Structural analysis of graphene and h-BN: A molecular dynamics approach

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

Thomas, Siby; Ajith, K. M., E-mail: ajith@nitk.ac.in; Valsakumar, M. C.

2016-05-06

Classical molecular dynamics simulation is employed to analyze pair correlations in graphene and h-BN at various temperatures to explore the integrity of their respective structures. As the temperature increases, the height fluctuations in the out-of-plane direction of both graphene and h-BN are found to increase. The positional spread of atoms also increases with temperature. Thus the amplitude of the peak positions in the radial distribution function (RDF) decreases with temperature. It is found that FWHM of peaks in the RDF of h-BN is smaller as compared to those of graphene which implies that the structure of h-BN is more robustmore » as compared to that of graphene with respect to their respective empirical potential.« less

Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements.

PubMed

Haskett, Timothy L; Terpolilli, Jason J; Ramachandran, Vinoy K; Verdonk, Callum J; Poole, Phillip S; O'Hara, Graham W; Ramsay, Joshua P

2018-03-01

Tripartite integrative and conjugative elements (ICE3) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp. Prior to conjugative transfer the three ICE3 regions of M. ciceri WSM1271 ICEMcSym1271 combine and excise to form a single circular element. This assembly requires three coordinated recombination events involving three site-specific recombinases IntS, IntG and IntM. Here, we demonstrate that three excisionases-or recombination directionality factors-RdfS, RdfG and RdfM are required for ICE3 excision. Transcriptome sequencing revealed that expression of ICE3 transfer and conjugation genes was induced by quorum sensing. Quorum sensing activated expression of rdfS, and in turn RdfS stimulated transcription of both rdfG and rdfM. Therefore, RdfS acts as a "master controller" of ICE3 assembly and excision. The dependence of all three excisive reactions on RdfS ensures that ICE3 excision occurs via a stepwise sequence of recombination events that avoids splitting the chromosome into a non-viable configuration. These discoveries expose a surprisingly simple control system guiding molecular assembly of these novel and complex mobile genetic elements and highlight the diverse and critical functions of excisionase proteins in control of horizontal gene transfer.

Structural Physics of Bee Honeycomb

NASA Astrophysics Data System (ADS)

Kaatz, Forrest; Bultheel, Adhemar; Egami, Takeshi

2008-03-01

Honeybee combs have aroused interest in the ability of honeybees to form regular hexagonal geometric constructs since ancient times. Here we use a real space technique based on the pair distribution function (PDF) and radial distribution function (RDF), and a reciprocal space method utilizing the Debye-Waller Factor (DWF) to quantify the order for a range of honeycombs made by Apis mellifera. The PDFs and RDFs are fit with a series of Gaussian curves. We characterize the order in the honeycomb using a real space order parameter, OP3, to describe the order in the combs and a two-dimensional Fourier transform from which a Debye-Waller order parameter, u, is derived. Both OP3 and u take values from [0, 1] where the value one represents perfect order. The analyzed combs have values of OP3 from 0.33 to 0.60 and values of u from 0.83 to 0.98. RDF fits of honeycomb histograms show that naturally made comb can be crystalline in a 2D ordered structural sense, yet is more `liquid-like' than cells made on `foundation' wax. We show that with the assistance of man-made foundation wax, honeybees can manufacture highly ordered arrays of hexagonal cells.

Storage and Retrieval of Large RDF Graph Using Hadoop and MapReduce

NASA Astrophysics Data System (ADS)

Farhan Husain, Mohammad; Doshi, Pankil; Khan, Latifur; Thuraisingham, Bhavani

Handling huge amount of data scalably is a matter of concern for a long time. Same is true for semantic web data. Current semantic web frameworks lack this ability. In this paper, we describe a framework that we built using Hadoop to store and retrieve large number of RDF triples. We describe our schema to store RDF data in Hadoop Distribute File System. We also present our algorithms to answer a SPARQL query. We make use of Hadoop's MapReduce framework to actually answer the queries. Our results reveal that we can store huge amount of semantic web data in Hadoop clusters built mostly by cheap commodity class hardware and still can answer queries fast enough. We conclude that ours is a scalable framework, able to handle large amount of RDF data efficiently.

Master curves and radial distribution functions for shear dilatancy of liquid n-hexadecane via nonequilibrium molecular dynamics simulations.

PubMed

Tseng, Huan-Chang; Wu, Jiann-Shing; Chang, Rong-Yeu

2009-04-28

Shear dilatancy, a significant nonlinear behavior of nonequilibrium thermodynamics states, has been observed in nonequilibrium molecular dynamics (NEMD) simulations for liquid n-hexadecane fluid under extreme shear conditions. The existence of shear dilatancy is relevant to the relationship between the imposed shear rate gamma and the critical shear rate gamma(c). Consequently, as gammagamma(c), the intermolecular distance is lengthened substantially by strong shear deformation breaking the equilibrium thermodynamic state so that shear dilatancy takes place. Notably, a characteristic shear rate gamma(m), which depends on the root mean square molecular velocity and the average free molecular distance, is found in nonequilibrium thermodynamics state curves. Studies of the variations in the intermolecular radial distribution function (RDF) with respect to the shear rate provide a direct measure of the variation in the degree of intermolecular separation. Additionally, the variations of the RDF curve in the microscopic regime are consistent with those of the nonequilibrium thermodynamic state in the macroscopic world. By inspecting the overall shape of the RDF curve, it can be readily corroborated that the fluid of interest exists in the liquid state. More importantly, both primary characteristic values, the equilibrium thermodynamic state variable and a particular shear rate of gamma(p), are determined cautiously, with gamma(p) depending on the gamma(m) value and the square root of pressure. Thereby, the nonequilibrium thermodynamic state curves can be normalized as temperature-, pressure-, and density-invariant master curves, formulated by applying the Cross constitutive equation. Clearly, gamma(c) occurs at which a reduced shear rate gamma/gamma(p) approaches 0.1. Furthermore, the trends in the rates of shear dilatancy in both the constant-pressure and constant-volume NEMD systems under isothermal conditions conform to the cyclic rule of pressure, as a function of density and shear rate.

Structural behavior of supercritical fluids under confinement

NASA Astrophysics Data System (ADS)

Ghosh, Kanka; Krishnamurthy, C. V.

2018-01-01

The existence of the Frenkel line in the supercritical regime of a Lennard-Jones (LJ) fluid shown through molecular dynamics (MD) simulations initially and later corroborated by experiments on argon opens up possibilities of understanding the structure and dynamics of supercritical fluids in general and of the Frenkel line in particular. The location of the Frenkel line, which demarcates two distinct physical states, liquidlike and gaslike within the supercritical regime, has been established through MD simulations of the velocity autocorrelation (VACF) and radial distribution function (RDF). We, in this article, explore the changes in the structural features of supercritical LJ fluid under partial confinement using atomistic walls. The study is carried out across the Frenkel line through a series of MD simulations considering a set of thermodynamics states in the supercritical regime (P =5000 bar, 240 K ≤T ≤1500 K ) of argon well above the critical point. Confinement is partial, with atomistic walls located normal to z and extending to "infinity" along the x and y directions. In the "liquidlike" regime of the supercritical phase, particles are found to be distributed in distinct layers along the z axis with layer spacing less than one atomic diameter and the lateral RDF showing amorphous-like structure for specific spacings (packing frustration) and non-amorphous-like structure for other spacings. Increasing the rigidity of the atomistic walls is found to lead to stronger layering and increased structural order. For confinement with reflective walls, layers are found to form with one atomic diameter spacing and the lateral RDF showing close-packed structure for the smaller confinements. Translational order parameter and excess entropy assessment confirms the ordering taking place for atomistic wall and reflective wall confinements. In the "gaslike" regime of the supercritical phase, particle distribution along the spacing and the lateral RDF exhibit features not significantly different from that due to normal gas regime. The heterogeneity across the Frenkel line, found to be present both in bulk and confined systems, might cause the breakdown of the universal scaling between structure and dynamics of fluids necessitating the determination of a unique relationship between them.

Structural behavior of supercritical fluids under confinement.

PubMed

Ghosh, Kanka; Krishnamurthy, C V

2018-01-01

The existence of the Frenkel line in the supercritical regime of a Lennard-Jones (LJ) fluid shown through molecular dynamics (MD) simulations initially and later corroborated by experiments on argon opens up possibilities of understanding the structure and dynamics of supercritical fluids in general and of the Frenkel line in particular. The location of the Frenkel line, which demarcates two distinct physical states, liquidlike and gaslike within the supercritical regime, has been established through MD simulations of the velocity autocorrelation (VACF) and radial distribution function (RDF). We, in this article, explore the changes in the structural features of supercritical LJ fluid under partial confinement using atomistic walls. The study is carried out across the Frenkel line through a series of MD simulations considering a set of thermodynamics states in the supercritical regime (P=5000 bar, 240K≤T≤1500K) of argon well above the critical point. Confinement is partial, with atomistic walls located normal to z and extending to "infinity" along the x and y directions. In the "liquidlike" regime of the supercritical phase, particles are found to be distributed in distinct layers along the z axis with layer spacing less than one atomic diameter and the lateral RDF showing amorphous-like structure for specific spacings (packing frustration) and non-amorphous-like structure for other spacings. Increasing the rigidity of the atomistic walls is found to lead to stronger layering and increased structural order. For confinement with reflective walls, layers are found to form with one atomic diameter spacing and the lateral RDF showing close-packed structure for the smaller confinements. Translational order parameter and excess entropy assessment confirms the ordering taking place for atomistic wall and reflective wall confinements. In the "gaslike" regime of the supercritical phase, particle distribution along the spacing and the lateral RDF exhibit features not significantly different from that due to normal gas regime. The heterogeneity across the Frenkel line, found to be present both in bulk and confined systems, might cause the breakdown of the universal scaling between structure and dynamics of fluids necessitating the determination of a unique relationship between them.

