while judging the duration of a concurrently presented tone (500-950 ms in duration). Across all experiments, judgments of tone duration were attracted toward the duration of executed movements (i.e., tones were perceived to be longer when executing a movement of longer duration). Our results demonstrate that temporal information associated with movement biases perceived auditory duration, placing important constraints on theories modeling cue integration for state estimation, as well as models of time perception, action control and social cognition. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Enhancing Knowledge Integration: An Information System Capstone Project

ERIC Educational Resources Information Center

Steiger, David M.

2009-01-01

This database project focuses on learning through knowledge integration; i.e., sharing and applying specialized (database) knowledge within a group, and combining it with other business knowledge to create new knowledge. Specifically, the Tiny Tots, Inc. project described below requires students to design, build, and instantiate a database system…

Constraint treatment techniques and parallel algorithms for multibody dynamic analysis. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Chiou, Jin-Chern

1990-01-01

Computational procedures for kinematic and dynamic analysis of three-dimensional multibody dynamic (MBD) systems are developed from the differential-algebraic equations (DAE's) viewpoint. Constraint violations during the time integration process are minimized and penalty constraint stabilization techniques and partitioning schemes are developed. The governing equations of motion, a two-stage staggered explicit-implicit numerical algorithm, are treated which takes advantage of a partitioned solution procedure. A robust and parallelizable integration algorithm is developed. This algorithm uses a two-stage staggered central difference algorithm to integrate the translational coordinates and the angular velocities. The angular orientations of bodies in MBD systems are then obtained by using an implicit algorithm via the kinematic relationship between Euler parameters and angular velocities. It is shown that the combination of the present solution procedures yields a computationally more accurate solution. To speed up the computational procedures, parallel implementation of the present constraint treatment techniques, the two-stage staggered explicit-implicit numerical algorithm was efficiently carried out. The DAE's and the constraint treatment techniques were transformed into arrowhead matrices to which Schur complement form was derived. By fully exploiting the sparse matrix structural analysis techniques, a parallel preconditioned conjugate gradient numerical algorithm is used to solve the systems equations written in Schur complement form. A software testbed was designed and implemented in both sequential and parallel computers. This testbed was used to demonstrate the robustness and efficiency of the constraint treatment techniques, the accuracy of the two-stage staggered explicit-implicit numerical algorithm, and the speed up of the Schur-complement-based parallel preconditioned conjugate gradient algorithm on a parallel computer.

Science objectives and observing strategy for the OMEGA imaging spectrometer on Mars-Express

NASA Astrophysics Data System (ADS)

Erard, S.; Bibring, J.-P.; Drossart, P.; Forget, F.; Schmitt, B.; OMEGA Team

2003-04-01

The science objectives of OMEGA, which were first defined at the time of instruments selection for Mars-Express, were recently updated to integrate new results from MGS and Odyssey concerning three main fields: Martian surface and atmosphere, and polar processes. Thematic categories of observations are derived from the scientific objectives whenever spectral observations from OMEGA are expected to provide insights to Mars present situation and evolution. Targets within these categories are selected on the basis of their expected usefulness, which is related to their intrinsic properties and to the instrument capabilities. The whole surface will be mapped at low resolution (~5 km/pixel) in the course of the nominal mission, and possibly routinely at very coarse resolution to monitor time-varying processes from apocenter. However, only 5% of the surface can be observed at high resolution (up to 350 m/pixel) owing to constraints on telemetry rate. HR targets are therefore selected on the basis of telemetry constraints, orbital parameters, observing opportunities (visibility under given conditions), and spacecraft functionalities (e.g., depointing capacity), then prioritized within each category according to the probability to perform significant observations with OMEGA (in many situations, according to the estimated dust coverage). Target selection is performed interactively between OMEGA co-Is, in close contact with teams from other MEx experiments (mostly HRSC, PFS and Spicam) and other missions (e.g., MER and MRO). Most HR surface targets are selected on the basis of deep examination of Viking, THEMIS, and MOC HR images. Other surface targets include areas presenting unusual spectral properties in previous observations, or suspected to exhibit signatures of hydrothermal activity. Proposed landing sites and suggested source areas for the SNC meteorites are also included. Atmospheric/polar objectives more often translate as particular observing modes, sometimes at HR (e.g., limb observations, EPF sequences). The constraints are related to local time and seasonal occurrence of particular processes, and to spacecraft pointing. About 1000 HR targets are currently identified in the Southern hemisphere (first six month in orbit). The targets are described in a database with geographic coordinates in IAU-2000 system, context and detailed images, optimum observing conditions, science rationale and references. This database is currently being interfaced with ESA's MAPSS planning software.

Integrated systems optimization model for biofuel development: The influence of environmental constraints

NASA Astrophysics Data System (ADS)

Housh, M.; Ng, T.; Cai, X.

2012-12-01

The environmental impact is one of the major concerns of biofuel development. While many other studies have examined the impact of biofuel expansion on stream flow and water quality, this study examines the problem from the other side - will and how a biofuel production target be affected by given environmental constraints. For this purpose, an integrated model comprises of different sub-systems of biofuel refineries, transportation, agriculture, water resources and crops/ethanol market has been developed. The sub-systems are integrated into one large-scale model to guide the optimal development plan considering the interdependency between the subsystems. The optimal development plan includes biofuel refineries location and capacity, refinery operation, land allocation between biofuel and food crops, and the corresponding stream flow and nitrate load in the watershed. The watershed is modeled as a network flow, in which the nodes represent sub-watersheds and the arcs are defined as the linkage between the sub-watersheds. The runoff contribution of each sub-watershed is determined based on the land cover and the water uses in that sub-watershed. Thus, decisions of other sub-systems such as the land allocation in the land use sub-system and the water use in the refinery sub-system define the sources and the sinks of the network. Environmental policies will be addressed in the integrated model by imposing stream flow and nitrate load constraints. These constraints can be specified by location and time in the watershed to reflect the spatial and temporal variation of the regulations. Preliminary results show that imposing monthly water flow constraints and yearly nitrate load constraints will change the biofuel development plan dramatically. Sensitivity analysis is performed to examine how the environmental constraints and their spatial and the temporal distribution influence the overall biofuel development plan and the performance of each of the sub-systems. Additional scenarios are analyzed to show the synergies of crop pattern choice (first versus second generation of biofuel crops), refinery technology adaptation (particularly on water use), refinery plant distribution, and economic incentives in terms of balanced environmental protection and bioenergy development objectives.

Use of Remote Sensing Data to Enhance NWS Storm Damage Toolkit

NASA Technical Reports Server (NTRS)

Jedlove, Gary J.; Molthan, Andrew L.; White, Kris; Burks, Jason; Stellman, Keith; Smith, Mathew

2012-01-01

In the wake of a natural disaster such as a tornado, the National Weather Service (NWS) is required to provide a very detailed and timely storm damage assessment to local, state and federal homeland security officials. The Post ]Storm Data Acquisition (PSDA) procedure involves the acquisition and assembly of highly perishable data necessary for accurate post ]event analysis and potential integration into a geographic information system (GIS) available to its end users and associated decision makers. Information gained from the process also enables the NWS to increase its knowledge of extreme events, learn how to better use existing equipment, improve NWS warning programs, and provide accurate storm intensity and damage information to the news media and academia. To help collect and manage all of this information, forecasters in NWS Southern Region are currently developing a Storm Damage Assessment Toolkit (SDAT), which incorporates GIS ]capable phones and laptops into the PSDA process by tagging damage photography, location, and storm damage details with GPS coordinates for aggregation within the GIS database. However, this tool alone does not fully integrate radar and ground based storm damage reports nor does it help to identify undetected storm damage regions. In many cases, information on storm damage location (beginning and ending points, swath width, etc.) from ground surveys is incomplete or difficult to obtain. Geographic factors (terrain and limited roads in rural areas), manpower limitations, and other logistical constraints often prevent the gathering of a comprehensive picture of tornado or hail damage, and may allow damage regions to go undetected. Molthan et al. (2011) have shown that high resolution satellite data can provide additional valuable information on storm damage tracks to augment this database. This paper presents initial development to integrate satellitederived damage track information into the SDAT for near real ]time use by forecasters and decision makers.

Use of Remote Sensing Data to Enhance NWS Storm Damage Toolkit

NASA Astrophysics Data System (ADS)

Jedlovec, G.; Molthan, A.; White, K.; Burks, J.; Stellman, K.; Smith, M. R.

2012-12-01

In the wake of a natural disaster such as a tornado, the National Weather Service (NWS) is required to provide a very detailed and timely storm damage assessment to local, state and federal homeland security officials. The Post-Storm Data Acquisition (PSDA) procedure involves the acquisition and assembly of highly perishable data necessary for accurate post-event analysis and potential integration into a geographic information system (GIS) available to its end users and associated decision makers. Information gained from the process also enables the NWS to increase its knowledge of extreme events, learn how to better use existing equipment, improve NWS warning programs, and provide accurate storm intensity and damage information to the news media and academia. To help collect and manage all of this information, forecasters in NWS Southern Region are currently developing a Storm Damage Assessment Toolkit (SDAT), which incorporates GIS-capable phones and laptops into the PSDA process by tagging damage photography, location, and storm damage details with GPS coordinates for aggregation within the GIS database. However, this tool alone does not fully integrate radar and ground based storm damage reports nor does it help to identify undetected storm damage regions. In many cases, information on storm damage location (beginning and ending points, swath width, etc.) from ground surveys is incomplete or difficult to obtain. Geographic factors (terrain and limited roads in rural areas), manpower limitations, and other logistical constraints often prevent the gathering of a comprehensive picture of tornado or hail damage, and may allow damage regions to go undetected. Molthan et al. (2011) have shown that high resolution satellite data can provide additional valuable information on storm damage tracks to augment this database. This paper presents initial development to integrate satellite-derived damage track information into the SDAT for near real-time use by forecasters and decision makers.

Integrated Risk Management Within NASA Programs/Projects

NASA Technical Reports Server (NTRS)

Connley, Warren; Rad, Adrian; Botzum, Stephen

2004-01-01

As NASA Project Risk Management activities continue to evolve, the need to successfully integrate risk management processes across the life cycle, between functional disciplines, stakeholders, various management policies, and within cost, schedule and performance requirements/constraints become more evident and important. Today's programs and projects are complex undertakings that include a myriad of processes, tools, techniques, management arrangements and other variables all of which must function together in order to achieve mission success. The perception and impact of risk may vary significantly among stakeholders and may influence decisions that may have unintended consequences on the project during a future phase of the life cycle. In these cases, risks may be unintentionally and/or arbitrarily transferred to others without the benefit of a comprehensive systemic risk assessment. Integrating risk across people, processes, and project requirements/constraints serves to enhance decisions, strengthen communication pathways, and reinforce the ability of the project team to identify and manage risks across the broad spectrum of project management responsibilities. The ability to identify risks in all areas of project management increases the likelihood a project will identify significant issues before they become problems and allows projects to make effective and efficient use of shrinking resources. By getting a total team integrated risk effort, applying a disciplined and rigorous process, along with understanding project requirements/constraints provides the opportunity for more effective risk management. Applying an integrated approach to risk management makes it possible to do a better job at balancing safety, cost, schedule, operational performance and other elements of risk. This paper will examine how people, processes, and project requirements/constraints can be integrated across the project lifecycle for better risk management and ultimately improve the chances for mission success.

A systematic approach for finding the objective function and active constraints for dynamic flux balance analysis.

PubMed

Nikdel, Ali; Braatz, Richard D; Budman, Hector M

2018-05-01

Dynamic flux balance analysis (DFBA) has become an instrumental modeling tool for describing the dynamic behavior of bioprocesses. DFBA involves the maximization of a biologically meaningful objective subject to kinetic constraints on the rate of consumption/production of metabolites. In this paper, we propose a systematic data-based approach for finding both the biological objective function and a minimum set of active constraints necessary for matching the model predictions to the experimental data. The proposed algorithm accounts for the errors in the experiments and eliminates the need for ad hoc choices of objective function and constraints as done in previous studies. The method is illustrated for two cases: (1) for in silico (simulated) data generated by a mathematical model for Escherichia coli and (2) for actual experimental data collected from the batch fermentation of Bordetella Pertussis (whooping cough).

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

PubMed

Ahmadi, Farshid Farnood; Ebadi, Hamid

2009-01-01

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

Virtual Manufacturing Techniques Designed and Applied to Manufacturing Activities in the Manufacturing Integration and Technology Branch

NASA Technical Reports Server (NTRS)

Shearrow, Charles A.

1999-01-01

One of the identified goals of EM3 is to implement virtual manufacturing by the time the year 2000 has ended. To realize this goal of a true virtual manufacturing enterprise the initial development of a machinability database and the infrastructure must be completed. This will consist of the containment of the existing EM-NET problems and developing machine, tooling, and common materials databases. To integrate the virtual manufacturing enterprise with normal day to day operations the development of a parallel virtual manufacturing machinability database, virtual manufacturing database, virtual manufacturing paradigm, implementation/integration procedure, and testable verification models must be constructed. Common and virtual machinability databases will include the four distinct areas of machine tools, available tooling, common machine tool loads, and a materials database. The machine tools database will include the machine envelope, special machine attachments, tooling capacity, location within NASA-JSC or with a contractor, and availability/scheduling. The tooling database will include available standard tooling, custom in-house tooling, tool properties, and availability. The common materials database will include materials thickness ranges, strengths, types, and their availability. The virtual manufacturing databases will consist of virtual machines and virtual tooling directly related to the common and machinability databases. The items to be completed are the design and construction of the machinability databases, virtual manufacturing paradigm for NASA-JSC, implementation timeline, VNC model of one bridge mill and troubleshoot existing software and hardware problems with EN4NET. The final step of this virtual manufacturing project will be to integrate other production sites into the databases bringing JSC's EM3 into a position of becoming a clearing house for NASA's digital manufacturing needs creating a true virtual manufacturing enterprise.

General relativity in two dimensions: A Hamilton-Jacobi analysis

NASA Astrophysics Data System (ADS)

Bertin, M. C.; Pimentel, B. M.; Pompeia, P. J.

2010-11-01

We analyzed the constraint structure of the Einstein-Hilbert first-order action in two dimensions using the Hamilton-Jacobi approach. We were able to find a set of involutive, as well as a set of non-involutive constraints. Using generalized brackets we showed how to assure integrability of the theory, to eliminate the set of non-involutive constraints and how to build the field equations.

Integrated tokamak modeling: when physics informs engineering and research planning

NASA Astrophysics Data System (ADS)

Poli, Francesca

2017-10-01

Simulations that integrate virtually all the relevant engineering and physics aspects of a real tokamak experiment are a power tool for experimental interpretation, model validation and planning for both present and future devices. This tutorial will guide through the building blocks of an ``integrated'' tokamak simulation, such as magnetic flux diffusion, thermal, momentum and particle transport, external heating and current drive sources, wall particle sources and sinks. Emphasis is given to the connection and interplay between external actuators and plasma response, between the slow time scales of the current diffusion and the fast time scales of transport, and how reduced and high-fidelity models can contribute to simulate a whole device. To illustrate the potential and limitations of integrated tokamak modeling for discharge prediction, a helium plasma scenario for the ITER pre-nuclear phase is taken as an example. This scenario presents challenges because it requires core-edge integration and advanced models for interaction between waves and fast-ions, which are subject to a limited experimental database for validation and guidance. Starting from a scenario obtained by re-scaling parameters from the demonstration inductive ``ITER baseline'', it is shown how self-consistent simulations that encompass both core and edge plasma regions, as well as high-fidelity heating and current drive source models are needed to set constraints on the density, magnetic field and heating scheme. This tutorial aims at demonstrating how integrated modeling, when used with adequate level of criticism, can not only support design of operational scenarios, but also help to asses the limitations and gaps in the available models, thus indicating where improved modeling tools are required and how present experiments can help their validation and inform research planning. Work supported by DOE under DE-AC02-09CH1146.

Integrating digital topology in image-processing libraries.

PubMed

Lamy, Julien

2007-01-01

This paper describes a method to integrate digital topology informations in image-processing libraries. This additional information allows a library user to write algorithms respecting topological constraints, for example, a seed fill or a skeletonization algorithm. As digital topology is absent from most image-processing libraries, such constraints cannot be fulfilled. We describe and give code samples for all the structures necessary for this integration, and show a use case in the form of a homotopic thinning filter inside ITK. The obtained filter can be up to a hundred times as fast as ITK's thinning filter and works for any image dimension. This paper mainly deals of integration within ITK, but can be adapted with only minor modifications to other image-processing libraries.

The Application of Lidar to Synthetic Vision System Integrity

NASA Technical Reports Server (NTRS)

Campbell, Jacob L.; UijtdeHaag, Maarten; Vadlamani, Ananth; Young, Steve

2003-01-01

One goal in the development of a Synthetic Vision System (SVS) is to create a system that can be certified by the Federal Aviation Administration (FAA) for use at various flight criticality levels. As part of NASA s Aviation Safety Program, Ohio University and NASA Langley have been involved in the research and development of real-time terrain database integrity monitors for SVS. Integrity monitors based on a consistency check with onboard sensors may be required if the inherent terrain database integrity is not sufficient for a particular operation. Sensors such as the radar altimeter and weather radar, which are available on most commercial aircraft, are currently being investigated for use in a real-time terrain database integrity monitor. This paper introduces the concept of using a Light Detection And Ranging (LiDAR) sensor as part of a real-time terrain database integrity monitor. A LiDAR system consists of a scanning laser ranger, an inertial measurement unit (IMU), and a Global Positioning System (GPS) receiver. Information from these three sensors can be combined to generate synthesized terrain models (profiles), which can then be compared to the stored SVS terrain model. This paper discusses an initial performance evaluation of the LiDAR-based terrain database integrity monitor using LiDAR data collected over Reno, Nevada. The paper will address the consistency checking mechanism and test statistic, sensitivity to position errors, and a comparison of the LiDAR-based integrity monitor to a radar altimeter-based integrity monitor.

Compressible fluids with Maxwell-type equations, the minimal coupling with electromagnetic field and the Stefan–Boltzmann law

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

Mendes, Albert C.R., E-mail: albert@fisica.ufjf.br; Takakura, Flavio I., E-mail: takakura@fisica.ufjf.br; Abreu, Everton M.C., E-mail: evertonabreu@ufrrj.br

In this work we have obtained a higher-derivative Lagrangian for a charged fluid coupled with the electromagnetic fluid and the Dirac’s constraints analysis was discussed. A set of first-class constraints fixed by noncovariant gauge condition were obtained. The path integral formalism was used to obtain the partition function for the corresponding higher-derivative Hamiltonian and the Faddeev–Popov ansatz was used to construct an effective Lagrangian. Through the partition function, a Stefan–Boltzmann type law was obtained. - Highlights: • Higher-derivative Lagrangian for a charged fluid. • Electromagnetic coupling and Dirac’s constraint analysis. • Partition function through path integral formalism. • Stefan–Boltzmann-kind lawmore » through the partition function.« less

Integration of Information Retrieval and Database Management Systems.

ERIC Educational Resources Information Center

Deogun, Jitender S.; Raghavan, Vijay V.

1988-01-01

Discusses the motivation for integrating information retrieval and database management systems, and proposes a probabilistic retrieval model in which records in a file may be composed of attributes (formatted data items) and descriptors (content indicators). The details and resolutions of difficulties involved in integrating such systems are…

Linking Bibliographic Data Bases: A Discussion of the Battelle Technical Report.

ERIC Educational Resources Information Center

Jones, C. Lee

This document establishes the context, summarizes the contents, and discusses the Battelle technical report, noting certain constraints of the study. Further steps for the linking of bibliographic databases for use by academic and public libraries are suggested. (RAA)

A flexible computer aid for conceptual design based on constraint propagation and component-modeling. [of aircraft in three dimensions

NASA Technical Reports Server (NTRS)

Kolb, Mark A.

1988-01-01

The Rubber Airplane program, which combines two symbolic processing techniques with a component-based database of design knowledge, is proposed as a computer aid for conceptual design. Using object-oriented programming, programs are organized around the objects and behavior to be simulated, and using constraint propagation, declarative statements designate mathematical relationships among all the equation variables. It is found that the additional level of organizational structure resulting from the arrangement of the design information in terms of design components provides greater flexibility and convenience.

The NCBI BioSystems database.

PubMed

Geer, Lewis Y; Marchler-Bauer, Aron; Geer, Renata C; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H

2010-01-01

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI's Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets.

Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data.

PubMed

Miannay, Bertrand; Minvielle, Stéphane; Magrangeas, Florence; Guziolowski, Carito

2018-03-21

The integration of gene expression profiles (GEPs) and large-scale biological networks derived from pathways databases is a subject which is being widely explored. Existing methods are based on network distance measures among significantly measured species. Only a small number of them include the directionality and underlying logic existing in biological networks. In this study we approach the GEP-networks integration problem by considering the network logic, however our approach does not require a prior species selection according to their gene expression level. We start by modeling the biological network representing its underlying logic using Logic Programming. This model points to reachable network discrete states that maximize a notion of harmony between the molecular species active or inactive possible states and the directionality of the pathways reactions according to their activator or inhibitor control role. Only then, we confront these network states with the GEP. From this confrontation independent graph components are derived, each of them related to a fixed and optimal assignment of active or inactive states. These components allow us to decompose a large-scale network into subgraphs and their molecular species state assignments have different degrees of similarity when compared to the same GEP. We apply our method to study the set of possible states derived from a subgraph from the NCI-PID Pathway Interaction Database. This graph links Multiple Myeloma (MM) genes to known receptors for this blood cancer. We discover that the NCI-PID MM graph had 15 independent components, and when confronted to 611 MM GEPs, we find 1 component as being more specific to represent the difference between cancer and healthy profiles.

Using activity-based costing and theory of constraints to guide continuous improvement in managed care.

PubMed

Roybal, H; Baxendale, S J; Gupta, M

1999-01-01

Activity-based costing and the theory of constraints have been applied successfully in many manufacturing organizations. Recently, those concepts have been applied in service organizations. This article describes the application of activity-based costing and the theory of constraints in a managed care mental health and substance abuse organization. One of the unique aspects of this particular application was the integration of activity-based costing and the theory of constraints to guide process improvement efforts. This article describes the activity-based costing model and the application of the theory of constraint's focusing steps with an emphasis on unused capacities of activities in the organization.

Rapid HIS, RIS, PACS Integration Using Graphical CASE Tools

NASA Astrophysics Data System (ADS)

Taira, Ricky K.; Breant, Claudine M.; Stepczyk, Frank M.; Kho, Hwa T.; Valentino, Daniel J.; Tashima, Gregory H.; Materna, Anthony T.

1994-05-01

We describe the clinical requirements of the integrated federation of databases and present our client-mediator-server design. The main body of the paper describes five important aspects of integrating information systems: (1) global schema design, (2) establishing sessions with remote database servers, (3) development of schema translators, (4) integration of global system triggers, and (5) development of job workflow scripts.

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.

AN ENERGY SYSTEMS PERPECTIVE OF ECOLOGICAL INTEGRITY AND ECOSYSTEM HEALTH

EPA Science Inventory

The integrity and health of society's life-supporting ecosystems establishes a fundamental constraint on economic growth and development. Energy Systems Theory provides a theoretical basis for defining, measuring and interpreting the concepts of ecological integrity and ecosystem...

Automated Derivation of Complex System Constraints from User Requirements

NASA Technical Reports Server (NTRS)

Muery, Kim; Foshee, Mark; Marsh, Angela

2006-01-01

International Space Station (ISS) payload developers submit their payload science requirements for the development of on-board execution timelines. The ISS systems required to execute the payload science operations must be represented as constraints for the execution timeline. Payload developers use a software application, User Requirements Collection (URC), to submit their requirements by selecting a simplified representation of ISS system constraints. To fully represent the complex ISS systems, the constraints require a level of detail that is beyond the insight of the payload developer. To provide the complex representation of the ISS system constraints, HOSC operations personnel, specifically the Payload Activity Requirements Coordinators (PARC), manually translate the payload developers simplified constraints into detailed ISS system constraints used for scheduling the payload activities in the Consolidated Planning System (CPS). This paper describes the implementation for a software application, User Requirements Integration (URI), developed to automate the manual ISS constraint translation process.

Towards a Dynamic Digital Observatory: Synthesizing Community Data and Model Development in the Susquehanna River Basin and Chesapeake Bay

NASA Astrophysics Data System (ADS)

Dressler, K. A.; Piasecki, M.; Bhatt, G.; Duffy, C. J.; Reed, P. M.

2007-12-01

Physically-based fully-distributed hydrologic models simulate hydrologic state variables spatiotemporally using information on forcing (climate) and landscape (topography, land use, hydrogeology) heterogeneities. Incorporating physical data layers in the hydrologic model requires intensive data development. Traditionally, GIS has been used for data management, data analysis and visualization; however, proprietary data structures, platform dependence, isolated data model and non-dynamic data-interaction with pluggable software components of existing GIS frameworks, makes it restrictive to perform sophisticated numerical modeling. In this effort we present a "tightly-coupled" GIS interface to Penn State Integrated Hydrologic Model (PIHM; www.pihm.psu.edu) called PIHMgis which is open source, platform independent and extensible. The tight coupling between GIS and the model is achieved by developing a shared data-model and hydrologic-model data structure. Domain discretization is fundamental to the approach and an unstructured triangular irregular network (e.g. Delaunay triangles) is generated with both geometric and parametric constraints. A local prismatic control volume is formed by vertical projection of the Delaunay triangles forming each layer of the model. Given a set of constraints (e.g. river network support, watershed boundary, altitude zones, ecological regions, hydraulic properties, climate zones, etc), an "optimal" mesh is generated. Time variant forcing for the model is typically derived from time series data available at points that are transferred onto a grid. Therefore, the modeling environment can use the Observations Database model developed by the Hydrologic Information Systems group of the Consortium of Universities for the Advancement of Hydrologic Sciences, Inc. (CUAHSI). As part of a initial testbed series the database has been implemented in support for the Susquehanna and Chesapeake Bay watersheds and is now being populated by national (USGS-NWIS; EPA- STORET), regional (Chesapeake Information Management System, CIMS; National Air Deposition Program, NADP), and local (RTH-Net, Burd Run) datasets. The data can be searched side by side in a one-stop-querying- center, www.hydroseek.org , another application developed as part of the CUAHSI HIS effort. The ultimate goal is to populate the observations database with as many catalogues (i.e. collections of information on what data sources contain) as possible including the build out of the local data sources, i.e. the Susquehanna River Basin Hydrologic Observatory System (SRBHOS) time series server.

Integrating tracer-based metabolomics data and metabolic fluxes in a linear fashion via Elementary Carbon Modes.

PubMed

Pey, Jon; Rubio, Angel; Theodoropoulos, Constantinos; Cascante, Marta; Planes, Francisco J

2012-07-01

Constraints-based modeling is an emergent area in Systems Biology that includes an increasing set of methods for the analysis of metabolic networks. In order to refine its predictions, the development of novel methods integrating high-throughput experimental data is currently a key challenge in the field. In this paper, we present a novel set of constraints that integrate tracer-based metabolomics data from Isotope Labeling Experiments and metabolic fluxes in a linear fashion. These constraints are based on Elementary Carbon Modes (ECMs), a recently developed concept that generalizes Elementary Flux Modes at the carbon level. To illustrate the effect of our ECMs-based constraints, a Flux Variability Analysis approach was applied to a previously published metabolic network involving the main pathways in the metabolism of glucose. The addition of our ECMs-based constraints substantially reduced the under-determination resulting from a standard application of Flux Variability Analysis, which shows a clear progress over the state of the art. In addition, our approach is adjusted to deal with combinatorial explosion of ECMs in genome-scale metabolic networks. This extension was applied to infer the maximum biosynthetic capacity of non-essential amino acids in human metabolism. Finally, as linearity is the hallmark of our approach, its importance is discussed at a methodological, computational and theoretical level and illustrated with a practical application in the field of Isotope Labeling Experiments. Copyright © 2012 Elsevier Inc. All rights reserved.

The NCBI BioSystems database

PubMed Central

Geer, Lewis Y.; Marchler-Bauer, Aron; Geer, Renata C.; Han, Lianyi; He, Jane; He, Siqian; Liu, Chunlei; Shi, Wenyao; Bryant, Stephen H.

2010-01-01

The NCBI BioSystems database, found at http://www.ncbi.nlm.nih.gov/biosystems/, centralizes and cross-links existing biological systems databases, increasing their utility and target audience by integrating their pathways and systems into NCBI resources. This integration allows users of NCBI’s Entrez databases to quickly categorize proteins, genes and small molecules by metabolic pathway, disease state or other BioSystem type, without requiring time-consuming inference of biological relationships from the literature or multiple experimental datasets. PMID:19854944

The integrated web service and genome database for agricultural plants with biotechnology information.

PubMed

Kim, Changkug; Park, Dongsuk; Seol, Youngjoo; Hahn, Jangho

2011-01-01

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage.

CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002.

PubMed

Yang, Yaohua; Feng, Jie; Li, Tao; Ge, Feng; Zhao, Jindong

2015-01-01

Cyanobacteria are an important group of organisms that carry out oxygenic photosynthesis and play vital roles in both the carbon and nitrogen cycles of the Earth. The annotated genome of Synechococcus sp. PCC 7002, as an ideal model cyanobacterium, is available. A series of transcriptomic and proteomic studies of Synechococcus sp. PCC 7002 cells grown under different conditions have been reported. However, no database of such integrated omics studies has been constructed. Here we present CyanOmics, a database based on the results of Synechococcus sp. PCC 7002 omics studies. CyanOmics comprises one genomic dataset, 29 transcriptomic datasets and one proteomic dataset and should prove useful for systematic and comprehensive analysis of all those data. Powerful browsing and searching tools are integrated to help users directly access information of interest with enhanced visualization of the analytical results. Furthermore, Blast is included for sequence-based similarity searching and Cluster 3.0, as well as the R hclust function is provided for cluster analyses, to increase CyanOmics's usefulness. To the best of our knowledge, it is the first integrated omics analysis database for cyanobacteria. This database should further understanding of the transcriptional patterns, and proteomic profiling of Synechococcus sp. PCC 7002 and other cyanobacteria. Additionally, the entire database framework is applicable to any sequenced prokaryotic genome and could be applied to other integrated omics analysis projects. Database URL: http://lag.ihb.ac.cn/cyanomics. © The Author(s) 2015. Published by Oxford University Press.

Developing a database for pedestrians' earthquake emergency evacuation in indoor scenarios.

PubMed

Zhou, Junxue; Li, Sha; Nie, Gaozhong; Fan, Xiwei; Tan, Jinxian; Li, Huayue; Pang, Xiaoke

2018-01-01

With the booming development of evacuation simulation software, developing an extensive database in indoor scenarios for evacuation models is imperative. In this paper, we conduct a qualitative and quantitative analysis of the collected videotapes and aim to provide a complete and unitary database of pedestrians' earthquake emergency response behaviors in indoor scenarios, including human-environment interactions. Using the qualitative analysis method, we extract keyword groups and keywords that code the response modes of pedestrians and construct a general decision flowchart using chronological organization. Using the quantitative analysis method, we analyze data on the delay time, evacuation speed, evacuation route and emergency exit choices. Furthermore, we study the effect of classroom layout on emergency evacuation. The database for indoor scenarios provides reliable input parameters and allows the construction of real and effective constraints for use in software and mathematical models. The database can also be used to validate the accuracy of evacuation models.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

PubMed

Cotten, Cameron; Reed, Jennifer L

2013-01-30

Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

PubMed Central

2013-01-01

Background Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. Results In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. Conclusions This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets. PMID:23360254

A GIS-Enabled, Michigan-Specific, Hierarchical Groundwater Modeling and Visualization System

NASA Astrophysics Data System (ADS)

Liu, Q.; Li, S.; Mandle, R.; Simard, A.; Fisher, B.; Brown, E.; Ross, S.

2005-12-01

Efficient management of groundwater resources relies on a comprehensive database that represents the characteristics of the natural groundwater system as well as analysis and modeling tools to describe the impacts of decision alternatives. Many agencies in Michigan have spent several years compiling expensive and comprehensive surface water and groundwater inventories and other related spatial data that describe their respective areas of responsibility. However, most often this wealth of descriptive data has only been utilized for basic mapping purposes. The benefits from analyzing these data, using GIS analysis functions or externally developed analysis models or programs, has yet to be systematically realized. In this talk, we present a comprehensive software environment that allows Michigan groundwater resources managers and frontline professionals to make more effective use of the available data and improve their ability to manage and protect groundwater resources, address potential conflicts, design cleanup schemes, and prioritize investigation activities. In particular, we take advantage of the Interactive Ground Water (IGW) modeling system and convert it to a customized software environment specifically for analyzing, modeling, and visualizing the Michigan statewide groundwater database. The resulting Michigan IGW modeling system (IGW-M) is completely window-based, fully interactive, and seamlessly integrated with a GIS mapping engine. The system operates in real-time (on the fly) providing dynamic, hierarchical mapping, modeling, spatial analysis, and visualization. Specifically, IGW-M allows water resources and environmental professionals in Michigan to: * Access and utilize the extensive data from the statewide groundwater database, interactively manipulate GIS objects, and display and query the associated data and attributes; * Analyze and model the statewide groundwater database, interactively convert GIS objects into numerical model features, automatically extract data and attributes, and simulate unsteady groundwater flow and contaminant transport in response to water and land management decisions; * Visualize and map model simulations and predictions with data from the statewide groundwater database in a seamless interactive environment. IGW-M has the potential to significantly improve the productivity of Michigan groundwater management investigations. It changes the role of engineers and scientists in modeling and analyzing the statewide groundwater database from heavily physical to cognitive problem-solving and decision-making tasks. The seamless real-time integration, real-time visual interaction, and real-time processing capability allows a user to focus on critical management issues, conflicts, and constraints, to quickly and iteratively examine conceptual approximations, management and planning scenarios, and site characterization assumptions, to identify dominant processes, to evaluate data worth and sensitivity, and to guide further data-collection activities. We illustrate the power and effectiveness of the M-IGW modeling and visualization system with a real case study and a real-time, live demonstration.

The Role Of Moral Awareness In Computer Security

NASA Astrophysics Data System (ADS)

Stawinski, Arthur

1984-08-01

Maintaining security of databases and other computer systems requires constraining the behavior of those persons who are able to access these systems so that they do not obtain, alter, or abuse the information contained in these systems. Three types of constraints are available: Physical contraints are obstructions designed to prevent (or at least make difficult) access to data by unauthorized persons; external constraints restrict behavior through threat of detection and punishment; internal constraints are self-imposed limitations on behavior which are derived from a person's moral standards. This paper argues that an effective computer security program will require attention to internal constraints as well as physical and external ones. Recent developments in moral philosophy and the psychology of moral development have given us new understanding of how individuals grow in moral awareness and how this growth can be encouraged. These insights are the foundation for some practical proposals for encouraging morally responsible behavior by computer professionals and others with access to confidential data. The aim of this paper is to encourage computer security professionals to discuss, refine and incorporate systems of internal constraints in developing methods of maintaining security.

A distributed computing environment with support for constraint-based task scheduling and scientific experimentation

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

Ahrens, J.P.; Shapiro, L.G.; Tanimoto, S.L.

1997-04-01

This paper describes a computing environment which supports computer-based scientific research work. Key features include support for automatic distributed scheduling and execution and computer-based scientific experimentation. A new flexible and extensible scheduling technique that is responsive to a user`s scheduling constraints, such as the ordering of program results and the specification of task assignments and processor utilization levels, is presented. An easy-to-use constraint language for specifying scheduling constraints, based on the relational database query language SQL, is described along with a search-based algorithm for fulfilling these constraints. A set of performance studies show that the environment can schedule and executemore » program graphs on a network of workstations as the user requests. A method for automatically generating computer-based scientific experiments is described. Experiments provide a concise method of specifying a large collection of parameterized program executions. The environment achieved significant speedups when executing experiments; for a large collection of scientific experiments an average speedup of 3.4 on an average of 5.5 scheduled processors was obtained.« less

Sports science needs more interdisciplinary, constraints-led research programmes: The case of water safety in New Zealand.

PubMed

Button, C; Croft, J L

2017-12-01

In the lead article of this special issue, Paul Glazier proposes that Newell's constraints model has the potential to contribute to a grand unified theory of sports performance in that it can help to integrate the disciplinary silos that have typically operated in isolation in sports and exercise science. With a few caveats discussed in this commentary, we agree with Glazier's proposal. However, his ideas suggest that there is a need to demonstrate explicitly how such an integration might occur within applied scientific research. To help fill this perceived 'gap' and thereby illustrate the value of adopting a constraints-led approach, we offer an example of our own interdisciplinary research programme. We believe our research on water safety is ideally suited to this task due to the diverse range of interacting constraints present and as such provides a tangible example of how this approach can unify different disciplinary perspectives examining an important aspect of sport performance. Copyright © 2017 Elsevier B.V. All rights reserved.

Lexical interference effects in sentence processing: Evidence from the visual world paradigm and self-organizing models

PubMed Central

Kukona, Anuenue; Cho, Pyeong Whan; Magnuson, James S.; Tabor, Whitney

2014-01-01

Psycholinguistic research spanning a number of decades has produced diverging results with regard to the nature of constraint integration in online sentence processing. For example, evidence that language users anticipatorily fixate likely upcoming referents in advance of evidence in the speech signal supports rapid context integration. By contrast, evidence that language users activate representations that conflict with contextual constraints, or only indirectly satisfy them, supports non-integration or late integration. Here, we report on a self-organizing neural network framework that addresses one aspect of constraint integration: the integration of incoming lexical information (i.e., an incoming word) with sentence context information (i.e., from preceding words in an unfolding utterance). In two simulations, we show that the framework predicts both classic results concerned with lexical ambiguity resolution (Swinney, 1979; Tanenhaus, Leiman, & Seidenberg, 1979), which suggest late context integration, and results demonstrating anticipatory eye movements (e.g., Altmann & Kamide, 1999), which support rapid context integration. We also report two experiments using the visual world paradigm that confirm a new prediction of the framework. Listeners heard sentences like “The boy will eat the white…,” while viewing visual displays with objects like a white cake (i.e., a predictable direct object of “eat”), white car (i.e., an object not predicted by “eat,” but consistent with “white”), and distractors. Consistent with our simulation predictions, we found that while listeners fixated white cake most, they also fixated white car more than unrelated distractors in this highly constraining sentence (and visual) context. PMID:24245535

Loopedia, a database for loop integrals

NASA Astrophysics Data System (ADS)

Bogner, C.; Borowka, S.; Hahn, T.; Heinrich, G.; Jones, S. P.; Kerner, M.; von Manteuffel, A.; Michel, M.; Panzer, E.; Papara, V.

2018-04-01

Loopedia is a new database at loopedia.org for information on Feynman integrals, intended to provide both bibliographic information as well as results made available by the community. Its bibliometry is complementary to that of INSPIRE or arXiv in the sense that it admits searching for integrals by graph-theoretical objects, e.g. its topology.

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

PubMed

May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

2009-05-04

The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

COBRApy: COnstraints-Based Reconstruction and Analysis for Python.

PubMed

Ebrahim, Ali; Lerman, Joshua A; Palsson, Bernhard O; Hyduke, Daniel R

2013-08-08

COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely used for genome-scale modeling of metabolic networks in both prokaryotes and eukaryotes. Due to the successes with metabolism, there is an increasing effort to apply COBRA methods to reconstruct and analyze integrated models of cellular processes. The COBRA Toolbox for MATLAB is a leading software package for genome-scale analysis of metabolism; however, it was not designed to elegantly capture the complexity inherent in integrated biological networks and lacks an integration framework for the multiomics data used in systems biology. The openCOBRA Project is a community effort to promote constraints-based research through the distribution of freely available software. Here, we describe COBRA for Python (COBRApy), a Python package that provides support for basic COBRA methods. COBRApy is designed in an object-oriented fashion that facilitates the representation of the complex biological processes of metabolism and gene expression. COBRApy does not require MATLAB to function; however, it includes an interface to the COBRA Toolbox for MATLAB to facilitate use of legacy codes. For improved performance, COBRApy includes parallel processing support for computationally intensive processes. COBRApy is an object-oriented framework designed to meet the computational challenges associated with the next generation of stoichiometric constraint-based models and high-density omics data sets. http://opencobra.sourceforge.net/

Integrating stations from the North America Gravity Database into a local GPS-based land gravity survey

USGS Publications Warehouse

Shoberg, Thomas G.; Stoddard, Paul R.

2013-01-01

The ability to augment local gravity surveys with additional gravity stations from easily accessible national databases can greatly increase the areal coverage and spatial resolution of a survey. It is, however, necessary to integrate such data seamlessly with the local survey. One challenge to overcome in integrating data from national databases is that these data are typically of unknown quality. This study presents a procedure for the evaluation and seamless integration of gravity data of unknown quality from a national database with data from a local Global Positioning System (GPS)-based survey. The starting components include the latitude, longitude, elevation and observed gravity at each station location. Interpolated surfaces of the complete Bouguer anomaly are used as a means of quality control and comparison. The result is an integrated dataset of varying quality with many stations having GPS accuracy and other reliable stations of unknown origin, yielding a wider coverage and greater spatial resolution than either survey alone.

The EBI SRS server-new features.

PubMed

Zdobnov, Evgeny M; Lopez, Rodrigo; Apweiler, Rolf; Etzold, Thure

2002-08-01

Here we report on recent developments at the EBI SRS server (http://srs.ebi.ac.uk). SRS has become an integration system for both data retrieval and sequence analysis applications. The EBI SRS server is a primary gateway to major databases in the field of molecular biology produced and supported at EBI as well as European public access point to the MEDLINE database provided by US National Library of Medicine (NLM). It is a reference server for latest developments in data and application integration. The new additions include: concept of virtual databases, integration of XML databases like the Integrated Resource of Protein Domains and Functional Sites (InterPro), Gene Ontology (GO), MEDLINE, Metabolic pathways, etc., user friendly data representation in 'Nice views', SRSQuickSearch bookmarklets. SRS6 is a licensed product of LION Bioscience AG freely available for academics. The EBI SRS server (http://srs.ebi.ac.uk) is a free central resource for molecular biology data as well as a reference server for the latest developments in data integration.

Neighboring extremals of dynamic optimization problems with path equality constraints

NASA Technical Reports Server (NTRS)

Lee, A. Y.

1988-01-01

Neighboring extremals of dynamic optimization problems with path equality constraints and with an unknown parameter vector are considered in this paper. With some simplifications, the problem is reduced to solving a linear, time-varying two-point boundary-value problem with integral path equality constraints. A modified backward sweep method is used to solve this problem. Two example problems are solved to illustrate the validity and usefulness of the solution technique.

Reduced Order Podolsky Model

NASA Astrophysics Data System (ADS)

Thibes, Ronaldo

2017-02-01

We perform the canonical and path integral quantizations of a lower-order derivatives model describing Podolsky's generalized electrodynamics. The physical content of the model shows an auxiliary massive vector field coupled to the usual electromagnetic field. The equivalence with Podolsky's original model is studied at classical and quantum levels. Concerning the dynamical time evolution, we obtain a theory with two first-class and two second-class constraints in phase space. We calculate explicitly the corresponding Dirac brackets involving both vector fields. We use the Senjanovic procedure to implement the second-class constraints and the Batalin-Fradkin-Vilkovisky path integral quantization scheme to deal with the symmetries generated by the first-class constraints. The physical interpretation of the results turns out to be simpler due to the reduced derivatives order permeating the equations of motion, Dirac brackets and effective action.

Building An Integrated Neurodegenerative Disease Database At An Academic Health Center

PubMed Central

Xie, Sharon X.; Baek, Young; Grossman, Murray; Arnold, Steven E.; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M.-Y.; Trojanowski, John Q.

2010-01-01

Background It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). These comparative studies rely on powerful database tools to quickly generate data sets which match diverse and complementary criteria set by the studies. Methods In this paper, we present a novel Integrated NeuroDegenerative Disease (INDD) database developed at the University of Pennsylvania (Penn) through a consortium of Penn investigators. Since these investigators work on AD, PD, ALS and FTLD, this allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used Microsoft SQL Server as the platform with built-in “backwards” functionality to provide Access as a front-end client to interface with the database. We used PHP hypertext Preprocessor to create the “front end” web interface and then integrated individual neurodegenerative disease databases using a master lookup table. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Results We compare the results of a biomarker study using the INDD database to those using an alternative approach by querying individual database separately. Conclusions We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies across several neurodegenerative diseases. PMID:21784346

DBGC: A Database of Human Gastric Cancer

PubMed Central

Wang, Chao; Zhang, Jun; Cai, Mingdeng; Zhu, Zhenggang; Gu, Wenjie; Yu, Yingyan; Zhang, Xiaoyan

2015-01-01

The Database of Human Gastric Cancer (DBGC) is a comprehensive database that integrates various human gastric cancer-related data resources. Human gastric cancer-related transcriptomics projects, proteomics projects, mutations, biomarkers and drug-sensitive genes from different sources were collected and unified in this database. Moreover, epidemiological statistics of gastric cancer patients in China and clinicopathological information annotated with gastric cancer cases were also integrated into the DBGC. We believe that this database will greatly facilitate research regarding human gastric cancer in many fields. DBGC is freely available at http://bminfor.tongji.edu.cn/dbgc/index.do PMID:26566288

The integrated web service and genome database for agricultural plants with biotechnology information

PubMed Central

Kim, ChangKug; Park, DongSuk; Seol, YoungJoo; Hahn, JangHo

2011-01-01

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a Web based relational database for agricultural plants with biotechnology information. The NABIC has concentrated on functional genomics of major agricultural plants, building an integrated biotechnology database for agro-biotech information that focuses on genomics of major agricultural resources. This genome database provides annotated genome information from 1,039,823 records mapped to rice, Arabidopsis, and Chinese cabbage. PMID:21887015

Database constraints applied to metabolic pathway reconstruction tools.

PubMed

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.

Path integral measure, constraints and ghosts for massive gravitons with a cosmological constant

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

Metaxas, Dimitrios

2009-12-15

For massive gravity in a de Sitter background one encounters problems of stability when the curvature is larger than the graviton mass. I analyze this situation from the path integral point of view and show that it is related to the conformal factor problem of Euclidean quantum (massless) gravity. When a constraint for massive gravity is incorporated and the proper treatment of the path integral measure is taken into account one finds that, for particular choices of the DeWitt metric on the space of metrics (in fact, the same choices as in the massless case), one obtains the opposite boundmore » on the graviton mass.« less

Effects of using a posteriori methods for the conservation of integral invariants. [for weather forecasting

NASA Technical Reports Server (NTRS)

Takacs, Lawrence L.

1988-01-01

The nature and effect of using a posteriori adjustments to nonconservative finite-difference schemes to enforce integral invariants of the corresponding analytic system are examined. The method of a posteriori integral constraint restoration is analyzed for the case of linear advection, and the harmonic response associated with the a posteriori adjustments is examined in detail. The conservative properties of the shallow water system are reviewed, and the constraint restoration algorithm applied to the shallow water equations are described. A comparison is made between forecasts obtained using implicit and a posteriori methods for the conservation of mass, energy, and potential enstrophy in the complete nonlinear shallow-water system.

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

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.

Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the “generalist” (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions, prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thusmore » represents a generalist ME model reflecting both growth rate maximization and “hedging” against uncertain environments and stresses, as indicated by significant enrichment of these sectors for the general stress response sigma factor σS. Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally-related protein groups) as demonstrated here. Furthermore, this flexible formalism provides an accessible approach for narrowing the gap between the complexity captured by omics data and governing principles of proteome allocation described by systems-level models.« less

An Integrated Korean Biodiversity and Genetic Information Retrieval System

PubMed Central

Lim, Jeongheui; Bhak, Jong; Oh, Hee-Mock; Kim, Chang-Bae; Park, Yong-Ha; Paek, Woon Kee

2008-01-01

Background On-line biodiversity information databases are growing quickly and being integrated into general bioinformatics systems due to the advances of fast gene sequencing technologies and the Internet. These can reduce the cost and effort of performing biodiversity surveys and genetic searches, which allows scientists to spend more time researching and less time collecting and maintaining data. This will cause an increased rate of knowledge build-up and improve conservations. The biodiversity databases in Korea have been scattered among several institutes and local natural history museums with incompatible data types. Therefore, a comprehensive database and a nation wide web portal for biodiversity information is necessary in order to integrate diverse information resources, including molecular and genomic databases. Results The Korean Natural History Research Information System (NARIS) was built and serviced as the central biodiversity information system to collect and integrate the biodiversity data of various institutes and natural history museums in Korea. This database aims to be an integrated resource that contains additional biological information, such as genome sequences and molecular level diversity. Currently, twelve institutes and museums in Korea are integrated by the DiGIR (Distributed Generic Information Retrieval) protocol, with Darwin Core2.0 format as its metadata standard for data exchange. Data quality control and statistical analysis functions have been implemented. In particular, integrating molecular and genetic information from the National Center for Biotechnology Information (NCBI) databases with NARIS was recently accomplished. NARIS can also be extended to accommodate other institutes abroad, and the whole system can be exported to establish local biodiversity management servers. Conclusion A Korean data portal, NARIS, has been developed to efficiently manage and utilize biodiversity data, which includes genetic resources. NARIS aims to be integral in maximizing bio-resource utilization for conservation, management, research, education, industrial applications, and integration with other bioinformation data resources. It can be found at . PMID:19091024

PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology

PubMed Central

Gioutlakis, Aris; Klapa, Maria I.

2017-01-01

It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normalization; namely, PPIs are merged after converted to a certain target level. Hence, the node set of the integrated network depends each time on the number and type of the combined datasets. Moreover, the irreversible a priori normalization process hinders the identification of normalization artifacts in the integrated network, which originate from the nonlinearity characterizing the genetic information flow. PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database. Its main novel feature over the existing meta-databases is its approach to primary PPI dataset integration via genetic information ontology. Building upon the PICKLE principles of using the reviewed human complete proteome (RHCP) of UniProtKB/Swiss-Prot as the reference protein interactor set, and filtering out protein interactions with low probability of being direct based on the available evidence, PICKLE 2.0 first assembles the RHCP genetic information ontology network by connecting the corresponding genes, nucleotide sequences (mRNAs) and proteins (UniProt entries) and then integrates PPI datasets by superimposing them on the ontology network without any a priori transformations. Importantly, this process allows the resulting heterogeneous integrated network to be reversibly normalized to any level of genetic reference without loss of the original information, the latter being used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking. The PICKLE web-based interface (www.pickle.gr) allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein (UniProt) or the gene level, at three PPI filtering modes. PMID:29023571

Relativistic top: An application of the BFV quantization procedure for systems with degenerate constraints

NASA Astrophysics Data System (ADS)

Nielsen, N. K.; Quaade, U. J.

1995-07-01

The physical phase space of the relativistic top, as defined by Hansson and Regge, is expressed in terms of canonical coordinates of the Poincaré group manifold. The system is described in the Hamiltonian formalism by the mass-shell condition and constraints that reduce the number of spin degrees of freedom. The constraints are second class and are modified into a set of first class constraints by adding combinations of gauge-fixing functions. The Batalin-Fradkin-Vilkovisky method is then applied to quantize the system in the path integral formalism in Hamiltonian form. It is finally shown that different gauge choices produce different equivalent forms of the constraints.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.

PubMed

Xu, Weijia; Ozer, Stuart; Gutell, Robin R

2009-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure.

Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA

PubMed Central

Xu, Weijia; Ozer, Stuart; Gutell, Robin R.

2010-01-01

With an increasingly large amount of sequences properly aligned, comparative sequence analysis can accurately identify not only common structures formed by standard base pairing but also new types of structural elements and constraints. However, traditional methods are too computationally expensive to perform well on large scale alignment and less effective with the sequences from diversified phylogenetic classifications. We propose a new approach that utilizes coevolutional rates among pairs of nucleotide positions using phylogenetic and evolutionary relationships of the organisms of aligned sequences. With a novel data schema to manage relevant information within a relational database, our method, implemented with a Microsoft SQL Server 2005, showed 90% sensitivity in identifying base pair interactions among 16S ribosomal RNA sequences from Bacteria, at a scale 40 times bigger and 50% better sensitivity than a previous study. The results also indicated covariation signals for a few sets of cross-strand base stacking pairs in secondary structure helices, and other subtle constraints in the RNA structure. PMID:20502534

Memory color assisted illuminant estimation through pixel clustering

NASA Astrophysics Data System (ADS)

Zhang, Heng; Quan, Shuxue

2010-01-01

The under constrained nature of illuminant estimation determines that in order to resolve the problem, certain assumptions are needed, such as the gray world theory. Including more constraints in this process may help explore the useful information in an image and improve the accuracy of the estimated illuminant, providing that the constraints hold. Based on the observation that most personal images have contents of one or more of the following categories: neutral objects, human beings, sky, and plants, we propose a method for illuminant estimation through the clustering of pixels of gray and three dominant memory colors: skin tone, sky blue, and foliage green. Analysis shows that samples of the above colors cluster around small areas under different illuminants and their characteristics can be used to effectively detect pixels falling into each of the categories. The algorithm requires the knowledge of the spectral sensitivity response of the camera, and a spectral database consisted of the CIE standard illuminants and reflectance or radiance database of samples of the above colors.

Automated extraction of knowledge for model-based diagnostics

NASA Technical Reports Server (NTRS)

Gonzalez, Avelino J.; Myler, Harley R.; Towhidnejad, Massood; Mckenzie, Frederic D.; Kladke, Robin R.

1990-01-01

The concept of accessing computer aided design (CAD) design databases and extracting a process model automatically is investigated as a possible source for the generation of knowledge bases for model-based reasoning systems. The resulting system, referred to as automated knowledge generation (AKG), uses an object-oriented programming structure and constraint techniques as well as internal database of component descriptions to generate a frame-based structure that describes the model. The procedure has been designed to be general enough to be easily coupled to CAD systems that feature a database capable of providing label and connectivity data from the drawn system. The AKG system is capable of defining knowledge bases in formats required by various model-based reasoning tools.

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

PubMed

Fang, Yilin; Scheibe, Timothy D; Mahadevan, Radhakrishnan; Garg, Srinath; Long, Philip E; Lovley, Derek R

2011-03-25

The activity of microorganisms often plays an important role in dynamic natural attenuation or engineered bioremediation of subsurface contaminants, such as chlorinated solvents, metals, and radionuclides. To evaluate and/or design bioremediated systems, quantitative reactive transport models are needed. State-of-the-art reactive transport models often ignore the microbial effects or simulate the microbial effects with static growth yield and constant reaction rate parameters over simulated conditions, while in reality microorganisms can dynamically modify their functionality (such as utilization of alternative respiratory pathways) in response to spatial and temporal variations in environmental conditions. Constraint-based genome-scale microbial in silico models, using genomic data and multiple-pathway reaction networks, have been shown to be able to simulate transient metabolism of some well studied microorganisms and identify growth rate, substrate uptake rates, and byproduct rates under different growth conditions. These rates can be identified and used to replace specific microbially-mediated reaction rates in a reactive transport model using local geochemical conditions as constraints. We previously demonstrated the potential utility of integrating a constraint-based microbial metabolism model with a reactive transport simulator as applied to bioremediation of uranium in groundwater. However, that work relied on an indirect coupling approach that was effective for initial demonstration but may not be extensible to more complex problems that are of significant interest (e.g., communities of microbial species and multiple constraining variables). Here, we extend that work by presenting and demonstrating a method of directly integrating a reactive transport model (FORTRAN code) with constraint-based in silico models solved with IBM ILOG CPLEX linear optimizer base system (C library). The models were integrated with BABEL, a language interoperability tool. The modeling system is designed in such a way that constraint-based models targeting different microorganisms or competing organism communities can be easily plugged into the system. Constraint-based modeling is very costly given the size of a genome-scale reaction network. To save computation time, a binary tree is traversed to examine the concentration and solution pool generated during the simulation in order to decide whether the constraint-based model should be called. We also show preliminary results from the integrated model including a comparison of the direct and indirect coupling approaches and evaluated the ability of the approach to simulate field experiment. Published by Elsevier B.V.

The MELISSA food data base: space food preparation and process optimization

NASA Astrophysics Data System (ADS)

Creuly, Catherine; Poughon, Laurent; Pons, A.; Farges, Berangere; Dussap, Claude-Gilles

Life Support Systems have to deal with air, water and food requirement for a crew, waste management and also to the crew's habitability and safety constraints. Food can be provided from stocks (open loops) or produced during the space flight or on an extraterrestrial base (what implies usually a closed loop system). Finally it is admitted that only biological processes can fulfil the food requirement of life support system. Today, only a strictly vegetarian source range is considered, and this is limited to a very small number of crops compared to the variety available on Earth. Despite these constraints, a successful diet should have enough variety in terms of ingredients and recipes and sufficiently high acceptability in terms of acceptance ratings for individual dishes to remain interesting and palatable over a several months period and an adequate level of nutrients commensurate with the space nutritional requirements. In addition to the nutritional aspects, others parameters have to be considered for the pertinent selection of the dishes as energy consumption (for food production and transformation), quantity of generated waste, preparation time, food processes. This work concerns a global approach called MELISSA Food Database to facilitate the cre-ation and the management of these menus associated to the nutritional, mass, energy and time constraints. The MELISSA Food Database is composed of a database (MySQL based) con-taining multiple information among others crew composition, menu, dishes, recipes, plant and nutritional data and of a web interface (PHP based) to interactively access the database and manage its content. In its current version a crew is defined and a 10 days menu scenario can be created using dishes that could be cooked from a set of limited fresh plant assumed to be produced in the life support system. The nutritional covering, waste produced, mass, time and energy requirements are calculated allowing evaluation of the menu scenario and its interactions with the life support system and filled with the information on food processes and equipment suitable for use in Advanced Life Support System. The MELISSA database is available on the server of the University Blaise Pascal (Clermont Université) with an authorized access at the address http://marseating.univ-bpclermont.fr. In the future, the challenge is to complete this database with specific data related to the MELISSA project. Plants chambers in the pilot plant located in Universitat Aut`noma de Barcelona will give nutritional and process data on crops cultivation.

The Perfect Marriage: Integrated Word Processing and Data Base Management Programs.

ERIC Educational Resources Information Center

Pogrow, Stanley

1983-01-01

Discussion of database integration and how it operates includes recommendations on compatible brand name word processing and database management programs, and a checklist for evaluating essential and desirable features of the available programs. (MBR)

Integration of air traffic databases : a case study

DOT National Transportation Integrated Search

1995-03-01

This report describes a case study to show the benefits from maximum utilization of existing air traffic databases. The study demonstrates the utility of integrating available data through developing and demonstrating a methodology addressing the iss...

SUPERSITES INTEGRATED RELATIONAL DATABASE (SIRD)

EPA Science Inventory

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

Realization of Real-Time Clinical Data Integration Using Advanced Database Technology

PubMed Central

Yoo, Sooyoung; Kim, Boyoung; Park, Heekyong; Choi, Jinwook; Chun, Jonghoon

2003-01-01

As information & communication technologies have advanced, interest in mobile health care systems has grown. In order to obtain information seamlessly from distributed and fragmented clinical data from heterogeneous institutions, we need solutions that integrate data. In this article, we introduce a method for information integration based on real-time message communication using trigger and advanced database technologies. Messages were devised to conform to HL7, a standard for electronic data exchange in healthcare environments. The HL7 based system provides us with an integrated environment in which we are able to manage the complexities of medical data. We developed this message communication interface to generate and parse HL7 messages automatically from the database point of view. We discuss how easily real time data exchange is performed in the clinical information system, given the requirement for minimum loading of the database system. PMID:14728271

Barriers and facilitators to healthy eating for nurses in the workplace: an integrative review.

PubMed

Nicholls, Rachel; Perry, Lin; Duffield, Christine; Gallagher, Robyn; Pierce, Heather

2017-05-01

The aim was to conduct an integrative systematic review to identify barriers and facilitators to healthy eating for working nurses. There is growing recognition of the influence of the workplace environment on the eating habits of the workforce, which in turn may contribute to increased overweight and obesity. Overweight and obesity exact enormous costs in terms of reduced well-being, worker productivity and increased risk of non-communicable diseases. The workplace is an ideal place to intervene and support healthy behaviours. This review aimed to identify barriers and facilitators to nurses' healthy eating in the workplace. Integrative mixed method review. Five electronic databases were searched: CINAHL, MEDLINE, PROQUEST Health and Medicine, ScienceDirect and PsycINFO. Reference lists were searched. Included papers were published in English between 2000-2016. Of 26 included papers, 21 were qualitative and five quantitative. An integrative literature review was undertaken. Quality appraisal of included studies used standardized checklists. A social-ecological framework was used to examine workplace facilitators and constraints to healthy eating, derived from the literature. Emergent themes were identified by thematic analysis. Review participants were Registered, Enrolled and/or Nurse Assistants primarily working in hospitals in middle or high income countries. The majority of studies reported barriers to healthy eating related to adverse work schedules, individual barriers, aspects of the physical workplace environment and social eating practices at work. Few facilitators were reported. Overall, studies found the workplace exerts a considerable negative influence on nurses' dietary intake. Reorientation of the workplace to promote healthy eating among nurses is required. © 2016 John Wiley & Sons Ltd.

Integrated Arctic Observation System Development Under Horizon 2020

NASA Astrophysics Data System (ADS)

Sandven, S.

2016-12-01

The overall objective of INTAROS is to develop an integrated Arctic Observation System (iAOS) by extending, improving and unifying existing systems in the different regions of the Arctic. INTAROS will have a strong multidisciplinary focus, with tools for integration of data from atmosphere, ocean, cryosphere and terrestrial sciences, provided by institutions in Europe, North America and Asia. Satellite earth observation data plays an increasingly important role in such observing systems, because the amount of EO data for observing the global climate and environment grows year by year. In situ observing systems are much more limited due to logistical constraints and cost limitations. The sparseness of in situ data is therefore the largest gap in the overall observing system. INTAROS will assess strengths and weaknesses of existing observing systems and contribute with innovative solutions to fill some of the critical gaps in the in situ observing network. INTAROS will develop a platform, iAOS, to search for and access data from distributed databases. The evolution into a sustainable Arctic observing system requires coordination, mobilization and cooperation between the existing European and international infrastructures (in-situ and remote including space-based), the modeling communities and relevant stakeholder groups. INTAROS will include development of community-based observing systems, where local knowledge is merged with scientific data. An integrated Arctic Observation System will enable better-informed decisions and better-documented processes within key sectors (e.g. local communities, shipping, tourism, fishing), in order to strengthen the societal and economic role of the Arctic region and support the EU strategy for the Arctic and related maritime and environmental policies.

Evolution of Western Mediterranean Sea Surface Temperature between 1985 and 2005: a complementary study in situ, satellite and modelling approaches

NASA Astrophysics Data System (ADS)

Troupin, C.; Lenartz, F.; Sirjacobs, D.; Alvera-Azcárate, A.; Barth, A.; Ouberdous, M.; Beckers, J.-M.

2009-04-01

In order to evaluate the variability of the sea surface temperature (SST) in the Western Mediterranean Sea between 1985 and 2005, an integrated approach combining geostatistical tools and modelling techniques has been set up. The objectives are: underline the capability of each tool to capture characteristic phenomena, compare and assess the quality of their outputs, infer an interannual trend from the results. Diva (Data Interpolating Variationnal Analysis, Brasseur et al. (1996) Deep-Sea Res.) was applied on a collection of in situ data gathered from various sources (World Ocean Database 2005, Hydrobase2, Coriolis and MedAtlas2), from which duplicates and suspect values were removed. This provided monthly gridded fields in the region of interest. Heterogeneous time data coverage was taken into account by computing and removing the annual trend, provided by Diva detrending tool. Heterogeneous correlation length was applied through an advection constraint. Statistical technique DINEOF (Data Interpolation with Empirical Orthogonal Functions, Alvera-Azc

Spatial modeling of the geographic distribution of wildlife populations: A case study in the lower Mississippi River region

USGS Publications Warehouse

Ji, W.; Jeske, C.

2000-01-01

A geographic information system (GIS)-based spatial modeling approach was developed to study environmental and land use impacts on the geographic distribution of wintering northern pintails (Arias acuta) in the Lower Mississippi River region. Pintails were fitted with backpack radio transmitter packages at Catahoula Lake, LA, in October 1992-1994 and located weekly through the following March. Pintail survey data were converted into a digital database in ARC/INFO GIS format and integrated with environmental GIS data through a customized modeling interface. The study verified the relationship between pintail distributions and major environmental factors and developed a conceptual relation model. Visualization-based spatial simulations were used to display the movement patterns of specific population groups under spatial and temporal constraints. The spatial modeling helped understand the seasonal movement patterns of pintails in relation to their habitat usage in Arkansas and southwestern Louisiana for wintering and interchange situations among population groups wintering in Texas and southeastern Louisiana. (C) 2000 Elsevier Science B.V.

MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status

PubMed Central

Attimonelli, M.; Altamura, N.; Benne, R.; Brennicke, A.; Cooper, J. M.; D’Elia, D.; Montalvo, A. de; Pinto, B. de; De Robertis, M.; Golik, P.; Knoop, V.; Lanave, C.; Lazowska, J.; Licciulli, F.; Malladi, B. S.; Memeo, F.; Monnerot, M.; Pasimeni, R.; Pilbout, S.; Schapira, A. H. V.; Sloof, P.; Saccone, C.

2000-01-01

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mitochondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn from the primary databases and from the literature; value adding information has been structured, e.g., editing information on protist mtDNA genomes, pathological information for human mtDNA variants, etc. The different databases, some of which are structured using commercial packages (Microsoft Access, File Maker Pro) while others use a flat-file format, have been integrated under ORACLE. Ad hoc retrieval systems have been devised for some of the above listed databases keeping into account their peculiarities. The database is resident at the EBI and is available at the following site: http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl . The impact of this project is intended for both basic and applied research. The study of mitochondrial genetic diseases and mitochondrial DNA intraspecies diversity are key topics in several biotechnological fields. The database has been funded within the EU Biotechnology programme. PMID:10592207

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

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

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

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

PubMed

Yang, Jin Ok; Hwang, Sohyun; Oh, Jeongsu; Bhak, Jong; Sohn, Tae-Kwon

2008-12-12

Studies on the relationship between disease and genetic variations such as single nucleotide polymorphisms (SNPs) are important. Genetic variations can cause disease by influencing important biological regulation processes. Despite the needs for analyzing SNP and disease correlation, most existing databases provide information only on functional variants at specific locations on the genome, or deal with only a few genes associated with disease. There is no combined resource to widely support gene-, SNP-, and disease-related information, and to capture relationships among such data. Therefore, we developed an integrated database-pipeline system for studying SNPs and diseases. To implement the pipeline system for the integrated database, we first unified complicated and redundant disease terms and gene names using the Unified Medical Language System (UMLS) for classification and noun modification, and the HUGO Gene Nomenclature Committee (HGNC) and NCBI gene databases. Next, we collected and integrated representative databases for three categories of information. For genes and proteins, we examined the NCBI mRNA, UniProt, UCSC Table Track and MitoDat databases. For genetic variants we used the dbSNP, JSNP, ALFRED, and HGVbase databases. For disease, we employed OMIM, GAD, and HGMD databases. The database-pipeline system provides a disease thesaurus, including genes and SNPs associated with disease. The search results for these categories are available on the web page http://diseasome.kobic.re.kr/, and a genome browser is also available to highlight findings, as well as to permit the convenient review of potentially deleterious SNPs among genes strongly associated with specific diseases and clinical phenotypes. Our system is designed to capture the relationships between SNPs associated with disease and disease-causing genes. The integrated database-pipeline provides a list of candidate genes and SNP markers for evaluation in both epidemiological and molecular biological approaches to diseases-gene association studies. Furthermore, researchers then can decide semi-automatically the data set for association studies while considering the relationships between genetic variation and diseases. The database can also be economical for disease-association studies, as well as to facilitate an understanding of the processes which cause disease. Currently, the database contains 14,674 SNP records and 109,715 gene records associated with human diseases and it is updated at regular intervals.

Explosive Growth and Advancement of the NASA/IPAC Extragalactic Database (NED)

NASA Astrophysics Data System (ADS)

Mazzarella, Joseph M.; Ogle, P. M.; Fadda, D.; Madore, B. F.; Ebert, R.; Baker, K.; Chan, H.; Chen, X.; Frayer, C.; Helou, G.; Jacobson, J. D.; LaGue, C.; Lo, T. M.; Pevunova, O.; Schmitz, M.; Terek, S.; Steer, I.

2014-01-01

The NASA/IPAC Extragalactic Database (NED) is continuing to evolve in lock-step with the explosive growth of astronomical data and advancements in information technology. A new methodology is being used to fuse data from very large surveys. Selected parameters are first loaded into a new database layer and made available in areal searches before they are cross-matched with prior NED objects. Then a programmed, rule-based statistical approach is used to identify new objects and compute cross-identifications with existing objects where possible; otherwise associations between objects are derived based on positional uncertainties or spatial resolution differences. Approximately 62 million UV sources from the GALEX All-Sky Survey and Medium Imaging Survey catalogs have been integrated into NED using this new process. The December 2013 release also contains nearly half a billion sources from the 2MASS Point Source Catalog accessible in cone searches, while the large scale cross-matching is in progress. Forthcoming updates will fuse data from All-WISE, SDSS DR12, and other very large catalogs. This work is progressing in parallel with the equally important integration of data from the literature, which is also growing rapidly. Recent updates have also included H I and CO channel maps (data cubes), as well as substantial growth in redshifts, classifications, photometry, spectra and redshift-independent distances. The By Parameters search engine now incorporates a simplified form for entry of constraints, and support for long-running queries with machine-readable output. A new tool for exploring the environments of galaxies with measured radial velocities includes informative graphics and a method to assess the incompleteness of redshift measurements. The NED user interface is also undergoing a major transformation, providing more streamlined navigation and searching, and a modern development framework for future enhancements. For further information, please visit our poster (Fadda et al. 2014) and stop by the NED exhibit for a demo. NED is operated by the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration.

Extraction, integration and analysis of alternative splicing and protein structure distributed information

PubMed Central

D'Antonio, Matteo; Masseroli, Marco

2009-01-01

Background Alternative splicing has been demonstrated to affect most of human genes; different isoforms from the same gene encode for proteins which differ for a limited number of residues, thus yielding similar structures. This suggests possible correlations between alternative splicing and protein structure. In order to support the investigation of such relationships, we have developed the Alternative Splicing and Protein Structure Scrutinizer (PASS), a Web application to automatically extract, integrate and analyze human alternative splicing and protein structure data sparsely available in the Alternative Splicing Database, Ensembl databank and Protein Data Bank. Primary data from these databases have been integrated and analyzed using the Protein Identifier Cross-Reference, BLAST, CLUSTALW and FeatureMap3D software tools. Results A database has been developed to store the considered primary data and the results from their analysis; a system of Perl scripts has been implemented to automatically create and update the database and analyze the integrated data; a Web interface has been implemented to make the analyses easily accessible; a database has been created to manage user accesses to the PASS Web application and store user's data and searches. Conclusion PASS automatically integrates data from the Alternative Splicing Database with protein structure data from the Protein Data Bank. Additionally, it comprehensively analyzes the integrated data with publicly available well-known bioinformatics tools in order to generate structural information of isoform pairs. Further analysis of such valuable information might reveal interesting relationships between alternative splicing and protein structure differences, which may be significantly associated with different functions. PMID:19828075

KaBOB: ontology-based semantic integration of biomedical databases.

PubMed

Livingston, Kevin M; Bada, Michael; Baumgartner, William A; Hunter, Lawrence E

2015-04-23

The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources. We present five processes for semantic data integration that, when applied collectively, solve seven key problems. These processes include making explicit the differences between biomedical concepts and database records, aggregating sets of identifiers denoting the same biomedical concepts across data sources, and using declaratively represented forward-chaining rules to take information that is variably represented in source databases and integrating it into a consistent biomedical representation. We demonstrate these processes and solutions by presenting KaBOB (the Knowledge Base Of Biomedicine), a knowledge base of semantically integrated data from 18 prominent biomedical databases using common representations grounded in Open Biomedical Ontologies. An instance of KaBOB with data about humans and seven major model organisms can be built using on the order of 500 million RDF triples. All source code for building KaBOB is available under an open-source license. KaBOB is an integrated knowledge base of biomedical data representationally based in prominent, actively maintained Open Biomedical Ontologies, thus enabling queries of the underlying data in terms of biomedical concepts (e.g., genes and gene products, interactions and processes) rather than features of source-specific data schemas or file formats. KaBOB resolves many of the issues that routinely plague biomedical researchers intending to work with data from multiple data sources and provides a platform for ongoing data integration and development and for formal reasoning over a wealth of integrated biomedical data.

Heterogeneous Biomedical Database Integration Using a Hybrid Strategy: A p53 Cantcer Research Database

PubMed Central

Bichutskiy, Vadim Y.; Colman, Richard; Brachmann, Rainer K.; Lathrop, Richard H.

2006-01-01

Complex problems in life science research give rise to multidisciplinary collaboration, and hence, to the need for heterogeneous database integration. The tumor suppressor p53 is mutated in close to 50% of human cancers, and a small drug-like molecule with the ability to restore native function to cancerous p53 mutants is a long-held medical goal of cancer treatment. The Cancer Research DataBase (CRDB) was designed in support of a project to find such small molecules. As a cancer informatics project, the CRDB involved small molecule data, computational docking results, functional assays, and protein structure data. As an example of the hybrid strategy for data integration, it combined the mediation and data warehousing approaches. This paper uses the CRDB to illustrate the hybrid strategy as a viable approach to heterogeneous data integration in biomedicine, and provides a design method for those considering similar systems. More efficient data sharing implies increased productivity, and, hopefully, improved chances of success in cancer research. (Code and database schemas are freely downloadable, http://www.igb.uci.edu/research/research.html.) PMID:19458771

Adaptive NN Control Using Integral Barrier Lyapunov Functionals for Uncertain Nonlinear Block-Triangular Constraint Systems.

PubMed

Liu, Yan-Jun; Tong, Shaocheng; Chen, C L Philip; Li, Dong-Juan

2017-11-01

A neural network (NN) adaptive control design problem is addressed for a class of uncertain multi-input-multi-output (MIMO) nonlinear systems in block-triangular form. The considered systems contain uncertainty dynamics and their states are enforced to subject to bounded constraints as well as the couplings among various inputs and outputs are inserted in each subsystem. To stabilize this class of systems, a novel adaptive control strategy is constructively framed by using the backstepping design technique and NNs. The novel integral barrier Lyapunov functionals (BLFs) are employed to overcome the violation of the full state constraints. The proposed strategy can not only guarantee the boundedness of the closed-loop system and the outputs are driven to follow the reference signals, but also can ensure all the states to remain in the predefined compact sets. Moreover, the transformed constraints on the errors are used in the previous BLF, and accordingly it is required to determine clearly the bounds of the virtual controllers. Thus, it can relax the conservative limitations in the traditional BLF-based controls for the full state constraints. This conservatism can be solved in this paper and it is for the first time to control this class of MIMO systems with the full state constraints. The performance of the proposed control strategy can be verified through a simulation example.

Network-based drug discovery by integrating systems biology and computational technologies

PubMed Central

Leung, Elaine L.; Cao, Zhi-Wei; Jiang, Zhi-Hong; Zhou, Hua

2013-01-01

Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs. The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy. Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. However, optimization methods of drug combination are insufficient, owning to lacking of tighter integration across multiple ‘-omics’ databases. The newly developed algorithm- or network-based computational models can tightly integrate ‘-omics’ databases and optimize combinational regimens of drug development, which encourage using medicinal herbs to develop into new wave of network-based multi-target drugs. However, challenges on further integration across the databases of medicinal herbs with multiple system biology platforms for multi-target drug optimization remain to the uncertain reliability of individual data sets, width and depth and degree of standardization of herbal medicine. Standardization of the methodology and terminology of multiple system biology and herbal database would facilitate the integration. Enhance public accessible databases and the number of research using system biology platform on herbal medicine would be helpful. Further integration across various ‘-omics’ platforms and computational tools would accelerate development of network-based drug discovery and network medicine. PMID:22877768

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.

Region 9 Census Block 2010

EPA Pesticide Factsheets

Geography:The TIGER Line Files are feature classes and related database files (.) that are an extract of selected geographic and cartographic information from the U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB). The MTDB represents a seamless national file with no overlaps or gaps between parts, however, each TIGER Line File is designed to stand alone as an independent data set, or they can be combined to cover the entire nation. Census Blocks are statistical areas bounded on all sides by visible features, such as streets, roads, streams, and railroad tracks, and/or by non visible boundaries such as city, town, township, and county limits, and short line-of-sight extensions of streets and roads. Census blocks are relatively small in area; for example, a block in a city bounded by streets. However, census blocks in remote areas are often large and irregular and may even be many square miles in area. A common misunderstanding is that data users think census blocks are used geographically to build all other census geographic areas, rather all other census geographic areas are updated and then used as the primary constraints, along with roads and water features, to delineate the tabulation blocks. As a result, all 2010 Census blocks nest within every other 2010 Census geographic area, so that Census Bureau statistical data can be tabulated at the block level and aggregated up t

Small PACS implementation using publicly available software

NASA Astrophysics Data System (ADS)

Passadore, Diego J.; Isoardi, Roberto A.; Gonzalez Nicolini, Federico J.; Ariza, P. P.; Novas, C. V.; Omati, S. A.

1998-07-01

Building cost effective PACS solutions is a main concern in developing countries. Hardware and software components are generally much more expensive than in developed countries and also more tightened financial constraints are the main reasons contributing to a slow rate of implementation of PACS. The extensive use of Internet for sharing resources and information has brought a broad number of freely available software packages to an ever-increasing number of users. In the field of medical imaging is possible to find image format conversion packages, DICOM compliant servers for all kinds of service classes, databases, web servers, image visualization, manipulation and analysis tools, etc. This paper describes a PACS implementation for review and storage built on freely available software. It currently integrates four diagnostic modalities (PET, CT, MR and NM), a Radiotherapy Treatment Planning workstation and several computers in a local area network, for image storage, database management and image review, processing and analysis. It also includes a web-based application that allows remote users to query the archive for studies from any workstation and to view the corresponding images and reports. We conclude that the advantage of using this approach is twofold. It allows a full understanding of all the issues involved in the implementation of a PACS and also contributes to keep costs down while enabling the development of a functional system for storage, distribution and review that can prove to be helpful for radiologists and referring physicians.

Probability theory, not the very guide of life.

PubMed

Juslin, Peter; Nilsson, Håkan; Winman, Anders

2009-10-01

Probability theory has long been taken as the self-evident norm against which to evaluate inductive reasoning, and classical demonstrations of violations of this norm include the conjunction error and base-rate neglect. Many of these phenomena require multiplicative probability integration, whereas people seem more inclined to linear additive integration, in part, at least, because of well-known capacity constraints on controlled thought. In this article, the authors show with computer simulations that when based on approximate knowledge of probabilities, as is routinely the case in natural environments, linear additive integration can yield as accurate estimates, and as good average decision returns, as estimates based on probability theory. It is proposed that in natural environments people have little opportunity or incentive to induce the normative rules of probability theory and, given their cognitive constraints, linear additive integration may often offer superior bounded rationality.

The EUVE Proposal Database

NASA Astrophysics Data System (ADS)

Christian, C. A.; Olson, E. C.

1993-01-01

The proposal database and scheduling system for the Extreme Ultraviolet Explorer is described. The proposal database has been implemented to take input for approved observations selected by the EUVE Peer Review Panel and output target information suitable for the scheduling system to digest. The scheduling system is a hybrid of the SPIKE program and EUVE software which checks spacecraft constraints, produces a proposed schedule and selects spacecraft orientations with optimal configurations for acquiring star trackers, etc. This system is used to schedule the In Orbit Calibration activities that took place this summer, following the EUVE launch in early June 1992. The strategy we have implemented has implications for the selection of approved targets, which have impacted the Peer Review process. In addition, we will discuss how the proposal database, founded on Sybase, controls the processing of EUVE Guest Observer data.

Dimensional modeling: beyond data processing constraints.

PubMed

Bunardzic, A

1995-01-01

The focus of information processing requirements is shifting from the on-line transaction processing (OLTP) issues to the on-line analytical processing (OLAP) issues. While the former serves to ensure the feasibility of the real-time on-line transaction processing (which has already exceeded a level of up to 1,000 transactions per second under normal conditions), the latter aims at enabling more sophisticated analytical manipulation of data. The OLTP requirements, or how to efficiently get data into the system, have been solved by applying the Relational theory in the form of Entity-Relation model. There is presently no theory related to OLAP that would resolve the analytical processing requirements as efficiently as Relational theory provided for the transaction processing. The "relational dogma" also provides the mathematical foundation for the Centralized Data Processing paradigm in which mission-critical information is incorporated as 'one and only one instance' of data, thus ensuring data integrity. In such surroundings, the information that supports business analysis and decision support activities is obtained by running predefined reports and queries that are provided by the IS department. In today's intensified competitive climate, businesses are finding that this traditional approach is not good enough. The only way to stay on top of things, and to survive and prosper, is to decentralize the IS services. The newly emerging Distributed Data Processing, with its increased emphasis on empowering the end user, does not seem to find enough merit in the relational database model to justify relying upon it. Relational theory proved too rigid and complex to accommodate the analytical processing needs. In order to satisfy the OLAP requirements, or how to efficiently get the data out of the system, different models, metaphors, and theories have been devised. All of them are pointing to the need for simplifying the highly non-intuitive mathematical constraints found in the relational databases normalized to their 3rd normal form. Object-oriented approach insists on the importance of the common sense component of the data processing activities. But, particularly interesting, is the approach that advocates the necessity of 'flattening' the structure of the business models as we know them today. This discipline is called Dimensional Modeling and it enables users to form multidimensional views of the relevant facts which are stored in a 'flat' (non-structured), easy-to-comprehend and easy-to-access database. When using dimensional modeling, we relax many of the axioms inherent in a relational model. We focus on the knowledge of the relevant facts which are reflecting the business operations and are the real basis for the decision support and business analysis. At the core of the dimensional modeling are fact tables that contain the non-discrete, additive data. To determine the level of aggregation of these facts, we use granularity tables that specify the resolution, or the level/detail, that the user is allowed to entertain. The third component is dimension tables that embody the knowledge of the constraints to be used to form the views.

Building an integrated neurodegenerative disease database at an academic health center.