EAGLE: 'EAGLE'Is an' Algorithmic Graph Library for Exploration

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

2015-01-16

The Resource Description Framework (RDF) and SPARQL Protocol and RDF Query Language (SPARQL) were introduced about a decade ago to enable flexible schema-free data interchange on the Semantic Web. Today data scientists use the framework as a scalable graph representation for integrating, querying, exploring and analyzing data sets hosted at different sources. With increasing adoption, the need for graph mining capabilities for the Semantic Web has emerged. Today there is no tools to conduct "graph mining" on RDF standard data sets. We address that need through implementation of popular iterative Graph Mining algorithms (Triangle count, Connected component analysis, degree distribution,more » diversity degree, PageRank, etc.). We implement these algorithms as SPARQL queries, wrapped within Python scripts and call our software tool as EAGLE. In RDF style, EAGLE stands for "EAGLE 'Is an' algorithmic graph library for exploration. EAGLE is like 'MATLAB' for 'Linked Data.'« less

Disentangling neighbors and extended range density oscillations in monatomic amorphous semiconductors.

PubMed

Roorda, S; Martin, C; Droui, M; Chicoine, M; Kazimirov, A; Kycia, S

2012-06-22

High energy x-ray diffraction measurements of pure amorphous Ge were made and its radial distribution function (RDF) was determined at high resolution, revealing new information on the atomic structure of amorphous semiconductors. Fine structure in the second peak in the RDF provides evidence that a fraction of third neighbors are closer than some second neighbors; taking this into account leads to a narrow distribution of tetrahedral bond angles, (8.5 ± 0.1)°. A small peak which appears near 5 Å upon thermal annealing shows that some ordering in the dihedral bond-angle distribution takes place during structural relaxation. Extended range order is detected (in both a-Ge and a-Si) which persists to beyond 20 Å, and both the periodicity and its decay length increase upon thermal annealing. Previously, the effect of structural relaxation was only detected at intermediate range, involving reduced tetrahedral bond-angle distortions. These results enhance our understanding of the atomic order in continuous random networks and place significantly more stringent requirements on computer models intending to describe these networks, or their alternatives which attempt to describe the structure in terms of an arrangement of paracrystals.

Structure-based coarse-graining for inhomogeneous liquid polymer systems.

PubMed

Fukuda, Motoo; Zhang, Hedong; Ishiguro, Takahiro; Fukuzawa, Kenji; Itoh, Shintaro

2013-08-07

The iterative Boltzmann inversion (IBI) method is used to derive interaction potentials for coarse-grained (CG) systems by matching structural properties of a reference atomistic system. However, because it depends on such thermodynamic conditions as density and pressure of the reference system, the derived CG nonbonded potential is probably not applicable to inhomogeneous systems containing different density regimes. In this paper, we propose a structure-based coarse-graining scheme to devise CG nonbonded potentials that are applicable to different density bulk systems and inhomogeneous systems with interfaces. Similar to the IBI, the radial distribution function (RDF) of a reference atomistic bulk system is used for iteratively refining the CG nonbonded potential. In contrast to the IBI, however, our scheme employs an appropriately estimated initial guess and a small amount of refinement to suppress transfer of the many-body interaction effects included in the reference RDF into the CG nonbonded potential. To demonstrate the application of our approach to inhomogeneous systems, we perform coarse-graining for a liquid perfluoropolyether (PFPE) film coated on a carbon surface. The constructed CG PFPE model favorably reproduces structural and density distribution functions, not only for bulk systems, but also at the liquid-vacuum and liquid-solid interfaces, demonstrating that our CG scheme offers an easy and practical way to accurately determine nonbonded potentials for inhomogeneous systems.

XLWrap - Querying and Integrating Arbitrary Spreadsheets with SPARQL

NASA Astrophysics Data System (ADS)

Langegger, Andreas; Wöß, Wolfram

In this paper a novel approach is presented for generating RDF graphs of arbitrary complexity from various spreadsheet layouts. Currently, none of the available spreadsheet-to-RDF wrappers supports cross tables and tables where data is not aligned in rows. Similar to RDF123, XLWrap is based on template graphs where fragments of triples can be mapped to specific cells of a spreadsheet. Additionally, it features a full expression algebra based on the syntax of OpenOffice Calc and various shift operations, which can be used to repeat similar mappings in order to wrap cross tables including multiple sheets and spreadsheet files. The set of available expression functions includes most of the native functions of OpenOffice Calc and can be easily extended by users of XLWrap.

Comparison of fuel value and combustion characteristics of two different RDF samples.

PubMed

Sever Akdağ, A; Atımtay, A; Sanin, F D

2016-01-01

Generation of Municipal Solid Waste (MSW) tends to increase with the growing population and economic development of the society; therefore, establishing environmentally sustainable waste management strategies is crucial. In this sense, waste to energy strategies have come into prominence since they increase the resource efficiency and replace the fossil fuels with renewable energy sources by enabling material and energy recovery instead of landfill disposal of the wastes. Refuse Derived Fuel (RDF), which is an alternative fuel produced from energy-rich Municipal Solid Waste (MSW) materials diverted from landfills, is one of the waste to energy strategies gaining more and more attention. This study aims to investigate the thermal characteristics and co-combustion efficiency of two RDF samples in Turkey. Proximate, ultimate and thermogravimetric analyses (TGA) were conducted on these samples. Furthermore, elemental compositions of ash from RDF samples were determined by X-Ray Fluorescence (XRF) analysis. The RDF samples were combusted alone and co-combusted in mixtures with coal and petroleum coke in a lab scale reactor at certain percentages on energy basis (3%, 5%, 10%, 20% and 30%) where co-combustion processes and efficiencies were investigated. It was found that the calorific values of RDF samples on dry basis were close to that of coal and a little lower compared to petroleum coke used in this study. Furthermore, the analysis indicated that when RDF in the mixture was higher than 10%, the CO concentration in the flue gas increased and so the combustion efficiency decreased; furthermore, the combustion characteristics changed from char combustion to volatile combustion. However, RDF addition to the fuel mixtures decreased the SO2 emission and did not change the NOx profiles. Also, XRF analysis showed that the slagging and fouling potential of RDF combustion was a function of RDF portion in fuel blend. When the RDF was combusted alone, the slagging and fouling indices of its ash were found to be higher than the limit values producing slagging and fouling. Copyright © 2015 Elsevier Ltd. All rights reserved.

Exposing SAMOS Data and Vocabularies within the Semantic Web

NASA Astrophysics Data System (ADS)

Dockery, Nkemdirim; Elya, Jocelyn; Smith, Shawn

2014-05-01

As part of the Ocean Data Interoperability Platform (ODIP), we at the Center for Ocean-Atmospheric Prediction Studies (COAPS) will present the development process for the exposure of quality-controlled data and core vocabularies managed by the Shipboard Automated Meteorological Oceanographic System (SAMOS) initiative using Semantic Web technologies. Participants in the SAMOS initiative collect continuous navigational (position, course, heading, speed), meteorological (winds, pressure, temperature, humidity, radiation), and near-surface oceanographic (sea temperature, salinity) parameters while at sea. One-minute interval observations are packaged and transmitted back to COAPS via daily emails, where they undergo standardized formatting and quality control. The authors will present methods used to expose these daily datasets. The Semantic Web, a vision of the World Wide Web Consortium, focuses on extending the principles of the web from connecting documents to connecting data. The creation of a web of Linked Data that can be used across different applications in a machine-readable way is the ultimate goal. The Resource Description Framework (RDF) is the standard language and format used in the Semantic Web. RDF pages may be queried using the SPARQL Protocol and RDF Query Language (SPARQL). The authors will showcase the development of RDF resources that map SAMOS vocabularies to internationally served vocabularies such as those found in the Natural Environment Research Council (NERC) Vocabulary Server. Each individual SAMOS vocabulary term (data parameter and quality control flag) will be described in an RDF resource page. These RDF resources will define each SAMOS vocabulary term and provide a link to the mapped vocabulary term (or multiple terms) served externally. Along with enhanced retrieval by parameter, time, and location, we will be able to add additional parameters with the confidence that they follow an international standard. The production of RDF resources that link daily SAMOS data to descriptors such as parameters, time and location information, quality assurance reports, and cruise tracks will also be described. The data is housed on a Thematic Real-time Environmental Distributed Data Services (THREDDS) data server, so these RDF resources will enable enhanced retrieval by any of the linked descriptors. We will showcase our collaboration with the Rolling Deck to Repository (R2R) program to develop SPARQL endpoints that distribute SAMOS content. R2R packages and transmits data on a per cruise basis, so an immediate result of the SAMOS exposure will be the narrowing of the gap between expedition type data (e.g. R2R cruises) and SAMOS observatory type data. The authors will present the development of RDF resources that will collectively expose shipboard data, vocabularies, and quality assurance reports in an overall structure which will serve as the basis for a COAPS SPARQL endpoint, enabling easier programmatic access to SAMOS data.

A general representation scheme for crystalline solids based on Voronoi-tessellation real feature values and atomic property data

PubMed Central

Jalem, Randy; Nakayama, Masanobu; Noda, Yusuke; Le, Tam; Takeuchi, Ichiro; Tateyama, Yoshitaka; Yamazaki, Hisatsugu

2018-01-01

Abstract Increasing attention has been paid to materials informatics approaches that promise efficient and fast discovery and optimization of functional inorganic materials. Technical breakthrough is urgently requested to advance this field and efforts have been made in the development of materials descriptors to encode or represent characteristics of crystalline solids, such as chemical composition, crystal structure, electronic structure, etc. We propose a general representation scheme for crystalline solids that lifts restrictions on atom ordering, cell periodicity, and system cell size based on structural descriptors of directly binned Voronoi-tessellation real feature values and atomic/chemical descriptors based on the electronegativity of elements in the crystal. Comparison was made vs. radial distribution function (RDF) feature vector, in terms of predictive accuracy on density functional theory (DFT) material properties: cohesive energy (CE), density (d), electronic band gap (BG), and decomposition energy (Ed). It was confirmed that the proposed feature vector from Voronoi real value binning generally outperforms the RDF-based one for the prediction of aforementioned properties. Together with electronegativity-based features, Voronoi-tessellation features from a given crystal structure that are derived from second-nearest neighbor information contribute significantly towards prediction. PMID:29707064

A general representation scheme for crystalline solids based on Voronoi-tessellation real feature values and atomic property data.