PubMed

Xie, Sharon X; Baek, Young; Grossman, Murray; Arnold, Steven E; Karlawish, Jason; Siderowf, Andrew; Hurtig, Howard; Elman, Lauren; McCluskey, Leo; Van Deerlin, Vivianna; Lee, Virginia M-Y; Trojanowski, John Q

2011-07-01

It is becoming increasingly important to study common and distinct etiologies, clinical and pathological features, and mechanisms related to neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration. These comparative studies rely on powerful database tools to quickly generate data sets that match diverse and complementary criteria set by them. In this article, we present a novel integrated neurodegenerative disease (INDD) database, which was developed at the University of Pennsylvania (Penn) with the help of a consortium of Penn investigators. Because the work of these investigators are based on Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal lobar degeneration, it allowed us to achieve the goal of developing an INDD database for these major neurodegenerative disorders. We used the Microsoft SQL server as a platform, with built-in "backwards" functionality to provide Access as a frontend client to interface with the database. We used PHP Hypertext Preprocessor to create the "frontend" web interface and then used a master lookup table to integrate individual neurodegenerative disease databases. We also present methods of data entry, database security, database backups, and database audit trails for this INDD database. Using the INDD database, we compared the results of a biomarker study with those using an alternative approach by querying individual databases separately. We have demonstrated that the Penn INDD database has the ability to query multiple database tables from a single console with high accuracy and reliability. The INDD database provides a powerful tool for generating data sets in comparative studies on several neurodegenerative diseases. Copyright © 2011 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

A combined solar and geomagnetic index for thermospheric climate

PubMed Central

Mlynczak, Martin G; Hunt, Linda A; Marshall, B Thomas; Russell, James M; Mertens, Christopher J; Thompson, R Earl; Gordley, Larry L

2015-01-01

Infrared radiation from nitric oxide (NO) at 5.3 µm is a primary mechanism by which the thermosphere cools to space. The Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument on the NASA Thermosphere-Ionosphere-Mesosphere Energetics and Dynamics satellite has been measuring thermospheric cooling by NO for over 13 years. In this letter we show that the SABER time series of globally integrated infrared power (watts) radiated by NO can be replicated accurately by a multiple linear regression fit using the F10.7, Ap, and Dst indices. This allows reconstruction of the NO power time series back nearly 70 years with extant databases of these indices. The relative roles of solar ultraviolet and geomagnetic processes in determining the NO cooling are derived and shown to vary significantly over the solar cycle. The NO power is a fundamental integral constraint on the thermospheric climate, and the time series presented here can be used to test upper atmosphere models over seven different solar cycles. Key Points F10.7, Ap, and Dst replicate time series of radiative cooling by nitric oxide Quantified relative roles of solar irradiance, geomagnetism in radiative cooling Establish a new index and extend record of thermospheric cooling back 70 years PMID:26709319

A combined solar and geomagnetic index for thermospheric climate.

PubMed

Mlynczak, Martin G; Hunt, Linda A; Marshall, B Thomas; Russell, James M; Mertens, Christopher J; Thompson, R Earl; Gordley, Larry L

2015-05-28

Infrared radiation from nitric oxide (NO) at 5.3 µm is a primary mechanism by which the thermosphere cools to space. The Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument on the NASA Thermosphere-Ionosphere-Mesosphere Energetics and Dynamics satellite has been measuring thermospheric cooling by NO for over 13 years. In this letter we show that the SABER time series of globally integrated infrared power (watts) radiated by NO can be replicated accurately by a multiple linear regression fit using the F 10.7 , Ap , and Dst indices. This allows reconstruction of the NO power time series back nearly 70 years with extant databases of these indices. The relative roles of solar ultraviolet and geomagnetic processes in determining the NO cooling are derived and shown to vary significantly over the solar cycle. The NO power is a fundamental integral constraint on the thermospheric climate, and the time series presented here can be used to test upper atmosphere models over seven different solar cycles. F 10.7 , Ap , and Dst replicate time series of radiative cooling by nitric oxide Quantified relative roles of solar irradiance, geomagnetism in radiative cooling Establish a new index and extend record of thermospheric cooling back 70 years.

Global teaching and training initiatives for emerging cohort studies

PubMed Central

Paulus, Jessica K.; Santoyo-Vistrain, Rocío; Havelick, David; Cohen, Amy; Kalyesubula, Robert; Ajayi, Ikeoluwapo O.; Mattsson, Jens G.; Adami, Hans-Olov; Dalal, Shona

2015-01-01

A striking disparity exists across the globe, with essentially no large-scale longitudinal studies ongoing in regions that will be significantly affected by the oncoming non-communicable disease epidemic. The successful implementation of cohort studies in most low-resource research environments presents unique challenges that may be aided by coordinated training programs. Leaders of emerging cohort studies attending the First World Cohort Integration Workshop were surveyed about training priorities, unmet needs and potential cross-cohort solutions to these barriers through an electronic pre-workshop questionnaire and focus groups. Cohort studies representing India, Mexico, Nigeria, South Africa, Sweden, Tanzania and Uganda described similar training needs, including on-the-job training, data analysis software instruction, and database and bio-bank management. A lack of funding and protected time for training activities were commonly identified constraints. Proposed solutions include a collaborative cross-cohort teaching platform with web-based content and interactive teaching methods for a range of research personnel. An international network for research mentorship and idea exchange, and modifying the graduate thesis structure were also identified as key initiatives. Cross-cohort integrated educational initiatives will efficiently meet shared needs, catalyze the development of emerging cohorts, speed closure of the global disparity in cohort research, and may fortify scientific capacity development in low-resource settings. PMID:23856451

Data Entities and Information System Matrix for Integrated Agriculture Information System (IAIS)

NASA Astrophysics Data System (ADS)

Budi Santoso, Halim; Delima, Rosa

2018-03-01

Integrated Agriculture Information System is a system that is developed to process data, information, and knowledge in Agriculture sector. Integrated Agriculture Information System brings valuable information for farmers: (1) Fertilizer price; (2) Agriculture technique and practise; (3) Pest management; (4) Cultivation; (5) Irrigation; (6) Post harvest processing; (7) Innovation in agriculture processing. Integrated Agriculture Information System contains 9 subsystems. To bring an integrated information to the user and stakeholder, it needs an integrated database approach. Thus, researchers describes data entity and its matrix relate to subsystem in Integrated Agriculture Information System (IAIS). As a result, there are 47 data entities as entities in single and integrated database.

A Novel Face-on-Face Contact Method for Nonlinear Solid Mechanics

NASA Astrophysics Data System (ADS)

Wopschall, Steven Robert

The implicit solution to contact problems in nonlinear solid mechanics poses many difficulties. Traditional node-to-segment methods may suffer from locking and experience contact force chatter in the presence of sliding. More recent developments include mortar based methods, which resolve local contact interactions over face-pairs and feature a kinematic constraint in integral form that smoothes contact behavior, especially in the presence of sliding. These methods have been shown to perform well in the presence of geometric nonlinearities and are demonstratively more robust than node-to-segment methods. These methods are typically biased, however, interpolating contact tractions and gap equations on a designated non-mortar face, which leads to an asymmetry in the formulation. Another challenge is constraint enforcement. The general selection of the active set of constraints is brought with difficulty, often leading to non-physical solutions and easily resulting in missed face-pair interactions. Details on reliable constraint enforcement methods are lacking in the greater contact literature. This work presents an unbiased contact formulation utilizing a median-plane methodology. Up to linear polynomials are used for the discrete pressure representation and integral gap constraints are enforced using a novel subcycling procedure. This procedure reliably determines the active set of contact constraints leading to physical and kinematically admissible solutions void of heuristics and user action. The contact method presented herein successfully solves difficult quasi-static contact problems in the implicit computational setting. These problems feature finite deformations, material nonlinearity, and complex interface geometries, all of which are challenging characteristics for contact implementations and constraint enforcement algorithms. The subcycling procedure is a key feature of this method, handling active constraint selection for complex interfaces and mesh geometries.

Constraint Logic Programming approach to protein structure prediction.

PubMed

Dal Palù, Alessandro; Dovier, Agostino; Fogolari, Federico

2004-11-30

The protein structure prediction problem is one of the most challenging problems in biological sciences. Many approaches have been proposed using database information and/or simplified protein models. The protein structure prediction problem can be cast in the form of an optimization problem. Notwithstanding its importance, the problem has very seldom been tackled by Constraint Logic Programming, a declarative programming paradigm suitable for solving combinatorial optimization problems. Constraint Logic Programming techniques have been applied to the protein structure prediction problem on the face-centered cube lattice model. Molecular dynamics techniques, endowed with the notion of constraint, have been also exploited. Even using a very simplified model, Constraint Logic Programming on the face-centered cube lattice model allowed us to obtain acceptable results for a few small proteins. As a test implementation their (known) secondary structure and the presence of disulfide bridges are used as constraints. Simplified structures obtained in this way have been converted to all atom models with plausible structure. Results have been compared with a similar approach using a well-established technique as molecular dynamics. The results obtained on small proteins show that Constraint Logic Programming techniques can be employed for studying protein simplified models, which can be converted into realistic all atom models. The advantage of Constraint Logic Programming over other, much more explored, methodologies, resides in the rapid software prototyping, in the easy way of encoding heuristics, and in exploiting all the advances made in this research area, e.g. in constraint propagation and its use for pruning the huge search space.

Federated Search Tools in Fusion Centers: Bridging Databases in the Information Sharing Environment

DTIC Science & Technology

2012-09-01

considerable variation in how fusion centers plan for, gather requirements, select and acquire federated search tools to bridge disparate databases...centers, when considering integrating federated search tools; by evaluating the importance of the planning, requirements gathering, selection and...acquisition processes for integrating federated search tools; by acknowledging the challenges faced by some fusion centers during these integration processes

Integrated Database And Knowledge Base For Genomic Prospective Cohort Study In Tohoku Medical Megabank Toward Personalized Prevention And Medicine.

PubMed

Ogishima, Soichi; Takai, Takako; Shimokawa, Kazuro; Nagaie, Satoshi; Tanaka, Hiroshi; Nakaya, Jun

2015-01-01

The Tohoku Medical Megabank project is a national project to revitalization of the disaster area in the Tohoku region by the Great East Japan Earthquake, and have conducted large-scale prospective genome-cohort study. Along with prospective genome-cohort study, we have developed integrated database and knowledge base which will be key database for realizing personalized prevention and medicine.

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases.

PubMed

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-07-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org.

Integration of Oracle and Hadoop: Hybrid Databases Affordable at Scale

NASA Astrophysics Data System (ADS)

Canali, L.; Baranowski, Z.; Kothuri, P.

2017-10-01

This work reports on the activities aimed at integrating Oracle and Hadoop technologies for the use cases of CERN database services and in particular on the development of solutions for offloading data and queries from Oracle databases into Hadoop-based systems. The goal and interest of this investigation is to increase the scalability and optimize the cost/performance footprint for some of our largest Oracle databases. These concepts have been applied, among others, to build offline copies of CERN accelerator controls and logging databases. The tested solution allows to run reports on the controls data offloaded in Hadoop without affecting the critical production database, providing both performance benefits and cost reduction for the underlying infrastructure. Other use cases discussed include building hybrid database solutions with Oracle and Hadoop, offering the combined advantages of a mature relational database system with a scalable analytics engine.

Reactor design and integration into a nuclear electric spacecraft

NASA Technical Reports Server (NTRS)

Phillips, W. M.; Koenig, D. R.

1978-01-01

One of the well-defined applications for nuclear power in space is nuclear electric propulsion (NEP). Mission studies have identified the optimum power level (400 kWe). A single Shuttle launch requirement and science-package integration have added additional constraints to the design. A reactor design which will meet these constraints has been studied. The reactor employs 90 fuel elements, each heat pipe cooled. Reactor control is obtained with BeO/B4C drums in a BeO reflector. The balance of the spacecraft is shielded from the reactor with LiH. Power conditioning and reactor control drum drives are located behind the LiH with the power conditioning. Launch safety, mechanical design and integration with the power conversion subsystem are discussed.

Constraint-induced aphasia therapy in post-stroke aphasia rehabilitation: A systematic review and meta-analysis of randomized controlled trials.

PubMed

Zhang, Jiaqi; Yu, Jiadan; Bao, Yong; Xie, Qing; Xu, Yang; Zhang, Junmei; Wang, Pu

2017-01-01

Constraint-induced aphasia therapy (CIAT) has been widely used in post-stroke aphasia rehabilitation. An increasing number of clinical controlled trials have investigated the efficacy of the CIAT for the post-stroke aphasia. To systematically review the randomized controlled trials (RCTs) concerning the effect of the CIAT in post-stroke patients with aphasia, and to identify the useful components of CIAT in post-stroke aphasia rehabilitation. A computerized database search was performed through five databases (Pubmed, EMbase, Medline, ScienceDirect and Cochrane library). Cochrane handbook domains were used to evaluate the methodological quality of the included RCTs. Eight RCTs qualified in the inclusion criteria. Inconsistent results were found in comparing the CIAT with conventional therapies without any component from the CIAT based on the results of three RCTs. Five RCTs showed that the CIAT performed equally well as other intensive aphasia therapies, in terms of improving language performance. One RCT showed that therapies embedded with social interaction were likely to enhance the efficacy of the CIAT. CIAT may be useful for improving chronic post-stroke aphasia, however, limited evidence to support its superiority to other aphasia therapies. Massed practice is likely to be a useful component of CIAT, while the role of "constraint" is needed to be further explored. CIAT embedded with social interaction may gain more benefits.

A collaborative vendor-buyer production-inventory systems with imperfect quality items, inspection errors, and stochastic demand under budget capacity constraint: a Karush-Kuhn-Tucker conditions approach

NASA Astrophysics Data System (ADS)

Kurdhi, N. A.; Nurhayati, R. A.; Wiyono, S. B.; Handajani, S. S.; Martini, T. S.

2017-01-01

In this paper, we develop an integrated inventory model considering the imperfect quality items, inspection error, controllable lead time, and budget capacity constraint. The imperfect items were uniformly distributed and detected on the screening process. However there are two types of possibilities. The first is type I of inspection error (when a non-defective item classified as defective) and the second is type II of inspection error (when a defective item classified as non-defective). The demand during the lead time is unknown, and it follows the normal distribution. The lead time can be controlled by adding the crashing cost. Furthermore, the existence of the budget capacity constraint is caused by the limited purchasing cost. The purposes of this research are: to modify the integrated vendor and buyer inventory model, to establish the optimal solution using Kuhn-Tucker’s conditions, and to apply the models. Based on the result of application and the sensitivity analysis, it can be obtained minimum integrated inventory total cost rather than separated inventory.

Achieving Integration in Mixed Methods Designs—Principles and Practices

PubMed Central

Fetters, Michael D; Curry, Leslie A; Creswell, John W

2013-01-01

Mixed methods research offers powerful tools for investigating complex processes and systems in health and health care. This article describes integration principles and practices at three levels in mixed methods research and provides illustrative examples. Integration at the study design level occurs through three basic mixed method designs—exploratory sequential, explanatory sequential, and convergent—and through four advanced frameworks—multistage, intervention, case study, and participatory. Integration at the methods level occurs through four approaches. In connecting, one database links to the other through sampling. With building, one database informs the data collection approach of the other. When merging, the two databases are brought together for analysis. With embedding, data collection and analysis link at multiple points. Integration at the interpretation and reporting level occurs through narrative, data transformation, and joint display. The fit of integration describes the extent the qualitative and quantitative findings cohere. Understanding these principles and practices of integration can help health services researchers leverage the strengths of mixed methods. PMID:24279835

Achieving integration in mixed methods designs-principles and practices.

PubMed

Fetters, Michael D; Curry, Leslie A; Creswell, John W

2013-12-01

Mixed methods research offers powerful tools for investigating complex processes and systems in health and health care. This article describes integration principles and practices at three levels in mixed methods research and provides illustrative examples. Integration at the study design level occurs through three basic mixed method designs-exploratory sequential, explanatory sequential, and convergent-and through four advanced frameworks-multistage, intervention, case study, and participatory. Integration at the methods level occurs through four approaches. In connecting, one database links to the other through sampling. With building, one database informs the data collection approach of the other. When merging, the two databases are brought together for analysis. With embedding, data collection and analysis link at multiple points. Integration at the interpretation and reporting level occurs through narrative, data transformation, and joint display. The fit of integration describes the extent the qualitative and quantitative findings cohere. Understanding these principles and practices of integration can help health services researchers leverage the strengths of mixed methods. © Health Research and Educational Trust.

Integration of Web-based and PC-based clinical research databases.

PubMed

Brandt, C A; Sun, K; Charpentier, P; Nadkarni, P M

2004-01-01

We have created a Web-based repository or data library of information about measurement instruments used in studies of multi-factorial geriatric health conditions (the Geriatrics Research Instrument Library - GRIL) based upon existing features of two separate clinical study data management systems. GRIL allows browsing, searching, and selecting measurement instruments based upon criteria such as keywords and areas of applicability. Measurement instruments selected can be printed and/or included in an automatically generated standalone microcomputer database application, which can be downloaded by investigators for use in data collection and data management. Integration of database applications requires the creation of a common semantic model, and mapping from each system to this model. Various database schema conflicts at the table and attribute level must be identified and resolved prior to integration. Using a conflict taxonomy and a mapping schema facilitates this process. Critical conflicts at the table level that required resolution included name and relationship differences. A major benefit of integration efforts is the sharing of features and cross-fertilization of applications created for similar purposes in different operating environments. Integration of applications mandates some degree of metadata model unification.

Integrated Transportation-land Use Model For Indiana

DOT National Transportation Integrated Search

1997-01-01

Despite the recent research interest in integrating land use and transportation models inspired by federal legislation, no product had met the data, budget, and personnel constraints faced by the metropolitan planning organizations in Indiana. Conseq...

Content and Workflow Management for Library Websites: Case Studies

ERIC Educational Resources Information Center

Yu, Holly, Ed.

2005-01-01

Using database-driven web pages or web content management (WCM) systems to manage increasingly diverse web content and to streamline workflows is a commonly practiced solution recognized in libraries today. However, limited library web content management models and funding constraints prevent many libraries from purchasing commercially available…

Innovative Approach for Development of Drinking Water Research Data in the EPA Treatability Database

EPA Science Inventory

In recent years, funding for development of the TDB has been limited due to Federal budget constraints. As a result, EPA adopted an innovative approach to continue the development of new contaminants and maintenance of treatability information on over 60 existing drinking water ...

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.

Overcoming Dietary Assessment Challenges in Low-Income Countries: Technological Solutions Proposed by the International Dietary Data Expansion (INDDEX) Project.

PubMed

Coates, Jennifer C; Colaiezzi, Brooke A; Bell, Winnie; Charrondiere, U Ruth; Leclercq, Catherine

2017-03-16

An increasing number of low-income countries (LICs) exhibit high rates of malnutrition coincident with rising rates of overweight and obesity. Individual-level dietary data are needed to inform effective responses, yet dietary data from large-scale surveys conducted in LICs remain extremely limited. This discussion paper first seeks to highlight the barriers to collection and use of individual-level dietary data in LICs. Second, it introduces readers to new technological developments and research initiatives to remedy this situation, led by the International Dietary Data Expansion (INDDEX) Project. Constraints to conducting large-scale dietary assessments include significant costs, time burden, technical complexity, and limited investment in dietary research infrastructure, including the necessary tools and databases required to collect individual-level dietary data in large surveys. To address existing bottlenecks, the INDDEX Project is developing a dietary assessment platform for LICs, called INDDEX24, consisting of a mobile application integrated with a web database application, which is expected to facilitate seamless data collection and processing. These tools will be subject to rigorous testing including feasibility, validation, and cost studies. To scale up dietary data collection and use in LICs, the INDDEX Project will also invest in food composition databases, an individual-level dietary data dissemination platform, and capacity development activities. Although the INDDEX Project activities are expected to improve the ability of researchers and policymakers in low-income countries to collect, process, and use dietary data, the global nutrition community is urged to commit further significant investments in order to adequately address the range and scope of challenges described in this paper.

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

Overcoming Dietary Assessment Challenges in Low-Income Countries: Technological Solutions Proposed by the International Dietary Data Expansion (INDDEX) Project

PubMed Central

Coates, Jennifer C.; Colaiezzi, Brooke A.; Bell, Winnie; Charrondiere, U. Ruth; Leclercq, Catherine

2017-01-01

An increasing number of low-income countries (LICs) exhibit high rates of malnutrition coincident with rising rates of overweight and obesity. Individual-level dietary data are needed to inform effective responses, yet dietary data from large-scale surveys conducted in LICs remain extremely limited. This discussion paper first seeks to highlight the barriers to collection and use of individual-level dietary data in LICs. Second, it introduces readers to new technological developments and research initiatives to remedy this situation, led by the International Dietary Data Expansion (INDDEX) Project. Constraints to conducting large-scale dietary assessments include significant costs, time burden, technical complexity, and limited investment in dietary research infrastructure, including the necessary tools and databases required to collect individual-level dietary data in large surveys. To address existing bottlenecks, the INDDEX Project is developing a dietary assessment platform for LICs, called INDDEX24, consisting of a mobile application integrated with a web database application, which is expected to facilitate seamless data collection and processing. These tools will be subject to rigorous testing including feasibility, validation, and cost studies. To scale up dietary data collection and use in LICs, the INDDEX Project will also invest in food composition databases, an individual-level dietary data dissemination platform, and capacity development activities. Although the INDDEX Project activities are expected to improve the ability of researchers and policymakers in low-income countries to collect, process, and use dietary data, the global nutrition community is urged to commit further significant investments in order to adequately address the range and scope of challenges described in this paper. PMID:28300759

An investigation of constraint-based component-modeling for knowledge representation in computer-aided conceptual design

NASA Technical Reports Server (NTRS)

Kolb, Mark A.

1990-01-01

Originally, computer programs for engineering design focused on detailed geometric design. Later, computer programs for algorithmically performing the preliminary design of specific well-defined classes of objects became commonplace. However, due to the need for extreme flexibility, it appears unlikely that conventional programming techniques will prove fruitful in developing computer aids for engineering conceptual design. The use of symbolic processing techniques, such as object-oriented programming and constraint propagation, facilitate such flexibility. Object-oriented programming allows programs to be organized around the objects and behavior to be simulated, rather than around fixed sequences of function- and subroutine-calls. Constraint propagation allows declarative statements to be understood as designating multi-directional mathematical relationships among all the variables of an equation, rather than as unidirectional assignments to the variable on the left-hand side of the equation, as in conventional computer programs. The research has concentrated on applying these two techniques to the development of a general-purpose computer aid for engineering conceptual design. Object-oriented programming techniques are utilized to implement a user-extensible database of design components. The mathematical relationships which model both geometry and physics of these components are managed via constraint propagation. In addition, to this component-based hierarchy, special-purpose data structures are provided for describing component interactions and supporting state-dependent parameters. In order to investigate the utility of this approach, a number of sample design problems from the field of aerospace engineering were implemented using the prototype design tool, Rubber Airplane. The additional level of organizational structure obtained by representing design knowledge in terms of components is observed to provide greater convenience to the program user, and to result in a database of engineering information which is easier both to maintain and to extend.

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

Inferring Metadata for a Semantic Web Peer-to-Peer Environment

ERIC Educational Resources Information Center

Brase, Jan; Painter, Mark

2004-01-01

Learning Objects Metadata (LOM) aims at describing educational resources in order to allow better reusability and retrieval. In this article we show how additional inference rules allows us to derive additional metadata from existing ones. Additionally, using these rules as integrity constraints helps us to define the constraints on LOM elements,…

Finite BRST-BFV transformations for dynamical systems with second-class constraints

NASA Astrophysics Data System (ADS)

Batalin, Igor A.; Lavrov, Peter M.; Tyutin, Igor V.

2015-06-01

We study finite field-dependent BRST-BFV transformations for dynamical systems with first- and second-class constraints within the generalized Hamiltonian formalism. We find explicitly their Jacobians and the form of a solution to the compensation equation necessary for generating an arbitrary finite change of gauge-fixing functionals in the path integral.

Scheduling double round-robin tournaments with divisional play using constraint programming

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

Carlsson, Mats; Johansson, Mikael; Larson, Jeffrey

We study a tournament format that extends a traditional double round-robin format with divisional single round-robin tournaments. Elitserien, the top Swedish handball league, uses such a format for its league schedule. We present a constraint programming model that characterizes the general double round-robin plus divisional single round-robin format. This integrated model allows scheduling to be performed in a single step, as opposed to common multistep approaches that decompose scheduling into smaller problems and possibly miss optimal solutions. In addition to general constraints, we introduce Elitserien-specific requirements for its tournament. These general and league-specific constraints allow us to identify implicit andmore » symmetry-breaking properties that reduce the time to solution from hours to seconds. A scalability study of the number of teams shows that our approach is reasonably fast for even larger league sizes. The experimental evaluation of the integrated approach takes considerably less computational effort to schedule Elitserien than does the previous decomposed approach. (C) 2016 Elsevier B.V. All rights reserved« less

3-D model-based Bayesian classification

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

Soenneland, L.; Tenneboe, P.; Gehrmann, T.

1994-12-31

The challenging task of the interpreter is to integrate different pieces of information and combine them into an earth model. The sophistication level of this earth model might vary from the simplest geometrical description to the most complex set of reservoir parameters related to the geometrical description. Obviously the sophistication level also depend on the completeness of the available information. The authors describe the interpreter`s task as a mapping between the observation space and the model space. The information available to the interpreter exists in observation space and the task is to infer a model in model-space. It is well-knownmore » that this inversion problem is non-unique. Therefore any attempt to find a solution depend son constraints being added in some manner. The solution will obviously depend on which constraints are introduced and it would be desirable to allow the interpreter to modify the constraints in a problem-dependent manner. They will present a probabilistic framework that gives the interpreter the tools to integrate the different types of information and produce constrained solutions. The constraints can be adapted to the problem at hand.« less

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea.

PubMed

Martin, Stanton L; Blackmon, Barbara P; Rajagopalan, Ravi; Houfek, Thomas D; Sceeles, Robert G; Denn, Sheila O; Mitchell, Thomas K; Brown, Douglas E; Wing, Rod A; Dean, Ralph A

2002-01-01

We have created a federated database for genome studies of Magnaporthe grisea, the causal agent of rice blast disease, by integrating end sequence data from BAC clones, genetic marker data and BAC contig assembly data. A library of 9216 BAC clones providing >25-fold coverage of the entire genome was end sequenced and fingerprinted by HindIII digestion. The Image/FPC software package was then used to generate an assembly of 188 contigs covering >95% of the genome. The database contains the results of this assembly integrated with hybridization data of genetic markers to the BAC library. AceDB was used for the core database engine and a MySQL relational database, populated with numerical representations of BAC clones within FPC contigs, was used to create appropriately scaled images. The database is being used to facilitate sequencing efforts. The database also allows researchers mapping known genes or other sequences of interest, rapid and easy access to the fundamental organization of the M.grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm.

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.

Database Constraints Applied to Metabolic Pathway Reconstruction Tools

PubMed Central

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

Stationary properties of maximum-entropy random walks.

PubMed

Dixit, Purushottam D

2015-10-01

Maximum-entropy (ME) inference of state probabilities using state-dependent constraints is popular in the study of complex systems. In stochastic systems, how state space topology and path-dependent constraints affect ME-inferred state probabilities remains unknown. To that end, we derive the transition probabilities and the stationary distribution of a maximum path entropy Markov process subject to state- and path-dependent constraints. A main finding is that the stationary distribution over states differs significantly from the Boltzmann distribution and reflects a competition between path multiplicity and imposed constraints. We illustrate our results with particle diffusion on a two-dimensional landscape. Connections with the path integral approach to diffusion are discussed.

Principles of proteome allocation are revealed using proteomic data and genome-scale models

PubMed Central

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.; Ebrahim, Ali; Saunders, Michael A.; Palsson, Bernhard O.

2016-01-01

Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the “generalist” (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions, prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thus represents a generalist ME model reflecting both growth rate maximization and “hedging” against uncertain environments and stresses, as indicated by significant enrichment of these sectors for the general stress response sigma factor σS. Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally-related protein groups) as demonstrated here. This flexible formalism provides an accessible approach for narrowing the gap between the complexity captured by omics data and governing principles of proteome allocation described by systems-level models. PMID:27857205

Principles of proteome allocation are revealed using proteomic data and genome-scale models

DOE PAGES

Yang, Laurence; Yurkovich, James T.; Lloyd, Colton J.; ...

2016-11-18

Integrating omics data to refine or make context-specific models is an active field of constraint-based modeling. Proteomics now cover over 95% of the Escherichia coli proteome by mass. Genome-scale models of Metabolism and macromolecular Expression (ME) compute proteome allocation linked to metabolism and fitness. Using proteomics data, we formulated allocation constraints for key proteome sectors in the ME model. The resulting calibrated model effectively computed the “generalist” (wild-type) E. coli proteome and phenotype across diverse growth environments. Across 15 growth conditions, prediction errors for growth rate and metabolic fluxes were 69% and 14% lower, respectively. The sector-constrained ME model thusmore » represents a generalist ME model reflecting both growth rate maximization and “hedging” against uncertain environments and stresses, as indicated by significant enrichment of these sectors for the general stress response sigma factor σS. Finally, the sector constraints represent a general formalism for integrating omics data from any experimental condition into constraint-based ME models. The constraints can be fine-grained (individual proteins) or coarse-grained (functionally-related protein groups) as demonstrated here. Furthermore, this flexible formalism provides an accessible approach for narrowing the gap between the complexity captured by omics data and governing principles of proteome allocation described by systems-level models.« less

Practical Cleanroom Operations Constraints

NASA Technical Reports Server (NTRS)

Hughes, David; Ginyard, Amani

2007-01-01

This viewgraph presentation reviews the GSFC Cleanroom Facility i.e., Spacecraft Systems Development and Integration Facility (SSDIF) with particular interest in its use during the development of the Wide Field Camera 3 (WFC3). The SSDIF is described and a diagram of the SSDIF is shown. A Constraint Table was created for consistency within Contamination Control Team. This table is shown. Another table that shows the activities that were allowed during the integration under given WFC3 condition and activity location is presented. Three decision trees are shown for different phases of the work: (1) Hardware Relocation, Hardware Work, and Contamination Control Operations.

Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.

PubMed

Kuhn, Stefan; Schlörer, Nils E

2015-08-01

nmrshiftdb2 supports with its laboratory information management system the integration of an electronic lab administration and management into academic NMR facilities. Also, it offers the setup of a local database, while full access to nmrshiftdb2's World Wide Web database is granted. This freely available system allows on the one hand the submission of orders for measurement, transfers recorded data automatically or manually, and enables download of spectra via web interface, as well as the integrated access to prediction, search, and assignment tools of the NMR database for lab users. On the other hand, for the staff and lab administration, flow of all orders can be supervised; administrative tools also include user and hardware management, a statistic functionality for accounting purposes, and a 'QuickCheck' function for assignment control, to facilitate quality control of assignments submitted to the (local) database. Laboratory information management system and database are based on a web interface as front end and are therefore independent of the operating system in use. Copyright © 2015 John Wiley & Sons, Ltd.

Structator: fast index-based search for RNA sequence-structure patterns

PubMed Central

2011-01-01

Background The secondary structure of RNA molecules is intimately related to their function and often more conserved than the sequence. Hence, the important task of searching databases for RNAs requires to match sequence-structure patterns. Unfortunately, current tools for this task have, in the best case, a running time that is only linear in the size of sequence databases. Furthermore, established index data structures for fast sequence matching, like suffix trees or arrays, cannot benefit from the complementarity constraints introduced by the secondary structure of RNAs. Results We present a novel method and readily applicable software for time efficient matching of RNA sequence-structure patterns in sequence databases. Our approach is based on affix arrays, a recently introduced index data structure, preprocessed from the target database. Affix arrays support bidirectional pattern search, which is required for efficiently handling the structural constraints of the pattern. Structural patterns like stem-loops can be matched inside out, such that the loop region is matched first and then the pairing bases on the boundaries are matched consecutively. This allows to exploit base pairing information for search space reduction and leads to an expected running time that is sublinear in the size of the sequence database. The incorporation of a new chaining approach in the search of RNA sequence-structure patterns enables the description of molecules folding into complex secondary structures with multiple ordered patterns. The chaining approach removes spurious matches from the set of intermediate results, in particular of patterns with little specificity. In benchmark experiments on the Rfam database, our method runs up to two orders of magnitude faster than previous methods. Conclusions The presented method's sublinear expected running time makes it well suited for RNA sequence-structure pattern matching in large sequence databases. RNA molecules containing several stem-loop substructures can be described by multiple sequence-structure patterns and their matches are efficiently handled by a novel chaining method. Beyond our algorithmic contributions, we provide with Structator a complete and robust open-source software solution for index-based search of RNA sequence-structure patterns. The Structator software is available at http://www.zbh.uni-hamburg.de/Structator. PMID:21619640

Spatial Data Integration Using Ontology-Based Approach

NASA Astrophysics Data System (ADS)

Hasani, S.; Sadeghi-Niaraki, A.; Jelokhani-Niaraki, M.

2015-12-01

In today's world, the necessity for spatial data for various organizations is becoming so crucial that many of these organizations have begun to produce spatial data for that purpose. In some circumstances, the need to obtain real time integrated data requires sustainable mechanism to process real-time integration. Case in point, the disater management situations that requires obtaining real time data from various sources of information. One of the problematic challenges in the mentioned situation is the high degree of heterogeneity between different organizations data. To solve this issue, we introduce an ontology-based method to provide sharing and integration capabilities for the existing databases. In addition to resolving semantic heterogeneity, better access to information is also provided by our proposed method. Our approach is consisted of three steps, the first step is identification of the object in a relational database, then the semantic relationships between them are modelled and subsequently, the ontology of each database is created. In a second step, the relative ontology will be inserted into the database and the relationship of each class of ontology will be inserted into the new created column in database tables. Last step is consisted of a platform based on service-oriented architecture, which allows integration of data. This is done by using the concept of ontology mapping. The proposed approach, in addition to being fast and low cost, makes the process of data integration easy and the data remains unchanged and thus takes advantage of the legacy application provided.

The integration of digital orthophotographs with GISs in a microcomputer environment

NASA Technical Reports Server (NTRS)

Steiner, David R.

1992-01-01

The issues involved in the use of orthoimages as a data source for GIS databases are examined. The integration of digital photographs into a GIS is discussed. A prototype PC-based program for the production of GIS databases using orthoimages is described.

MEPD: a Medaka gene expression pattern database

PubMed Central

Henrich, Thorsten; Ramialison, Mirana; Quiring, Rebecca; Wittbrodt, Beate; Furutani-Seiki, Makoto; Wittbrodt, Joachim; Kondoh, Hisato

2003-01-01

The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensity, category and comments and through a comprehensive, hierarchically organized dictionary of anatomical terms. Sequences of the ESTs are available and searchable through BLAST. ESTs in the database are clustered upon entry and have been blasted against public data-bases. The BLAST results are updated regularly, stored within the database and searchable. The MEPD is a project within the Medaka Genome Initiative (MGI) and entries will be interconnected to integrated genomic map databases. MEPD is accessible through the WWW at http://medaka.dsp.jst.go.jp/MEPD. PMID:12519950

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

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

PubMed Central

Maier, Christopher W; Long, Jeffrey G; Hemminger, Bradley M; Giddings, Morgan C

2009-01-01

Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these factors, systems designed to manage and integrate modern biological data sets often end up as large, unwieldy databases that become difficult to maintain or evolve. The novel rule-based approach of the Ultra-Structure design methodology presents a potential solution to this problem. By representing both data and processes as formal rules within a database, an Ultra-Structure system constitutes a flexible framework that enables users to explicitly store domain knowledge in both a machine- and human-readable form. End users themselves can change the system's capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modified. This provides flexibility in adapting to change, and allows integration of disparate, heterogenous data sets within a small core set of database tables, facilitating joint analysis and visualization without becoming unwieldy. Here, we examine the application of Ultra-Structure to our ongoing research program for the integration of large proteomic and genomic data sets (proteogenomic mapping). Results We transitioned our proteogenomic mapping information system from a traditional entity-relationship design to one based on Ultra-Structure. Our system integrates tandem mass spectrum data, genomic annotation sets, and spectrum/peptide mappings, all within a small, general framework implemented within a standard relational database system. General software procedures driven by user-modifiable rules can perform tasks such as logical deduction and location-based computations. The system is not tied specifically to proteogenomic research, but is rather designed to accommodate virtually any kind of biological research. Conclusion We find Ultra-Structure offers substantial benefits for biological information systems, the largest being the integration of diverse information sources into a common framework. This facilitates systems biology research by integrating data from disparate high-throughput techniques. It also enables us to readily incorporate new data types, sources, and domain knowledge with no change to the database structure or associated computer code. Ultra-Structure may be a significant step towards solving the hard problem of data management and integration in the systems biology era. PMID:19691849

Evaluation of the Role of Functional Constraints on the Integrity of an Ultraconserved Region in the Genus Drosophila

PubMed Central

Díaz-Castillo, Carlos; Xia, Xiao-Qin; Ranz, José M.

2012-01-01

Why gene order is conserved over long evolutionary timespans remains elusive. A common interpretation is that gene order conservation might reflect the existence of functional constraints that are important for organismal performance. Alteration of the integrity of genomic regions, and therefore of those constraints, would result in detrimental effects. This notion seems especially plausible in those genomes that can easily accommodate gene reshuffling via chromosomal inversions since genomic regions free of constraints are likely to have been disrupted in one or more lineages. Nevertheless, no empirical test has been performed to this notion. Here, we disrupt one of the largest conserved genomic regions of the Drosophila genome by chromosome engineering and examine the phenotypic consequences derived from such disruption. The targeted region exhibits multiple patterns of functional enrichment suggestive of the presence of constraints. The carriers of the disrupted collinear block show no defects in their viability, fertility, and parameters of general homeostasis, although their odorant perception is altered. This change in odorant perception does not correlate with modifications of the level of expression and sex bias of the genes within the genomic region disrupted. Our results indicate that even in highly rearranged genomes, like those of Diptera, unusually high levels of gene order conservation cannot be systematically attributed to functional constraints, which raises the possibility that other mechanisms can be in place and therefore the underpinnings of the maintenance of gene organization might be more diverse than previously thought. PMID:22319453

A DBMS-based medical teleconferencing system.

PubMed

Chun, J; Kim, H; Lee, S; Choi, J; Cho, H

2001-01-01

This article presents the design of a medical teleconferencing system that is integrated with a multimedia patient database and incorporates easy-to-use tools and functions to effectively support collaborative work between physicians in remote locations. The design provides a virtual workspace that allows physicians to collectively view various kinds of patient data. By integrating the teleconferencing function into this workspace, physicians are able to conduct conferences using the same interface and have real-time access to the database during conference sessions. The authors have implemented a prototype based on this design. The prototype uses a high-speed network test bed and a manually created substitute for the integrated patient database.

A DBMS-based Medical Teleconferencing System

PubMed Central

Chun, Jonghoon; Kim, Hanjoon; Lee, Sang-goo; Choi, Jinwook; Cho, Hanik

2001-01-01

This article presents the design of a medical teleconferencing system that is integrated with a multimedia patient database and incorporates easy-to-use tools and functions to effectively support collaborative work between physicians in remote locations. The design provides a virtual workspace that allows physicians to collectively view various kinds of patient data. By integrating the teleconferencing function into this workspace, physicians are able to conduct conferences using the same interface and have real-time access to the database during conference sessions. The authors have implemented a prototype based on this design. The prototype uses a high-speed network test bed and a manually created substitute for the integrated patient database. PMID:11522766

GraDit: graph-based data repair algorithm for multiple data edits rule violations

NASA Astrophysics Data System (ADS)

Ode Zuhayeni Madjida, Wa; Gusti Bagus Baskara Nugraha, I.

2018-03-01

Constraint-based data cleaning captures data violation to a set of rule called data quality rules. The rules consist of integrity constraint and data edits. Structurally, they are similar, where the rule contain left hand side and right hand side. Previous research proposed a data repair algorithm for integrity constraint violation. The algorithm uses undirected hypergraph as rule violation representation. Nevertheless, this algorithm can not be applied for data edits because of different rule characteristics. This study proposed GraDit, a repair algorithm for data edits rule. First, we use bipartite-directed hypergraph as model representation of overall defined rules. These representation is used for getting interaction between violation rules and clean rules. On the other hand, we proposed undirected graph as violation representation. Our experimental study showed that algorithm with undirected graph as violation representation model gave better data quality than algorithm with undirected hypergraph as representation model.

Option pricing, stochastic volatility, singular dynamics and constrained path integrals

NASA Astrophysics Data System (ADS)

Contreras, Mauricio; Hojman, Sergio A.

2014-01-01

Stochastic volatility models have been widely studied and used in the financial world. The Heston model (Heston, 1993) [7] is one of the best known models to deal with this issue. These stochastic volatility models are characterized by the fact that they explicitly depend on a correlation parameter ρ which relates the two Brownian motions that drive the stochastic dynamics associated to the volatility and the underlying asset. Solutions to the Heston model in the context of option pricing, using a path integral approach, are found in Lemmens et al. (2008) [21] while in Baaquie (2007,1997) [12,13] propagators for different stochastic volatility models are constructed. In all previous cases, the propagator is not defined for extreme cases ρ=±1. It is therefore necessary to obtain a solution for these extreme cases and also to understand the origin of the divergence of the propagator. In this paper we study in detail a general class of stochastic volatility models for extreme values ρ=±1 and show that in these two cases, the associated classical dynamics corresponds to a system with second class constraints, which must be dealt with using Dirac’s method for constrained systems (Dirac, 1958,1967) [22,23] in order to properly obtain the propagator in the form of a Euclidean Hamiltonian path integral (Henneaux and Teitelboim, 1992) [25]. After integrating over momenta, one gets an Euclidean Lagrangian path integral without constraints, which in the case of the Heston model corresponds to a path integral of a repulsive radial harmonic oscillator. In all the cases studied, the price of the underlying asset is completely determined by one of the second class constraints in terms of volatility and plays no active role in the path integral.

Feasibility and acceptability of delivering adolescent health interventions alongside HPV vaccination in Tanzania

PubMed Central

Watson-Jones, Deborah; Lees, Shelley; Mwanga, Joseph; Neke, Nyasule; Changalucha, John; Broutet, Nathalie; Maduhu, Ibrahim; Kapiga, Saidi; Chandra-Mouli, Venkatraman; Bloem, Paul; Ross, David A

2016-01-01

Background: Human papillomavirus (HPV) vaccination offers an opportunity to strengthen provision of adolescent health interventions (AHI). We explored the feasibility of integrating other AHI with HPV vaccination in Tanzania. Methods: A desk review of 39 policy documents was preceded by a stakeholder meeting with 38 policy makers and partners. Eighteen key informant interviews (KIIs) with health and education policy makers and district officials were conducted to further explore perceptions of current programs, priorities and AHI that might be suitable for integration with HPV vaccination. Results: Fourteen school health interventions (SHI) or AHI are currently being implemented by the Government of Tanzania. Most are delivered as vertical programmes. Coverage of current programs is not universal, and is limited by financial, human resource and logistic constraints. Limited community engagement, rumours, and lack of strategic advocacy has affected uptake of some interventions, e.g. tetanus toxoid (TT) immunization. Stakeholder and KI perceptions and opinions were limited by a lack of experience with integrated delivery and AHI that were outside an individual’s area of expertise and experience. Deworming and educational sessions including reproductive health education were the most frequently mentioned interventions that respondents considered suitable for integrated delivery with HPV vaccine. Conclusions: Given programme constraints, limited experience with integrated delivery and concern about real or perceived side-effects being attributed to the vaccine, it will be very important to pilot-test integration of AHI/SHI with HPV vaccination. Selected interventions will need to be simple and quick to deliver since health workers are likely to face significant logistic and time constraints during vaccination visits. PMID:26768827

Genetic constraints predict evolutionary divergence in Dalechampia blossoms.

PubMed

Bolstad, Geir H; Hansen, Thomas F; Pélabon, Christophe; Falahati-Anbaran, Mohsen; Pérez-Barrales, Rocío; Armbruster, W Scott

2014-08-19

If genetic constraints are important, then rates and direction of evolution should be related to trait evolvability. Here we use recently developed measures of evolvability to test the genetic constraint hypothesis with quantitative genetic data on floral morphology from the Neotropical vine Dalechampia scandens (Euphorbiaceae). These measures were compared against rates of evolution and patterns of divergence among 24 populations in two species in the D. scandens species complex. We found clear evidence for genetic constraints, particularly among traits that were tightly phenotypically integrated. This relationship between evolvability and evolutionary divergence is puzzling, because the estimated evolvabilities seem too large to constitute real constraints. We suggest that this paradox can be explained by a combination of weak stabilizing selection around moving adaptive optima and small realized evolvabilities relative to the observed additive genetic variance.

DSSTox EPA Integrated Risk Information System Structure-Index Locator File: SDF File and Documentation

EPA Science Inventory

EPA's Integrated Risk Information System (IRIS) database was developed and is maintained by EPA's Office of Research and Developement, National Center for Environmental Assessment. IRIS is a database of human health effects that may result from exposure to various substances fou...

Version 2.0 AERONET Dust Aerosol properties, Constraints and Application to Asian Dust Observations

NASA Technical Reports Server (NTRS)

Holben, Brent; Eck, Tom; Holben, Brent; Eck, Tom; Siniuk, Aliaksander; Huangand, Jianping; Zang, Wu

2007-01-01

In November 2006, AERONET released Version 2 of the Dubovik and King sky radiance and optical depth inversion. Reanalysis of the entire AERONET database revealed marked differences in aerosol properties in arid and semi arid regions with dust dominated aerosols. The change will be illustrated through sensitivity analysis and examples from the UAE2 (United Arab Emirates Unified Aerosol Experiment) field campaign. Properties of dust dominated aerosols will be presented from regional AERONET sites in China showing variations in dust aerosol properties. The constraints and limitations of the AERONET inversion will be presented that will facilitate analysis by the user community of these data.

Optimization of heterogeneous Bin packing using adaptive genetic algorithm

NASA Astrophysics Data System (ADS)

Sridhar, R.; Chandrasekaran, M.; Sriramya, C.; Page, Tom

2017-03-01

This research is concentrates on a very interesting work, the bin packing using hybrid genetic approach. The optimal and feasible packing of goods for transportation and distribution to various locations by satisfying the practical constraints are the key points in this project work. As the number of boxes for packing can not be predicted in advance and the boxes may not be of same category always. It also involves many practical constraints that are why the optimal packing makes much importance to the industries. This work presents a combinational of heuristic Genetic Algorithm (HGA) for solving Three Dimensional (3D) Single container arbitrary sized rectangular prismatic bin packing optimization problem by considering most of the practical constraints facing in logistic industries. This goal was achieved in this research by optimizing the empty volume inside the container using genetic approach. Feasible packing pattern was achieved by satisfying various practical constraints like box orientation, stack priority, container stability, weight constraint, overlapping constraint, shipment placement constraint. 3D bin packing problem consists of ‘n’ number of boxes being to be packed in to a container of standard dimension in such a way to maximize the volume utilization and in-turn profit. Furthermore, Boxes to be packed may be of arbitrary sizes. The user input data are the number of bins, its size, shape, weight, and constraints if any along with standard container dimension. This user input were stored in the database and encoded to string (chromosomes) format which were normally acceptable by GA. GA operators were allowed to act over these encoded strings for finding the best solution.

PlanWorks: A Debugging Environment for Constraint Based Planning Systems

NASA Technical Reports Server (NTRS)

Daley, Patrick; Frank, Jeremy; Iatauro, Michael; McGann, Conor; Taylor, Will

2005-01-01

Numerous planning and scheduling systems employ underlying constraint reasoning systems. Debugging such systems involves the search for errors in model rules, constraint reasoning algorithms, search heuristics, and the problem instance (initial state and goals). In order to effectively find such problems, users must see why each state or action is in a plan by tracking causal chains back to part of the initial problem instance. They must be able to visualize complex relationships among many different entities and distinguish between those entities easily. For example, a variable can be in the scope of several constraints, as well as part of a state or activity in a plan; the activity can arise as a consequence of another activity and a model rule. Finally, they must be able to track each logical inference made during planning. We have developed PlanWorks, a comprehensive system for debugging constraint-based planning and scheduling systems. PlanWorks assumes a strong transaction model of the entire planning process, including adding and removing parts of the constraint network, variable assignment, and constraint propagation. A planner logs all transactions to a relational database that is tailored to support queries for of specialized views to display different forms of data (e.g. constraints, activities, resources, and causal links). PlanWorks was specifically developed for the Extensible Universal Remote Operations Planning Architecture (EUROPA(sub 2)) developed at NASA, but the underlying principles behind PlanWorks make it useful for many constraint-based planning systems. The paper is organized as follows. We first describe some fundamentals of EUROPA(sub 2). We then describe PlanWorks' principal components. We then discuss each component in detail, and then describe inter-component navigation features. We close with a discussion of how PlanWorks is used to find model flaws.

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

PubMed Central

Kobayashi, Norio; Ishii, Manabu; Takahashi, Satoshi; Mochizuki, Yoshiki; Matsushima, Akihiro; Toyoda, Tetsuro

2011-01-01

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org. PMID:21632604

A General Connectionist Model of Attitude Structure and Change: The ACS (Attitudes as Constraint Satisfaction) Model

ERIC Educational Resources Information Center

Monroe, Brian M.; Read, Stephen J.

2008-01-01

A localist, parallel constraint satisfaction, artificial neural network model is presented that accounts for a broad collection of attitude and attitude-change phenomena. The network represents the attitude object and cognitions and beliefs related to the attitude, as well as how to integrate a persuasive message into this network. Short-term…

A Partial Test of Agnew's General Theory of Crime and Delinquency

ERIC Educational Resources Information Center

Zhang, Yan; Day, George; Cao, Liqun

2012-01-01

In 2005, Agnew introduced a new integrated theory, which he labels a general theory of crime and delinquency. He proposes that delinquency is more likely to occur when constraints against delinquency are low and motivations for delinquency are high. In addition, he argues that constraints and motivations are influenced by variables in five life…

A Systematic Review of Dropout from Organized Sport among Children and Youth

ERIC Educational Resources Information Center

Crane, Jeff; Temple, Viviene

2015-01-01

Leisure constraints theory was used as a framework to systematically review factors associated with dropout of organized sport among children and adolescents. Keyword searches for the population, context and construct of interest (i.e. dropout) identified articles from the entire contents of the following databases: Academic Search Complete, ERIC,…

Effect of workplace incivility on end-of-work negative affect: examining individual and organizational moderators in a daily diary study.

PubMed

Zhou, Zhiqing E; Yan, Yu; Che, Xin Xuan; Meier, Laurenz L

2015-01-01

Although previous studies have linked workplace incivility with various negative outcomes, they mainly focused on the long-term effects of chronic exposure to workplace incivility, whereas targets' short-term reactions to incivility episodes have been largely neglected. Using a daily diary design, the current study examined effects of daily workplace incivility on end-of-work negative affect and explored potential individual and organizational moderators. Data collected from 76 full-time employees across 10 consecutive working days revealed that daily workplace incivility positively predicted end-of-work negative affect while controlling for before-work negative affect. Further, the relationship was stronger for people with low emotional stability, high hostile attribution bias, external locus of control, and people experiencing low chronic workload and more chronic organizational constraints, as compared with people with high emotional stability, low hostile attribution bias, internal locus of control, and people experiencing high chronic workload and fewer chronic organizational constraints, respectively. (PsycINFO Database Record (c) 2014 APA, all rights reserved). PsycINFO Database Record (c) 2014 APA, all rights reserved.

Free text databases in an Integrated Academic Information System (IAIMS) at Columbia Presbyterian Medical Center.

PubMed Central

Clark, A. S.; Shea, S.

1991-01-01

The use of Folio Views, a PC DOS based product for free text databases, is explored in three applications in an Integrated Academic Information System (IAIMS): (1) a telephone directory, (2) a grants and contracts newsletter, and (3) nursing care plans. PMID:1666967

IN SILICO METHODOLOGIES FOR PREDICTIVE EVALUATION OF TOXICITY BASED ON INTEGRATION OF DATABASES

EPA Science Inventory

In silico methodologies for predictive evaluation of toxicity based on integration of databases

Chihae Yang1 and Ann M. Richard2, 1LeadScope, Inc. 1245 Kinnear Rd. Columbus, OH. 43212 2National Health & Environmental Effects Research Lab, U.S. EPA, Research Triangle Park, ...

Integrative medicine for managing the symptoms of lupus nephritis: A protocol for systematic review and meta-analysis.

PubMed

Choi, Tae-Young; Jun, Ji Hee; Lee, Myeong Soo

2018-03-01

Integrative medicine is claimed to improve symptoms of lupus nephritis. No systematic reviews have been performed for the application of integrative medicine for lupus nephritis on patients with systemic lupus erythematosus (SLE). Thus, this review will aim to evaluate the current evidence on the efficacy of integrative medicine for the management of lupus nephritis in patients with SLE. The following electronic databases will be searched for studies published from their dates of inception February 2018: Medline, EMBASE and the Cochrane Central Register of Controlled Trials (CENTRAL), as well as 6 Korean medical databases (Korea Med, the Oriental Medicine Advanced Search Integrated System [OASIS], DBpia, the Korean Medical Database [KM base], the Research Information Service System [RISS], and the Korean Studies Information Services System [KISS]), and 1 Chinese medical database (the China National Knowledge Infrastructure [CNKI]). Study selection, data extraction, and assessment will be performed independently by 2 researchers. The risk of bias (ROB) will be assessed using the Cochrane ROB tool. This systematic review will be published in a peer-reviewed journal and disseminated both electronically and in print. The review will be updated to inform and guide healthcare practice and policy. PROSPERO 2018 CRD42018085205.

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

[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.

Discrete Event Simulation-Based Resource Modelling in Health Technology Assessment.

PubMed

Salleh, Syed; Thokala, Praveen; Brennan, Alan; Hughes, Ruby; Dixon, Simon

2017-10-01

The objective of this article was to conduct a systematic review of published research on the use of discrete event simulation (DES) for resource modelling (RM) in health technology assessment (HTA). RM is broadly defined as incorporating and measuring effects of constraints on physical resources (e.g. beds, doctors, nurses) in HTA models. Systematic literature searches were conducted in academic databases (JSTOR, SAGE, SPRINGER, SCOPUS, IEEE, Science Direct, PubMed, EMBASE) and grey literature (Google Scholar, NHS journal library), enhanced by manual searchers (i.e. reference list checking, citation searching and hand-searching techniques). The search strategy yielded 4117 potentially relevant citations. Following the screening and manual searches, ten articles were included. Reviewing these articles provided insights into the applications of RM: firstly, different types of economic analyses, model settings, RM and cost-effectiveness analysis (CEA) outcomes were identified. Secondly, variation in the characteristics of the constraints such as types and nature of constraints and sources of data for the constraints were identified. Thirdly, it was found that including the effects of constraints caused the CEA results to change in these articles. The review found that DES proved to be an effective technique for RM but there were only a small number of studies applied in HTA. However, these studies showed the important consequences of modelling physical constraints and point to the need for a framework to be developed to guide future applications of this approach.

An Algorithm for Interactive Modeling of Space-Transportation Engine Simulations: A Constraint Satisfaction Approach

NASA Technical Reports Server (NTRS)

Mitra, Debasis; Thomas, Ajai; Hemminger, Joseph; Sakowski, Barbara

2001-01-01

In this research we have developed an algorithm for the purpose of constraint processing by utilizing relational algebraic operators. Van Beek and others have investigated in the past this type of constraint processing from within a relational algebraic framework, producing some unique results. Apart from providing new theoretical angles, this approach also gives the opportunity to use the existing efficient implementations of relational database management systems as the underlying data structures for any relevant algorithm. Our algorithm here enhances that framework. The algorithm is quite general in its current form. Weak heuristics (like forward checking) developed within the Constraint-satisfaction problem (CSP) area could be also plugged easily within this algorithm for further enhancements of efficiency. The algorithm as developed here is targeted toward a component-oriented modeling problem that we are currently working on, namely, the problem of interactive modeling for batch-simulation of engineering systems (IMBSES). However, it could be adopted for many other CSP problems as well. The research addresses the algorithm and many aspects of the problem IMBSES that we are currently handling.

Constraint processing in our extensible language for cooperative imaging system

NASA Astrophysics Data System (ADS)

Aoki, Minoru; Murao, Yo; Enomoto, Hajime

1996-02-01

The extensible WELL (Window-based elaboration language) has been developed using the concept of common platform, where both client and server can communicate with each other with support from a communication manager. This extensible language is based on an object oriented design by introducing constraint processing. Any kind of services including imaging in the extensible language is controlled by the constraints. Interactive functions between client and server are extended by introducing agent functions including a request-respond relation. Necessary service integrations are satisfied with some cooperative processes using constraints. Constraints are treated similarly to data, because the system should have flexibilities in the execution of many kinds of services. The similar control process is defined by using intentional logic. There are two kinds of constraints, temporal and modal constraints. Rendering the constraints, the predicate format as the relation between attribute values can be a warrant for entities' validity as data. As an imaging example, a processing procedure of interaction between multiple objects is shown as an image application for the extensible system. This paper describes how the procedure proceeds in the system, and that how the constraints work for generating moving pictures.

Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

PubMed

Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

2015-01-01

Recently, various types of biological data, including genomic sequences, have been rapidly accumulating. To discover biological knowledge from such growing heterogeneous data, a flexible framework for data integration is necessary. Ortholog information is a central resource for interlinking corresponding genes among different organisms, and the Semantic Web provides a key technology for the flexible integration of heterogeneous data. We have constructed an ortholog database using the Semantic Web technology, aiming at the integration of numerous genomic data and various types of biological information. To formalize the structure of the ortholog information in the Semantic Web, we have constructed the Ortholog Ontology (OrthO). While the OrthO is a compact ontology for general use, it is designed to be extended to the description of database-specific concepts. On the basis of OrthO, we described the ortholog information from our Microbial Genome Database for Comparative Analysis (MBGD) in the form of Resource Description Framework (RDF) and made it available through the SPARQL endpoint, which accepts arbitrary queries specified by users. In this framework based on the OrthO, the biological data of different organisms can be integrated using the ortholog information as a hub. Besides, the ortholog information from different data sources can be compared with each other using the OrthO as a shared ontology. Here we show some examples demonstrating that the ortholog information described in RDF can be used to link various biological data such as taxonomy information and Gene Ontology. Thus, the ortholog database using the Semantic Web technology can contribute to biological knowledge discovery through integrative data analysis.

The sense of body ownership relaxes temporal constraints for multisensory integration.

PubMed

Maselli, Antonella; Kilteni, Konstantina; López-Moliner, Joan; Slater, Mel

2016-08-03

Experimental work on body ownership illusions showed how simple multisensory manipulation can generate the illusory experience of an artificial limb as being part of the own-body. This work highlighted how own-body perception relies on a plastic brain representation emerging from multisensory integration. The flexibility of this representation is reflected in the short-term modulations of physiological states and perceptual processing observed during these illusions. Here, we explore the impact of ownership illusions on the temporal dimension of multisensory integration. We show that, during the illusion, the temporal window for integrating touch on the physical body with touch seen on a virtual body representation, increases with respect to integration with visual events seen close but separated from the virtual body. We show that this effect is mediated by the ownership illusion. Crucially, the temporal window for visuotactile integration was positively correlated with participants' scores rating the illusory experience of owning the virtual body and touching the object seen in contact with it. Our results corroborate the recently proposed causal inference mechanism for illusory body ownership. As a novelty, they show that the ensuing illusory causal binding between stimuli from the real and fake body relaxes constraints for the integration of bodily signals.

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

PubMed Central

Liu, Zhi-Ping; Wu, Canglin; Miao, Hongyu; Wu, Hulin

2015-01-01

Transcriptional and post-transcriptional regulation of gene expression is of fundamental importance to numerous biological processes. Nowadays, an increasing amount of gene regulatory relationships have been documented in various databases and literature. However, to more efficiently exploit such knowledge for biomedical research and applications, it is necessary to construct a genome-wide regulatory network database to integrate the information on gene regulatory relationships that are widely scattered in many different places. Therefore, in this work, we build a knowledge-based database, named ‘RegNetwork’, of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among transcription factors (TFs), microRNAs (miRNAs) and target genes from 25 selected databases. Moreover, we also inferred and incorporated potential regulatory relationships based on transcription factor binding site (TFBS) motifs into RegNetwork. As a result, RegNetwork contains a comprehensive set of experimentally observed or predicted transcriptional and post-transcriptional regulatory relationships, and the database framework is flexibly designed for potential extensions to include gene regulatory networks for other organisms in the future. Based on RegNetwork, we characterized the statistical and topological properties of genome-wide regulatory networks for human and mouse, we also extracted and interpreted simple yet important network motifs that involve the interplays between TF-miRNA and their targets. In summary, RegNetwork provides an integrated resource on the prior information for gene regulatory relationships, and it enables us to further investigate context-specific transcriptional and post-transcriptional regulatory interactions based on domain-specific experimental data. Database URL: http://www.regnetworkweb.org PMID:26424082

iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation.

PubMed

Komaki, Shohei; Shiwa, Yuh; Furukawa, Ryohei; Hachiya, Tsuyoshi; Ohmomo, Hideki; Otomo, Ryo; Satoh, Mamoru; Hitomi, Jiro; Sobue, Kenji; Sasaki, Makoto; Shimizu, Atsushi

2018-01-01

We launched an integrative multi-omics database, iMETHYL (http://imethyl.iwate-megabank.org). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14 000 genes) data for CD4 + T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database.

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

USDA-ARS?s Scientific Manuscript database

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

Nonplanar on-shell diagrams and leading singularities of scattering amplitudes

NASA Astrophysics Data System (ADS)

Chen, Baoyi; Chen, Gang; Cheung, Yeuk-Kwan E.; Li, Yunxuan; Xie, Ruofei; Xin, Yuan

2017-02-01

Bipartite on-shell diagrams are the latest tool in constructing scattering amplitudes. In this paper we prove that a Britto-Cachazo-Feng-Witten (BCFW) decomposable on-shell diagram process a rational top form if and only if the algebraic ideal comprised the geometrical constraints are shifted linearly during successive BCFW integrations. With a proper geometric interpretation of the constraints in the Grassmannian manifold, the rational top form integration contours can thus be obtained, and understood, in a straightforward way. All rational top form integrands of arbitrary higher loops leading singularities can therefore be derived recursively, as long as the corresponding on-shell diagram is BCFW decomposable.

The capability and constraint model of recoverability: An integrated theory of continuity planning.

PubMed

Lindstedt, David

2017-01-01

While there are best practices, good practices, regulations and standards for continuity planning, there is no single model to collate and sort their various recommended activities. To address this deficit, this paper presents the capability and constraint model of recoverability - a new model to provide an integrated foundation for business continuity planning. The model is non-linear in both construct and practice, thus allowing practitioners to remain adaptive in its application. The paper presents each facet of the model, outlines the model's use in both theory and practice, suggests a subsequent approach that arises from the model, and discusses some possible ramifications to the industry.

Relationship mapping

NASA Astrophysics Data System (ADS)

Benachenhou, D.

2009-04-01

Information-technology departments in large enterprises spend 40% of budget on information integration-combining information from different data sources into a coherent form. IDC, a market-intelligence firm, estimates that the market for data integration and access software (which includes the key enabling technology for information integration) was about 2.5 billion in 2007, and is expected to grow to 3.8 billion in 2012. This is only the cost estimate for structured or traditional database information integration. Just imagine the market for transforming text into structured information and subsequent fusion with traditional databases.

Integrated Analytic and Linearized Inverse Kinematics for Precise Full Body Interactions

NASA Astrophysics Data System (ADS)

Boulic, Ronan; Raunhardt, Daniel

Despite the large success of games grounded on movement-based interactions the current state of full body motion capture technologies still prevents the exploitation of precise interactions with complex environments. This paper focuses on ensuring a precise spatial correspondence between the user and the avatar. We build upon our past effort in human postural control with a Prioritized Inverse Kinematics framework. One of its key advantage is to ease the dynamic combination of postural and collision avoidance constraints. However its reliance on a linearized approximation of the problem makes it vulnerable to the well-known full extension singularity of the limbs. In such context the tracking performance is reduced and/or less believable intermediate postural solutions are produced. We address this issue by introducing a new type of analytic constraint that smoothly integrates within the prioritized Inverse Kinematics framework. The paper first recalls the background of full body 3D interactions and the advantages and drawbacks of the linearized IK solution. Then the Flexion-EXTension constraint (FLEXT in short) is introduced for the partial position control of limb-like articulated structures. Comparative results illustrate the interest of this new type of integrated analytical and linearized IK control.

Advances in the integration of transcriptional regulatory information into genome-scale metabolic models.

PubMed

Vivek-Ananth, R P; Samal, Areejit

2016-09-01

A major goal of systems biology is to build predictive computational models of cellular metabolism. Availability of complete genome sequences and wealth of legacy biochemical information has led to the reconstruction of genome-scale metabolic networks in the last 15 years for several organisms across the three domains of life. Due to paucity of information on kinetic parameters associated with metabolic reactions, the constraint-based modelling approach, flux balance analysis (FBA), has proved to be a vital alternative to investigate the capabilities of reconstructed metabolic networks. In parallel, advent of high-throughput technologies has led to the generation of massive amounts of omics data on transcriptional regulation comprising mRNA transcript levels and genome-wide binding profile of transcriptional regulators. A frontier area in metabolic systems biology has been the development of methods to integrate the available transcriptional regulatory information into constraint-based models of reconstructed metabolic networks in order to increase the predictive capabilities of computational models and understand the regulation of cellular metabolism. Here, we review the existing methods to integrate transcriptional regulatory information into constraint-based models of metabolic networks. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Integrated Attitude Control Strategy for the Asteroid Redirect Mission

NASA Technical Reports Server (NTRS)

Lopez, Pedro, Jr.; Price, Hoppy; San Martin, Miguel

2014-01-01

A deep-space mission has been proposed to redirect an asteroid to a distant retrograde orbit around the moon using a robotic vehicle, the Asteroid Redirect Vehicle (ARV). In this orbit, astronauts will rendezvous with the ARV using the Orion spacecraft. The integrated attitude control concept that Orion will use for approach and docking and for mated operations will be described. Details of the ARV's attitude control system and its associated constraints for redirecting the asteroid to the distant retrograde orbit around the moon will be provided. Once Orion is docked to the ARV, an overall description of the mated stack attitude during all phases of the mission will be presented using a coordinate system that was developed for this mission. Next, the thermal and power constraints of both the ARV and Orion will be discussed as well as how they are used to define the optimal integrated stack attitude. Lastly, the lighting and communications constraints necessary for the crew's extravehicular activity planned to retrieve samples from the asteroid will be examined. Similarly, the joint attitude control strategy that employs both the Orion and the ARV attitude control assets prior, during, and after each extravehicular activity will also be thoroughly discussed.

VIGOR: Interactive Visual Exploration of Graph Query Results.

PubMed

Pienta, Robert; Hohman, Fred; Endert, Alex; Tamersoy, Acar; Roundy, Kevin; Gates, Chris; Navathe, Shamkant; Chau, Duen Horng

2018-01-01

Finding patterns in graphs has become a vital challenge in many domains from biological systems, network security, to finance (e.g., finding money laundering rings of bankers and business owners). While there is significant interest in graph databases and querying techniques, less research has focused on helping analysts make sense of underlying patterns within a group of subgraph results. Visualizing graph query results is challenging, requiring effective summarization of a large number of subgraphs, each having potentially shared node-values, rich node features, and flexible structure across queries. We present VIGOR, a novel interactive visual analytics system, for exploring and making sense of query results. VIGOR uses multiple coordinated views, leveraging different data representations and organizations to streamline analysts sensemaking process. VIGOR contributes: (1) an exemplar-based interaction technique, where an analyst starts with a specific result and relaxes constraints to find other similar results or starts with only the structure (i.e., without node value constraints), and adds constraints to narrow in on specific results; and (2) a novel feature-aware subgraph result summarization. Through a collaboration with Symantec, we demonstrate how VIGOR helps tackle real-world problems through the discovery of security blindspots in a cybersecurity dataset with over 11,000 incidents. We also evaluate VIGOR with a within-subjects study, demonstrating VIGOR's ease of use over a leading graph database management system, and its ability to help analysts understand their results at higher speed and make fewer errors.

Integration deficiencies associated with continuous limb movement sequences in Parkinson's disease.

PubMed

Park, Jin-Hoon; Stelmach, George E

2009-11-01

The present study examined the extent to which Parkinson's disease (PD) influences integration of continuous limb movement sequences. Eight patients with idiopathic PD and 8 age-matched normal subjects were instructed to perform repetitive sequential aiming movements to specified targets under three-accuracy constraints: 1) low accuracy (W = 7 cm) - minimal accuracy constraint, 2) high accuracy (W = 0.64 cm) - maximum accuracy constraint, and 3) mixed accuracy constraint - one target of high accuracy and another target of low accuracy. The characteristic of sequential movements in the low accuracy condition was mostly cyclical, whereas in the high accuracy condition it was discrete in both groups. When the accuracy constraint was mixed, the sequential movements were executed by assembling discrete and cyclical movements in both groups, suggesting that for PD patients the capability to combine discrete and cyclical movements to meet a task requirement appears to be intact. However, such functional linkage was not as pronounced as was in normal subjects. Close examination of movement from the mixed accuracy condition revealed marked movement hesitations in the vicinity of the large target in PD patients, resulting in a bias toward discrete movement. These results suggest that PD patients may have deficits in ongoing planning and organizing processes during movement execution when the tasks require to assemble various accuracy requirements into more complex movement sequences.

Genetic constraints predict evolutionary divergence in Dalechampia blossoms

PubMed Central

Bolstad, Geir H.; Hansen, Thomas F.; Pélabon, Christophe; Falahati-Anbaran, Mohsen; Pérez-Barrales, Rocío; Armbruster, W. Scott

2014-01-01

If genetic constraints are important, then rates and direction of evolution should be related to trait evolvability. Here we use recently developed measures of evolvability to test the genetic constraint hypothesis with quantitative genetic data on floral morphology from the Neotropical vine Dalechampia scandens (Euphorbiaceae). These measures were compared against rates of evolution and patterns of divergence among 24 populations in two species in the D. scandens species complex. We found clear evidence for genetic constraints, particularly among traits that were tightly phenotypically integrated. This relationship between evolvability and evolutionary divergence is puzzling, because the estimated evolvabilities seem too large to constitute real constraints. We suggest that this paradox can be explained by a combination of weak stabilizing selection around moving adaptive optima and small realized evolvabilities relative to the observed additive genetic variance. PMID:25002700

Impulse and constraint: perspectives from personality psychology, convergence with theory in other areas, and potential for integration.

PubMed

Carver, Charles S

2005-01-01

A behavioral dimension of impulse versus constraint has long been observed by personality psychologists. This article begins by reviewing processes underlying this dimension from the perspectives of several personality theories. Some cases of constraint reflect inhibition due to anxiety, but some theories suggest other roots for constraint. Theories from developmental psychology accommodate both possibilities by positing 2 sorts of control over action. These modes of influence strongly resemble those predicated in some personality theories and also 2 modes of function that are asserted by some cognitive and social psychological theories. Several further literatures are considered, to which 2-mode models seem to contribute meaningfully. The article closes by addressing questions raised by these ideas, including whether the issue of impulse versus constraint applies to avoidance as well as to approach.

Integrating forensic information in a crime intelligence database.

PubMed

Rossy, Quentin; Ioset, Sylvain; Dessimoz, Damien; Ribaux, Olivier

2013-07-10

Since 2008, intelligence units of six states of the western part of Switzerland have been sharing a common database for the analysis of high volume crimes. On a daily basis, events reported to the police are analysed, filtered and classified to detect crime repetitions and interpret the crime environment. Several forensic outcomes are integrated in the system such as matches of traces with persons, and links between scenes detected by the comparison of forensic case data. Systematic procedures have been settled to integrate links assumed mainly through DNA profiles, shoemarks patterns and images. A statistical outlook on a retrospective dataset of series from 2009 to 2011 of the database informs for instance on the number of repetition detected or confirmed and increased by forensic case data. Time needed to obtain forensic intelligence in regard with the type of marks treated, is seen as a critical issue. Furthermore, the underlying integration process of forensic intelligence into the crime intelligence database raised several difficulties in regards of the acquisition of data and the models used in the forensic databases. Solutions found and adopted operational procedures are described and discussed. This process form the basis to many other researches aimed at developing forensic intelligence models. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

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

Lessons learned while building the Deepwater Horizon Database: Toward improved data sharing in coastal science

NASA Astrophysics Data System (ADS)

Thessen, Anne E.; McGinnis, Sean; North, Elizabeth W.

2016-02-01

Process studies and coupled-model validation efforts in geosciences often require integration of multiple data types across time and space. For example, improved prediction of hydrocarbon fate and transport is an important societal need which fundamentally relies upon synthesis of oceanography and hydrocarbon chemistry. Yet, there are no publically accessible databases which integrate these diverse data types in a georeferenced format, nor are there guidelines for developing such a database. The objective of this research was to analyze the process of building one such database to provide baseline information on data sources and data sharing and to document the challenges and solutions that arose during this major undertaking. The resulting Deepwater Horizon Database was approximately 2.4 GB in size and contained over 8 million georeferenced data points collected from industry, government databases, volunteer networks, and individual researchers. The major technical challenges that were overcome were reconciliation of terms, units, and quality flags which were necessary to effectively integrate the disparate data sets. Assembling this database required the development of relationships with individual researchers and data managers which often involved extensive e-mail contacts. The average number of emails exchanged per data set was 7.8. Of the 95 relevant data sets that were discovered, 38 (40%) were obtained, either in whole or in part. Over one third (36%) of the requests for data went unanswered. The majority of responses were received after the first request (64%) and within the first week of the first request (67%). Although fewer than half of the potentially relevant datasets were incorporated into the database, the level of sharing (40%) was high compared to some other disciplines where sharing can be as low as 10%. Our suggestions for building integrated databases include budgeting significant time for e-mail exchanges, being cognizant of the cost versus benefits of pursuing reticent data providers, and building trust through clear, respectful communication and with flexible and appropriate attributions.

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

NASA Technical Reports Server (NTRS)

Kulkarni, Deepak; Marietta, Roberta

1998-01-01

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

The Relationship between Treatment Integrity and Acceptability of Reading Interventions for Children with Attention-Deficit/Hyperactivity Disorder

ERIC Educational Resources Information Center

Mautone, Jennifer A.; DuPaul, George J.; Jitendra, Asha K.; Tresco, Katy E.; Junod, Rosemary Vile; Volpe, Robert J.

2009-01-01

This study examined the relationship between treatment integrity and acceptability for reading interventions across two consultation models, intensive data-based academic intervention (IDAI) and traditional data-based academic intervention (TDAI). Participants included 83 first- through fourth-grade students who met research criteria for…

The Problem with the Delta Cost Project Database

ERIC Educational Resources Information Center

Jaquette, Ozan; Parra, Edna

2016-01-01

The Integrated Postsecondary Education System (IPEDS) collects data on Title IV institutions. The Delta Cost Project (DCP) integrated data from multiple IPEDS survey components into a public-use longitudinal dataset. The DCP Database was the basis for dozens of journal articles and a series of influential policy reports. Unfortunately, a flaw in…

Integrated remote sensing and visualization (IRSV) system for transportation infrastructure operations and management, phase two, volume 4 : web-based bridge information database--visualization analytics and distributed sensing.

DOT National Transportation Integrated Search

2012-03-01

This report introduces the design and implementation of a Web-based bridge information visual analytics system. This : project integrates Internet, multiple databases, remote sensing, and other visualization technologies. The result : combines a GIS ...

Service Management Database for DSN Equipment

NASA Technical Reports Server (NTRS)

Zendejas, Silvino; Bui, Tung; Bui, Bach; Malhotra, Shantanu; Chen, Fannie; Wolgast, Paul; Allen, Christopher; Luong, Ivy; Chang, George; Sadaqathulla, Syed

2009-01-01

This data- and event-driven persistent storage system leverages the use of commercial software provided by Oracle for portability, ease of maintenance, scalability, and ease of integration with embedded, client-server, and multi-tiered applications. In this role, the Service Management Database (SMDB) is a key component of the overall end-to-end process involved in the scheduling, preparation, and configuration of the Deep Space Network (DSN) equipment needed to perform the various telecommunication services the DSN provides to its customers worldwide. SMDB makes efficient use of triggers, stored procedures, queuing functions, e-mail capabilities, data management, and Java integration features provided by the Oracle relational database management system. SMDB uses a third normal form schema design that allows for simple data maintenance procedures and thin layers of integration with client applications. The software provides an integrated event logging system with ability to publish events to a JMS messaging system for synchronous and asynchronous delivery to subscribed applications. It provides a structured classification of events and application-level messages stored in database tables that are accessible by monitoring applications for real-time monitoring or for troubleshooting and analysis over historical archives.

Integrating Sociological Practice into Traditional Sociology Courses.

ERIC Educational Resources Information Center

Basirico, Laurence A.

1990-01-01

Outlines a model of instruction that uses Marvin Olsen's reconceptualization of sociology as "sociological practice" to integrate sociological practice into traditional courses. States that this approach helps students gain a critical perspective and overcome personal and cultural ideological constraints in dealing with real issues…

Atlas - a data warehouse for integrative bioinformatics.

PubMed

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire M S; Ling, John; Ouellette, B F Francis

2005-02-21

We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: http://bioinformatics.ubc.ca/atlas/

Atlas – a data warehouse for integrative bioinformatics

PubMed Central

Shah, Sohrab P; Huang, Yong; Xu, Tao; Yuen, Macaire MS; Ling, John; Ouellette, BF Francis

2005-01-01

Background We present a biological data warehouse called Atlas that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. The goal of the system is to provide data, as well as a software infrastructure for bioinformatics research and development. Description The Atlas system is based on relational data models that we developed for each of the source data types. Data stored within these relational models are managed through Structured Query Language (SQL) calls that are implemented in a set of Application Programming Interfaces (APIs). The APIs include three languages: C++, Java, and Perl. The methods in these API libraries are used to construct a set of loader applications, which parse and load the source datasets into the Atlas database, and a set of toolbox applications which facilitate data retrieval. Atlas stores and integrates local instances of GenBank, RefSeq, UniProt, Human Protein Reference Database (HPRD), Biomolecular Interaction Network Database (BIND), Database of Interacting Proteins (DIP), Molecular Interactions Database (MINT), IntAct, NCBI Taxonomy, Gene Ontology (GO), Online Mendelian Inheritance in Man (OMIM), LocusLink, Entrez Gene and HomoloGene. The retrieval APIs and toolbox applications are critical components that offer end-users flexible, easy, integrated access to this data. We present use cases that use Atlas to integrate these sources for genome annotation, inference of molecular interactions across species, and gene-disease associations. Conclusion The Atlas biological data warehouse serves as data infrastructure for bioinformatics research and development. It forms the backbone of the research activities in our laboratory and facilitates the integration of disparate, heterogeneous biological sources of data enabling new scientific inferences. Atlas achieves integration of diverse data sets at two levels. First, Atlas stores data of similar types using common data models, enforcing the relationships between data types. Second, integration is achieved through a combination of APIs, ontology, and tools. The Atlas software is freely available under the GNU General Public License at: PMID:15723693

TIGER/Line Shapefile, 2010, 2010 Census Block State-based

EPA Pesticide Factsheets

The TIGER/Line Files are shapefiles and related database files (.dbf) that are an extract of selected geographic and cartographic information from the U.S. Census Bureau's Master Address File / Topologically Integrated Geographic Encoding and Referencing (MAF/TIGER) Database (MTDB). The MTDB represents a seamless national file with no overlaps or gaps between parts, however, each TIGER/Line File is designed to stand alone as an independent data set, or they can be combined to cover the entire nation. Census Blocks are statistical areas bounded on all sides by visible features, such as streets, roads, streams, and railroad tracks, and/or by nonvisible boundaries such as city, town, township, and county limits, and short line-of-sight extensions of streets and roads. Census blocks are relatively small in area; for example, a block in a city bounded by streets. However, census blocks in remote areas are often large and irregular and may even be many square miles in area. A common misunderstanding is that data users think census blocks are used geographically to build all other census geographic areas, rather all other census geographic areas are updated and then used as the primary constraints, along with roads and water features, to delineate the tabulation blocks. As a result, all 2010 Census blocks nest within every other 2010 Census geographic area, so that Census Bureau statistical data can be tabulated at the block level and aggregated up to the appropr

The NASA NEESPI Data Portal: Products, Information, and Services

NASA Technical Reports Server (NTRS)

Shen, Suhung; Leptoukh, Gregory; Loboda, Tatiana; Csiszar, Ivan; Romanov, Peter; Gerasimov, Irina

2008-01-01

Studies have indicated that land cover and use changes in Northern Eurasia influence global climate system. However, the procedures are not fully understood and it is challenging to understand the interactions between the land changes in this region and the global climate. Having integrated data collections form multiple disciplines are important for studies of climate and environmental changes. Remote sensed and model data are particularly important die to sparse in situ measurements in many Eurasia regions especially in Siberia. The NASA GES DISC (Goddard Earth Sciences Data and Information Services Center) NEESPI data portal has generated infrastructure to provide satellite remote sensing and numerical model data for atmospheric, land surface, and cryosphere. Data searching, subsetting, and downloading functions are available. ONe useful tool is the Web-based online data analysis and visualization system, Giovanni (Goddard Interactive Online Visualization ANd aNalysis Infrastructure), which allows scientists to assess easily the state and dynamics of terrestrial ecosystems in Northern Eurasia and their interactions with global climate system. Recently, we have created a metadata database prototype to expand the NASA NEESPI data portal for providing a venue for NEESPI scientists fo find the desired data easily and leveraging data sharing within NEESPI projects. The database provides product level information. The desired data can be found through navigation and free text search and narrowed down by filtering with a number of constraints. In addition, we have developed a Web Map Service (WMS) prototype to allow access data and images from difference data resources.

New insights on entrainment and condensation in volcanic plumes: Constraints from independent observations of explosive eruptions and implications for assessing their impacts

NASA Astrophysics Data System (ADS)

Aubry, Thomas J.; Jellinek, A. Mark

2018-05-01

The turbulent entrainment of atmosphere and the condensation of water vapor govern the heights of explosive volcanic plumes. These processes thus determine the delivery and the lifetime of volcanic ash and aerosols into the atmosphere. Predictions of plume heights using one-dimensional "integral" models of volcanic plumes, however, suffer from very large uncertainties, related to parameterizations for entrainment and condensation. In particular, the wind entrainment coefficient β, which governs the contribution of crosswinds to turbulent entrainment, is subject to uncertainties of one order of magnitude, leading to relative uncertainties of the order of 50% on plume height. In this study, we use a database of 94 eruptive phases with independent estimates of mass eruption rate and plume height to constrain and evaluate four popular 1D models. We employ re-sampling methods to account for observational uncertainties. We show that plume height predictions are significantly improved when: i) the contribution of water vapor condensation to the plume buoyancy flux is excluded; and ii) the wind entrainment coefficient β is held constant between 0.1 and 0.4. We explore implications of these results for predicting the climate impacts of explosive eruptions and the likelihood that eruptions will form stable umbrella clouds or devastating pyroclastic flows. Last, we discuss the sensitivity of our results to the definition of plume height in the model in light of a recent set of laboratory experiments and draw conclusions for improving future databases of eruption parameters.

Integral approximations to classical diffusion and smoothed particle hydrodynamics

DOE PAGES

Du, Qiang; Lehoucq, R. B.; Tartakovsky, A. M.

2014-12-31

The contribution of the paper is the approximation of a classical diffusion operator by an integral equation with a volume constraint. A particular focus is on classical diffusion problems associated with Neumann boundary conditions. By exploiting this approximation, we can also approximate other quantities such as the flux out of a domain. Our analysis of the model equation on the continuum level is closely related to the recent work on nonlocal diffusion and peridynamic mechanics. In particular, we elucidate the role of a volumetric constraint as an approximation to a classical Neumann boundary condition in the presence of physical boundary.more » The volume-constrained integral equation then provides the basis for accurate and robust discretization methods. As a result, an immediate application is to the understanding and improvement of the Smoothed Particle Hydrodynamics (SPH) method.« less

Feasibility and acceptability of delivering adolescent health interventions alongside HPV vaccination in Tanzania.