PubMed

Jalem, Randy; Nakayama, Masanobu; Noda, Yusuke; Le, Tam; Takeuchi, Ichiro; Tateyama, Yoshitaka; Yamazaki, Hisatsugu

2018-01-01

Increasing attention has been paid to materials informatics approaches that promise efficient and fast discovery and optimization of functional inorganic materials. Technical breakthrough is urgently requested to advance this field and efforts have been made in the development of materials descriptors to encode or represent characteristics of crystalline solids, such as chemical composition, crystal structure, electronic structure, etc. We propose a general representation scheme for crystalline solids that lifts restrictions on atom ordering, cell periodicity, and system cell size based on structural descriptors of directly binned Voronoi-tessellation real feature values and atomic/chemical descriptors based on the electronegativity of elements in the crystal. Comparison was made vs. radial distribution function (RDF) feature vector, in terms of predictive accuracy on density functional theory (DFT) material properties: cohesive energy (CE), density ( d ), electronic band gap (BG), and decomposition energy (Ed). It was confirmed that the proposed feature vector from Voronoi real value binning generally outperforms the RDF-based one for the prediction of aforementioned properties. Together with electronegativity-based features, Voronoi-tessellation features from a given crystal structure that are derived from second-nearest neighbor information contribute significantly towards prediction.

In-Memory Graph Databases for Web-Scale Data

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

Castellana, Vito G.; Morari, Alessandro; Weaver, Jesse R.

RDF databases have emerged as one of the most relevant way for organizing, integrating, and managing expo- nentially growing, often heterogeneous, and not rigidly structured data for a variety of scientific and commercial fields. In this paper we discuss the solutions integrated in GEMS (Graph database Engine for Multithreaded Systems), a software framework for implementing RDF databases on commodity, distributed-memory high-performance clusters. Unlike the majority of current RDF databases, GEMS has been designed from the ground up to primarily employ graph-based methods. This is reflected in all the layers of its stack. The GEMS framework is composed of: a SPARQL-to-C++more » compiler, a library of data structures and related methods to access and modify them, and a custom runtime providing lightweight software multithreading, network messages aggregation and a partitioned global address space. We provide an overview of the framework, detailing its component and how they have been closely designed and customized to address issues of graph methods applied to large-scale datasets on clusters. We discuss in details the principles that enable automatic translation of the queries (expressed in SPARQL, the query language of choice for RDF databases) to graph methods, and identify differences with respect to other RDF databases.« less

Dioxin and trace metal emissions from combustion of carbonized RDF slurry fuels

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

Klosky, M.; Fisher, M.; Singhania, A.

1997-12-01

In 1994, the U.S. generated approximately 209 million tons of Municipal Solid Waste (MSW), with 61% landfilled, 24% recycled, and 15% processed through Municipal Waste Combustion (MWC). In order to divert a larger portion of this generated MSW from landfills, MWC will have to play a growing role in MSW disposal. However, recently promulgated New Source Performance Standards (NSPS) for MWC will add an additional financial burden, through mandated emission reductions and air pollution control technologies, to an already financially pressured MWC marketplace. In the past, Refuse Derived Fuel (RDF), a solid fuel produced from MSW, has been fired inmore » industrial and coal boilers as an alternative means of MWC. While lower sulfur dioxide (SO{sub 2}) emissions provided the impetus, firing RDF in industrial and coal boilers frequently suffered from several disadvantages including increased solids handling, increased excess air requirements, increased air emissions, increased slag formation in the boiler, and higher fly ash resistivity. This paper summarizes the latest emissions and combustion tests with the carbonized RDF slurry fuel. With EnerTech`s SlurryCarb{trademark} process, a pumpable slurry of RDF is continuously pressurized with a pump to between 1200 and 2500 psi. The RDF slurry is pressurized above the saturated steam curve to maintain a liquid state when the slurry is heated to approximately 480-660{degrees}F. Slurry pressure and temperature then are maintained for less than 30 minutes in plug-flow reactors. At this temperature and pressure, oxygen functional groups in the molecular structure of the RDF are split off as carbon dioxide gas. This evolved carbon dioxide gas comprises a significant weight percentage of the feed RDF, but only a minimal percentage of the heating value.« less

Bringing Clouds into Our Lab! - The Influence of Turbulence on the Early Stage Rain Droplets

NASA Astrophysics Data System (ADS)

Yavuz, Mehmet Altug; Kunnen, Rudie; Heijst, Gertjan; Clercx, Herman

2015-11-01

We are investigating a droplet-laden flow in an air-filled turbulence chamber, forced by speaker-driven air jets. The speakers are running in a random manner; yet they allow us to control and define the statistics of the turbulence. We study the motion of droplets with tunable size (Stokes numbers ~ 0.13 - 9) in a turbulent flow, mimicking the early stages of raindrop formation. 3D Particle Tracking Velocimetry (PTV) together with Laser Induced Fluorescence (LIF) methods are chosen as the experimental method to track the droplets and collect data for statistical analysis. Thereby it is possible to study the spatial distribution of the droplets in turbulence using the so-called Radial Distribution Function (RDF), a statistical measure to quantify the clustering of particles. Additionally, 3D-PTV technique allows us to measure velocity statistics of the droplets and the influence of the turbulence on droplet trajectories, both individually and collectively. In this contribution, we will present the clustering probability quantified by the RDF for different Stokes numbers. We will explain the physics underlying the influence of turbulence on droplet cluster behavior. This study supported by FOM/NWO Netherlands.

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

PubMed Central

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

2017-01-01

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

Stochastic Theory for the Clustering of Rapidly Settling, Low-Inertia Particle Pairs in Isotropic Turbulence - I

NASA Astrophysics Data System (ADS)

Gupta, Vijay; Rani, Sarma; Koch, Donald

2017-11-01

A stochastic theory is developed to predict the Radial Distribution Function (RDF) of monodisperse, rapidly settling, low-inertia particle pairs in isotropic turbulence. The theory is based on approximating the turbulent flow in a reference frame following an aerosol particle as a locally linear velocity field. In the first version of the theory (referred to as T1), the fluid velocity gradient tensor ``seen'' by the primary aerosol particle is further assumed to be Gaussian. Analytical closures are then derived for the drift and diffusive fluxes controling the RDF, in the asymptotic limits of small particle Stokes number (St =τp /τη << 1), and large dimensionless settling velocity (Sv = gτp /uη >> 1). It is seen that the RDF for rapidly settling pairs has an inverse power dependency on pair separation r with an exponent, c1, that is proportional to St2 . However, the c1 predicted by T1 for Sv >> 1 particles is higher than the c1 of even non-settling (Sv = 0) particles obtained from DNS of particle-laden isotropic turbulence. Thus, the Gaussian velocity gradient in T1 leads to the unphysical effect that gravity enhances pair clustering. To address this inconsistency, a second version (T2) was developed. Funding from the CBET Division of the National Science Foundation is gratefully acknowledged.

Gravity influence on the clustering of charged particles in turbulence

NASA Astrophysics Data System (ADS)

Lu, Jiang; Nordsiek, Hansen; Shaw, Raymond

2010-11-01

We report results aimed at studying the interactions of bidisperse charged inertial particles in homogeneous, isotropic turbulence, under the influence of gravitational settling. We theoretically and experimentally investigate the impact of gravititational settling on particle clustering, which is quantified by the radial distribution function (RDF). The theory is based on a drift-diffusion (Fokker-Planck) model with gravitational settling appearing as a diffusive term depending on a dimensionless settling parameter. The experiments are carried out in a laboratory chamber with nearly homogeneous, isotropic turbulence in which the flow is seeded with charged particles and digital holography used to obtain 3D particle positions and velocities. The derived radial distribution function for bidisperse settling charged particles is compared to the experimental RDFs.

Building pathway graphs from BioPAX data in R.

PubMed

Benis, Nirupama; Schokker, Dirkjan; Kramer, Frank; Smits, Mari A; Suarez-Diez, Maria

2016-01-01

Biological pathways are increasingly available in the BioPAX format which uses an RDF model for data storage. One can retrieve the information in this data model in the scripting language R using the package rBiopaxParser , which converts the BioPAX format to one readable in R. It also has a function to build a regulatory network from the pathway information. Here we describe an extension of this function. The new function allows the user to build graphs of entire pathways, including regulated as well as non-regulated elements, and therefore provides a maximum of information. This function is available as part of the rBiopaxParser distribution from Bioconductor.

Spatiotemporal-Thematic Data Processing for the Semantic Web

NASA Astrophysics Data System (ADS)

Hakimpour, Farshad; Aleman-Meza, Boanerges; Perry, Matthew; Sheth, Amit

This chapter presents practical approaches to data processing in the space, time and theme dimensions using existing Semantic Web technologies. It describes how we obtain geographic and event data from Internet sources and also how we integrate them into an RDF store. We briefly introduce a set of functionalities in space, time and semantics. These functionalities are implemented based on our existing technology for main-memory-based RDF data processing developed at the LSDIS Lab. A number of these functionalities are exposed as REST Web services. We present two sample client-side applications that are developed using a combination of our services with Google Maps service.