PubMed

Watson-Jones, Deborah; Lees, Shelley; Mwanga, Joseph; Neke, Nyasule; Changalucha, John; Broutet, Nathalie; Maduhu, Ibrahim; Kapiga, Saidi; Chandra-Mouli, Venkatraman; Bloem, Paul; Ross, David A

2016-07-01

Human papillomavirus (HPV) vaccination offers an opportunity to strengthen provision of adolescent health interventions (AHI). We explored the feasibility of integrating other AHI with HPV vaccination in Tanzania. A desk review of 39 policy documents was preceded by a stakeholder meeting with 38 policy makers and partners. Eighteen key informant interviews (KIIs) with health and education policy makers and district officials were conducted to further explore perceptions of current programs, priorities and AHI that might be suitable for integration with HPV vaccination. Fourteen school health interventions (SHI) or AHI are currently being implemented by the Government of Tanzania. Most are delivered as vertical programmes. Coverage of current programs is not universal, and is limited by financial, human resource and logistic constraints. Limited community engagement, rumours, and lack of strategic advocacy has affected uptake of some interventions, e.g. tetanus toxoid (TT) immunization. Stakeholder and KI perceptions and opinions were limited by a lack of experience with integrated delivery and AHI that were outside an individual's area of expertise and experience. Deworming and educational sessions including reproductive health education were the most frequently mentioned interventions that respondents considered suitable for integrated delivery with HPV vaccine. Given programme constraints, limited experience with integrated delivery and concern about real or perceived side-effects being attributed to the vaccine, it will be very important to pilot-test integration of AHI/SHI with HPV vaccination. Selected interventions will need to be simple and quick to deliver since health workers are likely to face significant logistic and time constraints during vaccination visits. © The Author 2016. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.

MIPS PlantsDB: a database framework for comparative plant genome research.

PubMed

Nussbaumer, Thomas; Martis, Mihaela M; Roessner, Stephan K; Pfeifer, Matthias; Bader, Kai C; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB-plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834-D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB.

MIPS PlantsDB: a database framework for comparative plant genome research

PubMed Central

Nussbaumer, Thomas; Martis, Mihaela M.; Roessner, Stephan K.; Pfeifer, Matthias; Bader, Kai C.; Sharma, Sapna; Gundlach, Heidrun; Spannagl, Manuel

2013-01-01

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.helmholtz-muenchen.de/plant/genomes.jsp) was initially described in NAR in 2007 [Spannagl,M., Noubibou,O., Haase,D., Yang,L., Gundlach,H., Hindemitt, T., Klee,K., Haberer,G., Schoof,H. and Mayer,K.F. (2007) MIPSPlantsDB–plant database resource for integrative and comparative plant genome research. Nucleic Acids Res., 35, D834–D840] and was set up from the start to provide data and information resources for individual plant species as well as a framework for integrative and comparative plant genome research. PlantsDB comprises database instances for tomato, Medicago, Arabidopsis, Brachypodium, Sorghum, maize, rice, barley and wheat. Building up on that, state-of-the-art comparative genomics tools such as CrowsNest are integrated to visualize and investigate syntenic relationships between monocot genomes. Results from novel genome analysis strategies targeting the complex and repetitive genomes of triticeae species (wheat and barley) are provided and cross-linked with model species. The MIPS Repeat Element Database (mips-REdat) and Catalog (mips-REcat) as well as tight connections to other databases, e.g. via web services, are further important components of PlantsDB. PMID:23203886

Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow.

PubMed

Stockton, David B; Santamaria, Fidel

2017-10-01

We developed software tools to download, extract features, and organize the Cell Types Database from the Allen Brain Institute (ABI) in order to integrate its whole cell patch clamp characterization data into the automated modeling/data analysis cycle. To expand the potential user base we employed both Python and MATLAB. The basic set of tools downloads selected raw data and extracts cell, sweep, and spike features, using ABI's feature extraction code. To facilitate data manipulation we added a tool to build a local specialized database of raw data plus extracted features. Finally, to maximize automation, we extended our NeuroManager workflow automation suite to include these tools plus a separate investigation database. The extended suite allows the user to integrate ABI experimental and modeling data into an automated workflow deployed on heterogeneous computer infrastructures, from local servers, to high performance computing environments, to the cloud. Since our approach is focused on workflow procedures our tools can be modified to interact with the increasing number of neuroscience databases being developed to cover all scales and properties of the nervous system.

Plug-in Plan Tool v3.0.3.1

NASA Technical Reports Server (NTRS)

Andrea-Liner, Kathleen E.; Au, Brion J.; Fisher, Blake R.; Rodbumrung, Watchara; Hamic, Jeffrey C.; Smith, Kary; Beadle, David S.

2012-01-01

The role of PLUTO (Plug-in Port UTilization Officer) and the growth of the International Space Station (ISS) have exceeded the capabilities of the current tool PiP (Plug-in Plan). Its users (crew and flight controllers) have expressed an interest in a new, easy-to-use tool with a higher level of interactivity and functionality that is not bound by the limitations of Excel. The PiP Tool assists crewmembers and ground controllers in making real-time decisions concerning the safety and compatibility of hardware plugged into the UOPs (Utility Outlet Panels) onboard the ISS. The PiP Tool also provides a reference to the current configuration of the hardware plugged in to the UOPs, and enables the PLUTO and crew to test Plug-in locations for constraint violations (such as cable connector mismatches or amp limit violations), to see the amps and volts for an end item, to see whether or not the end item uses 1553 data, and the cable length between the outlet and the end item. As new equipment is flown or returned, the database can be updated appropriately as needed. The current tool is a macroheavy Excel spreadsheet with its own database and reporting functionality. The new tool captures the capabilities of the original tool, ports them to new software, defines a new dataset, and compensates for ever-growing unique constraints associated with the Plug-in Plan. New constraints were designed into the tool, and updates to existing constraints were added to provide more flexibility and customizability. In addition, there is an option to associate a "Flag" with each device that will let the user know there is a unique constraint associated with it when they use it. This helps improve the safety and efficiency of real-time calls by limiting the amount of "corporate knowledge" overhead that has to be trained and learned through use. The tool helps save time by automating previous manual processes, such as calculating connector types and deciding which cables are required and in what order.

Hard and Soft Constraints in Reliability-Based Design Optimization

NASA Technical Reports Server (NTRS)

Crespo, L.uis G.; Giesy, Daniel P.; Kenny, Sean P.

2006-01-01

This paper proposes a framework for the analysis and design optimization of models subject to parametric uncertainty where design requirements in the form of inequality constraints are present. Emphasis is given to uncertainty models prescribed by norm bounded perturbations from a nominal parameter value and by sets of componentwise bounded uncertain variables. These models, which often arise in engineering problems, allow for a sharp mathematical manipulation. Constraints can be implemented in the hard sense, i.e., constraints must be satisfied for all parameter realizations in the uncertainty model, and in the soft sense, i.e., constraints can be violated by some realizations of the uncertain parameter. In regard to hard constraints, this methodology allows (i) to determine if a hard constraint can be satisfied for a given uncertainty model and constraint structure, (ii) to generate conclusive, formally verifiable reliability assessments that allow for unprejudiced comparisons of competing design alternatives and (iii) to identify the critical combination of uncertain parameters leading to constraint violations. In regard to soft constraints, the methodology allows the designer (i) to use probabilistic uncertainty models, (ii) to calculate upper bounds to the probability of constraint violation, and (iii) to efficiently estimate failure probabilities via a hybrid method. This method integrates the upper bounds, for which closed form expressions are derived, along with conditional sampling. In addition, an l(sub infinity) formulation for the efficient manipulation of hyper-rectangular sets is also proposed.

New optimization strategies of pavement maintenance: A case study for national road network in Indonesia using integrated road management system

NASA Astrophysics Data System (ADS)

Hamdi, Hadiwardoyo, Sigit P.; Correia, A. Gomes; Pereira, Paulo

2017-06-01

A road network requires timely maintenance to keep the road surface in good condition onward better services to improve accessibility and mobility. Strategies and maintenance techniques must be chosen in order to maximize road service level through cost-effective interventions. This approach requires an updated database, which the road network in Indonesia is supported by a manual and visual survey, also using NAASRA profiler. Furthermore, in this paper, the deterministic model of deterioration was used. This optimization model uses life cycle cost analysis (LCCA), applied in an integrated manner, using IRI indicator, and allows determining the priority of treatment, type of treatment and its relation to the cost. The purpose of this paper was focussed on the aspects of road maintenance management, i.e., maintenance optimization models for different levels of traffic and various initial of road distress conditions on the national road network in Indonesia. The implementation of Integrated Road Management System (IRMS) can provide a solution to the problem of cost constraints in the maintenance of the national road network. The results from this study found that as the lowest as agency cost, it will affect the increasing of user cost. With the achievement of the target plan scenario Pl000 with initial value IRI 2, it was found that the routine management throughout the year and in early reconstruction and periodic maintenance with a 30 mm thick overlay, will simultaneously provide a higher net benefit value and has the lowest total cost of transportation.

Integrated vector management: a critical strategy for combating vector-borne diseases in South Sudan.

PubMed

Chanda, Emmanuel; Govere, John M; Macdonald, Michael B; Lako, Richard L; Haque, Ubydul; Baba, Samson P; Mnzava, Abraham

2013-10-25

Integrated vector management (IVM) based vector control is encouraged by the World Health Organization (WHO). However, operational experience with the IVM strategy has mostly come from countries with relatively well-established health systems and with malaria control focused programmes. Little is known about deployment of IVM for combating multiple vector-borne diseases in post-emergency settings, where delivery structures are less developed or absent. This manuscript reports on the feasibility of operational IVM for combating vector-borne diseases in South Sudan. A methodical review of published and unpublished documents on vector-borne diseases for South Sudan was conducted via systematic literature search of online electronic databases, Google Scholar, PubMed and WHO, using a combination of search terms. Additional, non-peer reviewed literature was examined for information related to the subject. South Sudan is among the heartlands of vector-borne diseases in the world, characterized by enormous infrastructure, human and financial resource constraints and a weak health system against an increasing number of refugees, returnees and internally displaced people. The presence of a multiplicity of vector-borne diseases in this post-conflict situation presents a unique opportunity to explore the potential of a rational IVM strategy for multiple disease control and optimize limited resource utilization, while maximizing the benefits and providing a model for countries in a similar situation. The potential of integrating vector-borne disease control is enormous in South Sudan. However, strengthened coordination, intersectoral collaboration and institutional and technical capacity for entomological monitoring and evaluation, including enforcement of appropriate legislation are crucial.

Integrated vector management: a critical strategy for combating vector-borne diseases in South Sudan

PubMed Central

2013-01-01

Background Integrated vector management (IVM) based vector control is encouraged by the World Health Organization (WHO). However, operational experience with the IVM strategy has mostly come from countries with relatively well-established health systems and with malaria control focused programmes. Little is known about deployment of IVM for combating multiple vector-borne diseases in post-emergency settings, where delivery structures are less developed or absent. This manuscript reports on the feasibility of operational IVM for combating vector-borne diseases in South Sudan. Case description A methodical review of published and unpublished documents on vector-borne diseases for South Sudan was conducted via systematic literature search of online electronic databases, Google Scholar, PubMed and WHO, using a combination of search terms. Additional, non-peer reviewed literature was examined for information related to the subject. Discussion South Sudan is among the heartlands of vector-borne diseases in the world, characterized by enormous infrastructure, human and financial resource constraints and a weak health system against an increasing number of refugees, returnees and internally displaced people. The presence of a multiplicity of vector-borne diseases in this post-conflict situation presents a unique opportunity to explore the potential of a rational IVM strategy for multiple disease control and optimize limited resource utilization, while maximizing the benefits and providing a model for countries in a similar situation. Conclusion The potential of integrating vector-borne disease control is enormous in South Sudan. However, strengthened coordination, intersectoral collaboration and institutional and technical capacity for entomological monitoring and evaluation, including enforcement of appropriate legislation are crucial. PMID:24156749

Reducing perceived stigma: Work integration of people with severe mental disorders in Italian social enterprise.

PubMed

Villotti, Patrizia; Zaniboni, Sara; Corbière, Marc; Guay, Stéphane; Fraccaroli, Franco

2018-06-01

People with mental illnesses face stigma that hinders their full integration into society. Work is a major determinant of social inclusion, however, people with mental disorders have fewer opportunities to work. Emerging evidence suggests that social enterprises help disadvantaged people with their work integration process. The purpose of this study is to enhance our understanding about how perceptions of stigma can be decreased for people with mental disorders throughout their work experience in a social enterprise. Using a longitudinal study design, 310 individuals with mental disorders employed in Italian social enterprises completed a battery of questionnaires on individual (e.g., severity of symptoms; occupational self-efficacy) and environmental (e.g., social support; organizational constraints) variables. Of the 223 individuals potentially eligible at the 12-month follow up, 139 completed a battery of questionnaires on social and working skills, perceived work productivity and perceived stigma. Path analyses were used to test a model delineating how people with mental disorders working in social enterprises improve social and work outcomes (i.e., motivation, skills and productivity), and reduce the perception of being stigmatized. Working in a social enterprise enhances working social skills, which leads to a perception of higher productivity and, consequently, the perception of being discriminated against and stigmatized is reduced. Social enterprise provides a context in which people with mental disorders reach a sense of work-related and social competence. This sense of competence helps them to reduce perceived stigma, which is a crucial step toward social inclusion. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

The integration of quantitative information with an intelligent decision support system for residential energy retrofits

NASA Astrophysics Data System (ADS)

Mo, Yunjeong

The purpose of this research is to support the development of an intelligent Decision Support System (DSS) by integrating quantitative information with expert knowledge in order to facilitate effective retrofit decision-making. To achieve this goal, the Energy Retrofit Decision Process Framework is analyzed. Expert system shell software, a retrofit measure cost database, and energy simulation software are needed for developing the DSS; Exsys Corvid, the NREM database and BEopt were chosen for implementing an integration model. This integration model demonstrates the holistic function of a residential energy retrofit system for existing homes, by providing a prioritized list of retrofit measures with cost information, energy simulation and expert advice. The users, such as homeowners and energy auditors, can acquire all of the necessary retrofit information from this unified system without having to explore several separate systems. The integration model plays the role of a prototype for the finalized intelligent decision support system. It implements all of the necessary functions for the finalized DSS, including integration of the database, energy simulation and expert knowledge.

Development of SRS.php, a Simple Object Access Protocol-based library for data acquisition from integrated biological databases.

PubMed

Barbosa-Silva, A; Pafilis, E; Ortega, J M; Schneider, R

2007-12-11

Data integration has become an important task for biological database providers. The current model for data exchange among different sources simplifies the manner that distinct information is accessed by users. The evolution of data representation from HTML to XML enabled programs, instead of humans, to interact with biological databases. We present here SRS.php, a PHP library that can interact with the data integration Sequence Retrieval System (SRS). The library has been written using SOAP definitions, and permits the programmatic communication through webservices with the SRS. The interactions are possible by invoking the methods described in WSDL by exchanging XML messages. The current functions available in the library have been built to access specific data stored in any of the 90 different databases (such as UNIPROT, KEGG and GO) using the same query syntax format. The inclusion of the described functions in the source of scripts written in PHP enables them as webservice clients to the SRS server. The functions permit one to query the whole content of any SRS database, to list specific records in these databases, to get specific fields from the records, and to link any record among any pair of linked databases. The case study presented exemplifies the library usage to retrieve information regarding registries of a Plant Defense Mechanisms database. The Plant Defense Mechanisms database is currently being developed, and the proposal of SRS.php library usage is to enable the data acquisition for the further warehousing tasks related to its setup and maintenance.

Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

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

Gaponov, Yu.A.; Igarashi, N.; Hiraki, M.

2004-05-12

An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view,more » create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments.« less

Analysis of effect of internal and operating variables on performance of SVDS constraint model (ABIND)

NASA Technical Reports Server (NTRS)

Pendergrass, J. R.; Walsh, R. L.

1975-01-01

An examination of the factors which modify the simulation of a constraint in the motion of the aft attach points of the orbiter and external tank during separation has been made. The factors considered were both internal (spring and damper constants) and external (friction coefficient and dynamic pressure). The results show that an acceptable choice of spring/damper constant combinations exist over the expected range of the external factors and that the choice is consistent with a practical integration interval. The constraint model is shown to produce about a 10 percent increase in the relative body pitch angles over the unconstrained case whereas the MDC-STL constraint model is shown to produce about a 38 percent increase.

Deep Neural Networks for Speech Separation With Application to Robust Speech Recognition

DTIC Science & Technology

acoustic -phonetic features. The second objective is integration of spectrotemporal context for improved separation performance. Conditional random fields...will be used to encode contextual constraints. The third objective is to achieve robust ASR in the DNN framework through integrated acoustic modeling

Fully integrated aerodynamic/dynamic optimization of helicopter rotor blades

NASA Technical Reports Server (NTRS)

Walsh, Joanne L.; Lamarsh, William J., II; Adelman, Howard M.

1992-01-01

This paper describes a fully integrated aerodynamic/dynamic optimization procedure for helicopter rotor blades. The procedure combines performance and dynamics analyses with a general purpose optimizer. The procedure minimizes a linear combination of power required (in hover, forward flight, and maneuver) and vibratory hub shear. The design variables include pretwist, taper initiation, taper ratio, root chord, blade stiffnesses, tuning masses, and tuning mass locations. Aerodynamic constraints consist of limits on power required in hover, forward flight and maneuver; airfoil section stall; drag divergence Mach number; minimum tip chord; and trim. Dynamic constraints are on frequencies, minimum autorotational inertia, and maximum blade weight. The procedure is demonstrated for two cases. In the first case the objective function involves power required (in hover, forward flight, and maneuver) and dynamics. The second case involves only hover power and dynamics. The designs from the integrated procedure are compared with designs from a sequential optimization approach in which the blade is first optimized for performance and then for dynamics. In both cases, the integrated approach is superior.

Fully integrated aerodynamic/dynamic optimization of helicopter rotor blades

NASA Technical Reports Server (NTRS)

Walsh, Joanne L.; Lamarsh, William J., II; Adelman, Howard M.

1992-01-01

A fully integrated aerodynamic/dynamic optimization procedure is described for helicopter rotor blades. The procedure combines performance and dynamic analyses with a general purpose optimizer. The procedure minimizes a linear combination of power required (in hover, forward flight, and maneuver) and vibratory hub shear. The design variables include pretwist, taper initiation, taper ratio, root chord, blade stiffnesses, tuning masses, and tuning mass locations. Aerodynamic constraints consist of limits on power required in hover, forward flight and maneuvers; airfoil section stall; drag divergence Mach number; minimum tip chord; and trim. Dynamic constraints are on frequencies, minimum autorotational inertia, and maximum blade weight. The procedure is demonstrated for two cases. In the first case, the objective function involves power required (in hover, forward flight and maneuver) and dynamics. The second case involves only hover power and dynamics. The designs from the integrated procedure are compared with designs from a sequential optimization approach in which the blade is first optimized for performance and then for dynamics. In both cases, the integrated approach is superior.

Acceleration constraints in modeling and control of nonholonomic systems

NASA Astrophysics Data System (ADS)

Bajodah, Abdulrahman H.

2003-10-01

Acceleration constraints are used to enhance modeling techniques for dynamical systems. In particular, Kane's equations of motion subjected to bilateral constraints, unilateral constraints, and servo-constraints are modified by utilizing acceleration constraints for the purpose of simplifying the equations and increasing their applicability. The tangential properties of Kane's method provide relationships between the holonomic and the nonholonomic partial velocities, and hence allow one to describe nonholonomic generalized active and inertia forces in terms of their holonomic counterparts, i.e., those which correspond to the system without constraints. Therefore, based on the modeling process objectives, the holonomic and the nonholonomic vector entities in Kane's approach are used interchangeably to model holonomic and nonholonomic systems. When the holonomic partial velocities are used to model nonholonomic systems, the resulting models are full-order (also called nonminimal or unreduced) and separated in accelerations. As a consequence, they are readily integrable and can be used for generic system analysis. Other related topics are constraint forces, numerical stability of the nonminimal equations of motion, and numerical constraint stabilization. Two types of unilateral constraints considered are impulsive and friction constraints. Impulsive constraints are modeled by means of a continuous-in-velocities and impulse-momentum approaches. In controlled motion, the acceleration form of constraints is utilized with the Moore-Penrose generalized inverse of the corresponding constraint matrix to solve for the inverse dynamics of servo-constraints, and for the redundancy resolution of overactuated manipulators. If control variables are involved in the algebraic constraint equations, then these tools are used to modify the controlled equations of motion in order to facilitate control system design. An illustrative example of spacecraft stabilization is presented.

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

PubMed Central

2010-01-01

Background Genome-scale metabolic reconstructions under the Constraint Based Reconstruction and Analysis (COBRA) framework are valuable tools for analyzing the metabolic capabilities of organisms and interpreting experimental data. As the number of such reconstructions and analysis methods increases, there is a greater need for data uniformity and ease of distribution and use. Description We describe BiGG, a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest. Conclusions BiGG addresses a need in the systems biology community to have access to high quality curated metabolic models and reconstructions. It is freely available for academic use at http://bigg.ucsd.edu. PMID:20426874

Lost in search: (Mal-)adaptation to probabilistic decision environments in children and adults.

PubMed

Betsch, Tilmann; Lehmann, Anne; Lindow, Stefanie; Lang, Anna; Schoemann, Martin

2016-02-01

Adaptive decision making in probabilistic environments requires individuals to use probabilities as weights in predecisional information searches and/or when making subsequent choices. Within a child-friendly computerized environment (Mousekids), we tracked 205 children's (105 children 5-6 years of age and 100 children 9-10 years of age) and 103 adults' (age range: 21-22 years) search behaviors and decisions under different probability dispersions (.17; .33, .83 vs. .50, .67, .83) and constraint conditions (instructions to limit search: yes vs. no). All age groups limited their depth of search when instructed to do so and when probability dispersion was high (range: .17-.83). Unlike adults, children failed to use probabilities as weights for their searches, which were largely not systematic. When examining choices, however, elementary school children (unlike preschoolers) systematically used probabilities as weights in their decisions. This suggests that an intuitive understanding of probabilities and the capacity to use them as weights during integration is not a sufficient condition for applying simple selective search strategies that place one's focus on weight distributions. PsycINFO Database Record (c) 2016 APA, all rights reserved.

Knowledge management: An abstraction of knowledge base and database management systems

NASA Technical Reports Server (NTRS)

Riedesel, Joel D.

1990-01-01

Artificial intelligence application requirements demand powerful representation capabilities as well as efficiency for real-time domains. Many tools exist, the most prevalent being expert systems tools such as ART, KEE, OPS5, and CLIPS. Other tools just emerging from the research environment are truth maintenance systems for representing non-monotonic knowledge, constraint systems, object oriented programming, and qualitative reasoning. Unfortunately, as many knowledge engineers have experienced, simply applying a tool to an application requires a large amount of effort to bend the application to fit. Much work goes into supporting work to make the tool integrate effectively. A Knowledge Management Design System (KNOMAD), is described which is a collection of tools built in layers. The layered architecture provides two major benefits; the ability to flexibly apply only those tools that are necessary for an application, and the ability to keep overhead, and thus inefficiency, to a minimum. KNOMAD is designed to manage many knowledge bases in a distributed environment providing maximum flexibility and expressivity to the knowledge engineer while also providing support for efficiency.

Building continental-scale 3D subsurface layers in the Digital Crust project: constrained interpolation and uncertainty estimation.

NASA Astrophysics Data System (ADS)

Yulaeva, E.; Fan, Y.; Moosdorf, N.; Richard, S. M.; Bristol, S.; Peters, S. E.; Zaslavsky, I.; Ingebritsen, S.

2015-12-01

The Digital Crust EarthCube building block creates a framework for integrating disparate 3D/4D information from multiple sources into a comprehensive model of the structure and composition of the Earth's upper crust, and to demonstrate the utility of this model in several research scenarios. One of such scenarios is estimation of various crustal properties related to fluid dynamics (e.g. permeability and porosity) at each node of any arbitrary unstructured 3D grid to support continental-scale numerical models of fluid flow and transport. Starting from Macrostrat, an existing 4D database of 33,903 chronostratigraphic units, and employing GeoDeepDive, a software system for extracting structured information from unstructured documents, we construct 3D gridded fields of sediment/rock porosity, permeability and geochemistry for large sedimentary basins of North America, which will be used to improve our understanding of large-scale fluid flow, chemical weathering rates, and geochemical fluxes into the ocean. In this talk, we discuss the methods, data gaps (particularly in geologically complex terrain), and various physical and geological constraints on interpolation and uncertainty estimation.

Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance

PubMed Central

Squires, R. Burke; Noronha, Jyothi; Hunt, Victoria; García‐Sastre, Adolfo; Macken, Catherine; Baumgarth, Nicole; Suarez, David; Pickett, Brett E.; Zhang, Yun; Larsen, Christopher N.; Ramsey, Alvin; Zhou, Liwei; Zaremba, Sam; Kumar, Sanjeev; Deitrich, Jon; Klem, Edward; Scheuermann, Richard H.

2012-01-01

Please cite this paper as: Squires et al. (2012) Influenza research database: an integrated bioinformatics resource for influenza research and surveillance. Influenza and Other Respiratory Viruses 6(6), 404–416. Background  The recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics. Design  The Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly‐accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user‐friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in‐protected ‘workbench’ spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. Results  To demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross‐protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks. Conclusions  The IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics. PMID:22260278

Enabling heterogenous multi-scale database for emergency service functions through geoinformation technologies

NASA Astrophysics Data System (ADS)

Bhanumurthy, V.; Venugopala Rao, K.; Srinivasa Rao, S.; Ram Mohan Rao, K.; Chandra, P. Satya; Vidhyasagar, J.; Diwakar, P. G.; Dadhwal, V. K.

2014-11-01

Geographical Information Science (GIS) is now graduated from traditional desktop system to Internet system. Internet GIS is emerging as one of the most promising technologies for addressing Emergency Management. Web services with different privileges are playing an important role in dissemination of the emergency services to the decision makers. Spatial database is one of the most important components in the successful implementation of Emergency Management. It contains spatial data in the form of raster, vector, linked with non-spatial information. Comprehensive data is required to handle emergency situation in different phases. These database elements comprise core data, hazard specific data, corresponding attribute data, and live data coming from the remote locations. Core data sets are minimum required data including base, thematic, infrastructure layers to handle disasters. Disaster specific information is required to handle a particular disaster situation like flood, cyclone, forest fire, earth quake, land slide, drought. In addition to this Emergency Management require many types of data with spatial and temporal attributes that should be made available to the key players in the right format at right time. The vector database needs to be complemented with required resolution satellite imagery for visualisation and analysis in disaster management. Therefore, the database is interconnected and comprehensive to meet the requirement of an Emergency Management. This kind of integrated, comprehensive and structured database with appropriate information is required to obtain right information at right time for the right people. However, building spatial database for Emergency Management is a challenging task because of the key issues such as availability of data, sharing policies, compatible geospatial standards, data interoperability etc. Therefore, to facilitate using, sharing, and integrating the spatial data, there is a need to define standards to build emergency database systems. These include aspects such as i) data integration procedures namely standard coding scheme, schema, meta data format, spatial format ii) database organisation mechanism covering data management, catalogues, data models iii) database dissemination through a suitable environment, as a standard service for effective service dissemination. National Database for Emergency Management (NDEM) is such a comprehensive database for addressing disasters in India at the national level. This paper explains standards for integrating, organising the multi-scale and multi-source data with effective emergency response using customized user interfaces for NDEM. It presents standard procedure for building comprehensive emergency information systems for enabling emergency specific functions through geospatial technologies.

Integrative medicine for managing the symptoms of lupus nephritis

PubMed Central

Choi, Tae-Young; Jun, Ji Hee; Lee, Myeong Soo

2018-01-01

Abstract Background: Integrative medicine is claimed to improve symptoms of lupus nephritis. No systematic reviews have been performed for the application of integrative medicine for lupus nephritis on patients with systemic lupus erythematosus (SLE). Thus, this review will aim to evaluate the current evidence on the efficacy of integrative medicine for the management of lupus nephritis in patients with SLE. Methods and analyses: The following electronic databases will be searched for studies published from their dates of inception February 2018: Medline, EMBASE and the Cochrane Central Register of Controlled Trials (CENTRAL), as well as 6 Korean medical databases (Korea Med, the Oriental Medicine Advanced Search Integrated System [OASIS], DBpia, the Korean Medical Database [KM base], the Research Information Service System [RISS], and the Korean Studies Information Services System [KISS]), and 1 Chinese medical database (the China National Knowledge Infrastructure [CNKI]). Study selection, data extraction, and assessment will be performed independently by 2 researchers. The risk of bias (ROB) will be assessed using the Cochrane ROB tool. Dissemination: This systematic review will be published in a peer-reviewed journal and disseminated both electronically and in print. The review will be updated to inform and guide healthcare practice and policy. Trial registration number: PROSPERO 2018 CRD42018085205 PMID:29595669

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

PubMed Central

Nascimento, Leandro Costa; Salazar, Marcela Mendes; Lepikson-Neto, Jorge; Camargo, Eduardo Leal Oliveira; Parreiras, Lucas Salera; Carazzolle, Marcelo Falsarella

2017-01-01

Abstract Tree species of the genus Eucalyptus are the most valuable and widely planted hardwoods in the world. Given the economic importance of Eucalyptus trees, much effort has been made towards the generation of specimens with superior forestry properties that can deliver high-quality feedstocks, customized to the industrýs needs for both cellulosic (paper) and lignocellulosic biomass production. In line with these efforts, large sets of molecular data have been generated by several scientific groups, providing invaluable information that can be applied in the development of improved specimens. In order to fully explore the potential of available datasets, the development of a public database that provides integrated access to genomic and transcriptomic data from Eucalyptus is needed. EUCANEXT is a database that analyses and integrates publicly available Eucalyptus molecular data, such as the E. grandis genome assembly and predicted genes, ESTs from several species and digital gene expression from 26 RNA-Seq libraries. The database has been implemented in a Fedora Linux machine running MySQL and Apache, while Perl CGI was used for the web interfaces. EUCANEXT provides a user-friendly web interface for easy access and analysis of publicly available molecular data from Eucalyptus species. This integrated database allows for complex searches by gene name, keyword or sequence similarity and is publicly accessible at http://www.lge.ibi.unicamp.br/eucalyptusdb. Through EUCANEXT, users can perform complex analysis to identify genes related traits of interest using RNA-Seq libraries and tools for differential expression analysis. Moreover, all the bioinformatics pipeline here described, including the database schema and PERL scripts, are readily available and can be applied to any genomic and transcriptomic project, regardless of the organism. Database URL: http://www.lge.ibi.unicamp.br/eucalyptusdb PMID:29220468

The Mouse Heart Attack Research Tool (mHART) 1.0 Database.

PubMed

DeLeon-Pennell, Kristine Y; Iyer, Rugmani Padmanabhan; Ma, Yonggang; Yabluchanskiy, Andriy; Zamilpa, Rogelio; Chiao, Ying Ann; Cannon, Presley; Cates, Courtney; Flynn, Elizabeth R; Halade, Ganesh V; de Castro Bras, Lisandra E; Lindsey, Merry L

2018-05-18

The generation of Big Data has enabled systems-level dissections into the mechanisms of cardiovascular pathology. Integration of genetic, proteomic, and pathophysiological variables across platforms and laboratories fosters discoveries through multidisciplinary investigations and minimizes unnecessary redundancy in research efforts. The Mouse Heart Attack Research Tool (mHART) consolidates a large dataset of over 10 years of experiments from a single laboratory for cardiovascular investigators to generate novel hypotheses and identify new predictive markers of progressive left ventricular remodeling following myocardial infarction (MI) in mice. We designed the mHART REDCap database using our own data to integrate cardiovascular community participation. We generated physiological, biochemical, cellular, and proteomic outputs from plasma and left ventricles obtained from post-MI and no MI (naïve) control groups. We included both male and female mice ranging in age from 3 to 36 months old. After variable collection, data underwent quality assessment for data curation (e.g. eliminate technical errors, check for completeness, remove duplicates, and define terms). Currently, mHART 1.0 contains >888,000 data points and includes results from >2,100 unique mice. Database performance was tested and an example provided to illustrate database utility. This report explains how the first version of the mHART database was established and provides researchers with a standard framework to aid in the integration of their data into our database or in the development of a similar database.

Columba: an integrated database of proteins, structures, and annotations.

PubMed

Trissl, Silke; Rother, Kristian; Müller, Heiko; Steinke, Thomas; Koch, Ina; Preissner, Robert; Frömmel, Cornelius; Leser, Ulf

2005-03-31

Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annotation. Compiling such sets using current web resources is tedious because the necessary data are spread over many different databases. To facilitate this task, we have created COLUMBA, an integrated database of annotations of protein structures. COLUMBA currently integrates twelve different databases, including PDB, KEGG, Swiss-Prot, CATH, SCOP, the Gene Ontology, and ENZYME. The database can be searched using either keyword search or data source-specific web forms. Users can thus quickly select and download PDB entries that, for instance, participate in a particular pathway, are classified as containing a certain CATH architecture, are annotated as having a certain molecular function in the Gene Ontology, and whose structures have a resolution under a defined threshold. The results of queries are provided in both machine-readable extensible markup language and human-readable format. The structures themselves can be viewed interactively on the web. The COLUMBA database facilitates the creation of protein structure data sets for many structure-based studies. It allows to combine queries on a number of structure-related databases not covered by other projects at present. Thus, information on both many and few protein structures can be used efficiently. The web interface for COLUMBA is available at http://www.columba-db.de.

78 FR 2363 - Notification of Deletion of a System of Records; Automated Trust Funds Database

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-11

... Database AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Notice of deletion of a system... establishing the Automated Trust Funds (ATF) database system of records. The Federal Information Security... Integrity Act of 1982, Public Law 97-255, provided authority for the system. The ATF database has been...

A User's Applications of Imaging Techniques: The University of Maryland Historic Textile Database.

ERIC Educational Resources Information Center

Anderson, Clarita S.

1991-01-01

Describes the incorporation of textile images into the University of Maryland Historic Textile Database by a computer user rather than a computer expert. Selection of a database management system is discussed, and PICTUREPOWER, a system that integrates photographic quality images with text and numeric information in databases, is described. (three…

Integrating Databases with Maps: The Delivery of Cultural Data through TimeMap.

ERIC Educational Resources Information Center

Johnson, Ian

TimeMap is a unique integration of database management, metadata and interactive maps, designed to contextualise and deliver cultural data through maps. TimeMap extends conventional maps with the time dimension, creating and animating maps "on-the-fly"; delivers them as a kiosk application or embedded in Web pages; links flexibly to…

Information integration for a sky survey by data warehousing

NASA Astrophysics Data System (ADS)

Luo, A.; Zhang, Y.; Zhao, Y.

The virtualization service of data system for a sky survey LAMOST is very important for astronomers The service needs to integrate information from data collections catalogs and references and support simple federation of a set of distributed files and associated metadata Data warehousing has been in existence for several years and demonstrated superiority over traditional relational database management systems by providing novel indexing schemes that supported efficient on-line analytical processing OLAP of large databases Now relational database systems such as Oracle etc support the warehouse capability which including extensions to the SQL language to support OLAP operations and a number of metadata management tools have been created The information integration of LAMOST by applying data warehousing is to effectively provide data and knowledge on-line

Missing Modality Transfer Learning via Latent Low-Rank Constraint.

PubMed

Ding, Zhengming; Shao, Ming; Fu, Yun

2015-11-01

Transfer learning is usually exploited to leverage previously well-learned source domain for evaluating the unknown target domain; however, it may fail if no target data are available in the training stage. This problem arises when the data are multi-modal. For example, the target domain is in one modality, while the source domain is in another. To overcome this, we first borrow an auxiliary database with complete modalities, then consider knowledge transfer across databases and across modalities within databases simultaneously in a unified framework. The contributions are threefold: 1) a latent factor is introduced to uncover the underlying structure of the missing modality from the known data; 2) transfer learning in two directions allows the data alignment between both modalities and databases, giving rise to a very promising recovery; and 3) an efficient solution with theoretical guarantees to the proposed latent low-rank transfer learning algorithm. Comprehensive experiments on multi-modal knowledge transfer with missing target modality verify that our method can successfully inherit knowledge from both auxiliary database and source modality, and therefore significantly improve the recognition performance even when test modality is inaccessible in the training stage.

Charting a Path to Location Intelligence for STD Control.

PubMed

Gerber, Todd M; Du, Ping; Armstrong-Brown, Janelle; McNutt, Louise-Anne; Coles, F Bruce

2009-01-01

This article describes the New York State Department of Health's GeoDatabase project, which developed new methods and techniques for designing and building a geocoding and mapping data repository for sexually transmitted disease (STD) control. The GeoDatabase development was supported through the Centers for Disease Control and Prevention's Outcome Assessment through Systems of Integrated Surveillance workgroup. The design and operation of the GeoDatabase relied upon commercial-off-the-shelf tools that other public health programs may also use for disease-control systems. This article provides a blueprint of the structure and software used to build the GeoDatabase and integrate location data from multiple data sources into the everyday activities of STD control programs.

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

Basso, Benjamin; Dixon, Lance J.

We use integrability at weak coupling to compute fishnet diagrams for four-point correlation functions in planar Φ 4 theory. Our results are always multilinear combinations of ladder integrals, which are in turn built out of classical polylogarithms. The Steinmann relations provide a powerful constraint on such linear combinations, which leads to a natural conjecture for any fishnet diagram as the determinant of a matrix of ladder integrals.

A programing system for research and applications in structural optimization

NASA Technical Reports Server (NTRS)

Sobieszczanski-Sobieski, J.; Rogers, J. L., Jr.

1981-01-01

The flexibility necessary for such diverse utilizations is achieved by combining, in a modular manner, a state-of-the-art optimization program, a production level structural analysis program, and user supplied and problem dependent interface programs. Standard utility capabilities in modern computer operating systems are used to integrate these programs. This approach results in flexibility of the optimization procedure organization and versatility in the formulation of constraints and design variables. Features shown in numerical examples include: variability of structural layout and overall shape geometry, static strength and stiffness constraints, local buckling failure, and vibration constraints.

Integrated optimization of nonlinear R/C frames with reliability constraints

NASA Technical Reports Server (NTRS)

Soeiro, Alfredo; Hoit, Marc

1989-01-01

A structural optimization algorithm was researched including global displacements as decision variables. The algorithm was applied to planar reinforced concrete frames with nonlinear material behavior submitted to static loading. The flexural performance of the elements was evaluated as a function of the actual stress-strain diagrams of the materials. Formation of rotational hinges with strain hardening were allowed and the equilibrium constraints were updated accordingly. The adequacy of the frames was guaranteed by imposing as constraints required reliability indices for the members, maximum global displacements for the structure and a maximum system probability of failure.

RNAcentral: an international database of ncRNA sequences

DOE PAGES

Williams, Kelly Porter

2014-10-28

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

Constraints in Implementation of HIV and AIDS Curriculum Integration in Primary Schools in Bungoma County, Kenya

ERIC Educational Resources Information Center

Mbach, Florence; Oboka, Wycliffe; Simiyu, Ruth; Wakhungu, Jacob

2016-01-01

Education was identified as the critical means of achieving behaviour change in and out of the classroom in order to prevent and mitigate the spread of HIV and AIDS among the youth. This study sought to investigate the constraints during HIV and AIDS curriculum implementation, the study was guided by social cognitive approach theories, survey and…

Staggered solution procedures for multibody dynamics simulation

NASA Technical Reports Server (NTRS)

Park, K. C.; Chiou, J. C.; Downer, J. D.

1990-01-01

The numerical solution procedure for multibody dynamics (MBD) systems is termed a staggered MBD solution procedure that solves the generalized coordinates in a separate module from that for the constraint force. This requires a reformulation of the constraint conditions so that the constraint forces can also be integrated in time. A major advantage of such a partitioned solution procedure is that additional analysis capabilities such as active controller and design optimization modules can be easily interfaced without embedding them into a monolithic program. After introducing the basic equations of motion for MBD system in the second section, Section 3 briefly reviews some constraint handling techniques and introduces the staggered stabilized technique for the solution of the constraint forces as independent variables. The numerical direct time integration of the equations of motion is described in Section 4. As accurate damping treatment is important for the dynamics of space structures, we have employed the central difference method and the mid-point form of the trapezoidal rule since they engender no numerical damping. This is in contrast to the current practice in dynamic simulations of ground vehicles by employing a set of backward difference formulas. First, the equations of motion are partitioned according to the translational and the rotational coordinates. This sets the stage for an efficient treatment of the rotational motions via the singularity-free Euler parameters. The resulting partitioned equations of motion are then integrated via a two-stage explicit stabilized algorithm for updating both the translational coordinates and angular velocities. Once the angular velocities are obtained, the angular orientations are updated via the mid-point implicit formula employing the Euler parameters. When the two algorithms, namely, the two-stage explicit algorithm for the generalized coordinates and the implicit staggered procedure for the constraint Lagrange multipliers, are brought together in a staggered manner, they constitute a staggered explicit-implicit procedure which is summarized in Section 5. Section 6 presents some example problems and discussions concerning several salient features of the staggered MBD solution procedure are offered in Section 7.

Towards a Semantically-Enabled Control Strategy for Building Simulations: Integration of Semantic Technologies and Model Predictive Control

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

Delgoshaei, Parastoo; Austin, Mark A.; Pertzborn, Amanda J.

State-of-the-art building simulation control methods incorporate physical constraints into their mathematical models, but omit implicit constraints associated with policies of operation and dependency relationships among rules representing those constraints. To overcome these shortcomings, there is a recent trend in enabling the control strategies with inference-based rule checking capabilities. One solution is to exploit semantic web technologies in building simulation control. Such approaches provide the tools for semantic modeling of domains, and the ability to deduce new information based on the models through use of Description Logic (DL). In a step toward enabling this capability, this paper presents a cross-disciplinary data-drivenmore » control strategy for building energy management simulation that integrates semantic modeling and formal rule checking mechanisms into a Model Predictive Control (MPC) formulation. The results show that MPC provides superior levels of performance when initial conditions and inputs are derived from inference-based rules.« less

The Proposal of the Model for Developing Dispatch System for Nationwide One-Day Integrative Planning

NASA Astrophysics Data System (ADS)

Kim, Hyun Soo; Choi, Hyung Rim; Park, Byung Kwon; Jung, Jae Un; Lee, Jin Wook

The problems of dispatch planning for container truck are classified as the pickup and delivery problems, which are highly complex issues that consider various constraints in the real world. However, in case of the current situation, it is developed by the control system so that it requires the automated planning system under the view of nationwide integrative planning. Therefore, the purpose of this study is to suggest model to develop the automated dispatch system through the constraint satisfaction problem and meta-heuristic technique-based algorithm. In the further study, the practical system is developed and evaluation is performed in aspect of various results. This study suggests model to undergo the study which promoted the complexity of the problems by considering the various constraints which were not considered in the early study. However, it is suggested that it is necessary to add the study which includes the real-time monitoring function for vehicles and cargos based on the information technology.

An integrated production-inventory model for the singlevendor two-buyer problem with partial backorder, stochastic demand, and service level constraints

NASA Astrophysics Data System (ADS)

Arfawi Kurdhi, Nughthoh; Adi Diwiryo, Toray; Sutanto

2016-02-01

This paper presents an integrated single-vendor two-buyer production-inventory model with stochastic demand and service level constraints. Shortage is permitted in the model, and partial backordered partial lost sale. The lead time demand is assumed follows a normal distribution and the lead time can be reduced by adding crashing cost. The lead time and ordering cost reductions are interdependent with logaritmic function relationship. A service level constraint policy corresponding to each buyer is considered in the model in order to limit the level of inventory shortages. The purpose of this research is to minimize joint total cost inventory model by finding the optimal order quantity, safety stock, lead time, and the number of lots delivered in one production run. The optimal production-inventory policy gained by the Lagrange method is shaped to account for the service level restrictions. Finally, a numerical example and effects of the key parameters are performed to illustrate the results of the proposed model.

Beyond mechanistic interaction: value-based constraints on meaning in language.

PubMed

Rączaszek-Leonardi, Joanna; Nomikou, Iris

2015-01-01

According to situated, embodied, and distributed approaches to cognition, language is a crucial means for structuring social interactions. Recent approaches that emphasize this coordinative function treat language as a system of replicable constraints on individual and interactive dynamics. In this paper, we argue that the integration of the replicable-constraints approach to language with the ecological view on values allows for a deeper insight into processes of meaning creation in interaction. Such a synthesis of these frameworks draws attention to important sources of structuring interactions beyond the sheer efficiency of a collective system in its current task situation. Most importantly, the workings of linguistic constraints will be shown as embedded in more general fields of values, which are realized on multiple timescales. Because the ontogenetic timescale offers a convenient window into the emergence of linguistic constraints, we present illustrations of concrete mechanisms through which values may become embodied in language use in development.

National Vulnerability Database (NVD)

National Institute of Standards and Technology Data Gateway

National Vulnerability Database (NVD) (Web, free access)   NVD is a comprehensive cyber security vulnerability database that integrates all publicly available U.S. Government vulnerability resources and provides references to industry resources. It is based on and synchronized with the CVE vulnerability naming standard.

Computer Databases as an Educational Tool in the Basic Sciences.

ERIC Educational Resources Information Center

Friedman, Charles P.; And Others

1990-01-01

The University of North Carolina School of Medicine developed a computer database, INQUIRER, containing scientific information in bacteriology, and then integrated the database into routine educational activities for first-year medical students in their microbiology course. (Author/MLW)

Integrated design of the CSI evolutionary structure: A verification of the design methodology

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.; Joshi, S. M.; Elliott, Kenny B.; Walz, J. E.

1993-01-01

One of the main objectives of the Controls-Structures Interaction (CSI) program is to develop and evaluate integrated controls-structures design methodology for flexible space structures. Thus far, integrated design methodologies for a class of flexible spacecraft, which require fine attitude pointing and vibration suppression with no payload articulation, have been extensively investigated. Various integrated design optimization approaches, such as single-objective optimization, and multi-objective optimization, have been implemented with an array of different objectives and constraints involving performance and cost measures such as total mass, actuator mass, steady-state pointing performance, transient performance, control power, and many more. These studies have been performed using an integrated design software tool (CSI-DESIGN CODE) which is under development by the CSI-ADM team at the NASA Langley Research Center. To date, all of these studies, irrespective of the type of integrated optimization posed or objectives and constraints used, have indicated that integrated controls-structures design results in an overall spacecraft design which is considerably superior to designs obtained through a conventional sequential approach. Consequently, it is believed that validation of some of these results through fabrication and testing of a structure which is designed through an integrated design approach is warranted. The objective of this paper is to present and discuss the efforts that have been taken thus far for the validation of the integrated design methodology.

The GLIMS Glacier Database

NASA Astrophysics Data System (ADS)

Raup, B. H.; Khalsa, S. S.; Armstrong, R.

2007-12-01

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We have implemented two web-based interfaces to the database; one enables exploration of the data via interactive maps (web map server), while the other allows searches based on text-field constraints. The web map server is an Open Geospatial Consortium (OGC) compliant Web Map Server (WMS) and Web Feature Server (WFS). This means that other web sites can display glacier layers from our site over the Internet, or retrieve glacier features in vector format. All components of the system are implemented using Open Source software: Linux, PostgreSQL, PostGIS (geospatial extensions to the database), MapServer (WMS and WFS), and several supporting components such as Proj.4 (a geographic projection library) and PHP. These tools are robust and provide a flexible and powerful framework for web mapping applications. As a service to the GLIMS community, the database contains metadata on all ASTER imagery acquired over glacierized terrain. Reduced-resolution of the images (browse imagery) can be viewed either as a layer in the MapServer application, or overlaid on the virtual globe within Google Earth. The interactive map application allows the user to constrain by time what data appear on the map. For example, ASTER or glacier outlines from 2002 only, or from Autumn in any year, can be displayed. The system allows users to download their selected glacier data in a choice of formats. The results of a query based on spatial selection (using a mouse) or text-field constraints can be downloaded in any of these formats: ESRI shapefiles, KML (Google Earth), MapInfo, GML (Geography Markup Language) and GMT (Generic Mapping Tools). This "clip-and-ship" function allows users to download only the data they are interested in. Our flexible web interfaces to the database, which includes various support layers (e.g. a layer to help collaborators identify satellite imagery over their region of expertise) will facilitate enhanced analysis to be undertaken on glacier systems, their distribution, and their impacts on other Earth systems.

The Integrated Farm System Model: A Tool for Whole Farm Nutrient Management Analysis

USDA-ARS?s Scientific Manuscript database

With tighter profit margins and increasing environmental constraints, strategic planning of farm production systems is becoming both more important and more difficult. This is especially true for integrated crop and animal production systems. Animal production is complex with a number of interacting...

Automated Planning and Scheduling for Space Mission Operations

NASA Technical Reports Server (NTRS)

Chien, Steve; Jonsson, Ari; Knight, Russell

2005-01-01

Research Trends: a) Finite-capacity scheduling under more complex constraints and increased problem dimensionality (subcontracting, overtime, lot splitting, inventory, etc.) b) Integrated planning and scheduling. c) Mixed-initiative frameworks. d) Management of uncertainty (proactive and reactive). e) Autonomous agent architectures and distributed production management. e) Integration of machine learning capabilities. f) Wider scope of applications: 1) analysis of supplier/buyer protocols & tradeoffs; 2) integration of strategic & tactical decision-making; and 3) enterprise integration.

V-band integrated quadriphase modulator

NASA Technical Reports Server (NTRS)

Grote, A.; Chang, K.

1983-01-01

A V-band integrated circuit quadriphase shift keyed modulator/exciter for space communications systems was developed. Intersatellite communications systems require direct modulation at 60 GHz to enhance signal processing capability. For most systems, particularly space applications, small and lightweight components are essential to alleviate severe system design constraints. Thus to achieve wideband, high data rate systems, direct modulation techniques at millimeter waves using solid state integrated circuit technology are an integral part of the overall technology developments.

Establishment of an international database for genetic variants in esophageal cancer.

PubMed

Vihinen, Mauno

2016-10-01

The establishment of a database has been suggested in order to collect, organize, and distribute genetic information about esophageal cancer. The World Organization for Specialized Studies on Diseases of the Esophagus and the Human Variome Project will be in charge of a central database of information about esophageal cancer-related variations from publications, databases, and laboratories; in addition to genetic details, clinical parameters will also be included. The aim will be to get all the central players in research, clinical, and commercial laboratories to contribute. The database will follow established recommendations and guidelines. The database will require a team of dedicated curators with different backgrounds. Numerous layers of systematics will be applied to facilitate computational analyses. The data items will be extensively integrated with other information sources. The database will be distributed as open access to ensure exchange of the data with other databases. Variations will be reported in relation to reference sequences on three levels--DNA, RNA, and protein-whenever applicable. In the first phase, the database will concentrate on genetic variations including both somatic and germline variations for susceptibility genes. Additional types of information can be integrated at a later stage. © 2016 New York Academy of Sciences.

Developing an ontological explosion knowledge base for business continuity planning purposes.

PubMed

Mohammadfam, Iraj; Kalatpour, Omid; Golmohammadi, Rostam; Khotanlou, Hasan

2013-01-01

Industrial accidents are among the most known challenges to business continuity. Many organisations have lost their reputation following devastating accidents. To manage the risks of such accidents, it is necessary to accumulate sufficient knowledge regarding their roots, causes and preventive techniques. The required knowledge might be obtained through various approaches, including databases. Unfortunately, many databases are hampered by (among other things) static data presentations, a lack of semantic features, and the inability to present accident knowledge as discrete domains. This paper proposes the use of Protégé software to develop a knowledge base for the domain of explosion accidents. Such a structure has a higher capability to improve information retrieval compared with common accident databases. To accomplish this goal, a knowledge management process model was followed. The ontological explosion knowledge base (EKB) was built for further applications, including process accident knowledge retrieval and risk management. The paper will show how the EKB has a semantic feature that enables users to overcome some of the search constraints of existing accident databases.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

[LONI & Co: about the epistemic specificity of digital spaces of knowledge in cognitive neuroscience].

PubMed

Huber, Lara

2011-06-01

In the neurosciences digital databases more and more are becoming important tools of data rendering and distributing. This development is due to the growing impact of imaging based trial design in cognitive neuroscience, including morphological as much as functional imaging technologies. As the case of the 'Laboratory of Neuro Imaging' (LONI) is showing, databases are attributed a specific epistemological power: Since the 1990s databasing is seen to foster the integration of neuroscientific data, although local regimes of data production, -manipulation and--interpretation are also challenging this development. Databasing in the neurosciences goes along with the introduction of new structures of integrating local data, hence establishing digital spaces of knowledge (epistemic spaces): At this stage, inherent norms of digital databases are affecting regimes of imaging-based trial design, for example clinical research into Alzheimer's disease.

SU-E-I-97: Smart Auto-Planning Framework in An EMR Environment (SAFEE)

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

Zhang, B; Chen, S; Mutaf, Y

2014-06-01

Purpose: Our Radiation Oncology Department uses clinical practice guidelines for patient treatment, including normal tissue sparing and other dosimetric constraints. These practice guidelines were adapted from national guidelines, clinical trials, literature reviews, and practitioner's own experience. Modern treatment planning systems (TPS) have the capability of incorporating these practice guidelines to automatically create radiation therapy treatment plans with little human intervention. We are developing a software infrastructure to integrate clinical practice guidelines and radiation oncology electronic medical record (EMR) system into radiation therapy treatment planning system (TPS) for auto planning. Methods: Our Smart Auto-Planning Framework in an EMR environment (SAFEE) usesmore » a software pipeline framework to integrate practice guidelines,EMR, and TPS together. The SAFEE system starts with retrieving diagnosis information and physician's prescription from the EMR system. After approval of contouring, SAFEE will automatically create plans according to our guidelines. Based on clinical objectives, SAFEE will automatically select treatment delivery techniques (such as, 3DRT/IMRT/VMAT) and optimize plans. When necessary, SAFEE will create multiple treatment plans with different combinations of parameters. SAFEE's pipeline structure makes it very flexible to integrate various techniques, such as, Model-Base Segmentation (MBS) and plan optimization algorithms, e.g., Multi-Criteria Optimization (MCO). In addition, SAFEE uses machine learning, data mining techniques, and an integrated database to create clinical knowledgebase and then answer clinical questions, such as, how to score plan quality or how volume overlap affects physicians' decision in beam and treatment technique selection. Results: In our institution, we use Varian Aria EMR system and RayStation TPS from RaySearch, whose ScriptService API allows control by external programs. These applications are the building blocks of our SAFEE system. Conclusion: SAFEE is a feasible method of integrating clinical information to develop an auto-planning paradigm to improve clinical workflow in cancer patient care.« less

Exploring the roles of cannot-link constraint in community detection via Multi-variance Mixed Gaussian Generative Model.

PubMed

Yang, Liang; Ge, Meng; Jin, Di; He, Dongxiao; Fu, Huazhu; Wang, Jing; Cao, Xiaochun

2017-01-01

Due to the demand for performance improvement and the existence of prior information, semi-supervised community detection with pairwise constraints becomes a hot topic. Most existing methods have been successfully encoding the must-link constraints, but neglect the opposite ones, i.e., the cannot-link constraints, which can force the exclusion between nodes. In this paper, we are interested in understanding the role of cannot-link constraints and effectively encoding pairwise constraints. Towards these goals, we define an integral generative process jointly considering the network topology, must-link and cannot-link constraints. We propose to characterize this process as a Multi-variance Mixed Gaussian Generative (MMGG) Model to address diverse degrees of confidences that exist in network topology and pairwise constraints and formulate it as a weighted nonnegative matrix factorization problem. The experiments on artificial and real-world networks not only illustrate the superiority of our proposed MMGG, but also, most importantly, reveal the roles of pairwise constraints. That is, though the must-link is more important than cannot-link when either of them is available, both must-link and cannot-link are equally important when both of them are available. To the best of our knowledge, this is the first work on discovering and exploring the importance of cannot-link constraints in semi-supervised community detection.

Exploring the roles of cannot-link constraint in community detection via Multi-variance Mixed Gaussian Generative Model

PubMed Central

Ge, Meng; Jin, Di; He, Dongxiao; Fu, Huazhu; Wang, Jing; Cao, Xiaochun

2017-01-01

Due to the demand for performance improvement and the existence of prior information, semi-supervised community detection with pairwise constraints becomes a hot topic. Most existing methods have been successfully encoding the must-link constraints, but neglect the opposite ones, i.e., the cannot-link constraints, which can force the exclusion between nodes. In this paper, we are interested in understanding the role of cannot-link constraints and effectively encoding pairwise constraints. Towards these goals, we define an integral generative process jointly considering the network topology, must-link and cannot-link constraints. We propose to characterize this process as a Multi-variance Mixed Gaussian Generative (MMGG) Model to address diverse degrees of confidences that exist in network topology and pairwise constraints and formulate it as a weighted nonnegative matrix factorization problem. The experiments on artificial and real-world networks not only illustrate the superiority of our proposed MMGG, but also, most importantly, reveal the roles of pairwise constraints. That is, though the must-link is more important than cannot-link when either of them is available, both must-link and cannot-link are equally important when both of them are available. To the best of our knowledge, this is the first work on discovering and exploring the importance of cannot-link constraints in semi-supervised community detection. PMID:28678864

IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data.

PubMed

Legehar, Ashenafi; Xhaard, Henri; Ghemtio, Leo

2016-01-01

The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failure of drug candidates and has led to the withdrawal of approved drugs. Computational methods are effective approaches to reduce the number of safety issues by analyzing possible links between chemical structures and ADMET or adverse effects, but this is limited by the size, quality, and heterogeneity of the data available from individual sources. Thus, large, clean and integrated databases of approved drug data, associated with fast and efficient predictive tools are desirable early in the drug discovery process. We have built a relational database (IDAAPM) to integrate available approved drug data such as drug approval information, ADMET and adverse effects, chemical structures and molecular descriptors, targets, bioactivity and related references. The database has been coupled with a searchable web interface and modern data analytics platform (KNIME) to allow data access, data transformation, initial analysis and further predictive modeling. Data were extracted from FDA resources and supplemented from other publicly available databases. Currently, the database contains information regarding about 19,226 FDA approval applications for 31,815 products (small molecules and biologics) with their approval history, 2505 active ingredients, together with as many ADMET properties, 1629 molecular structures, 2.5 million adverse effects and 36,963 experimental drug-target bioactivity data. IDAAPM is a unique resource that, in a single relational database, provides detailed information on FDA approved drugs including their ADMET properties and adverse effects, the corresponding targets with bioactivity data, coupled with a data analytics platform. It can be used to perform basic to complex drug-target ADMET or adverse effects analysis and predictive modeling. IDAAPM is freely accessible at http://idaapm.helsinki.fi and can be exploited through a KNIME workflow connected to the database.Graphical abstractFDA approved drug data integration for predictive modeling.

Development of the Lymphoma Enterprise Architecture Database: A caBIG(tm) Silver level compliant System

PubMed Central

Huang, Taoying; Shenoy, Pareen J.; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W.; Flowers, Christopher R.

2009-01-01

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid™ (caBIG™) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system™ (LEAD™), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute’s Center for Bioinformatics to establish the LEAD™ platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD™ could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG™ can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG™ to the management of clinical and biological data. PMID:19492074

Development of the Lymphoma Enterprise Architecture Database: a caBIG Silver level compliant system.

PubMed

Huang, Taoying; Shenoy, Pareen J; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W; Flowers, Christopher R

2009-04-03

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid (caBIG) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system (LEAD), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute's Center for Bioinformatics to establish the LEAD platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG to the management of clinical and biological data.

A National Virtual Specimen Database for Early Cancer Detection

NASA Technical Reports Server (NTRS)

Crichton, Daniel; Kincaid, Heather; Kelly, Sean; Thornquist, Mark; Johnsey, Donald; Winget, Marcy

2003-01-01

Access to biospecimens is essential for enabling cancer biomarker discovery. The National Cancer Institute's (NCI) Early Detection Research Network (EDRN) comprises and integrates a large number of laboratories into a network in order to establish a collaborative scientific environment to discover and validate disease markers. The diversity of both the institutions and the collaborative focus has created the need for establishing cross-disciplinary teams focused on integrating expertise in biomedical research, computational and biostatistics, and computer science. Given the collaborative design of the network, the EDRN needed an informatics infrastructure. The Fred Hutchinson Cancer Research Center, the National Cancer Institute,and NASA's Jet Propulsion Laboratory (JPL) teamed up to build an informatics infrastructure creating a collaborative, science-driven research environment despite the geographic and morphology differences of the information systems that existed within the diverse network. EDRN investigators identified the need to share biospecimen data captured across the country managed in disparate databases. As a result, the informatics team initiated an effort to create a virtual tissue database whereby scientists could search and locate details about specimens located at collaborating laboratories. Each database, however, was locally implemented and integrated into collection processes and methods unique to each institution. This meant that efforts to integrate databases needed to be done in a manner that did not require redesign or re-implementation of existing system

An integrated chronostratigraphic data system for the twenty-first century

USGS Publications Warehouse

Sikora, P.J.; Ogg, James G.; Gary, A.; Cervato, C.; Gradstein, Felix; Huber, B.T.; Marshall, C.; Stein, J.A.; Wardlaw, B.

2006-01-01

Research in stratigraphy is increasingly multidisciplinary and conducted by diverse research teams whose members can be widely separated. This developing distributed-research process, facilitated by the availability of the Internet, promises tremendous future benefits to researchers. However, its full potential is hindered by the absence of a development strategy for the necessary infrastructure. At a National Science Foundation workshop convened in November 2001, thirty quantitative stratigraphers and database specialists from both academia and industry met to discuss how best to integrate their respective chronostratigraphic databases. The main goal was to develop a strategy that would allow efficient distribution and integration of existing data relevant to the study of geologic time. Discussions concentrated on three major themes: database standards and compatibility, strategies and tools for information retrieval and analysis of all types of global and regional stratigraphic data, and future directions for database integration and centralization of currently distributed depositories. The result was a recommendation to establish an integrated chronostratigraphic database, to be called Chronos, which would facilitate greater efficiency in stratigraphic studies (http://www.chronos.org/) . The Chronos system will both provide greater ease of data gathering and allow for multidisciplinary synergies, functions of fundamental importance in a variety of research, including time scale construction, paleoenvironmental analysis, paleoclimatology and paleoceanography. Beyond scientific research, Chronos will also provide educational and societal benefits by providing an accessible source of information of general interest (e.g., mass extinctions) and concern (e.g., climatic change). The National Science Foundation has currently funded a three-year program for implementing Chronos.. ?? 2006 Geological Society of America. All rights reserved.

CSRQ: Communication-Efficient Secure Range Queries in Two-Tiered Sensor Networks

PubMed Central

Dai, Hua; Ye, Qingqun; Yang, Geng; Xu, Jia; He, Ruiliang

2016-01-01

In recent years, we have seen many applications of secure query in two-tiered wireless sensor networks. Storage nodes are responsible for storing data from nearby sensor nodes and answering queries from Sink. It is critical to protect data security from a compromised storage node. In this paper, the Communication-efficient Secure Range Query (CSRQ)—a privacy and integrity preserving range query protocol—is proposed to prevent attackers from gaining information of both data collected by sensor nodes and queries issued by Sink. To preserve privacy and integrity, in addition to employing the encoding mechanisms, a novel data structure called encrypted constraint chain is proposed, which embeds the information of integrity verification. Sink can use this encrypted constraint chain to verify the query result. The performance evaluation shows that CSRQ has lower communication cost than the current range query protocols. PMID:26907293

Kinematics of velocity and vorticity correlations in turbulent flow

NASA Technical Reports Server (NTRS)

Bernard, P. S.

1983-01-01

The kinematic problem of calculating second-order velocity moments from given values of the vorticity covariance is examined. Integral representation formulas for second-order velocity moments in terms of the two-point vorticity correlation tensor are derived. The special relationships existing between velocity moments in isotropic turbulence are expressed in terms of the integral formulas yielding several kinematic constraints on the two-point vorticity correlation tensor in isotropic turbulence. Numerical evaluation of these constraints suggests that a Gaussian curve may be the only form of the longitudinal velocity correlation coefficient which is consistent with the requirement of isotropy. It is shown that if this is the case, then a family of exact solutions to the decay of isotropic turbulence may be obtained which contains Batchelor's final period solution as a special case. In addition, the computed results suggest a method of approximating the integral representation formulas in general turbulent shear flows.

Quality assessment of clinical practice guidelines for integrative medicine in China: A systematic review.

PubMed

Yao, Sha; Wei, Dang; Chen, Yao-Long; Wang, Qi; Wang, Xiao-Qin; Zeng, Zhao; Li, Hui

2017-05-01

To assess the quality of integrative medicine clinical practice guidelines (CPGs) published before 2014. A systematic search of the scientific literature published before 2014 was conducted to select integrative medicine CPGs. Four major Chinese integrated databases and one guideline database were searched: the Chinese Biomedical Literature Database (CBM), the China National Knowledge Infrastructure (CNKI), China Science and Technology Journal Database (VIP), Wanfang Data, and the China Guideline Clearinghouse (CGC). Four reviewers independently assessed the quality of the included guidelines using the Appraisal of Guidelines for Research and Evaluation (AGREE) II Instrument. Overall consensus among the reviewers was assessed using the intra-class correlation coefficient (ICC). A total of 41 guidelines published from 2003 to 2014 were included. The overall consensus among the reviewers was good [ICC: 0.928; 95% confifi dence interval (CI): 0.920 to 0.935]. The scores on the 6 AGREE domains were: 17% for scope and purpose (range: 6% to 32%), 11% for stakeholder involvement (range: 0 to 24%), 10% for rigor of development (range: 3% to 22%), 39% for clarity and presentation (range: 25% to 64%), 11% for applicability (range: 4% to 24%), and 1% for editorial independence (range: 0 to 15%). The quality of integrative medicine CPGs was low, the development of integrative medicine CPGs should be guided by systematic methodology. More emphasis should be placed on multi-disciplinary guideline development groups, quality of evidence, management of funding and conflfl icts of interest, and guideline updates in the process of developing integrative medicine CPGs in China.

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

PubMed Central

Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PubMed

Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo; Dobson, Paul D; Dunstan, Mark; Jervis, Adrian J; Vinaixa, Maria; Williams, Alan R; Ananiadou, Sophia; Faulon, Jean-Loup; Mendes, Pedro; Kell, Douglas B; Scrutton, Nigel S; Breitling, Rainer

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

PubMed Central

Batista-Navarro, Riza; Dunstan, Mark; Jervis, Adrian J.; Vinaixa, Maria; Ananiadou, Sophia; Faulon, Jean-Loup; Kell, Douglas B.

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and–crucially–the relationships between them. Such a resource should be extensible, such that newly discovered relationships–for example, those between novel, synthetic enzymes and non-natural products–can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists. PMID:28708831

Design of a Multi Dimensional Database for the Archimed DataWarehouse.

PubMed

Bréant, Claudine; Thurler, Gérald; Borst, François; Geissbuhler, Antoine

2005-01-01

The Archimed data warehouse project started in 1993 at the Geneva University Hospital. It has progressively integrated seven data marts (or domains of activity) archiving medical data such as Admission/Discharge/Transfer (ADT) data, laboratory results, radiology exams, diagnoses, and procedure codes. The objective of the Archimed data warehouse is to facilitate the access to an integrated and coherent view of patient medical in order to support analytical activities such as medical statistics, clinical studies, retrieval of similar cases and data mining processes. This paper discusses three principal design aspects relative to the conception of the database of the data warehouse: 1) the granularity of the database, which refers to the level of detail or summarization of data, 2) the database model and architecture, describing how data will be presented to end users and how new data is integrated, 3) the life cycle of the database, in order to ensure long term scalability of the environment. Both, the organization of patient medical data using a standardized elementary fact representation and the use of the multi dimensional model have proved to be powerful design tools to integrate data coming from the multiple heterogeneous database systems part of the transactional Hospital Information System (HIS). Concurrently, the building of the data warehouse in an incremental way has helped to control the evolution of the data content. These three design aspects bring clarity and performance regarding data access. They also provide long term scalability to the system and resilience to further changes that may occur in source systems feeding the data warehouse.

EXPERIMENTAL EVALUATION OF DEFORMATION AND CONSTRAINT CHARACTERISTICS IN PRECRACKED CHARPY AND OTHER THREE-POINT BEND SPECIMENS

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

Nanstad, Randy K; Sokolov, Mikhail A; Merkle, John Graham

2007-01-01

To enable determination of the fracture toughness reference temperature, T0, with reactor pressure vessel surveillance specimens, the precracked Charpy (PCVN) three-point bend, SE(B), specimen is of interest. Compared with the 25-mm (1 in.) thick compact, 1TC(T), specimen, tests with the PCVN specimen (10x10x55 mm) have resulted in T0 temperatures as much as 40 XC lower (a so-called specimen bias effect). The Heavy-Section Steel Irradiation (HSSI) Program at Oak Ridge National Laboratory developed a two-part project to evaluate the C(T) versus PCVN differences, (1) calibration experiments concentrating on test practices, and (2) a matrix of transition range tests with various specimenmore » geometries and sizes, including 1T SE(B) and 1TC(T). The test material selected was a plate of A533 grade B class 1 steel. The calibration experiments included assessment of the computational validity of J-integral determinations, while the constraint characteristics of various specimen types and sizes were evaluated using key curves and notch strength determinations. The results indicate that J-integral solutions for the small PCVN specimen are comparable in terms of J-integral validity with 1T bend specimens. Regarding constraint evaluations, Phase I deformation is defined where plastic deformation is confined to crack tip plastic zone development, whereas Phase II deformation is defined where plastic hinging deformation develops. In Phase II deformation, the 0.5T SE(B) B B specimen (slightly larger than the PCVN specimen) consistently showed the highest constraint of all SE(B) specimens evaluated for constraint comparisons. The PCVN specimen begins the Phase II type of deformation at relatively low KR levels, with the result that KJc values above about 70 MPa m from precracked Charpy specimens are under extensive plastic hinging deformation.« less

Do Developmental Constraints and High Integration Limit the Evolution of the Marsupial Oral Apparatus?

PubMed

Goswami, Anjali; Randau, Marcela; Polly, P David; Weisbecker, Vera; Bennett, C Verity; Hautier, Lionel; Sánchez-Villagra, Marcelo R

2016-09-01

Developmental constraints can have significant influence on the magnitude and direction of evolutionary change, and many studies have demonstrated that these effects are manifested on macroevolutionary scales. Phenotypic integration, or the strong interactions among traits, has been similarly invoked as a major influence on morphological variation, and many studies have demonstrated that trait integration changes through ontogeny, in many cases decreasing with age. Here, we unify these perspectives in a case study of the ontogeny of the mammalian cranium, focusing on a comparison between marsupials and placentals. Marsupials are born at an extremely altricial state, requiring, in most cases, the use of the forelimbs to climb to the pouch, and, in all cases, an extended period of continuous suckling, during which most of their development occurs. Previous work has shown that marsupials are less disparate in adult cranial form than are placentals, particularly in the oral apparatus, and in forelimb ontogeny and adult morphology, presumably due to functional selection pressures on these two systems during early postnatal development. Using phenotypic trajectory analysis to quantify prenatal and early postnatal cranial ontogeny in 10 species of therian mammals, we demonstrate that this pattern of limited variation is also apparent in the development of the oral apparatus of marsupials, relative to placentals, but not in the skull more generally. Combined with the observation that marsupials show extremely high integration of the oral apparatus in early postnatal ontogeny, while other cranial regions show similar levels of integration to that observed in placentals, we suggest that high integration may compound the effects of the functional constraints for continuous suckling to ultimately limit the ontogenetic and adult disparity of the marsupial oral apparatus throughout their evolutionary history. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology.

The prevalence of co-morbid depression among employees with type 2 diabetes in a Japanese corporation: a descriptive study using an integrated health database.

PubMed

Arima, Hideaki; Miwa, Makiko; Kawahara, Kazuo

2007-03-01

To determine the prevalence of comorbid depression among people with type 2 diabetes using the integrated health database. A total of 6543 people aged 18-65 years were selected from the employees of a Japanese corporation. Using the corporation's integrated health database, which consisted of medical claims data and a self-reported questionnaire from the fiscal year 2000, this study was undertaken to identify the prevalence, the odds ratio and some related factors. The prevalence of co-morbid depression among people with type 2 diabetes was 2.6%. The crude odds ratio of co-morbid depression among those with type 2 diabetes was 2.20 (95% CI 0.88-5.50). After adjustment for covariates (gender, age, alcohol drinking, smoking, exercise, and dietary restriction), the odds ratio of co-morbid depression among those with type 2 diabetes was 2.33 (0.86-6.33). Using the integrated health database, it was suggested that patients with type 2 diabetes were more likely to suffer from depression and there was a relationship between depression and dietary restriction of portion control.

The designing and implementation of PE teaching information resource database based on broadband network

NASA Astrophysics Data System (ADS)

Wang, Jian

2017-01-01

In order to change traditional PE teaching mode and realize the interconnection, interworking and sharing of PE teaching resources, a distance PE teaching platform based on broadband network is designed and PE teaching information resource database is set up. The designing of PE teaching information resource database takes Windows NT 4/2000Server as operating system platform, Microsoft SQL Server 7.0 as RDBMS, and takes NAS technology for data storage and flow technology for video service. The analysis of system designing and implementation shows that the dynamic PE teaching information resource sharing platform based on Web Service can realize loose coupling collaboration, realize dynamic integration and active integration and has good integration, openness and encapsulation. The distance PE teaching platform based on Web Service and the design scheme of PE teaching information resource database can effectively solve and realize the interconnection, interworking and sharing of PE teaching resources and adapt to the informatization development demands of PE teaching.

Comparison of Integrated Testlet and Constructed-Response Question Formats

ERIC Educational Resources Information Center

Slepkov, Aaron D.; Shiell, Ralph C.

2014-01-01

Constructed-response (CR) questions are a mainstay of introductory physics textbooks and exams. However, because of the time, cost, and scoring reliability constraints associated with this format, CR questions are being increasingly replaced by multiple-choice (MC) questions in formal exams. The integrated testlet (IT) is a recently developed…

Gestalt Therapy and Feminist Therapy: A Proposed Integration.

ERIC Educational Resources Information Center

Enns, Carolyn Zerbe

1987-01-01

Offers a proposal for integrating the Gestalt goals of self-responsibility with a feminist perspective that places value on the web of relationships in women's lives and focuses attention on the environmental constraints and socialization that affect women's choices. Discusses Gestalt techniques for enhancing women's growth and examines…

Constraint-Driven Software Design: An Escape from the Waterfall Model.

ERIC Educational Resources Information Center

de Hoog, Robert; And Others

1994-01-01

Presents the principles of a development methodology for software design based on a nonlinear, product-driven approach that integrates quality aspects. Two examples are given to show that the flexibility needed for building high quality systems leads to integrated development environments in which methodology, product, and tools are closely…

Perspectives of teachers regarding the integration of mathematics and science at the secondary school level

NASA Astrophysics Data System (ADS)

Zolnierczyk, Joanna Asia

The integration of mathematics and science in secondary schools in the 21st century continues to be an important topic of practice and research. The purpose of my research study, which builds on studies by Frykholm and Glasson (2005) and Berlin and White (2010), is to explore the potential constraints and benefits of integrating mathematics and science in Ontario secondary schools based on the perspectives of in-service and pre-service teachers with various math and/or science backgrounds. A qualitative and quantitative research design with an exploratory approach was used. The qualitative data was collected from a sample of 12 in-service teachers with various math and/or science backgrounds recruited from two school boards in Eastern Ontario. The quantitative and some qualitative data was collected from a sample of 81 pre-service teachers from the Queen's University Bachelor of Education (B.Ed) program. Semi-structured interviews were conducted with the in-service teachers while a survey and a focus group was conducted with the pre-service teachers. Once the data was collected, the qualitative data were abductively analyzed. For the quantitative data, descriptive and inferential statistics (one-way ANOVAs and Pearson Chi Square analyses) were calculated to examine perspectives of teachers regardless of teaching background and to compare groups of teachers based on teaching background. The findings of this study suggest that in-service and pre-service teachers have a positive attitude towards the integration of math and science and view it as valuable to student learning and success. The pre-service teachers viewed the integration as easy and did not express concerns to this integration. On the other hand, the in-service teachers highlighted concerns and challenges such as resources, scheduling, and time constraints. My results illustrate when teachers perceive it is valuable to integrate math and science and which aspects of the classroom benefit best from the integration. Furthermore, the results highlight barriers and possible solutions to better the integration of math and science. In addition to the benefits and constraints of integration, my results illustrate why some teachers may opt out of integrating math and science and the different strategies teachers have incorporated to integrate math and science in their classroom.

Policy Review of the Primary and Junior Secondary Education Sub-Sectors in East Java. Educational Policy and Planning Project. A Government of Indonesia-USAID Project.

ERIC Educational Resources Information Center

Soebagio, Retno L.; And Others

Indonesian representatives and the Educational Research and Development Center studied East Javanese primary and junior secondary schools to develop a database for future planning and to identify deficiencies, constraints, and areas for fruitful reform. Issues of enrollment, personnel, curriculum, facilities and equipment, cost, and financing were…

Energetic and ecological constraints on population density of reef fishes.

PubMed

Barneche, D R; Kulbicki, M; Floeter, S R; Friedlander, A M; Allen, A P

2016-01-27

Population ecology has classically focused on pairwise species interactions, hindering the description of general patterns and processes of population abundance at large spatial scales. Here we use the metabolic theory of ecology as a framework to formulate and test a model that yields predictions linking population density to the physiological constraints of body size and temperature on individual metabolism, and the ecological constraints of trophic structure and species richness on energy partitioning among species. Our model was tested by applying Bayesian quantile regression to a comprehensive reef-fish community database, from which we extracted density data for 5609 populations spread across 49 sites around the world. Our results indicate that population density declines markedly with increases in community species richness and that, after accounting for richness, energetic constraints are manifested most strongly for the most abundant species, which generally are of small body size and occupy lower trophic groups. Overall, our findings suggest that, at the global scale, factors associated with community species richness are the major drivers of variation in population density. Given that populations of species-rich tropical systems exhibit markedly lower maximum densities, they may be particularly susceptible to stochastic extinction. © 2016 The Author(s).

Energetic and ecological constraints on population density of reef fishes

PubMed Central

Barneche, D. R.; Kulbicki, M.; Floeter, S. R.; Friedlander, A. M.; Allen, A. P.

2016-01-01

Population ecology has classically focused on pairwise species interactions, hindering the description of general patterns and processes of population abundance at large spatial scales. Here we use the metabolic theory of ecology as a framework to formulate and test a model that yields predictions linking population density to the physiological constraints of body size and temperature on individual metabolism, and the ecological constraints of trophic structure and species richness on energy partitioning among species. Our model was tested by applying Bayesian quantile regression to a comprehensive reef-fish community database, from which we extracted density data for 5609 populations spread across 49 sites around the world. Our results indicate that population density declines markedly with increases in community species richness and that, after accounting for richness, energetic constraints are manifested most strongly for the most abundant species, which generally are of small body size and occupy lower trophic groups. Overall, our findings suggest that, at the global scale, factors associated with community species richness are the major drivers of variation in population density. Given that populations of species-rich tropical systems exhibit markedly lower maximum densities, they may be particularly susceptible to stochastic extinction. PMID:26791611

Gluing Ladder Feynman Diagrams into Fishnets

DOE PAGES

Basso, Benjamin; Dixon, Lance J.

2017-08-14

We use integrability at weak coupling to compute fishnet diagrams for four-point correlation functions in planar Φ 4 theory. Our results are always multilinear combinations of ladder integrals, which are in turn built out of classical polylogarithms. The Steinmann relations provide a powerful constraint on such linear combinations, which leads to a natural conjecture for any fishnet diagram as the determinant of a matrix of ladder integrals.

Topological materials discovery using electron filling constraints

NASA Astrophysics Data System (ADS)

Chen, Ru; Po, Hoi Chun; Neaton, Jeffrey B.; Vishwanath, Ashvin

2018-01-01

Nodal semimetals are classes of topological materials that have nodal-point or nodal-line Fermi surfaces, which give them novel transport and topological properties. Despite being highly sought after, there are currently very few experimental realizations, and identifying new materials candidates has mainly relied on exhaustive database searches. Here we show how recent studies on the interplay between electron filling and nonsymmorphic space-group symmetries can guide the search for filling-enforced nodal semimetals. We recast the previously derived constraints on the allowed band-insulator fillings in any space group into a new form, which enables effective screening of materials candidates based solely on their space group, electron count in the formula unit, and multiplicity of the formula unit. This criterion greatly reduces the computation load for discovering topological materials in a database of previously synthesized compounds. As a demonstration, we focus on a few selected nonsymmorphic space groups which are predicted to host filling-enforced Dirac semimetals. Of the more than 30,000 entires listed, our filling criterion alone eliminates 96% of the entries before they are passed on for further analysis. We discover a handful of candidates from this guided search; among them, the monoclinic crystal Ca2Pt2Ga is particularly promising.

Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants

PubMed Central

Bagley, Steven C.; Sirota, Marina; Chen, Richard; Butte, Atul J.; Altman, Russ B.

2016-01-01

Patterns of disease co-occurrence that deviate from statistical independence may represent important constraints on biological mechanism, which sometimes can be explained by shared genetics. In this work we study the relationship between disease co-occurrence and commonly shared genetic architecture of disease. Records of pairs of diseases were combined from two different electronic medical systems (Columbia, Stanford), and compared to a large database of published disease-associated genetic variants (VARIMED); data on 35 disorders were available across all three sources, which include medical records for over 1.2 million patients and variants from over 17,000 publications. Based on the sources in which they appeared, disease pairs were categorized as having predominant clinical, genetic, or both kinds of manifestations. Confounding effects of age on disease incidence were controlled for by only comparing diseases when they fall in the same cluster of similarly shaped incidence patterns. We find that disease pairs that are overrepresented in both electronic medical record systems and in VARIMED come from two main disease classes, autoimmune and neuropsychiatric. We furthermore identify specific genes that are shared within these disease groups. PMID:27115429

Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants.

PubMed

Bagley, Steven C; Sirota, Marina; Chen, Richard; Butte, Atul J; Altman, Russ B

2016-04-01

Patterns of disease co-occurrence that deviate from statistical independence may represent important constraints on biological mechanism, which sometimes can be explained by shared genetics. In this work we study the relationship between disease co-occurrence and commonly shared genetic architecture of disease. Records of pairs of diseases were combined from two different electronic medical systems (Columbia, Stanford), and compared to a large database of published disease-associated genetic variants (VARIMED); data on 35 disorders were available across all three sources, which include medical records for over 1.2 million patients and variants from over 17,000 publications. Based on the sources in which they appeared, disease pairs were categorized as having predominant clinical, genetic, or both kinds of manifestations. Confounding effects of age on disease incidence were controlled for by only comparing diseases when they fall in the same cluster of similarly shaped incidence patterns. We find that disease pairs that are overrepresented in both electronic medical record systems and in VARIMED come from two main disease classes, autoimmune and neuropsychiatric. We furthermore identify specific genes that are shared within these disease groups.

A Dynamic Non Energy Storing Guidance Constraint with Motion Redirection for Robot Assisted Surgery

DTIC Science & Technology

2016-12-01

Abstract— Haptically enabled hands-on or tele-operated surgical robotic systems provide a unique opportunity to integrate pre- and intra... robot -assisted surgical systems aim at improving and extending human capabilities, by exploiting the advantages of robotic systems while keeping the...move during the operation. Robot -assisted beating heart surgery is an example of procedures that can benefit from dynamic constraints. Their

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.