RDF-GL: A SPARQL-Based Graphical Query Language for RDF

NASA Astrophysics Data System (ADS)

Hogenboom, Frederik; Milea, Viorel; Frasincar, Flavius; Kaymak, Uzay

This chapter presents RDF-GL, a graphical query language (GQL) for RDF. The GQL is based on the textual query language SPARQL and mainly focuses on SPARQL SELECT queries. The advantage of a GQL over textual query languages is that complexity is hidden through the use of graphical symbols. RDF-GL is supported by a Java-based editor, SPARQLinG, which is presented as well. The editor does not only allow for RDF-GL query creation, but also converts RDF-GL queries to SPARQL queries and is able to subsequently execute these. Experiments show that using the GQL in combination with the editor makes RDF querying more accessible for end users.

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

Ding, Jun; Ma, Evan; Asta, Mark

Using molecular dynamics simulations, we have studied the atomic correlations characterizing the second peak in the radial distribution function (RDF) of metallic glasses and liquids. The analysis was conducted from the perspective of different connection schemes of atomic packing motifs, based on the number of shared atoms between two linked coordination polyhedra. The results demonstrate that the cluster connections by face-sharing, specifically with three common atoms, are most favored when transitioning from the liquid to glassy state, and exhibit the stiffest elastic response during shear deformation. These properties of the connections and the resultant atomic correlations are generally the samemore » for different types of packing motifs in different alloys. Splitting of the second RDF peak was observed for the inherent structure of the equilibrium liquid, originating solely from cluster connections; this trait can then be inherited in the metallic glass formed via subsequent quenching of the parent liquid through the glass transition, in the absence of any additional type of local structural order. In conclusion, increasing ordering and cluster connection during cooling, however, may tune the position and intensity of the split peaks.« less

The STP (Solar-Terrestrial Physics) Semantic Web based on the RSS1.0 and the RDF

NASA Astrophysics Data System (ADS)

Kubo, T.; Murata, K. T.; Kimura, E.; Ishikura, S.; Shinohara, I.; Kasaba, Y.; Watari, S.; Matsuoka, D.

2006-12-01

In the Solar-Terrestrial Physics (STP), it is pointed out that circulation and utilization of observation data among researchers are insufficient. To archive interdisciplinary researches, we need to overcome this circulation and utilization problems. Under such a background, authors' group has developed a world-wide database that manages meta-data of satellite and ground-based observation data files. It is noted that retrieving meta-data from the observation data and registering them to database have been carried out by hand so far. Our goal is to establish the STP Semantic Web. The Semantic Web provides a common framework that allows a variety of data shared and reused across applications, enterprises, and communities. We also expect that the secondary information related with observations, such as event information and associated news, are also shared over the networks. The most fundamental issue on the establishment is who generates, manages and provides meta-data in the Semantic Web. We developed an automatic meta-data collection system for the observation data using the RSS (RDF Site Summary) 1.0. The RSS1.0 is one of the XML-based markup languages based on the RDF (Resource Description Framework), which is designed for syndicating news and contents of news-like sites. The RSS1.0 is used to describe the STP meta-data, such as data file name, file server address and observation date. To describe the meta-data of the STP beyond RSS1.0 vocabulary, we defined original vocabularies for the STP resources using the RDF Schema. The RDF describes technical terms on the STP along with the Dublin Core Metadata Element Set, which is standard for cross-domain information resource descriptions. Researchers' information on the STP by FOAF, which is known as an RDF/XML vocabulary, creates a machine-readable metadata describing people. Using the RSS1.0 as a meta-data distribution method, the workflow from retrieving meta-data to registering them into the database is automated. This technique is applied for several database systems, such as the DARTS database system and NICT Space Weather Report Service. The DARTS is a science database managed by ISAS/JAXA in Japan. We succeeded in generating and collecting the meta-data automatically for the CDF (Common data Format) data, such as Reimei satellite data, provided by the DARTS. We also create an RDF service for space weather report and real-time global MHD simulation 3D data provided by the NICT. Our Semantic Web system works as follows: The RSS1.0 documents generated on the data sites (ISAS and NICT) are automatically collected by a meta-data collection agent. The RDF documents are registered and the agent extracts meta-data to store them in the Sesame, which is an open source RDF database with support for RDF Schema inferencing and querying. The RDF database provides advanced retrieval processing that has considered property and relation. Finally, the STP Semantic Web provides automatic processing or high level search for the data which are not only for observation data but for space weather news, physical events, technical terms and researches information related to the STP.

Comparison of coal/solid recovered fuel (SRF) with coal/refuse derived fuel (RDF) in a fluidised bed reactor

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

Wagland, S.T.; Kilgallon, P.; Coveney, R.

2011-06-15

An experimental study was undertaken to compare the differences between municipal solid waste (MSW) derived solid recovered fuel (SRF) (complying with CEN standards) and refuse derived fuel (RDF). Both fuels were co-combusted with coal in a 50 kW fluidised bed combustor and the metal emissions were compared. Synthetic SRF was prepared in the laboratory by grinding major constituents of MSW such as paper, plastic, textile and wood. RDF was obtained from a local mechanical treatment plant. Heavy metal emissions in flue gas and ash samples from the (coal + 10% SRF) fuel mixture were found to be within the acceptablemore » range and were generally lower than that obtained for coal + 10% RDF fuel mixture. The relative distribution of heavy metals in ash components and the flue gas stream shows the presence of a large fraction (up to 98%) of most of the metals in the ash (except Hg and As). Thermo-gravimetric (TG) analysis of SRF constituents was performed to understand the behaviour of fuel mixtures in the absence and presence of air. The results obtained from the experimental study will enhance the confidence of fuel users towards using MSW-derived SRF as an alternative fuel.« less

Processing SPARQL queries with regular expressions in RDF databases

PubMed Central

2011-01-01

Background As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users’ requests for extracting information from the RDF data as well as the lack of users’ knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. Results In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Conclusions Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns. PMID:21489225

Processing SPARQL queries with regular expressions in RDF databases.

PubMed

Lee, Jinsoo; Pham, Minh-Duc; Lee, Jihwan; Han, Wook-Shin; Cho, Hune; Yu, Hwanjo; Lee, Jeong-Hoon

2011-03-29

As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users' requests for extracting information from the RDF data as well as the lack of users' knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns.

AlzPharm: integration of neurodegeneration data using RDF.

PubMed

Lam, Hugo Y K; Marenco, Luis; Clark, Tim; Gao, Yong; Kinoshita, June; Shepherd, Gordon; Miller, Perry; Wu, Elizabeth; Wong, Gwendolyn T; Liu, Nian; Crasto, Chiquito; Morse, Thomas; Stephens, Susie; Cheung, Kei-Hoi

2007-05-09

Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data. We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion. Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields.

AlzPharm: integration of neurodegeneration data using RDF

PubMed Central

Lam, Hugo YK; Marenco, Luis; Clark, Tim; Gao, Yong; Kinoshita, June; Shepherd, Gordon; Miller, Perry; Wu, Elizabeth; Wong, Gwendolyn T; Liu, Nian; Crasto, Chiquito; Morse, Thomas; Stephens, Susie; Cheung, Kei-Hoi

2007-01-01

Background Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data. Results We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion. Conclusion Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields. PMID:17493287

Information-computational system for storage, search and analytical processing of environmental datasets based on the Semantic Web technologies

NASA Astrophysics Data System (ADS)

Titov, A.; Gordov, E.; Okladnikov, I.

2009-04-01

In this report the results of the work devoted to the development of working model of the software system for storage, semantically-enabled search and retrieval along with processing and visualization of environmental datasets containing results of meteorological and air pollution observations and mathematical climate modeling are presented. Specially designed metadata standard for machine-readable description of datasets related to meteorology, climate and atmospheric pollution transport domains is introduced as one of the key system components. To provide semantic interoperability the Resource Description Framework (RDF, http://www.w3.org/RDF/) technology means have been chosen for metadata description model realization in the form of RDF Schema. The final version of the RDF Schema is implemented on the base of widely used standards, such as Dublin Core Metadata Element Set (http://dublincore.org/), Directory Interchange Format (DIF, http://gcmd.gsfc.nasa.gov/User/difguide/difman.html), ISO 19139, etc. At present the system is available as a Web server (http://climate.risks.scert.ru/metadatabase/) based on the web-portal ATMOS engine [1] and is implementing dataset management functionality including SeRQL-based semantic search as well as statistical analysis and visualization of selected data archives [2,3]. The core of the system is Apache web server in conjunction with Tomcat Java Servlet Container (http://jakarta.apache.org/tomcat/) and Sesame Server (http://www.openrdf.org/) used as a database for RDF and RDF Schema. At present statistical analysis of meteorological and climatic data with subsequent visualization of results is implemented for such datasets as NCEP/NCAR Reanalysis, Reanalysis NCEP/DOE AMIP II, JMA/CRIEPI JRA-25, ECMWF ERA-40 and local measurements obtained from meteorological stations on the territory of Russia. This functionality is aimed primarily at finding of main characteristics of regional climate dynamics. The proposed system represents a step in the process of development of a distributed collaborative information-computational environment to support multidisciplinary investigations of Earth regional environment [4]. Partial support of this work by SB RAS Integration Project 34, SB RAS Basic Program Project 4.5.2.2, APN Project CBA2007-08NSY and FP6 Enviro-RISKS project (INCO-CT-2004-013427) is acknowledged. References 1. E.P. Gordov, V.N. Lykosov, and A.Z. Fazliev. Web portal on environmental sciences "ATMOS" // Advances in Geosciences. 2006. Vol. 8. p. 33 - 38. 2. Gordov E.P., Okladnikov I.G., Titov A.G. Development of elements of web based information-computational system supporting regional environment processes investigations // Journal of Computational Technologies, Vol. 12, Special Issue #3, 2007, pp. 20 - 28. 3. Okladnikov I.G., Titov A.G. Melnikova V.N., Shulgina T.M. Web-system for processing and visualization of meteorological and climatic data // Journal of Computational Technologies, Vol. 13, Special Issue #3, 2008, pp. 64 - 69. 4. Gordov E.P., Lykosov V.N. Development of information-computational infrastructure for integrated study of Siberia environment // Journal of Computational Technologies, Vol. 12, Special Issue #2, 2007, pp. 19 - 30.

Order parameters from image analysis: a honeycomb example

NASA Astrophysics Data System (ADS)

Kaatz, Forrest H.; Bultheel, Adhemar; Egami, Takeshi

2008-11-01

Honeybee combs have aroused interest in the ability of honeybees to form regular hexagonal geometric constructs since ancient times. Here we use a real space technique based on the pair distribution function (PDF) and radial distribution function (RDF), and a reciprocal space method utilizing the Debye-Waller Factor (DWF) to quantify the order for a range of honeycombs made by Apis mellifera ligustica. The PDFs and RDFs are fit with a series of Gaussian curves. We characterize the order in the honeycomb using a real space order parameter, OP 3 , to describe the order in the combs and a two-dimensional Fourier transform from which a Debye-Waller order parameter, u, is derived. Both OP 3 and u take values from [0, 1] where the value one represents perfect order. The analyzed combs have values of OP 3 from 0.33 to 0.60 and values of u from 0.59 to 0.69. RDF fits of honeycomb histograms show that naturally made comb can be crystalline in a 2D ordered structural sense, yet is more ‘liquid-like’ than cells made on ‘foundation’ wax. We show that with the assistance of man-made foundation wax, honeybees can manufacture highly ordered arrays of hexagonal cells. This is the first description of honeycomb utilizing the Debye-Waller Factor, and provides a complete analysis of the order in comb from a real-space order parameter and a reciprocal space order parameter. It is noted that the techniques used are general in nature and could be applied to any digital photograph of an ordered array.

SAFE: SPARQL Federation over RDF Data Cubes with Access Control.

PubMed

Khan, Yasar; Saleem, Muhammad; Mehdi, Muntazir; Hogan, Aidan; Mehmood, Qaiser; Rebholz-Schuhmann, Dietrich; Sahay, Ratnesh

2017-02-01

Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stakeholders; consequently, privacy is a major concern when federating queries over such datasets. In the Healthcare and Life Sciences (HCLS) domain real-world datasets contain sensitive statistical information: strict ownership is granted to individuals working in hospitals, research labs, clinical trial organisers, etc. Therefore, the legal and ethical concerns on (i) preserving the anonymity of patients (or clinical subjects); and (ii) respecting data ownership through access control; are key challenges faced by the data analytics community working within the HCLS domain. Likewise statistical data play a key role in the domain, where the RDF Data Cube Vocabulary has been proposed as a standard format to enable the exchange of such data. However, to the best of our knowledge, no existing approach has looked to optimise federated queries over such statistical data. We present SAFE: a query federation engine that enables policy-aware access to sensitive statistical datasets represented as RDF data cubes. SAFE is designed specifically to query statistical RDF data cubes in a distributed setting, where access control is coupled with source selection, user profiles and their access rights. SAFE proposes a join-aware source selection method that avoids wasteful requests to irrelevant and unauthorised data sources. In order to preserve anonymity and enforce stricter access control, SAFE's indexing system does not hold any data instances-it stores only predicates and endpoints. The resulting data summary has a significantly lower index generation time and size compared to existing engines, which allows for faster updates when sources change. We validate the performance of the system with experiments over real-world datasets provided by three clinical organisations as well as legacy linked datasets. We show that SAFE enables granular graph-level access control over distributed clinical RDF data cubes and efficiently reduces the source selection and overall query execution time when compared with general-purpose SPARQL query federation engines in the targeted setting.

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

PubMed Central

Kinjo, Akira R.; Suzuki, Hirofumi; Yamashita, Reiko; Ikegawa, Yasuyo; Kudou, Takahiro; Igarashi, Reiko; Kengaku, Yumiko; Cho, Hasumi; Standley, Daron M.; Nakagawa, Atsushi; Nakamura, Haruki

2012-01-01

The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources. PMID:21976737

Towards the novel reasoning among particles in PSO by the use of RDF and SPARQL.

PubMed

Fister, Iztok; Yang, Xin-She; Ljubič, Karin; Fister, Dušan; Brest, Janez; Fister, Iztok

2014-01-01

The significant development of the Internet has posed some new challenges and many new programming tools have been developed to address such challenges. Today, semantic web is a modern paradigm for representing and accessing knowledge data on the Internet. This paper tries to use the semantic tools such as resource definition framework (RDF) and RDF query language (SPARQL) for the optimization purpose. These tools are combined with particle swarm optimization (PSO) and the selection of the best solutions depends on its fitness. Instead of the local best solution, a neighborhood of solutions for each particle can be defined and used for the calculation of the new position, based on the key ideas from semantic web domain. The preliminary results by optimizing ten benchmark functions showed the promising results and thus this method should be investigated further.

Channel doping concentration and cell program state dependence on random telegraph noise spatial and statistical distribution in 30 nm NAND flash memory

NASA Astrophysics Data System (ADS)

Tomita, Toshihiro; Miyaji, Kousuke

2015-04-01

The dependence of spatial and statistical distribution of random telegraph noise (RTN) in a 30 nm NAND flash memory on channel doping concentration NA and cell program state Vth is comprehensively investigated using three-dimensional Monte Carlo device simulation considering random dopant fluctuation (RDF). It is found that single trap RTN amplitude ΔVth is larger at the center of the channel region in the NAND flash memory, which is closer to the jellium (uniform) doping results since NA is relatively low to suppress junction leakage current. In addition, ΔVth peak at the center of the channel decreases in the higher Vth state due to the current concentration at the shallow trench isolation (STI) edges induced by the high vertical electrical field through the fringing capacitance between the channel and control gate. In such cases, ΔVth distribution slope λ cannot be determined by only considering RDF and single trap.

The RDF/SRF torrefaction: An effect of temperature on characterization of the product - Carbonized Refuse Derived Fuel.

PubMed

Białowiec, Andrzej; Pulka, Jakub; Stępień, Paweł; Manczarski, Piotr; Gołaszewski, Janusz

2017-12-01

The influence of Refuse Derived Fuel (RDF)/Solid Recovery Fuel (SRF) torrefaction temperature on product characteristic was investigated. RDF/SRF thermal treatment experiment was conducted with 1-h residence time, under given temperatures: 200, 220, 240, 260, 280 and 300°C. Sawdust was used as reference material. The following parameters of torrefaction char from sawdust and Carbonized Refuse Derived Fuel (CRDF) from RDF/SRF were measured: moisture, calorific value, ash content, volatile compounds and sulfur content. Sawdust biochar was confirmed as a good quality solid fuel, due to significant fuel property increase. The study also indicated that RDF torrefaction reduced moisture significantly from 22.9% to 1.4% and therefore increased lower heating value (LHV) from 19.6 to 25.3MJ/kg. Results suggest that RDF torrefaction may be a good method for increasing attractiveness of RDF as an energy source, and it could help unify RDF properties on the market. Copyright © 2017 Elsevier Ltd. All rights reserved.

Japanese RDF-fired power generation system and fundamental research on RDF combustion

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

Narukawa, Kimihito; Goto, Hidenori; Chen, Y.

1997-12-31

Power generation from refuse derived fuel (RDF) is one of the new technologies for municipal solid waste (MSW) management. This technology is strongly attracting the attention of the Japanese government. The results of a feasibility study of this system in Japan is presented. To develop this highly efficient RDF-fired CFB generating process, combustibility and dechlorination characteristics of RDF were investigated by both the thermo-balance technique and combustion tests with an electric furnace. RDF combustion tests by a bench scale CFBC were carried out and then the following experimental results were obtained: (1) RDF can be combusted almost completely even inmore » small scale CFBC; (2) HCl and N{sub 2}O emissions are quite low at any conditions; and (3) NO{sub x} emissions are a little higher in single stage combustion, however they are reduced at 50% air bias ratio. Some of the results can be explained by a RDF combustion model.« less

Soft materials design via self assembly of functionalized icosahedral particles

NASA Astrophysics Data System (ADS)

Muthukumar, Vidyalakshmi Chockalingam

In this work we simulate self assembly of icosahedral building blocks using a coarse grained model of the icosahedral capsid of virus 1m1c. With significant advancements in site-directed functionalization of these macromolecules [1], we propose possible application of such self-assembled materials for drug delivery. While there have been some reports on organization of viral particles in solution through functionalization, exploiting this behaviour for obtaining well-ordered stoichiometric structures has not yet been explored. Our work is in well agreement with the earlier simulation studies of icosahedral gold nanocrystals, giving chain like patterns [5] and also broadly in agreement with the wet lab works of Finn, M.G. et al., who have shown small predominantly chain-like aggregates with mannose-decorated Cowpea Mosaic Virus (CPMV) [22] and small two dimensional aggregates with oligonucleotide functionalization on the CPMV capsid [1]. To quantify the results of our Coarse Grained Molecular Dynamics Simulations I developed analysis routines in MATLAB using which we found the most preferable nearest neighbour distances (from the radial distribution function (RDF) calculations) for different lengths of the functional groups and under different implicit solvent conditions, and the most frequent coordination number for a virus particle (histogram plots further using the information from RDF). Visual inspection suggests that our results most likely span the low temperature limits explored in the works of Finn, M.G. et al., and show a good degree of agreement with the experimental results in [1] at an annealing temperature of 4°C. Our work also reveals the possibility of novel stoichiometric N-mer type aggregates which could be synthesized using these capsids with appropriate functionalization and solvent conditions.

Advanced SPARQL querying in small molecule databases.