PubMed

Xu, Huilei; Baroukh, Caroline; Dannenfelser, Ruth; Chen, Edward Y; Tan, Christopher M; Kou, Yan; Kim, Yujin E; Lemischka, Ihor R; Ma'ayan, Avi

2013-01-01

High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE

Global search tool for the Advanced Photon Source Integrated Relational Model of Installed Systems (IRMIS) database.

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

Quock, D. E. R.; Cianciarulo, M. B.; APS Engineering Support Division

2007-01-01

The Integrated Relational Model of Installed Systems (IRMIS) is a relational database tool that has been implemented at the Advanced Photon Source to maintain an updated account of approximately 600 control system software applications, 400,000 process variables, and 30,000 control system hardware components. To effectively display this large amount of control system information to operators and engineers, IRMIS was initially built with nine Web-based viewers: Applications Organizing Index, IOC, PLC, Component Type, Installed Components, Network, Controls Spares, Process Variables, and Cables. However, since each viewer is designed to provide details from only one major category of the control system, themore » necessity for a one-stop global search tool for the entire database became apparent. The user requirements for extremely fast database search time and ease of navigation through search results led to the choice of Asynchronous JavaScript and XML (AJAX) technology in the implementation of the IRMIS global search tool. Unique features of the global search tool include a two-tier level of displayed search results, and a database data integrity validation and reporting mechanism.« less

The ChEMBL database as linked open data

PubMed Central

2013-01-01

Background Making data available as Linked Data using Resource Description Framework (RDF) promotes integration with other web resources. RDF documents can natively link to related data, and others can link back using Uniform Resource Identifiers (URIs). RDF makes the data machine-readable and uses extensible vocabularies for additional information, making it easier to scale up inference and data analysis. Results This paper describes recent developments in an ongoing project converting data from the ChEMBL database into RDF triples. Relative to earlier versions, this updated version of ChEMBL-RDF uses recently introduced ontologies, including CHEMINF and CiTO; exposes more information from the database; and is now available as dereferencable, linked data. To demonstrate these new features, we present novel use cases showing further integration with other web resources, including Bio2RDF, Chem2Bio2RDF, and ChemSpider, and showing the use of standard ontologies for querying. Conclusions We have illustrated the advantages of using open standards and ontologies to link the ChEMBL database to other databases. Using those links and the knowledge encoded in standards and ontologies, the ChEMBL-RDF resource creates a foundation for integrated semantic web cheminformatics applications, such as the presented decision support. PMID:23657106

A DBMS architecture for global change research

NASA Astrophysics Data System (ADS)

Hachem, Nabil I.; Gennert, Michael A.; Ward, Matthew O.

1993-08-01

The goal of this research is the design and development of an integrated system for the management of very large scientific databases, cartographic/geographic information processing, and exploratory scientific data analysis for global change research. The system will represent both spatial and temporal knowledge about natural and man-made entities on the eath's surface, following an object-oriented paradigm. A user will be able to derive, modify, and apply, procedures to perform operations on the data, including comparison, derivation, prediction, validation, and visualization. This work represents an effort to extend the database technology with an intrinsic class of operators, which is extensible and responds to the growing needs of scientific research. Of significance is the integration of many diverse forms of data into the database, including cartography, geography, hydrography, hypsography, images, and urban planning data. Equally important is the maintenance of metadata, that is, data about the data, such as coordinate transformation parameters, map scales, and audit trails of previous processing operations. This project will impact the fields of geographical information systems and global change research as well as the database community. It will provide an integrated database management testbed for scientific research, and a testbed for the development of analysis tools to understand and predict global change.

A web-based system architecture for ontology-based data integration in the domain of IT benchmarking

NASA Astrophysics Data System (ADS)

Pfaff, Matthias; Krcmar, Helmut

2018-03-01

In the domain of IT benchmarking (ITBM), a variety of data and information are collected. Although these data serve as the basis for business analyses, no unified semantic representation of such data yet exists. Consequently, data analysis across different distributed data sets and different benchmarks is almost impossible. This paper presents a system architecture and prototypical implementation for an integrated data management of distributed databases based on a domain-specific ontology. To preserve the semantic meaning of the data, the ITBM ontology is linked to data sources and functions as the central concept for database access. Thus, additional databases can be integrated by linking them to this domain-specific ontology and are directly available for further business analyses. Moreover, the web-based system supports the process of mapping ontology concepts to external databases by introducing a semi-automatic mapping recommender and by visualizing possible mapping candidates. The system also provides a natural language interface to easily query linked databases. The expected result of this ontology-based approach of knowledge representation and data access is an increase in knowledge and data sharing in this domain, which will enhance existing business analysis methods.

Real Time Computation of Kinetic Constraints to Support Equilibrium Reconstruction

NASA Astrophysics Data System (ADS)

Eggert, W. J.; Kolemen, E.; Eldon, D.

2016-10-01

A new method for quickly and automatically applying kinetic constraints to EFIT equilibrium reconstructions using readily available data is presented. The ultimate goal is to produce kinetic equilibrium reconstructions in real time and use them to constrain the DCON stability code as part of a disruption avoidance scheme. A first effort presented here replaces CPU-time expensive modules, such as the fast ion pressure profile calculation, with a simplified model. We show with a DIII-D database analysis that we can achieve reasonable predictions for selected applications by modeling the fast ion pressure profile and determining the fit parameters as functions of easily measured quantities including neutron rate and electron temperature on axis. Secondly, we present a strategy for treating Thomson scattering and Charge Exchange Recombination data to automatically form constraints for a kinetic equilibrium reconstruction, a process that historically was performed by hand. Work supported by US DOE DE-AC02-09CH11466 and DE-FC02-04ER54698.

A New Approach To Secure Federated Information Bases Using Agent Technology.

ERIC Educational Resources Information Center

Weippi, Edgar; Klug, Ludwig; Essmayr, Wolfgang

2003-01-01

Discusses database agents which can be used to establish federated information bases by integrating heterogeneous databases. Highlights include characteristics of federated information bases, including incompatible database management systems, schemata, and frequently changing context; software agent technology; Java agents; system architecture;…

Using ontology databases for scalable query answering, inconsistency detection, and data integration

PubMed Central

Dou, Dejing

2011-01-01

An ontology database is a basic relational database management system that models an ontology plus its instances. To reason over the transitive closure of instances in the subsumption hierarchy, for example, an ontology database can either unfold views at query time or propagate assertions using triggers at load time. In this paper, we use existing benchmarks to evaluate our method—using triggers—and we demonstrate that by forward computing inferences, we not only improve query time, but the improvement appears to cost only more space (not time). However, we go on to show that the true penalties were simply opaque to the benchmark, i.e., the benchmark inadequately captures load-time costs. We have applied our methods to two case studies in biomedicine, using ontologies and data from genetics and neuroscience to illustrate two important applications: first, ontology databases answer ontology-based queries effectively; second, using triggers, ontology databases detect instance-based inconsistencies—something not possible using views. Finally, we demonstrate how to extend our methods to perform data integration across multiple, distributed ontology databases. PMID:22163378

Arrhythmia Evaluation in Wearable ECG Devices

PubMed Central

Sadrawi, Muammar; Lin, Chien-Hung; Hsieh, Yita; Kuo, Chia-Chun; Chien, Jen Chien; Haraikawa, Koichi; Abbod, Maysam F.; Shieh, Jiann-Shing

2017-01-01

This study evaluates four databases from PhysioNet: The American Heart Association database (AHADB), Creighton University Ventricular Tachyarrhythmia database (CUDB), MIT-BIH Arrhythmia database (MITDB), and MIT-BIH Noise Stress Test database (NSTDB). The ANSI/AAMI EC57:2012 is used for the evaluation of the algorithms for the supraventricular ectopic beat (SVEB), ventricular ectopic beat (VEB), atrial fibrillation (AF), and ventricular fibrillation (VF) via the evaluation of the sensitivity, positive predictivity and false positive rate. Sample entropy, fast Fourier transform (FFT), and multilayer perceptron neural network with backpropagation training algorithm are selected for the integrated detection algorithms. For this study, the result for SVEB has some improvements compared to a previous study that also utilized ANSI/AAMI EC57. In further, VEB sensitivity and positive predictivity gross evaluations have greater than 80%, except for the positive predictivity of the NSTDB database. For AF gross evaluation of MITDB database, the results show very good classification, excluding the episode sensitivity. In advanced, for VF gross evaluation, the episode sensitivity and positive predictivity for the AHADB, MITDB, and CUDB, have greater than 80%, except for MITDB episode positive predictivity, which is 75%. The achieved results show that the proposed integrated SVEB, VEB, AF, and VF detection algorithm has an accurate classification according to ANSI/AAMI EC57:2012. In conclusion, the proposed integrated detection algorithm can achieve good accuracy in comparison with other previous studies. Furthermore, more advanced algorithms and hardware devices should be performed in future for arrhythmia detection and evaluation. PMID:29068369

An Integrated Molecular Database on Indian Insects.

PubMed

Pratheepa, Maria; Venkatesan, Thiruvengadam; Gracy, Gandhi; Jalali, Sushil Kumar; Rangheswaran, Rajagopal; Antony, Jomin Cruz; Rai, Anil

2018-01-01

MOlecular Database on Indian Insects (MODII) is an online database linking several databases like Insect Pest Info, Insect Barcode Information System (IBIn), Insect Whole Genome sequence, Other Genomic Resources of National Bureau of Agricultural Insect Resources (NBAIR), Whole Genome sequencing of Honey bee viruses, Insecticide resistance gene database and Genomic tools. This database was developed with a holistic approach for collecting information about phenomic and genomic information of agriculturally important insects. This insect resource database is available online for free at http://cib.res.in. http://cib.res.in/.

Searching Across the International Space Station Databases

NASA Technical Reports Server (NTRS)

Maluf, David A.; McDermott, William J.; Smith, Ernest E.; Bell, David G.; Gurram, Mohana

2007-01-01

Data access in the enterprise generally requires us to combine data from different sources and different formats. It is advantageous thus to focus on the intersection of the knowledge across sources and domains; keeping irrelevant knowledge around only serves to make the integration more unwieldy and more complicated than necessary. A context search over multiple domain is proposed in this paper to use context sensitive queries to support disciplined manipulation of domain knowledge resources. The objective of a context search is to provide the capability for interrogating many domain knowledge resources, which are largely semantically disjoint. The search supports formally the tasks of selecting, combining, extending, specializing, and modifying components from a diverse set of domains. This paper demonstrates a new paradigm in composition of information for enterprise applications. In particular, it discusses an approach to achieving data integration across multiple sources, in a manner that does not require heavy investment in database and middleware maintenance. This lean approach to integration leads to cost-effectiveness and scalability of data integration with an underlying schemaless object-relational database management system. This highly scalable, information on demand system framework, called NX-Search, which is an implementation of an information system built on NETMARK. NETMARK is a flexible, high-throughput open database integration framework for managing, storing, and searching unstructured or semi-structured arbitrary XML and HTML used widely at the National Aeronautics Space Administration (NASA) and industry.

Integrated radiologist's workstation enabling the radiologist as an effective clinical consultant

NASA Astrophysics Data System (ADS)

McEnery, Kevin W.; Suitor, Charles T.; Hildebrand, Stan; Downs, Rebecca; Thompson, Stephen K.; Shepard, S. Jeff

2002-05-01

Since February 2000, radiologists at the M. D. Anderson Cancer Center have accessed clinical information through an internally developed radiologist's clinical interpretation workstation called RadStation. This project provides a fully integrated digital dictation workstation with clinical data review. RadStation enables the radiologist as an effective clinical consultant with access to pertinent sources of clinical information at the time of dictation. Data sources not only include prior radiology reports from the radiology information system (RIS) but access to pathology data, laboratory data, history and physicals, clinic notes, and operative reports. With integrated clinical information access, a radiologists's interpretation not only comments on morphologic findings but also can enable evaluation of study findings in the context of pertinent clinical presentation and history. Image access is enabled through the integration of an enterprise image archive (Stentor, San Francisco). Database integration is achieved by a combination of real time HL7 messaging and queries to SQL-based legacy databases. A three-tier system architecture accommodates expanding access to additional databases including real-time patient schedule as well as patient medications and allergies.

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.

PubMed

Cserhati, Matyas F; Pandey, Sanjit; Beaudoin, James J; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. © The Author(s) 2015. Published by Oxford University Press.

Database citation in full text biomedical articles.

PubMed

Kafkas, Şenay; Kim, Jee-Hyub; McEntyre, Johanna R

2013-01-01

Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles, based on analysis of the full text Open Access articles available from Europe PMC. Focusing on citation of entries in the European Nucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text mining doubles the number of structured annotations of database record citations supplied in journal articles by publishers. Many thousands of new literature-database relationships are found by text mining, since these relationships are also not present in the set of articles cited by database records. We recommend that structured annotation of database records in articles is extended to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the literature. The very high precision and high-throughput of this text-mining pipeline makes this activity possible both accurately and at low cost, which will allow the development of new integrated data services.

Database Citation in Full Text Biomedical Articles

PubMed Central

Kafkas, Şenay; Kim, Jee-Hyub; McEntyre, Johanna R.

2013-01-01

Molecular biology and literature databases represent essential infrastructure for life science research. Effective integration of these data resources requires that there are structured cross-references at the level of individual articles and biological records. Here, we describe the current patterns of how database entries are cited in research articles, based on analysis of the full text Open Access articles available from Europe PMC. Focusing on citation of entries in the European Nucleotide Archive (ENA), UniProt and Protein Data Bank, Europe (PDBe), we demonstrate that text mining doubles the number of structured annotations of database record citations supplied in journal articles by publishers. Many thousands of new literature-database relationships are found by text mining, since these relationships are also not present in the set of articles cited by database records. We recommend that structured annotation of database records in articles is extended to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the literature. The very high precision and high-throughput of this text-mining pipeline makes this activity possible both accurately and at low cost, which will allow the development of new integrated data services. PMID:23734176

PIGD: a database for intronless genes in the Poaceae.

PubMed

Yan, Hanwei; Jiang, Cuiping; Li, Xiaoyu; Sheng, Lei; Dong, Qing; Peng, Xiaojian; Li, Qian; Zhao, Yang; Jiang, Haiyang; Cheng, Beijiu

2014-10-01

Intronless genes are a feature of prokaryotes; however, they are widespread and unequally distributed among eukaryotes and represent an important resource to study the evolution of gene architecture. Although many databases on exons and introns exist, there is currently no cohesive database that collects intronless genes in plants into a single database. In this study, we present the Poaceae Intronless Genes Database (PIGD), a user-friendly web interface to explore information on intronless genes from different plants. Five Poaceae species, Sorghum bicolor, Zea mays, Setaria italica, Panicum virgatum and Brachypodium distachyon, are included in the current release of PIGD. Gene annotations and sequence data were collected and integrated from different databases. The primary focus of this study was to provide gene descriptions and gene product records. In addition, functional annotations, subcellular localization prediction and taxonomic distribution are reported. PIGD allows users to readily browse, search and download data. BLAST and comparative analyses are also provided through this online database, which is available at http://pigd.ahau.edu.cn/. PIGD provides a solid platform for the collection, integration and analysis of intronless genes in the Poaceae. As such, this database will be useful for subsequent bio-computational analysis in comparative genomics and evolutionary studies.

Connectionism, parallel constraint satisfaction processes, and gestalt principles: (re) introducing cognitive dynamics to social psychology.

PubMed

Read, S J; Vanman, E J; Miller, L C

1997-01-01

We argue that recent work in connectionist modeling, in particular the parallel constraint satisfaction processes that are central to many of these models, has great importance for understanding issues of both historical and current concern for social psychologists. We first provide a brief description of connectionist modeling, with particular emphasis on parallel constraint satisfaction processes. Second, we examine the tremendous similarities between parallel constraint satisfaction processes and the Gestalt principles that were the foundation for much of modem social psychology. We propose that parallel constraint satisfaction processes provide a computational implementation of the principles of Gestalt psychology that were central to the work of such seminal social psychologists as Asch, Festinger, Heider, and Lewin. Third, we then describe how parallel constraint satisfaction processes have been applied to three areas that were key to the beginnings of modern social psychology and remain central today: impression formation and causal reasoning, cognitive consistency (balance and cognitive dissonance), and goal-directed behavior. We conclude by discussing implications of parallel constraint satisfaction principles for a number of broader issues in social psychology, such as the dynamics of social thought and the integration of social information within the narrow time frame of social interaction.

On the BRST Quantization of the Massless Bosonic Particle in Twistor-Like Formulation

NASA Astrophysics Data System (ADS)

Bandos, Igor; Maznytsia, Alexey; Rudychev, Igor; Sorokin, Dmitri

We study some features of bosonic-particle path-integral quantization in a twistor-like approach by the use of the BRST-BFV-quantization prescription. In the course of the Hamiltonian analysis we observe links between various formulations of the twistor-like particle by performing a conversion of the Hamiltonian constraints of one formulation to another. A particular feature of the conversion procedure applied to turn the second-class constraints into first-class constraints is that the simplest Lorentz-covariant way to do this is to convert a full mixed set of the initial first- and second-class constraints rather than explicitly extracting and converting only the second-class constraints. Another novel feature of the conversion procedure applied below is that in the case of the D = 4 and D = 6 twistor-like particle the number of new auxiliary Lorentz-covariant coordinates, which one introduces to get a system of first-class constraints in an extended phase space, exceeds the number of independent second-class constraints of the original dynamical system. We calculate the twistor-like particle propagator in D = 3,4,6 space-time dimensions and show that it coincides with that of a conventional massless bosonic particle.

Why don't zebras have machine guns? Adaptation, selection, and constraints in evolutionary theory.

PubMed

Shanahan, Timothy

2008-03-01

In an influential paper, Stephen Jay Gould and Richard Lewontin (1979) contrasted selection-driven adaptation with phylogenetic, architectural, and developmental constraints as distinct causes of phenotypic evolution. In subsequent publications Gould (e.g., 1997a,b, 2002) has elaborated this distinction into one between a narrow "Darwinian Fundamentalist" emphasis on "external functionalist" processes, and a more inclusive "pluralist" emphasis on "internal structuralist" principles. Although theoretical integration of functionalist and structuralist explanations is the ultimate aim, natural selection and internal constraints are treated as distinct causes of evolutionary change. This distinction is now routinely taken for granted in the literature in evolutionary biology. I argue that this distinction is problematic because the effects attributed to non-selective constraints are more parsimoniously explained as the ordinary effects of selection itself. Although it may still be a useful shorthand to speak of phylogenetic, architectural, and developmental constraints on phenotypic evolution, it is important to understand that such "constraints" do not constitute an alternative set of causes of evolutionary change. The result of this analysis is a clearer understanding of the relationship between adaptation, selection and constraints as explanatory concepts in evolutionary theory.

From r-spin intersection numbers to Hodge integrals

NASA Astrophysics Data System (ADS)

Ding, Xiang-Mao; Li, Yuping; Meng, Lingxian

2016-01-01

Generalized Kontsevich Matrix Model (GKMM) with a certain given potential is the partition function of r-spin intersection numbers. We represent this GKMM in terms of fermions and expand it in terms of the Schur polynomials by boson-fermion correspondence, and link it with a Hurwitz partition function and a Hodge partition by operators in a widehat{GL}(∞) group. Then, from a W 1+∞ constraint of the partition function of r-spin intersection numbers, we get a W 1+∞ constraint for the Hodge partition function. The W 1+∞ constraint completely determines the Schur polynomials expansion of the Hodge partition function.

Model-based control strategies for systems with constraints of the program type

NASA Astrophysics Data System (ADS)

Jarzębowska, Elżbieta

2006-08-01

The paper presents a model-based tracking control strategy for constrained mechanical systems. Constraints we consider can be material and non-material ones referred to as program constraints. The program constraint equations represent tasks put upon system motions and they can be differential equations of orders higher than one or two, and be non-integrable. The tracking control strategy relies upon two dynamic models: a reference model, which is a dynamic model of a system with arbitrary order differential constraints and a dynamic control model. The reference model serves as a motion planner, which generates inputs to the dynamic control model. It is based upon a generalized program motion equations (GPME) method. The method enables to combine material and program constraints and merge them both into the motion equations. Lagrange's equations with multipliers are the peculiar case of the GPME, since they can be applied to systems with constraints of first orders. Our tracking strategy referred to as a model reference program motion tracking control strategy enables tracking of any program motion predefined by the program constraints. It extends the "trajectory tracking" to the "program motion tracking". We also demonstrate that our tracking strategy can be extended to a hybrid program motion/force tracking.

Ethics across the computer science curriculum: privacy modules in an introductory database course.

PubMed

Appel, Florence

2005-10-01

This paper describes the author's experience of infusing an introductory database course with privacy content, and the on-going project entitled Integrating Ethics Into the Database Curriculum, that evolved from that experience. The project, which has received funding from the National Science Foundation, involves the creation of a set of privacy modules that can be implemented systematically by database educators throughout the database design thread of an undergraduate course.

XML Technology Assessment

DTIC Science & Technology

2001-01-01

System (GCCS) Track Database Management System (TDBM) (3) GCCS Integrated Imagery and Intelligence (3) Intelligence Shared Data Server (ISDS) General ...The CTH is a powerful model that will allow more than just message systems to exchange information. It could be used for object-oriented databases, as...of the Naval Integrated Tactical Environmental System I (NITES I) is used as a case study to demonstrate the utility of this distributed component

IRIS Toxicological Review of Ethylene Glycol Mono-Butyl ...

EPA Pesticide Factsheets

EPA has conducted a peer review of the scientific basis supporting the human health hazard and dose-response assessment of ethylene glycol monobutyl ether that will appear on the Integrated Risk Information System (IRIS) database. EPA is conducting a peer review of the scientific basis supporting the human health hazard and dose-response assessment of propionaldehyde that will appear on the Integrated Risk Information System (IRIS) database.

EPA U.S. NATIONAL MARKAL DATABASE: DATABASE DOCUMENTATION

EPA Science Inventory

This document describes in detail the U.S. Energy System database developed by EPA's Integrated Strategic Assessment Work Group for use with the MARKAL model. The group is part of the Office of Research and Development and is located in the National Risk Management Research Labor...

Urban Neighborhood Information Systems: Crime Prevention and Control Applications.

ERIC Educational Resources Information Center

Pattavina, April; Pierce, Glenn; Saiz, Alan

2002-01-01

Chronicles the need for and development of an interdisciplinary, integrated neighborhood-level database for Boston, Massachusetts, discussing database content and potential applications of this database to a range of criminal justice problems and initiatives (e.g., neighborhood crime patterns, needs assessment, and program planning and…

Brain evolution and development: adaptation, allometry and constraint

PubMed Central

Barton, Robert A.

2016-01-01

Phenotypic traits are products of two processes: evolution and development. But how do these processes combine to produce integrated phenotypes? Comparative studies identify consistent patterns of covariation, or allometries, between brain and body size, and between brain components, indicating the presence of significant constraints limiting independent evolution of separate parts. These constraints are poorly understood, but in principle could be either developmental or functional. The developmental constraints hypothesis suggests that individual components (brain and body size, or individual brain components) tend to evolve together because natural selection operates on relatively simple developmental mechanisms that affect the growth of all parts in a concerted manner. The functional constraints hypothesis suggests that correlated change reflects the action of selection on distributed functional systems connecting the different sub-components, predicting more complex patterns of mosaic change at the level of the functional systems and more complex genetic and developmental mechanisms. These hypotheses are not mutually exclusive but make different predictions. We review recent genetic and neurodevelopmental evidence, concluding that functional rather than developmental constraints are the main cause of the observed patterns. PMID:27629025

The gene expression database for mouse development (GXD): putting developmental expression information at your fingertips.

PubMed

Smith, Constance M; Finger, Jacqueline H; Kadin, James A; Richardson, Joel E; Ringwald, Martin

2014-10-01

Because molecular mechanisms of development are extraordinarily complex, the understanding of these processes requires the integration of pertinent research data. Using the Gene Expression Database for Mouse Development (GXD) as an example, we illustrate the progress made toward this goal, and discuss relevant issues that apply to developmental databases and developmental research in general. Since its first release in 1998, GXD has served the scientific community by integrating multiple types of expression data from publications and electronic submissions and by making these data freely and widely available. Focusing on endogenous gene expression in wild-type and mutant mice and covering data from RNA in situ hybridization, in situ reporter (knock-in), immunohistochemistry, reverse transcriptase-polymerase chain reaction, Northern blot, and Western blot experiments, the database has grown tremendously over the years in terms of data content and search utilities. Currently, GXD includes over 1.4 million annotated expression results and over 260,000 images. All these data and images are readily accessible to many types of database searches. Here we describe the data and search tools of GXD; explain how to use the database most effectively; discuss how we acquire, curate, and integrate developmental expression information; and describe how the research community can help in this process. Copyright © 2014 The Authors Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists.

SInCRe—structural interactome computational resource for Mycobacterium tuberculosis

PubMed Central

Metri, Rahul; Hariharaputran, Sridhar; Ramakrishnan, Gayatri; Anand, Praveen; Raghavender, Upadhyayula S.; Ochoa-Montaño, Bernardo; Higueruelo, Alicia P.; Sowdhamini, Ramanathan; Chandra, Nagasuma R.; Blundell, Tom L.; Srinivasan, Narayanaswamy

2015-01-01

We have developed an integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with protein–protein and protein–small molecule interactions. SInCRe (Structural Interactome Computational Resource) is developed out of CamBan (Cambridge and Bangalore) collaboration. The motivation for development of this database is to provide an integrated platform to allow easily access and interpretation of data and results obtained by all the groups in CamBan in the field of Mtb informatics. In-house algorithms and databases developed independently by various academic groups in CamBan are used to generate Mtb-specific datasets and are integrated in this database to provide a structural dimension to studies on tuberculosis. The SInCRe database readily provides information on identification of functional domains, genome-scale modelling of structures of Mtb proteins and characterization of the small-molecule binding sites within Mtb. The resource also provides structure-based function annotation, information on small-molecule binders including FDA (Food and Drug Administration)-approved drugs, protein–protein interactions (PPIs) and natural compounds that bind to pathogen proteins potentially and result in weakening or elimination of host–pathogen protein–protein interactions. Together they provide prerequisites for identification of off-target binding. Database URL: http://proline.biochem.iisc.ernet.in/sincre PMID:26130660

PosMed-plus: an intelligent search engine that inferentially integrates cross-species information resources for molecular breeding of plants.

PubMed

Makita, Yuko; Kobayashi, Norio; Mochizuki, Yoshiki; Yoshida, Yuko; Asano, Satomi; Heida, Naohiko; Deshpande, Mrinalini; Bhatia, Rinki; Matsushima, Akihiro; Ishii, Manabu; Kawaguchi, Shuji; Iida, Kei; Hanada, Kosuke; Kuromori, Takashi; Seki, Motoaki; Shinozaki, Kazuo; Toyoda, Tetsuro

2009-07-01

Molecular breeding of crops is an efficient way to upgrade plant functions useful to mankind. A key step is forward genetics or positional cloning to identify the genes that confer useful functions. In order to accelerate the whole research process, we have developed an integrated database system powered by an intelligent data-retrieval engine termed PosMed-plus (Positional Medline for plant upgrading science), allowing us to prioritize highly promising candidate genes in a given chromosomal interval(s) of Arabidopsis thaliana and rice, Oryza sativa. By inferentially integrating cross-species information resources including genomes, transcriptomes, proteomes, localizomes, phenomes and literature, the system compares a user's query, such as phenotypic or functional keywords, with the literature associated with the relevant genes located within the interval. By utilizing orthologous and paralogous correspondences, PosMed-plus efficiently integrates cross-species information to facilitate the ranking of rice candidate genes based on evidence from other model species such as Arabidopsis. PosMed-plus is a plant science version of the PosMed system widely used by mammalian researchers, and provides both a powerful integrative search function and a rich integrative display of the integrated databases. PosMed-plus is the first cross-species integrated database that inferentially prioritizes candidate genes for forward genetics approaches in plant science, and will be expanded for wider use in plant upgrading in many species.

Aerodynamic Characteristics and Glide-Back Performance of Langley Glide-Back Booster

NASA Technical Reports Server (NTRS)

Pamadi, Bandu N.; Covell, Peter F.; Tartabini, Paul V.; Murphy, Kelly J.

2004-01-01

NASA-Langley Research Center is conducting system level studies on an-house concept of a small launch vehicle to address NASA's needs for rapid deployment of small payloads to Low Earth Orbit. The vehicle concept is a three-stage system with a reusable first stage and expendable upper stages. The reusable first stage booster, which glides back to launch site after staging around Mach 3 is named the Langley Glide-Back Booster (LGBB). This paper discusses the aerodynamic characteristics of the LGBB from subsonic to supersonic speeds, development of the aerodynamic database and application of this database to evaluate the glide back performance of the LGBB. The aerodynamic database was assembled using a combination of wind tunnel test data and engineering level analysis. The glide back performance of the LGBB was evaluated using a trajectory optimization code and subject to constraints on angle of attack, dynamic pressure and normal acceleration.

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

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2013-12-01

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

Integrating Geographic Information Systems (GIS) Applications into Business Courses Using Online Business Geographics Modules

ERIC Educational Resources Information Center

Miller, Fred; Mangold, W. Glynn; Holmes, Terry

2006-01-01

Although the value of geographic information systems (GIS) technologies is recognized by practitioners and educators alike, GIS instruction has yet to make significant inroads into business curricula. In this article, the authors discuss the constraints of integrating GIS tools into business education. They develop a prototype module for…

Integrating Guided Inquiry into a Traditional Chemistry Curricular Framework

ERIC Educational Resources Information Center

Smithenry, Dennis William

2010-01-01

The case study presented in this paper examines the work of one high school chemistry teacher who has integrated guided inquiry into a yearlong, traditional curricular framework in ways that take into account the constraints and realities of her classroom. The study's findings suggest (1) the extent and frequency to which teachers can…

Integrating CALL into an Iranian EAP Course: Constraints and Affordances

ERIC Educational Resources Information Center

Mehran, Parisa; Alizadeh, Mehrasa

2015-01-01

Iranian universities have recently displayed a growing interest in integrating Computer-Assisted Language Learning (CALL) into teaching/learning English. The English for Academic Purposes (EAP) context, however, is not keeping pace with the current changes since EAP courses are strictly text-based and exam-oriented, and little research has thus…

Integrating Service and Experience: When Education Meets Admissions

ERIC Educational Resources Information Center

Stafne, Marcos

2010-01-01

In the past five years the Rubin Museum of Art has had significant shifts in the organizational structure and interrelation of visitor services and education due to various financial and administrative changes. Though varying levels of integration have existed in the institution's history, due to budget constraints in early 2009, the two separate…

Organizational Support of Technology Integration in One School in Lebanon

ERIC Educational Resources Information Center

Zgheib, Rosine S.

2013-01-01

Technology has been at the center of heated debates in educational settings driving schools to compete for the best technological equipments. However, in Lebanon there is a lag in technology integration matching twenty first century advances. Several barriers related to teacher attitudes, lack of technical skills and organizational constraints to…

The Integrated Medical Model - A Risk Assessment and Decision Support Tool for Human Space Flight Missions

NASA Technical Reports Server (NTRS)

Kerstman, Eric; Minard, Charles G.; Saile, Lynn; FreiredeCarvalho, Mary; Myers, Jerry; Walton, Marlei; Butler, Douglas; Lopez, Vilma

2010-01-01

The Integrated Medical Model (IMM) is a decision support tool that is useful to space flight mission planners and medical system designers in assessing risks and optimizing medical systems. The IMM employs an evidence-based, probabilistic risk assessment (PRA) approach within the operational constraints of space flight.

Information management and analysis system for groundwater data in Thailand

NASA Astrophysics Data System (ADS)

Gill, D.; Luckananurung, P.

1992-01-01

The Ground Water Division of the Thai Department of Mineral Resources maintains a large archive of groundwater data with information on some 50,000 water wells. Each well file contains information on well location, well completion, borehole geology, water levels, water quality, and pumping tests. In order to enable efficient use of this information a computer-based system for information management and analysis was created. The project was sponsored by the United Nations Development Program and the Thai Department of Mineral Resources. The system was designed to serve users who lack prior training in automated data processing. Access is through a friendly user/system dialogue. Tasks are segmented into a number of logical steps, each of which is managed by a separate screen. Selective retrieval is possible by four different methods of area definition and by compliance with user-specified constraints on any combination of database variables. The main types of outputs are: (1) files of retrieved data, screened according to users' specifications; (2) an assortment of pre-formatted reports; (3) computed geochemical parameters and various diagrams of water chemistry derived therefrom; (4) bivariate scatter diagrams and linear regression analysis; (5) posting of data and computed results on maps; and (6) hydraulic aquifer characteristics as computed from pumping tests. Data are entered directly from formatted screens. Most records can be copied directly from hand-written documents. The database-management program performs data integrity checks in real time, enabling corrections at the time of input. The system software can be grouped into: (1) database administration and maintenance—these functions are carried out by the SIR/DBMS software package; (2) user communication interface for task definition and execution control—the interface is written in the operating system command language (VMS/DCL) and in FORTRAN 77; and (3) scientific data-processing programs, written in FORTRAN 77. The system was implemented on a DEC MicroVAX II computer.

CottonGen: a genomics, genetics and breeding database for cotton research

USDA-ARS?s Scientific Manuscript database

CottonGen (http://www.cottongen.org) is a curated and integrated web-based relational database providing access to publicly available genomic, genetic and breeding data for cotton. CottonGen supercedes CottonDB and the Cotton Marker Database, with enhanced tools for easier data sharing, mining, vis...

Integrating Borrowed Records into a Database: Impact on Thesaurus Development and Retrieval.

ERIC Educational Resources Information Center

And Others; Kirtland, Monika

1980-01-01

Discusses three approaches to thesaurus and indexing/retrieval language maintenance for combined databases: reindexing, merging, and initial standardization. Two thesauri for a combined database are evaluated in terms of their compatibility, and indexing practices are compared. Tables and figures help illustrate aspects of the comparison. (SW)

An integrated approach to reservoir modeling

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

Donaldson, K.

1993-08-01

The purpose of this research is to evaluate the usefulness of the following procedural and analytical methods in investigating the heterogeneity of the oil reserve for the Mississipian Big Injun Sandstone of the Granny Creek field, Clay and Roane counties, West Virginia: (1) relational database, (2) two-dimensional cross sections, (3) true three-dimensional modeling, (4) geohistory analysis, (5) a rule-based expert system, and (6) geographical information systems. The large data set could not be effectively integrated and interpreted without this approach. A relational database was designed to fully integrate three- and four-dimensional data. The database provides an effective means for maintainingmore » and manipulating the data. A two-dimensional cross section program was designed to correlate stratigraphy, depositional environments, porosity, permeability, and petrographic data. This flexible design allows for additional four-dimensional data. Dynamic Graphics[sup [trademark

The Relationship Between Constraint and Ductile Fracture Initiation as Defined by Micromechanical Analyses

NASA Technical Reports Server (NTRS)

Panontin, Tina L.; Sheppard, Sheri D.

1994-01-01

The use of small laboratory specimens to predict the integrity of large, complex structures relies on the validity of single parameter fracture mechanics. Unfortunately, the constraint loss associated with large scale yielding, whether in a laboratory specimen because of its small size or in a structure because it contains shallow flaws loaded in tension, can cause the breakdown of classical fracture mechanics and the loss of transferability of critical, global fracture parameters. Although the issue of constraint loss can be eliminated by testing actual structural configurations, such an approach can be prohibitively costly. Hence, a methodology that can correct global fracture parameters for constraint effects is desirable. This research uses micromechanical analyses to define the relationship between global, ductile fracture initiation parameters and constraint in two specimen geometries (SECT and SECB with varying a/w ratios) and one structural geometry (circumferentially cracked pipe). Two local fracture criteria corresponding to ductile fracture micromechanisms are evaluated: a constraint-modified, critical strain criterion for void coalescence proposed by Hancock and Cowling and a critical void ratio criterion for void growth based on the Rice and Tracey model. Crack initiation is assumed to occur when the critical value in each case is reached over some critical length. The primary material of interest is A516-70, a high-hardening pressure vessel steel sensitive to constraint; however, a low-hardening structural steel that is less sensitive to constraint is also being studied. Critical values of local fracture parameters are obtained by numerical analysis and experimental testing of circumferentially notched tensile specimens of varying constraint (e.g., notch radius). These parameters are then used in conjunction with large strain, large deformation, two- and three-dimensional finite element analyses of the geometries listed above to predict crack initiation loads and to calculate the associated (critical) global fracture parameters. The loads are verified experimentally, and microscopy is used to measure pre-crack length, crack tip opening displacement (CTOD), and the amount of stable crack growth. Results for A516-70 steel indicate that the constraint-modified, critical strain criterion with a critical length approximately equal to the grain size (0.0025 inch) provides accurate predictions of crack initiation. The critical void growth criterion is shown to considerably underpredict crack initiation loads with the same critical length. The relationship between the critical value of the J-integral for ductile crack initiation and crack depth for SECT and SECB specimens has been determined using the constraint-modified, critical strain criterion, demonstrating that this micromechanical model can be used to correct in-plane constraint effects due to crack depth and bending vs. tension loading. Finally, the relationship developed for the SECT specimens is used to predict the behavior of circumferentially cracked pipe specimens.

An automated system for terrain database construction

NASA Technical Reports Server (NTRS)

Johnson, L. F.; Fretz, R. K.; Logan, T. L.; Bryant, N. A.

1987-01-01

An automated Terrain Database Preparation System (TDPS) for the construction and editing of terrain databases used in computerized wargaming simulation exercises has been developed. The TDPS system operates under the TAE executive, and it integrates VICAR/IBIS image processing and Geographic Information System software with CAD/CAM data capture and editing capabilities. The terrain database includes such features as roads, rivers, vegetation, and terrain roughness.

3D automatic Cartesian grid generation for Euler flows

NASA Technical Reports Server (NTRS)

Melton, John E.; Enomoto, Francis Y.; Berger, Marsha J.

1993-01-01

We describe a Cartesian grid strategy for the study of three dimensional inviscid flows about arbitrary geometries that uses both conventional and CAD/CAM surface geometry databases. Initial applications of the technique are presented. The elimination of the body-fitted constraint allows the grid generation process to be automated, significantly reducing the time and effort required to develop suitable computational grids for inviscid flowfield simulations.

Web-based software tool for constraint-based design specification of synthetic biological systems.

PubMed

Oberortner, Ernst; Densmore, Douglas

2015-06-19

miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

PubMed Central

2013-01-01

Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

High performance techniques for space mission scheduling

NASA Technical Reports Server (NTRS)

Smith, Stephen F.

1994-01-01

In this paper, we summarize current research at Carnegie Mellon University aimed at development of high performance techniques and tools for space mission scheduling. Similar to prior research in opportunistic scheduling, our approach assumes the use of dynamic analysis of problem constraints as a basis for heuristic focusing of problem solving search. This methodology, however, is grounded in representational assumptions more akin to those adopted in recent temporal planning research, and in a problem solving framework which similarly emphasizes constraint posting in an explicitly maintained solution constraint network. These more general representational assumptions are necessitated by the predominance of state-dependent constraints in space mission planning domains, and the consequent need to integrate resource allocation and plan synthesis processes. First, we review the space mission problems we have considered to date and indicate the results obtained in these application domains. Next, we summarize recent work in constraint posting scheduling procedures, which offer the promise of better future solutions to this class of problems.

Design and implementation of a biomedical image database (BDIM).

PubMed

Aubry, F; Badaoui, S; Kaplan, H; Di Paola, R

1988-01-01

We developed a biomedical image database (BDIM) which proposes a standardized representation of value arrays such as images and curves, and of their associated parameters, independently of their acquisition mode to make their transmission and processing easier. It includes three kinds of interactions, oriented to the users. The network concept was kept as a constraint to incorporate the BDIM in a distributed structure and we maintained compatibility with the ACR/NEMA communication protocol. The management of arrays and their associated parameters includes two distinct bases of objects, linked together via a gateway. The first one manages arrays according to their storage mode: long term storage on optionally on-line mass storage devices, and, for consultations, partial copies of long term stored arrays on hard disk. The second one manages the associated parameters and the gateway by means of the relational DBMS ORACLE. Parameters are grouped into relations. Some of them are in agreement with groups defined by the ACR/NEMA. The other relations describe objects resulting from processed initial objects. These new objects are not described by the ACR/NEMA but they can be inserted as shadow groups of ACR/NEMA description. The relations describing the storage and their pathname constitute the gateway. ORACLE distributed tools and the two-level storage technique will allow the integration of the BDIM into a distributed structure, Queries and array (alone or in sequences) retrieval module has access to the relations via a level in which a dictionary managed by ORACLE is included. This dictionary translates ACR/NEMA objects into objects that can be handled by the DBMS.(ABSTRACT TRUNCATED AT 250 WORDS)

Evaluation of atomic pressure in the multiple time-step integration algorithm.

PubMed

Andoh, Yoshimichi; Yoshii, Noriyuki; Yamada, Atsushi; Okazaki, Susumu

2017-04-15

In molecular dynamics (MD) calculations, reduction in calculation time per MD loop is essential. A multiple time-step (MTS) integration algorithm, the RESPA (Tuckerman and Berne, J. Chem. Phys. 1992, 97, 1990-2001), enables reductions in calculation time by decreasing the frequency of time-consuming long-range interaction calculations. However, the RESPA MTS algorithm involves uncertainties in evaluating the atomic interaction-based pressure (i.e., atomic pressure) of systems with and without holonomic constraints. It is not clear which intermediate forces and constraint forces in the MTS integration procedure should be used to calculate the atomic pressure. In this article, we propose a series of equations to evaluate the atomic pressure in the RESPA MTS integration procedure on the basis of its equivalence to the Velocity-Verlet integration procedure with a single time step (STS). The equations guarantee time-reversibility even for the system with holonomic constrants. Furthermore, we generalize the equations to both (i) arbitrary number of inner time steps and (ii) arbitrary number of force components (RESPA levels). The atomic pressure calculated by our equations with the MTS integration shows excellent agreement with the reference value with the STS, whereas pressures calculated using the conventional ad hoc equations deviated from it. Our equations can be extended straightforwardly to the MTS integration algorithm for the isothermal NVT and isothermal-isobaric NPT ensembles. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

The Future of Asset Management for Human Space Exploration: Supply Classification and an Integrated Database

NASA Technical Reports Server (NTRS)

Shull, Sarah A.; Gralla, Erica L.; deWeck, Olivier L.; Shishko, Robert

2006-01-01

One of the major logistical challenges in human space exploration is asset management. This paper presents observations on the practice of asset management in support of human space flight to date and discusses a functional-based supply classification and a framework for an integrated database that could be used to improve asset management and logistics for human missions to the Moon, Mars and beyond.