PubMed

Galgonek, Jakub; Hurt, Tomáš; Michlíková, Vendula; Onderka, Petr; Schwarz, Jan; Vondrášek, Jiří

2016-01-01

In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics and bioinformatics databases. These technologies allow better interoperability of various data sources and powerful searching facilities. However, we identified several deficiencies that make usage of such RDF databases restrictive or challenging for common users. We extended a SPARQL engine to be able to use special procedures inside SPARQL queries. This allows the user to work with data that cannot be simply precomputed and thus cannot be directly stored in the database. We designed an algorithm that checks a query against data ontology to identify possible user errors. This greatly improves query debugging. We also introduced an approach to visualize retrieved data in a user-friendly way, based on templates describing visualizations of resource classes. To integrate all of our approaches, we developed a simple web application. Our system was implemented successfully, and we demonstrated its usability on the ChEBI database transformed into RDF form. To demonstrate procedure call functions, we employed compound similarity searching based on OrChem. The application is publicly available at https://bioinfo.uochb.cas.cz/projects/chemRDF.

Sample preparation for thermo-gravimetric determination and thermo-gravimetric characterization of refuse derived fuel.

PubMed

Robinson, T; Bronson, B; Gogolek, P; Mehrani, P

2016-02-01

Thermo-gravimetric analysis (TGA) is a useful method for characterizing fuels. In the past it has been applied to the study of refuse derived fuel (RDF) and related materials. However, the heterogeneity of RDF makes the preparation of small representative samples very difficult and this difficulty has limited the effectiveness of TGA for characterization of RDF. A TGA method was applied to a variety of materials prepared from a commercially available RDF using a variety of procedures. Applicability of TGA method to the determination of the renewable content of RDF was considered. Cryogenic ball milling was found to be an effective means of preparing RDF samples for TGA. When combined with an effective sample preparation, TGA could be used as an alternative method for assessing the renewable content of RDF. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Combustion characterization of carbonized RDF, Joint Venture Task No. 7. Topical Report

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

None, None

1995-04-30

The overall objective of this research program was to demonstrate EnerTech's and the Energy & Environmental Research Center's (EERC) process of slurry carbonization for producing homogeneous, pumpable titels from refuse-derived fuel (RDF) with continuous pilot plant facilities, and to characterize flue gas and ash emissions from combustion of the carbonizd RDF slurry fuel. Please note that "Wet Thermal Oxidation" is EnerTech's trademark mme for combustion of the carbonized RDF slurry fuel. Carbonized RDF slurry fuels were produced with the EERC'S 7.5-tpd (wet basis) pilot plant facility. A hose diaphragm pump pressurized a 7- lo-wt% feed RDF slurry, with a viscositymore » of 500 cP, to approximately 2500 psig. The pressurized RDF slurry was heated by indirect heat exchangers to between 5850 -626°F, and its temperature and pressure was maintained in a downflow reactor. The carbonized slurry was flashed, concentrated in a filter press, and ground in an attritor. During operation of the pilot plant, samples of the feed RDF slurry, carbonization gas, condensate, carbonized solids, and filtrate were taken and analyzed. Pilot-scale slurry carbonization experiments with RDF produced a homogeneous pumpable slurry fuel with a higher heating value (HHV) of 3,000-6,600 Btu/lb (as-received basis), at a viscosity of 500 CP at 100 Hz decreasing, and ambient temperature. Greater-heating-value slurry fuels were produced at higher slurry carbonization temperatures. During slurry carbonization, polyvinyl chloride (PVC) plastics in the feed RDF also decompose to form hydrochloric acid and salts. Pilot-scale slurty carbonization experiments extracted 82-94% of the feed RDF chlorine content as chloride salts. Higher carbonization temperatures and higher alkali additions to the feed slurry produced a higher chlorine extraction.« less

Modeling and validating HL7 FHIR profiles using semantic web Shape Expressions (ShEx).

PubMed

Solbrig, Harold R; Prud'hommeaux, Eric; Grieve, Grahame; McKenzie, Lloyd; Mandel, Joshua C; Sharma, Deepak K; Jiang, Guoqian

2017-03-01

HL7 Fast Healthcare Interoperability Resources (FHIR) is an emerging open standard for the exchange of electronic healthcare information. FHIR resources are defined in a specialized modeling language. FHIR instances can currently be represented in either XML or JSON. The FHIR and Semantic Web communities are developing a third FHIR instance representation format in Resource Description Framework (RDF). Shape Expressions (ShEx), a formal RDF data constraint language, is a candidate for describing and validating the FHIR RDF representation. Create a FHIR to ShEx model transformation and assess its ability to describe and validate FHIR RDF data. We created the methods and tools that generate the ShEx schemas modeling the FHIR to RDF specification being developed by HL7 ITS/W3C RDF Task Force, and evaluated the applicability of ShEx in the description and validation of FHIR to RDF transformations. The ShEx models contributed significantly to workgroup consensus. Algorithmic transformations from the FHIR model to ShEx schemas and FHIR example data to RDF transformations were incorporated into the FHIR build process. ShEx schemas representing 109 FHIR resources were used to validate 511 FHIR RDF data examples from the Standards for Trial Use (STU 3) Ballot version. We were able to uncover unresolved issues in the FHIR to RDF specification and detect 10 types of errors and root causes in the actual implementation. The FHIR ShEx representations have been included in the official FHIR web pages for the STU 3 Ballot version since September 2016. ShEx can be used to define and validate the syntax of a FHIR resource, which is complementary to the use of RDF Schema (RDFS) and Web Ontology Language (OWL) for semantic validation. ShEx proved useful for describing a standard model of FHIR RDF data. The combination of a formal model and a succinct format enabled comprehensive review and automated validation. Copyright © 2017 Elsevier Inc. All rights reserved.

Study of the hard-disk system at high densities: the fluid-hexatic phase transition.

PubMed

Mier-Y-Terán, Luis; Machorro-Martínez, Brian Ignacio; Chapela, Gustavo A; Del Río, Fernando

2018-06-21

Integral equations of uniform fluids have been considered unable to predict any characteristic feature of the fluid-solid phase transition, including the shoulder that arises in the second peak of the fluid-phase radial distribution function, RDF, of hard-core systems obtained by computer simulations, at fluid densities very close to the structural two-step phase transition. This reasoning is based on the results of traditional integral approximations, like Percus-Yevick, PY, which does not show such a shoulder in hard-core systems, neither in two nor three dimensions. In this work, we present results of three Ansätze, based on the PY theory, that were proposed to remedy the lack of PY analytical solutions in two dimensions. This comparative study shows that one of those Ansätze does develop a shoulder in the second peak of the RDF at densities very close to the phase transition, qualitatively describing this feature. Since the shoulder grows into a peak at still higher densities, this integral equation approach predicts the appearance of an orientational order characteristic of the hexatic phase in a continuous fluid-hexatic phase transition.

Knowledge represented using RDF semantic network in the concept of semantic web

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

Lukasova, A., E-mail: alena.lukasova@osu.cz; Vajgl, M., E-mail: marek.vajgl@osu.cz; Zacek, M., E-mail: martin.zacek@osu.cz

The RDF(S) model has been declared as the basic model to capture knowledge of the semantic web. It provides a common and flexible way to decompose composed knowledge to elementary statements, which can be represented by RDF triples or by RDF graph vectors. From the logical point of view, elements of knowledge can be expressed using at most binary predicates, which can be converted to RDF-triples or graph vectors. However, it is not able to capture implicit knowledge representable by logical formulas. This contribution shows how existing approaches (semantic networks and clausal form logic) can be combined together with RDFmore » to obtain RDF-compatible system with ability to represent implicit knowledge and inference over knowledge base.« less

Waste-to-Chemicals for a Circular Economy: The Case of Urea Production (Waste-to-Urea).

PubMed

Antonetti, Elena; Iaquaniello, Gaetano; Salladini, Annarita; Spadaccini, Luca; Perathoner, Siglinda; Centi, Gabriele

2017-03-09

The economics and environmental impact of a new technology for the production of urea from municipal solid waste, particularly the residue-derived fuel (RdF) fraction, is analyzed. Estimates indicate a cost of production of approximately €135 per ton of urea (internal rate of return more than 10 %) and savings of approximately 0.113 tons of CH 4 and approximately 0.78 tons of CO 2 per ton of urea produced. Thus, the results show that this waste-to-urea (WtU) technology is both economically valuable and environmentally advantageous (in terms of saving resources and limiting carbon footprint) for the production of chemicals from municipal solid waste in comparison with both the production of urea with conventional technology (starting from natural gas) and the use of RdF to produce electrical energy (waste-to-energy). A further benefit is the lower environmental impact of the solid residue produced from RdF conversion. The further benefit of this technology is the possibility to realize distributed fertilizer production. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrating XQuery-Enabled SCORM XML Metadata Repositories into an RDF-Based E-Learning P2P Network

ERIC Educational Resources Information Center

Qu, Changtao; Nejdl, Wolfgang

2004-01-01

Edutella is an RDF-based E-Learning P2P network that is aimed to accommodate heterogeneous learning resource metadata repositories in a P2P manner and further facilitate the exchange of metadata between these repositories based on RDF. Whereas Edutella provides RDF metadata repositories with a quite natural integration approach, XML metadata…

NCBI2RDF: enabling full RDF-based access to NCBI databases.

PubMed

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments.

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

GlycoRDF: an ontology to standardize glycomics data in RDF

PubMed Central

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F.; Campbell, Matthew P.; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-01-01

Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). Contact: rene@ccrc.uga.edu or kkiyoko@soka.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388145

GlycoRDF: an ontology to standardize glycomics data in RDF.

PubMed

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-03-15

Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Health and environmental effects of refuse derived fuel (RDF) production and RDF/coal co-firing technologies

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

O'Toole, J.J.; Wessels, T.E.; Lynch, J.F.

1981-10-01

Six facilities, representing the scope of different co-firing techniques with their associated RDF production systems were reviewed in detail for combustion equipment, firing modes, emission control systems, residue handling/disposal, and effluent wastewater treatment. These facilities encompass all currently operational or soon to be operational co-firing plants and associated RDF production systems. Occupational health and safety risks for these plants were evaluated on the basis of fatal and nonfatal accidents and disease arising from the respective fuel cycles, coal and RDF. Occupational risks include exposure to pathogenic organisms in the workplace. Unusual events that are life threatening in the RDF processingmore » industry (e.g., explosions) are also discussed and remedial and safety measures reviewed. 80 refs., 4 figs., 30 tabs.« less

Personality assessment inventory profile and predictors of elevations among dissociative disorder patients.

PubMed

Stadnik, Ryan D; Brand, Bethany; Savoca, Angela

2013-01-01

Assessing patients with dissociative disorders (DD) using personality tests is difficult. On the Minnesota Multiphasic Personality Inventory-2 ( J. N. Butcher, W. G. Dahlstrom, J. R. Graham, A. Tellegen, & B. Kaemmer, 1989 ), DD patients often obtain elevations on multiple clinical scales as well as on validity scales that were thought to indicate exaggeration yet have been shown to be elevated among traumatized individuals, including those with DD. No research has been conducted to determine how DD patients score on the Personality Assessment Inventory (PAI; L. C. Morey, 1991 ), which includes the symptom exaggeration scale Negative Impression (NIM) and the malingering scales Malingering Index (MAL) and Rogers Discriminant Function (RDF). The goals of this study were to document the PAI profile of dissociative identity disorder (DID) and dissociative disorder not otherwise specified (DDNOS) patients and to determine how the validity and Schizophrenia scales are related to other PAI scales as well as dissociation. A total of 42 inpatients with DID or DDNOS were assessed on the PAI as well as the Dissociative Experiences Scale-II. The DID/DDNOS patients were elevated on many PAI scales, including NIM and, to a lesser extent, MAL, but not RDF. Dissociation scores significantly and uniquely predicted NIM scores above and beyond Depression and Borderline Features. In addition, after we controlled for MAL and RDF, dissociation was positively associated with NIM. In contrast, after we controlled for the other 2 scales, dissociation was not related to MAL and was negatively related to RDF, indicating that RDF and, to a lesser extent, MAL are better correlates of feigning in DD patients than NIM.

Mobilizable RDF/d-RDF burning program

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

Niemann, K.; Campbell, J.

1982-03-01

The Mobilizable RDF/d-RDF Burning Program was conceived to promote the utilization of refuse-derived fuels (RDF) as a supplement to existing fossil fuel sources in industrial-sized boilers. The program explores the design, development, and eventual construction of densified-RDF (d-RDF) for use in boiler combustion testing as a supplement to stoker coal or wood wastes. The equipment would be mounted on trailers and assembled and operated at preselected sites throughout the country where approximately 750 tons of RDF would be produced and test burned in a local boiler. The equipment, to include a transportable RDF boiler metering and feed system, would thenmore » be moved and operated at two to three test sites annually. The program is intended to encourage the construction of permanent resource recovery facilities by involving local waste handling groups in operating the equipment and producing fuel, and potential local fuel users in testing the fuel in their boilers. The Mobilizable Program was developed from two separate tasks. The first task developed the concept behind the program and defined its operational and organizational structure. The second task, a follow-up to the first, was intended principally to finalize test locations, develop equipment designs and specifications, and formalize a management program. This report summarizes the principal findings of both tasks. It identifies the criteria used to identify test locations, outlines the program's management structure, presents design and performance specifications for both the fuel production equipment and boiler fuel feed systems, and provides a detailed evaluation of the parameters involved in burning RDF in industrial-sized boilers. Final conclusions and recommendations identify problem areas encountered in the program, and discuss possible future directions for such a program.« less

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments. PMID:23984425

Desiderata for an authoritative Representation of MeSH in RDF.

PubMed

Winnenburg, Rainer; Bodenreider, Olivier

2014-01-01

The Semantic Web provides a framework for the integration of resources on the web, which facilitates information integration and interoperability. RDF is the main representation format for Linked Open Data (LOD). However, datasets are not always made available in RDF by their producers and the Semantic Web community has had to convert some of these datasets to RDF in order for these datasets to participate in the LOD cloud. As a result, the LOD cloud sometimes contains outdated, partial and even inaccurate RDF datasets. We review the LOD landscape for one of these resources, MeSH, and analyze the characteristics of six existing representations in order to identify desirable features for an authoritative version, for which we create a prototype. We illustrate the suitability of this prototype on three common use cases. NLM intends to release an authoritative representation of MeSH in RDF (beta version) in the Fall of 2014.

Desiderata for an authoritative Representation of MeSH in RDF

PubMed Central

Winnenburg, Rainer; Bodenreider, Olivier

2014-01-01

The Semantic Web provides a framework for the integration of resources on the web, which facilitates information integration and interoperability. RDF is the main representation format for Linked Open Data (LOD). However, datasets are not always made available in RDF by their producers and the Semantic Web community has had to convert some of these datasets to RDF in order for these datasets to participate in the LOD cloud. As a result, the LOD cloud sometimes contains outdated, partial and even inaccurate RDF datasets. We review the LOD landscape for one of these resources, MeSH, and analyze the characteristics of six existing representations in order to identify desirable features for an authoritative version, for which we create a prototype. We illustrate the suitability of this prototype on three common use cases. NLM intends to release an authoritative representation of MeSH in RDF (beta version) in the Fall of 2014. PMID:25954433

SU-D-19A-05: The Dosimetric Impact of Using Xoft Axxent® Electronic Brachytherapy Source TG-43 Dosimetry Parameters for Treatment with the Xoft 30 Mm Diameter Vaginal Applicator

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

Simiele, S; Micka, J; Culberson, W

2014-06-01

Purpose: A full TG-43 dosimetric characterization has not been performed for the Xoft Axxent ® electronic brachytherapy source (Xoft, a subsidiary of iCAD, San Jose, CA) within the Xoft 30 mm diameter vaginal applicator. Currently, dose calculations are performed using the bare-source TG-43 parameters and do not account for the presence of the applicator. This work focuses on determining the difference between the bare-source and sourcein- applicator TG-43 parameters. Both the radial dose function (RDF) and polar anisotropy function (PAF) were computationally determined for the source-in-applicator and bare-source models to determine the impact of using the bare-source dosimetry data. Methods:more » MCNP5 was used to model the source and the Xoft 30 mm diameter vaginal applicator. All simulations were performed using 0.84p and 0.03e cross section libraries. All models were developed based on specifications provided by Xoft. The applicator is made of a proprietary polymer material and simulations were performed using the most conservative chemical composition. An F6 collision-kerma tally was used to determine the RDF and PAF values in water at various dwell positions. The RDF values were normalized to 2.0 cm from the source to accommodate the applicator radius. Source-in-applicator results were compared with bare-source results from this work as well as published baresource results. Results: For a 0 mm source pullback distance, the updated bare-source model and source-in-applicator RDF values differ by 2% at 3 cm and 4% at 5 cm. The largest PAF disagreements were observed at the distal end of the source and applicator with up to 17% disagreement at 2 cm and 8% at 8 cm. The bare-source model had RDF values within 2.6% of the published TG-43 data and PAF results within 7.2% at 2 cm. Conclusion: Results indicate that notable differences exist between the bare-source and source-in-applicator TG-43 simulated parameters. Xoft Inc. provided partial funding for this work.« less

Jet flames of a refuse derived fuel

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

Weber, Roman; Kupka, Tomasz; Zajac, Krzysztof

This paper is concerned with combustion of a refuse derived fuel in a small-scale flame. The objective is to provide a direct comparison of the RDF flame properties with properties of pulverized coal flames fired under similar boundary conditions. Measurements of temperature, gas composition (O{sub 2}, CO{sub 2}, CO, NO) and burnout have demonstrated fundamental differences between the coal flames and the RDF flames. The pulverized coals ignite in the close vicinity of the burner and most of the combustion is completed within the first 300 ms. Despite the high volatile content of the RDF, its combustion extends far intomore » the furnace and after 1.8 s residence time only a 94% burnout has been achieved. This effect has been attributed not only to the larger particle size of fluffy RDF particles but also to differences in RDF volatiles if compared to coal volatiles. Substantial amounts of oily tars have been observed in the RDF flames even though the flame temperatures exceeded 1300 C. The presence of these tars has enhanced the slagging propensity of RDF flames and rapidly growing deposits of high carbon content have been observed. (author)« less

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

PubMed

Kawano, Shin; Watanabe, Tsutomu; Mizuguchi, Sohei; Araki, Norie; Katayama, Toshiaki; Yamaguchi, Atsuko

2014-07-01

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

Madduri, Kamesh; Wu, Kesheng

The Resource Description Framework (RDF) is a popular data model for representing linked data sets arising from the web, as well as large scienti c data repositories such as UniProt. RDF data intrinsically represents a labeled and directed multi-graph. SPARQL is a query language for RDF that expresses subgraph pattern- nding queries on this implicit multigraph in a SQL- like syntax. SPARQL queries generate complex intermediate join queries; to compute these joins e ciently, we propose a new strategy based on bitmap indexes. We store the RDF data in column-oriented structures as compressed bitmaps along with two dictionaries. This papermore » makes three new contributions. (i) We present an e cient parallel strategy for parsing the raw RDF data, building dictionaries of unique entities, and creating compressed bitmap indexes of the data. (ii) We utilize the constructed bitmap indexes to e ciently answer SPARQL queries, simplifying the join evaluations. (iii) To quantify the performance impact of using bitmap indexes, we compare our approach to the state-of-the-art triple-store RDF-3X. We nd that our bitmap index-based approach to answering queries is up to an order of magnitude faster for a variety of SPARQL queries, on gigascale RDF data sets.« less

Effects of low-temperature pretreatment on enhancing properties of refuse-derived fuel via microwave irradiation.