The Integrated Medical Model: A Probabilistic Simulation Model for Predicting In-Flight Medical Risks

NASA Technical Reports Server (NTRS)

Keenan, Alexandra; Young, Millennia; Saile, Lynn; Boley, Lynn; Walton, Marlei; Kerstman, Eric; Shah, Ronak; Goodenow, Debra A.; Myers, Jerry G.

2015-01-01

The Integrated Medical Model (IMM) is a probabilistic model that uses simulation to predict mission medical risk. Given a specific mission and crew scenario, medical events are simulated using Monte Carlo methodology to provide estimates of resource utilization, probability of evacuation, probability of loss of crew, and the amount of mission time lost due to illness. Mission and crew scenarios are defined by mission length, extravehicular activity (EVA) schedule, and crew characteristics including: sex, coronary artery calcium score, contacts, dental crowns, history of abdominal surgery, and EVA eligibility. The Integrated Medical Evidence Database (iMED) houses the model inputs for one hundred medical conditions using in-flight, analog, and terrestrial medical data. Inputs include incidence, event durations, resource utilization, and crew functional impairment. Severity of conditions is addressed by defining statistical distributions on the dichotomized best and worst-case scenarios for each condition. The outcome distributions for conditions are bounded by the treatment extremes of the fully treated scenario in which all required resources are available and the untreated scenario in which no required resources are available. Upon occurrence of a simulated medical event, treatment availability is assessed, and outcomes are generated depending on the status of the affected crewmember at the time of onset, including any pre-existing functional impairments or ongoing treatment of concurrent conditions. The main IMM outcomes, including probability of evacuation and loss of crew life, time lost due to medical events, and resource utilization, are useful in informing mission planning decisions. To date, the IMM has been used to assess mission-specific risks with and without certain crewmember characteristics, to determine the impact of eliminating certain resources from the mission medical kit, and to design medical kits that maximally benefit crew health while meeting mass and volume constraints.

The Integrated Medical Model: A Probabilistic Simulation Model Predicting In-Flight Medical Risks

NASA Technical Reports Server (NTRS)

Keenan, Alexandra; Young, Millennia; Saile, Lynn; Boley, Lynn; Walton, Marlei; Kerstman, Eric; Shah, Ronak; Goodenow, Debra A.; Myers, Jerry G., Jr.

2015-01-01

The Integrated Medical Model (IMM) is a probabilistic model that uses simulation to predict mission medical risk. Given a specific mission and crew scenario, medical events are simulated using Monte Carlo methodology to provide estimates of resource utilization, probability of evacuation, probability of loss of crew, and the amount of mission time lost due to illness. Mission and crew scenarios are defined by mission length, extravehicular activity (EVA) schedule, and crew characteristics including: sex, coronary artery calcium score, contacts, dental crowns, history of abdominal surgery, and EVA eligibility. The Integrated Medical Evidence Database (iMED) houses the model inputs for one hundred medical conditions using in-flight, analog, and terrestrial medical data. Inputs include incidence, event durations, resource utilization, and crew functional impairment. Severity of conditions is addressed by defining statistical distributions on the dichotomized best and worst-case scenarios for each condition. The outcome distributions for conditions are bounded by the treatment extremes of the fully treated scenario in which all required resources are available and the untreated scenario in which no required resources are available. Upon occurrence of a simulated medical event, treatment availability is assessed, and outcomes are generated depending on the status of the affected crewmember at the time of onset, including any pre-existing functional impairments or ongoing treatment of concurrent conditions. The main IMM outcomes, including probability of evacuation and loss of crew life, time lost due to medical events, and resource utilization, are useful in informing mission planning decisions. To date, the IMM has been used to assess mission-specific risks with and without certain crewmember characteristics, to determine the impact of eliminating certain resources from the mission medical kit, and to design medical kits that maximally benefit crew health while meeting mass and volume constraints.

An integrated multi criteria approach for landfill siting in a conflicting environmental, economical and socio-cultural area.

PubMed

Eskandari, Mahnaz; Homaee, Mehdi; Mahmodi, Shahla

2012-08-01

Landfill site selection is a complicated multi criteria land use planning that should convince all related stakeholders with different insights. This paper addresses an integrating approach for landfill siting based on conflicting opinions among environmental, economical and socio-cultural expertise. In order to gain optimized siting decision, the issue was investigated in different viewpoints. At first step based on opinion sampling and questionnaire results of 35 experts familiar with local situations, the national environmental legislations and international practices, 13 constraints and 15 factors were built in hierarchical structure. Factors divided into three environmental, economical and socio-cultural groups. In the next step, the GIS-database was developed based on the designated criteria. In the third stage, the criteria standardization and criteria weighting were accomplished. The relative importance weights of criteria and subcriteria were estimated, respectively, using analytical hierarchy process and rank ordering methods based on different experts opinions. Thereafter, by using simple additive weighting method, the suitability maps for landfill siting in Marvdasht, Iran, was evaluated in environmental, economical and socio-cultural visions. The importance of each group of criteria in its own vision was assigned to be higher than two other groups. In the fourth stage, the final suitability map was obtained after crossing three resulted maps in different visions and reported in five suitability classes for landfill construction. This map indicated that almost 1224 ha of the study area can be considered as best suitable class for landfill siting considering all visions. In the last stage, a comprehensive field visit was performed to verify the selected site obtained from the proposed model. This field inspection has confirmed the proposed integrating approach for the landfill siting. Copyright © 2012 Elsevier Ltd. All rights reserved.

Integrating viscoelastic mass spring dampers into position-based dynamics to simulate soft tissue deformation in real time

PubMed Central

Lu, Yuhua; Liu, Qian

2018-01-01

We propose a novel method to simulate soft tissue deformation for virtual surgery applications. The method considers the mechanical properties of soft tissue, such as its viscoelasticity, nonlinearity and incompressibility; its speed, stability and accuracy also meet the requirements for a surgery simulator. Modifying the traditional equation for mass spring dampers (MSD) introduces nonlinearity and viscoelasticity into the calculation of elastic force. Then, the elastic force is used in the constraint projection step for naturally reducing constraint potential. The node position is enforced by the combined spring force and constraint conservative force through Newton's second law. We conduct a comparison study of conventional MSD and position-based dynamics for our new integrating method. Our approach enables stable, fast and large step simulation by freely controlling visual effects based on nonlinearity, viscoelasticity and incompressibility. We implement a laparoscopic cholecystectomy simulator to demonstrate the practicality of our method, in which liver and gallbladder deformation can be simulated in real time. Our method is an appropriate choice for the development of real-time virtual surgery applications. PMID:29515870

Integrating viscoelastic mass spring dampers into position-based dynamics to simulate soft tissue deformation in real time.

PubMed

Xu, Lang; Lu, Yuhua; Liu, Qian

2018-02-01

We propose a novel method to simulate soft tissue deformation for virtual surgery applications. The method considers the mechanical properties of soft tissue, such as its viscoelasticity, nonlinearity and incompressibility; its speed, stability and accuracy also meet the requirements for a surgery simulator. Modifying the traditional equation for mass spring dampers (MSD) introduces nonlinearity and viscoelasticity into the calculation of elastic force. Then, the elastic force is used in the constraint projection step for naturally reducing constraint potential. The node position is enforced by the combined spring force and constraint conservative force through Newton's second law. We conduct a comparison study of conventional MSD and position-based dynamics for our new integrating method. Our approach enables stable, fast and large step simulation by freely controlling visual effects based on nonlinearity, viscoelasticity and incompressibility. We implement a laparoscopic cholecystectomy simulator to demonstrate the practicality of our method, in which liver and gallbladder deformation can be simulated in real time. Our method is an appropriate choice for the development of real-time virtual surgery applications.

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

PubMed

Budinich, Marko; Bourdon, Jérémie; Larhlimi, Abdelhalim; Eveillard, Damien

2017-01-01

Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.

The depth estimation of 3D face from single 2D picture based on manifold learning constraints

NASA Astrophysics Data System (ADS)

Li, Xia; Yang, Yang; Xiong, Hailiang; Liu, Yunxia

2018-04-01

The estimation of depth is virtual important in 3D face reconstruction. In this paper, we propose a t-SNE based on manifold learning constraints and introduce K-means method to divide the original database into several subset, and the selected optimal subset to reconstruct the 3D face depth information can greatly reduce the computational complexity. Firstly, we carry out the t-SNE operation to reduce the key feature points in each 3D face model from 1×249 to 1×2. Secondly, the K-means method is applied to divide the training 3D database into several subset. Thirdly, the Euclidean distance between the 83 feature points of the image to be estimated and the feature point information before the dimension reduction of each cluster center is calculated. The category of the image to be estimated is judged according to the minimum Euclidean distance. Finally, the method Kong D will be applied only in the optimal subset to estimate the depth value information of 83 feature points of 2D face images. Achieving the final depth estimation results, thus the computational complexity is greatly reduced. Compared with the traditional traversal search estimation method, although the proposed method error rate is reduced by 0.49, the number of searches decreases with the change of the category. In order to validate our approach, we use a public database to mimic the task of estimating the depth of face images from 2D images. The average number of searches decreased by 83.19%.

A database perspective of the transition from single-use (ancillary-based) systems to integrated models supporting clinical care and research in a MUMPS-based system.

PubMed

Siegel, J; Kirkland, D

1991-01-01

The Composite Health Care System (CHCS), a MUMPS-based hospital information system (HIS), has evolved from the Decentralized Hospital Computer Program (DHCP) installed within VA Hospitals. The authors explore the evolution of an ancillary-based system toward an integrated model with a look at its current state and possible future. The history and relationships between orders of different types tie specific patient-related data into a logical and temporal model. Diagrams demonstrate how the database structure has evolved to support clinical needs for integration. It is suggested that a fully integrated model is capable of meeting traditional HIS needs.

FDT 2.0: Improving scalability of the fuzzy decision tree induction tool - integrating database storage.

PubMed

Durham, Erin-Elizabeth A; Yu, Xiaxia; Harrison, Robert W

2014-12-01

Effective machine-learning handles large datasets efficiently. One key feature of handling large data is the use of databases such as MySQL. The freeware fuzzy decision tree induction tool, FDT, is a scalable supervised-classification software tool implementing fuzzy decision trees. It is based on an optimized fuzzy ID3 (FID3) algorithm. FDT 2.0 improves upon FDT 1.0 by bridging the gap between data science and data engineering: it combines a robust decisioning tool with data retention for future decisions, so that the tool does not need to be recalibrated from scratch every time a new decision is required. In this paper we briefly review the analytical capabilities of the freeware FDT tool and its major features and functionalities; examples of large biological datasets from HIV, microRNAs and sRNAs are included. This work shows how to integrate fuzzy decision algorithms with modern database technology. In addition, we show that integrating the fuzzy decision tree induction tool with database storage allows for optimal user satisfaction in today's Data Analytics world.

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

PubMed Central

Lee, Ji-Hyun; Park, Kyoung Mii; Han, Dong-Jin; Bang, Nam Young; Kim, Do-Hee; Na, Hyeongjin; Lim, Semi; Kim, Tae Bum; Kim, Dae Gyu; Kim, Hyun-Jung; Chung, Yeonseok; Sung, Sang Hyun; Surh, Young-Joon; Kim, Sunghoon; Han, Byung Woo

2015-01-01

Despite the growing attention given to Traditional Medicine (TM) worldwide, there is no well-known, publicly available, integrated bio-pharmacological Traditional Korean Medicine (TKM) database for researchers in drug discovery. In this study, we have constructed PharmDB-K, which offers comprehensive information relating to TKM-associated drugs (compound), disease indication, and protein relationships. To explore the underlying molecular interaction of TKM, we integrated fourteen different databases, six Pharmacopoeias, and literature, and established a massive bio-pharmacological network for TKM and experimentally validated some cases predicted from the PharmDB-K analyses. Currently, PharmDB-K contains information about 262 TKMs, 7,815 drugs, 3,721 diseases, 32,373 proteins, and 1,887 side effects. One of the unique sets of information in PharmDB-K includes 400 indicator compounds used for standardization of herbal medicine. Furthermore, we are operating PharmDB-K via phExplorer (a network visualization software) and BioMart (a data federation framework) for convenient search and analysis of the TKM network. Database URL: http://pharmdb-k.org, http://biomart.i-pharm.org. PMID:26555441

Constructing distributed Hippocratic video databases for privacy-preserving online patient training and counseling.

PubMed

Peng, Jinye; Babaguchi, Noboru; Luo, Hangzai; Gao, Yuli; Fan, Jianping

2010-07-01

Digital video now plays an important role in supporting more profitable online patient training and counseling, and integration of patient training videos from multiple competitive organizations in the health care network will result in better offerings for patients. However, privacy concerns often prevent multiple competitive organizations from sharing and integrating their patient training videos. In addition, patients with infectious or chronic diseases may not want the online patient training organizations to identify who they are or even which video clips they are interested in. Thus, there is an urgent need to develop more effective techniques to protect both video content privacy and access privacy . In this paper, we have developed a new approach to construct a distributed Hippocratic video database system for supporting more profitable online patient training and counseling. First, a new database modeling approach is developed to support concept-oriented video database organization and assign a degree of privacy of the video content for each database level automatically. Second, a new algorithm is developed to protect the video content privacy at the level of individual video clip by filtering out the privacy-sensitive human objects automatically. In order to integrate the patient training videos from multiple competitive organizations for constructing a centralized video database indexing structure, a privacy-preserving video sharing scheme is developed to support privacy-preserving distributed classifier training and prevent the statistical inferences from the videos that are shared for cross-validation of video classifiers. Our experiments on large-scale video databases have also provided very convincing results.

Automatic liver segmentation from abdominal CT volumes using graph cuts and border marching.

PubMed

Liao, Miao; Zhao, Yu-Qian; Liu, Xi-Yao; Zeng, Ye-Zhan; Zou, Bei-Ji; Wang, Xiao-Fang; Shih, Frank Y

2017-05-01

Identifying liver regions from abdominal computed tomography (CT) volumes is an important task for computer-aided liver disease diagnosis and surgical planning. This paper presents a fully automatic method for liver segmentation from CT volumes based on graph cuts and border marching. An initial slice is segmented by density peak clustering. Based on pixel- and patch-wise features, an intensity model and a PCA-based regional appearance model are developed to enhance the contrast between liver and background. Then, these models as well as the location constraint estimated iteratively are integrated into graph cuts in order to segment the liver in each slice automatically. Finally, a vessel compensation method based on the border marching is used to increase the segmentation accuracy. Experiments are conducted on a clinical data set we created and also on the MICCAI2007 Grand Challenge liver data. The results show that the proposed intensity, appearance models, and the location constraint are significantly effective for liver recognition, and the undersegmented vessels can be compensated by the border marching based method. The segmentation performances in terms of VOE, RVD, ASD, RMSD, and MSD as well as the average running time achieved by our method on the SLIVER07 public database are 5.8 ± 3.2%, -0.1 ± 4.1%, 1.0 ± 0.5mm, 2.0 ± 1.2mm, 21.2 ± 9.3mm, and 4.7 minutes, respectively, which are superior to those of existing methods. The proposed method does not require time-consuming training process and statistical model construction, and is capable of dealing with complicated shapes and intensity variations successfully. Copyright © 2017 Elsevier B.V. All rights reserved.

InterAction Database (IADB)

Cancer.gov

The InterAction Database includes demographic and prescription information for more than 500,000 patients in the northern and middle Netherlands and has been integrated with other systems to enhance data collection and analysis.

Reflecting on the challenges of building a rich interconnected metadata database to describe the experiments of phase six of the coupled climate model intercomparison project (CMIP6) for the Earth System Documentation Project (ES-DOC) and anticipating the opportunities that tooling and services based on rich metadata can provide.

NASA Astrophysics Data System (ADS)

Pascoe, C. L.

2017-12-01

The Coupled Model Intercomparison Project (CMIP) has coordinated climate model experiments involving multiple international modelling teams since 1995. This has led to a better understanding of past, present, and future climate. The 2017 sixth phase of the CMIP process (CMIP6) consists of a suite of common experiments, and 21 separate CMIP-Endorsed Model Intercomparison Projects (MIPs) making a total of 244 separate experiments. Precise descriptions of the suite of CMIP6 experiments have been captured in a Common Information Model (CIM) database by the Earth System Documentation Project (ES-DOC). The database contains descriptions of forcings, model configuration requirements, ensemble information and citation links, as well as text descriptions and information about the rationale for each experiment. The database was built from statements about the experiments found in the academic literature, the MIP submissions to the World Climate Research Programme (WCRP), WCRP summary tables and correspondence with the principle investigators for each MIP. The database was collated using spreadsheets which are archived in the ES-DOC Github repository and then rendered on the ES-DOC website. A diagramatic view of the workflow of building the database of experiment metadata for CMIP6 is shown in the attached figure.The CIM provides the formalism to collect detailed information from diverse sources in a standard way across all the CMIP6 MIPs. The ES-DOC documentation acts as a unified reference for CMIP6 information to be used both by data producers and consumers. This is especially important given the federated nature of the CMIP6 project. Because the CIM allows forcing constraints and other experiment attributes to be referred to by more than one experiment, we can streamline the process of collecting information from modelling groups about how they set up their models for each experiment. End users of the climate model archive will be able to ask questions enabled by the interconnectedness of the metadata such as "Which MIPs make use of experiment A?" and "Which experiments use forcing constraint B?".

Integration of Evidence Base into a Probabilistic Risk Assessment

NASA Technical Reports Server (NTRS)

Saile, Lyn; Lopez, Vilma; Bickham, Grandin; Kerstman, Eric; FreiredeCarvalho, Mary; Byrne, Vicky; Butler, Douglas; Myers, Jerry; Walton, Marlei

2011-01-01

INTRODUCTION: A probabilistic decision support model such as the Integrated Medical Model (IMM) utilizes an immense amount of input data that necessitates a systematic, integrated approach for data collection, and management. As a result of this approach, IMM is able to forecasts medical events, resource utilization and crew health during space flight. METHODS: Inflight data is the most desirable input for the Integrated Medical Model. Non-attributable inflight data is collected from the Lifetime Surveillance for Astronaut Health study as well as the engineers, flight surgeons, and astronauts themselves. When inflight data is unavailable cohort studies, other models and Bayesian analyses are used, in addition to subject matters experts input on occasion. To determine the quality of evidence of a medical condition, the data source is categorized and assigned a level of evidence from 1-5; the highest level is one. The collected data reside and are managed in a relational SQL database with a web-based interface for data entry and review. The database is also capable of interfacing with outside applications which expands capabilities within the database itself. Via the public interface, customers can access a formatted Clinical Findings Form (CLiFF) that outlines the model input and evidence base for each medical condition. Changes to the database are tracked using a documented Configuration Management process. DISSCUSSION: This strategic approach provides a comprehensive data management plan for IMM. The IMM Database s structure and architecture has proven to support additional usages. As seen by the resources utilization across medical conditions analysis. In addition, the IMM Database s web-based interface provides a user-friendly format for customers to browse and download the clinical information for medical conditions. It is this type of functionality that will provide Exploratory Medicine Capabilities the evidence base for their medical condition list. CONCLUSION: The IMM Database in junction with the IMM is helping NASA aerospace program improve the health care and reduce risk for the astronauts crew. Both the database and model will continue to expand to meet customer needs through its multi-disciplinary evidence based approach to managing data. Future expansion could serve as a platform for a Space Medicine Wiki of medical conditions.

Eulerian Formulation of Spatially Constrained Elastic Rods

NASA Astrophysics Data System (ADS)

Huynen, Alexandre

Slender elastic rods are ubiquitous in nature and technology. For a vast majority of applications, the rod deflection is restricted by an external constraint and a significant part of the elastic body is in contact with a stiff constraining surface. The research work presented in this doctoral dissertation formulates a computational model for the solution of elastic rods constrained inside or around frictionless tube-like surfaces. The segmentation strategy adopted to cope with this complex class of problems consists in sequencing the global problem into, comparatively simpler, elementary problems either in continuous contact with the constraint or contact-free between their extremities. Within the conventional Lagrangian formulation of elastic rods, this approach is however associated with two major drawbacks. First, the boundary conditions specifying the locations of the rod centerline at both extremities of each elementary problem lead to the establishment of isoperimetric constraints, i.e., integral constraints on the unknown length of the rod. Second, the assessment of the unilateral contact condition requires, in principle, the comparison of two curves parametrized by distinct curvilinear coordinates, viz. the rod centerline and the constraint axis. Both conspire to burden the computations associated with the method. To streamline the solution along the elementary problems and rationalize the assessment of the unilateral contact condition, the rod governing equations are reformulated within the Eulerian framework of the constraint. The methodical exploration of both types of elementary problems leads to specific formulations of the rod governing equations that stress the profound connection between the mechanics of the rod and the geometry of the constraint surface. The proposed Eulerian reformulation, which restates the rod local equilibrium in terms of the curvilinear coordinate associated with the constraint axis, describes the rod deformed configuration by means of either its relative position with respect to the constraint axis (contact-free segments) or its angular position on the constraint surface (continuous contacts.) This formulation circumvents both drawbacks that afflict the conventional Lagrangian approach associated with the segmentation strategy. As the a priori unknown domain, viz. the rod length, is substituted for the known constraint axis, the free boundary problem and the associated isoperimetric constraints are converted into a classical two-point boundary value problem. Additionally, the description of the rod deflection by means of its eccentricity with respect to the constraint axis trivializes the assessment of the unilateral contact condition. Along continuous contacts, this formulation expresses the strain variables, measuring the rod change of shape, in terms of the geometric invariants of the constraint surface, and emphasizes the influence of the constraint local geometry on the reaction pressure. Formalizing the segmentation strategy, a computational model that exploits the Eulerian formulation of the rod governing equations is devised. To solve the quasi-static deflection of elastic rods constrained inside or around a tube-like surface, this computational model identifies the number of contacts, their nature (either discrete or continuous), and the rod configuration at the connections that satisfies the unilateral contact condition and preserves the rod integrity along the sequence of elementary problems.

dbPAF: an integrative database of protein phosphorylation in animals and fungi.

PubMed

Ullah, Shahid; Lin, Shaofeng; Xu, Yang; Deng, Wankun; Ma, Lili; Zhang, Ying; Liu, Zexian; Xue, Yu

2016-03-24

Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.

Special delivery: an analysis of mHealth in maternal and newborn health programs and their outcomes around the world.

PubMed

Tamrat, Tigest; Kachnowski, Stan

2012-07-01

Mobile health (mHealth) encompasses the use of mobile telecommunication and multimedia into increasingly mobile and wireless health care delivery systems and has the potential to improve tens of thousands of lives each year. The ubiquity and penetration of mobile phones presents the opportunity to leverage mHealth for maternal and newborn care, particularly in under-resourced health ecosystems. Moreover, the slow progress and funding constraints in attaining the Millennium Development Goals for child and maternal health encourage harnessing innovative measures, such as mHealth, to address these public health priorities. This literature review provides a schematic overview of the outcomes, barriers, and strategies of integrating mHealth to improve prenatal and neonatal health outcomes. Six electronic databases were methodically searched using predetermined search terms. Retrieved articles were then categorized according to themes identified in previous studies. A total of 34 articles and reports contributed to the findings with information about the use and limitations of mHealth for prenatal and neonatal healthcare access and delivery. Health systems have implemented mHealth programs to facilitate emergency medical responses, point-of-care support, health promotion and data collection. However, the policy infrastructure for funding, coordinating and guiding the sustainable adoption of prenatal and neonatal mHealth services remains under-developed. The integration of mobile health for prenatal and newborn health services has demonstrated positive outcomes, but the sustainability and scalability of operations requires further feedback from and evaluation of ongoing programs.

Assured crew return vehicle man-systems integration standards

NASA Technical Reports Server (NTRS)

1991-01-01

This is Volume 6 of the Man-Systems Integration Standards (MSIS) family of documents, which is contained in several volumes and a relational database. Each volume has a specific purpose, and each has been assembled from the data contained in the relational database. Volume 6 serves as the Assured Crew Return Vehicle project man-systems integration design requirements. The data in this document is a subset of the data found in Volume 1 and defines the requirements which are pertinent to the Assured Crew Return Vehicle as defined in the SPRD. Additional data and guidelines are provided to assist in the design.

Artificial Intelligence Support for Landing Site Selection on Mars

NASA Astrophysics Data System (ADS)

Rongier, G.; Pankratius, V.

2017-12-01

Mars is a key target for planetary exploration; a better understanding of its evolution and habitability requires roving in situ. Landing site selection is becoming more challenging for scientists as new instruments generate higher data volumes. The involved engineering and scientific constraints make site selection and the anticipation of possible onsite actions into a complex optimization problem: there may be multiple acceptable solutions depending on various goals and assumptions. Solutions must also account for missing data, errors, and potential biases. To address these problems, we propose an AI-informed decision support system that allows scientists, mission designers, engineers, and committees to explore alternative site selection choices based on data. In particular, we demonstrate first results of an exploratory case study using fuzzy logic and a simulation of a rover's mobility map based on the fast marching algorithm. Our system computes favorability maps of the entire planet to facilitate landing site selection and allows a definition of different configurations for rovers, science target priorities, landing ellipses, and other constraints. For a rover similar to NASA's Mars 2020 rover, we present results in form of a site favorability map as well as four derived exploration scenarios that depend on different prioritized scientific targets, all visualizing inherent tradeoffs. Our method uses the NASA PDS Geosciences Node and the NASA/ICA Integrated Database of Planetary Features. Under common assumptions, the data products reveal Eastern Margaritifer Terra and Meridiani Planum to be the most favorable sites due to a high concentration of scientific targets and a flat, easily navigable surface. Our method also allows mission designers to investigate which constraints have the highest impact on the mission exploration potential and to change parameter ranges. Increasing the elevation limit for landing, for example, provides access to many additional, more interesting sites on the southern terrains of Mars. The speed of current rovers is another limit to exploration capabilities: our system helps quantify how speed increases can improve the number of reachable targets in the search space. We acknowledge support from NASA AISTNNX15AG84G (PI Pankratius) and NSF ACI1442997 (PI Pankratius).

Comet: an open-source MS/MS sequence database search tool.

PubMed

Eng, Jimmy K; Jahan, Tahmina A; Hoopmann, Michael R

2013-01-01

Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Keyless Entry: Building a Text Database Using OCR Technology.

ERIC Educational Resources Information Center

Grotophorst, Clyde W.

1989-01-01

Discusses the use of optical character recognition (OCR) technology to produce an ASCII text database. A tutorial on digital scanning and OCR is provided, and a systems integration project which used the Calera CDP-3000XF scanner and text retrieval software to construct a database of dissertations at George Mason University is described. (four…

An Autonomic Framework for Integrating Security and Quality of Service Support in Databases

ERIC Educational Resources Information Center

Alomari, Firas

2013-01-01

The back-end databases of multi-tiered applications are a major data security concern for enterprises. The abundance of these systems and the emergence of new and different threats require multiple and overlapping security mechanisms. Therefore, providing multiple and diverse database intrusion detection and prevention systems (IDPS) is a critical…

Depth from Edge and Intensity Based Stereo.

DTIC Science & Technology

1982-09-01

a Mars Viking vehicle, and a random dotted coffee jar. Assessment of the algorithm is a bit difficult: it uses a fairly simple control structure with...correspondences. This use of an evaluation function estimator allowed the introduction of the extensive pruning of a branch and bound algorithm. Even with it...Figure 3-6). This is the edge reversal constraint, and was integral to the pruning . As it happens, this same constraint is the key to the use of the

Space station payload operations scheduling with ESP2

NASA Technical Reports Server (NTRS)

Stacy, Kenneth L.; Jaap, John P.

1988-01-01

The Mission Analysis Division of the Systems Analysis and Integration Laboratory at the Marshall Space Flight Center is developing a system of programs to handle all aspects of scheduling payload operations for Space Station. The Expert Scheduling Program (ESP2) is the heart of this system. The task of payload operations scheduling can be simply stated as positioning the payload activities in a mission so that they collect their desired data without interfering with other activities or violating mission constraints. ESP2 is an advanced version of the Experiment Scheduling Program (ESP) which was developed by the Mission Integration Branch beginning in 1979 to schedule Spacelab payload activities. The automatic scheduler in ESP2 is an expert system that embodies the rules that expert planners would use to schedule payload operations by hand. This scheduler uses depth-first searching, backtracking, and forward chaining techniques to place an activity so that constraints (such as crew, resources, and orbit opportunities) are not violated. It has an explanation facility to show why an activity was or was not scheduled at a certain time. The ESP2 user can also place the activities in the schedule manually. The program offers graphical assistance to the user and will advise when constraints are being violated. ESP2 also has an option to identify conflict introduced into an existing schedule by changes to payload requirements, mission constraints, and orbit opportunities.

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

PubMed

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

2016-01-01

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

Simplified, inverse, ejector design tool

NASA Technical Reports Server (NTRS)

Dechant, Lawrence J.

1993-01-01

A simple lumped parameter based inverse design tool has been developed which provides flow path geometry and entrainment estimates subject to operational, acoustic, and design constraints. These constraints are manifested through specification of primary mass flow rate or ejector thrust, fully-mixed exit velocity, and static pressure matching. Fundamentally, integral forms of the conservation equations coupled with the specified design constraints are combined to yield an easily invertible linear system in terms of the flow path cross-sectional areas. Entrainment is computed by back substitution. Initial comparison with experimental and analogous one-dimensional methods show good agreement. Thus, this simple inverse design code provides an analytically based, preliminary design tool with direct application to High Speed Civil Transport (HSCT) design studies.

Structural design optimization with survivability dependent constraints application: Primary wing box of a multi-role fighter

NASA Technical Reports Server (NTRS)

Dolvin, Douglas J.

1992-01-01

The superior survivability of a multirole fighter is dependent upon balanced integration of technologies for reduced vulnerability and susceptability. The objective is to develop a methodology for structural design optimization with survivability dependent constraints. The design criteria for optimization will be survivability in a tactical laser environment. The following analyses are studied to establish a dependent design relationship between structural weight and survivability: (1) develop a physically linked global design model of survivability variables; and (2) apply conventional constraints to quantify survivability dependent design. It was not possible to develop an exact approach which would include all aspects of survivability dependent design, therefore guidelines are offered for solving similar problems.

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis

PubMed Central

Gadelha, Luiz; Ribeiro-Alves, Marcelo; Porto, Fábio

2017-01-01

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were analyzed. The results are integrated into GeNNet-DB, a database about genes, clusters, experiments and their properties and relationships. The resulting graph database is explored with queries that demonstrate the expressiveness of this data model for reasoning about gene interaction networks. GeNNet is the first platform to integrate the analytical process of transcriptome data with graph databases. It provides a comprehensive set of tools that would otherwise be challenging for non-expert users to install and use. Developers can add new functionality to components of GeNNet. The derived data allows for testing previous hypotheses about an experiment and exploring new ones through the interactive graph database environment. It enables the analysis of different data on humans, rhesus, mice and rat coming from Affymetrix platforms. GeNNet is available as an open source platform at https://github.com/raquele/GeNNet and can be retrieved as a software container with the command docker pull quelopes/gennet. PMID:28695067

GeNNet: an integrated platform for unifying scientific workflows and graph databases for transcriptome data analysis.

PubMed

Costa, Raquel L; Gadelha, Luiz; Ribeiro-Alves, Marcelo; Porto, Fábio

2017-01-01

There are many steps in analyzing transcriptome data, from the acquisition of raw data to the selection of a subset of representative genes that explain a scientific hypothesis. The data produced can be represented as networks of interactions among genes and these may additionally be integrated with other biological databases, such as Protein-Protein Interactions, transcription factors and gene annotation. However, the results of these analyses remain fragmented, imposing difficulties, either for posterior inspection of results, or for meta-analysis by the incorporation of new related data. Integrating databases and tools into scientific workflows, orchestrating their execution, and managing the resulting data and its respective metadata are challenging tasks. Additionally, a great amount of effort is equally required to run in-silico experiments to structure and compose the information as needed for analysis. Different programs may need to be applied and different files are produced during the experiment cycle. In this context, the availability of a platform supporting experiment execution is paramount. We present GeNNet, an integrated transcriptome analysis platform that unifies scientific workflows with graph databases for selecting relevant genes according to the evaluated biological systems. It includes GeNNet-Wf, a scientific workflow that pre-loads biological data, pre-processes raw microarray data and conducts a series of analyses including normalization, differential expression inference, clusterization and gene set enrichment analysis. A user-friendly web interface, GeNNet-Web, allows for setting parameters, executing, and visualizing the results of GeNNet-Wf executions. To demonstrate the features of GeNNet, we performed case studies with data retrieved from GEO, particularly using a single-factor experiment in different analysis scenarios. As a result, we obtained differentially expressed genes for which biological functions were analyzed. The results are integrated into GeNNet-DB, a database about genes, clusters, experiments and their properties and relationships. The resulting graph database is explored with queries that demonstrate the expressiveness of this data model for reasoning about gene interaction networks. GeNNet is the first platform to integrate the analytical process of transcriptome data with graph databases. It provides a comprehensive set of tools that would otherwise be challenging for non-expert users to install and use. Developers can add new functionality to components of GeNNet. The derived data allows for testing previous hypotheses about an experiment and exploring new ones through the interactive graph database environment. It enables the analysis of different data on humans, rhesus, mice and rat coming from Affymetrix platforms. GeNNet is available as an open source platform at https://github.com/raquele/GeNNet and can be retrieved as a software container with the command docker pull quelopes/gennet.

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

PubMed

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

2015-09-01

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

Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

PubMed Central

2011-01-01

Background Solventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i) naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii) can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis). Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications. Results We present the first genome-scale metabolic model (iCM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test). Inhibition of the hydrogenase reaction was found to have a strong effect on butanol formation--as experimentally observed. Conclusions Microbial production of butanol by C. beijerinckii offers a promising, sustainable, method for generation of this important chemical and potential biofuel. iCM925 is a predictive model that can accurately reproduce physiological behavior and provide insight into the underlying mechanisms of microbial butanol production. As such, the model will be instrumental in efforts to better understand, and metabolically engineer, this microorganism for improved butanol production. PMID:21846360

Family Assessment/Treatment/Evaluation Methods Integrated for Helping Teen Suicide Attempters/Families in Short Term Psychiatric Hospitalization Programs.

ERIC Educational Resources Information Center

Shepard, Suzanne

The assessment process can be integrated with treatment and evaluation for helping teenage suicide attempters and families in short term psychiatric hospitalization programs. The method is an extremely efficient way for the therapist to work within a given time constraint. During family assessment sufficient information can be gathered to…

Digital Technologies in Mathematics Classrooms: Barriers, Lessons and Focus on Teachers

ERIC Educational Resources Information Center

Sacristán, Ana Isabel

2017-01-01

In this paper, drawing from data from several experiences and studies in which I have been involved in Mexico, I reflect on the constraints and inertia of classroom cultures, and the barriers to successful, meaningful and transformative technology integration in mathematics classroom. I focus on teachers as key players for this integration,…

Shuttle program. STS-7 feasibility assessment: IUS/TDRS-A

NASA Technical Reports Server (NTRS)

1979-01-01

This Space Transportation System 7 (STS-7) Flight Feasibility Assessment (FFA) provides a base from which the various design, operation, and integration elements associated with Tracking and Data Relay Satellite-A can perform mission planning and analysis. The STS-7 FFA identifies conflicts, issues, and concerns associated with the integrated flight design requirements and constraints.

IRIS Toxicological Review of Methanol (Non-Cancer) ...

EPA Pesticide Factsheets

EPA is conducting a peer review and public comment of the scientific basis supporting the human health hazard and dose-response assessment of methanol (non-cancer) that when finalized will appear on the Integrated Risk Information System (IRIS) database. EPA is conducting a peer review of the scientific basis supporting the human health hazard and dose-response assessment of methanol (non-cancer) that will appear in the Integrated Risk Information System (IRIS) database.

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.

RAIN: RNA–protein Association and Interaction Networks

PubMed Central

Junge, Alexander; Refsgaard, Jan C.; Garde, Christian; Pan, Xiaoyong; Santos, Alberto; Alkan, Ferhat; Anthon, Christian; von Mering, Christian; Workman, Christopher T.; Jensen, Lars Juhl; Gorodkin, Jan

2017-01-01

Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) as well. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA–RNA and ncRNA–protein interactions and its integration with the STRING database of protein–protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literature mining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessible web interface and all interaction data can be downloaded. Database URL: http://rth.dk/resources/rain PMID:28077569

Correlation functions of main-chain polymer nematics constrained by tensorial and vectorial conservation laws

NASA Astrophysics Data System (ADS)

Svenšek, Daniel; Podgornik, Rudolf

2015-09-01

We present and analyze correlation functions of a main-chain polymer nematic in a continuum worm-like chain description for two types of constraints formalized by the tensorial and vectorial conservation laws, both originating in the microscopic chain integrity, i.e., the connectivity of the polymer chains. In particular, our aim is to identify the features of the correlation functions that are most susceptible to the differences between the two constraints. Besides the density and director autocorrelations in both the tensorial and vectorial cases, we calculate also the density-director correlation functions, the latter being a direct signature of the presence of a specific constraint. Its amplitude is connected to the strength of the constraint and is zero if none of the constraints are present, i.e., for a standard non-polymeric nematic. Generally, the correlation functions with the constraints differ substantially from the correlation functions in the non-polymeric case, if the constraints are strong which in practice requires long chains. Moreover, for the tensorial conservation law to be well distinguishable from the vectorial one, the chain persistence length should be much smaller than the total length of the chain, so that hairpins (chain backfolding) are numerous and the polar order is small.

Development of a conceptual integrated traffic safety problem identification database

DOT National Transportation Integrated Search

1999-12-01

The project conceptualized a traffic safety risk management information system and statistical database for improved problem-driver identification, countermeasure development, and resource allocation. The California Department of Motor Vehicles Drive...

Critical assessment of human metabolic pathway databases: a stepping stone for future integration

PubMed Central

2011-01-01

Background Multiple pathway databases are available that describe the human metabolic network and have proven their usefulness in many applications, ranging from the analysis and interpretation of high-throughput data to their use as a reference repository. However, so far the various human metabolic networks described by these databases have not been systematically compared and contrasted, nor has the extent to which they differ been quantified. For a researcher using these databases for particular analyses of human metabolism, it is crucial to know the extent of the differences in content and their underlying causes. Moreover, the outcomes of such a comparison are important for ongoing integration efforts. Results We compared the genes, EC numbers and reactions of five frequently used human metabolic pathway databases. The overlap is surprisingly low, especially on reaction level, where the databases agree on 3% of the 6968 reactions they have combined. Even for the well-established tricarboxylic acid cycle the databases agree on only 5 out of the 30 reactions in total. We identified the main causes for the lack of overlap. Importantly, the databases are partly complementary. Other explanations include the number of steps a conversion is described in and the number of possible alternative substrates listed. Missing metabolite identifiers and ambiguous names for metabolites also affect the comparison. Conclusions Our results show that each of the five networks compared provides us with a valuable piece of the puzzle of the complete reconstruction of the human metabolic network. To enable integration of the networks, next to a need for standardizing the metabolite names and identifiers, the conceptual differences between the databases should be resolved. Considerable manual intervention is required to reach the ultimate goal of a unified and biologically accurate model for studying the systems biology of human metabolism. Our comparison provides a stepping stone for such an endeavor. PMID:21999653

Some thoughts on cartographic and geographic information systems for the 1980's

USGS Publications Warehouse

Starr, L.E.; Anderson, Kirk E.

1981-01-01

The U.S. Geological Survey is adopting computer techniques to meet the expanding need for cartographic base category data. Digital methods are becoming increasingly important in the mapmaking process, and the demand is growing for physical, social, and economic data. Recognizing these emerging needs, the National Mapping Division began, several years ago, an active program to develop advanced digital methods to support cartographic and geographic data processing. An integrated digital cartographic database would meet the anticipated needs. Such a database would contain data from various sources, and could provide a variety of standard and customized map and digital data file products. This cartographic database soon will be technologically feasible. The present trends in the economics of cartographic and geographic data handling and the growing needs for integrated physical, social, and economic data make such a database virtually mandatory.

World-wide precision airports for SVS

NASA Astrophysics Data System (ADS)

Schiefele, Jens; Lugsch, Bill; Launer, Marc; Baca, Diana

2004-08-01

Future cockpit and aviation applications require high quality airport databases. Accuracy, resolution, integrity, completeness, traceability, and timeliness [1] are key requirements. For most aviation applications, attributed vector databases are needed. The geometry is based on points, lines, and closed polygons. To document the needs for aviation industry RTCA and EUROCAE developed in a joint committee, the DO-272/ED-99 document. It states industry needs for data features, attributes, coding, and capture rules for Airport Mapping Databases (AMDB). This paper describes the technical approach Jeppesen has taken to generate a world-wide set of three-hundred AMDB airports. All AMDB airports are DO-200A/ED-76 [1] and DO-272/ED-99 [2] compliant. Jeppesen airports have a 5m (CE90) accuracy and an 10-3 integrity. World-wide all AMDB data is delivered in WGS84 coordinates. Jeppesen continually updates the databases.