PubMed

Liu, Zhen; Wang, Han-Qing; Zhou, Yue-Yun; Zhang, Xiao-Dong; Liu, Jian-Wen

2017-07-01

The present study focuses on pretreatment of enhancing the properties of refuse-derived fuel (RDF) via low-temperature microwave irradiation. These improved properties include lower chlorine content, a more porous surface structure and better combustion characteristics. In this study, low-temperature microwave irradiation was carried out in a modified microwave apparatus and the range of temperature was set to be 220-300℃. We found that the microwave absorbability of RDF was enhanced after being partly carbonized. Moreover, with the increasing of the final temperature, the organochlorine removal ratio was greatly increased to 80% and the content of chlorine was dramatically decreased to an extremely low level. It was also interesting to find that the chlorine of RDF was mainly released as HCl rather than organic chloride volatiles. The finding is just the same as the polyvinyl chloride pyrolysis process. In addition, pores and channels emerged during the modifying operation and the modified RDF has better combustibility and combustion stability than traditional RDF. This work revealed that low-temperature modification of RDF via microwave irradiation is significant for enhancing the quality of RDF and avoiding HCl erosion of equipment substantially.

Building a Semantic Framework for eScience

NASA Astrophysics Data System (ADS)

Movva, S.; Ramachandran, R.; Maskey, M.; Li, X.

2009-12-01

The e-Science vision focuses on the use of advanced computing technologies to support scientists. Recent research efforts in this area have focused primarily on “enabling” use of infrastructure resources for both data and computational access especially in Geosciences. One of the existing gaps in the existing e-Science efforts has been the failure to incorporate stable semantic technologies within the design process itself. In this presentation, we describe our effort in designing a framework for e-Science built using Service Oriented Architecture. Our framework provides users capabilities to create science workflows and mine distributed data. Our e-Science framework is being designed around a mass market tool to promote reusability across many projects. Semantics is an integral part of this framework and our design goal is to leverage the latest stable semantic technologies. The use of these stable semantic technologies will provide the users of our framework the useful features such as: allow search engines to find their content with RDFa tags; create RDF triple data store for their content; create RDF end points to share with others; and semantically mash their content with other online content available as RDF end point.

A molecular dynamics approach for predicting the glass transition temperature and plasticization effect in amorphous pharmaceuticals.

PubMed

Gupta, Jasmine; Nunes, Cletus; Jonnalagadda, Sriramakamal

2013-11-04

The objectives of this study were as follows: (i) To develop an in silico technique, based on molecular dynamics (MD) simulations, to predict glass transition temperatures (Tg) of amorphous pharmaceuticals. (ii) To computationally study the effect of plasticizer on Tg. (iii) To investigate the intermolecular interactions using radial distribution function (RDF). Amorphous sucrose and water were selected as the model compound and plasticizer, respectively. MD simulations were performed using COMPASS force field and isothermal-isobaric ensembles. The specific volumes of amorphous cells were computed in the temperature range of 440-265 K. The characteristic "kink" observed in volume-temperature curves, in conjunction with regression analysis, defined the Tg. The MD computed Tg values were 367 K, 352 K and 343 K for amorphous sucrose containing 0%, 3% and 5% w/w water, respectively. The MD technique thus effectively simulated the plasticization effect of water; and the corresponding Tg values were in reasonable agreement with theoretical models and literature reports. The RDF measurements revealed strong hydrogen bond interactions between sucrose hydroxyl oxygens and water oxygen. Steric effects led to weak interactions between sucrose acetal oxygens and water oxygen. MD is thus a powerful predictive tool for probing temperature and water effects on the stability of amorphous systems during drug development.

Bim-Gis Integrated Geospatial Information Model Using Semantic Web and Rdf Graphs

NASA Astrophysics Data System (ADS)

Hor, A.-H.; Jadidi, A.; Sohn, G.

2016-06-01

In recent years, 3D virtual indoor/outdoor urban modelling becomes a key spatial information framework for many civil and engineering applications such as evacuation planning, emergency and facility management. For accomplishing such sophisticate decision tasks, there is a large demands for building multi-scale and multi-sourced 3D urban models. Currently, Building Information Model (BIM) and Geographical Information Systems (GIS) are broadly used as the modelling sources. However, data sharing and exchanging information between two modelling domains is still a huge challenge; while the syntactic or semantic approaches do not fully provide exchanging of rich semantic and geometric information of BIM into GIS or vice-versa. This paper proposes a novel approach for integrating BIM and GIS using semantic web technologies and Resources Description Framework (RDF) graphs. The novelty of the proposed solution comes from the benefits of integrating BIM and GIS technologies into one unified model, so-called Integrated Geospatial Information Model (IGIM). The proposed approach consists of three main modules: BIM-RDF and GIS-RDF graphs construction, integrating of two RDF graphs, and query of information through IGIM-RDF graph using SPARQL. The IGIM generates queries from both the BIM and GIS RDF graphs resulting a semantically integrated model with entities representing both BIM classes and GIS feature objects with respect to the target-client application. The linkage between BIM-RDF and GIS-RDF is achieved through SPARQL endpoints and defined by a query using set of datasets and entity classes with complementary properties, relationships and geometries. To validate the proposed approach and its performance, a case study was also tested using IGIM system design.

A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties

NASA Astrophysics Data System (ADS)

Fu, Chia-Chun; Kulkarni, Pandurang M.; Scott Shell, M.; Gary Leal, L.

2012-10-01

Coarse-graining (CG) techniques have recently attracted great interest for providing descriptions at a mesoscopic level of resolution that preserve fluid thermodynamic and transport behaviors with a reduced number of degrees of freedom and hence less computational effort. One fundamental question arises: how well and to what extent can a "bottom-up" developed mesoscale model recover the physical properties of a molecular scale system? To answer this question, we explore systematically the properties of a CG model that is developed to represent an intermediate mesoscale model between the atomistic and continuum scales. This CG model aims to reduce the computational cost relative to a full atomistic simulation, and we assess to what extent it is possible to preserve both the thermodynamic and transport properties of an underlying reference all-atom Lennard-Jones (LJ) system. In this paper, only the thermodynamic properties are considered in detail. The transport properties will be examined in subsequent work. To coarse-grain, we first use the iterative Boltzmann inversion (IBI) to determine a CG potential for a (1-ϕ)N mesoscale particle system, where ϕ is the degree of coarse-graining, so as to reproduce the radial distribution function (RDF) of an N atomic particle system. Even though the uniqueness theorem guarantees a one to one relationship between the RDF and an effective pairwise potential, we find that RDFs are insensitive to the long-range part of the IBI-determined potentials, which provides some significant flexibility in further matching other properties. We then propose a reformulation of IBI as a robust minimization procedure that enables simultaneous matching of the RDF and the fluid pressure. We find that this new method mainly changes the attractive tail region of the CG potentials, and it improves the isothermal compressibility relative to pure IBI. We also find that there are optimal interaction cutoff lengths for the CG system, as a function of ϕ, that are required to attain an adequate potential while maintaining computational speedup. To demonstrate the universality of the method, we test a range of state points for the LJ liquid as well as several LJ chain fluids.

NO3- Coordination in Aqueous Solutions by 15N/ 14N and 18O/natO Isotopic Substitution: What Can We Learn from Molecular Simulation?

DOE PAGES

Chialvo, Ariel A.; Vlcek, Lukas

2014-12-16

We explore the deconvolution of the water-nitrate correlations by the first-order difference approach involving neutron diffraction of heavy- and null-aqueous solutions of KNO 3 under 14N 15N and natON 18ON substitutions to achieve a full characterization of the first water coordination around the nitrate ion. For that purpose we performed isobaric-isothermal simulations of 3.5m KNO 3 aqueous solutions at ambient conditions to generate the relevant radial distribution functions (RDF) required in the analysis (a) to identify the individual partial contributions to the total neutron weighted distribution function, (b) to isolate and assess the contribution of NO 3 -!K + pairmore » formation, (c) to test the accuracy of the NDIS-based coordination calculations and XRDbased assumptions, and (d) to describe the water coordination around both the nitrogen and oxygen sites of the nitrate ion.« less

Production and characterization refuse derived fuel (RDF) from high organic and moisture contents of municipal solid waste (MSW)

NASA Astrophysics Data System (ADS)

Dianda, P.; Mahidin; Munawar, E.

2018-03-01

Many cities in developing countries is facing a serious problems to dealing with huge municipal solid waste (MSW) generated. The main approach to manage MSW is causes environmental impact associated with the leachate and landfill gas emissions. On the other hand, the energy available also limited by rapid growth of population and economic development due to shortage of the natural resource. In this study, the potential utilized of MSW to produce refuse derived fuel (RDF) was investigate. The RDF was produced with various organic waste content. Then, the RDF was subjected to laboratory analysis to determine its characteristic including the calorific value. The results shows the moisture content was increased by increasing organic waste content, while the calorific value was found 17-36 MJ/kg. The highest calorific value was about 36 MJ/kg obtained at RDF with 40% organic waste content. This results indicated that the RDF can be use to substitute coal in main burning process and calcinations of cement industry.

Foundations of RDF Databases

NASA Astrophysics Data System (ADS)

Arenas, Marcelo; Gutierrez, Claudio; Pérez, Jorge

The goal of this paper is to give an overview of the basics of the theory of RDF databases. We provide a formal definition of RDF that includes the features that distinguish this model from other graph data models. We then move into the fundamental issue of querying RDF data. We start by considering the RDF query language SPARQL, which is a W3C Recommendation since January 2008. We provide an algebraic syntax and a compositional semantics for this language, study the complexity of the evaluation problem for different fragments of SPARQL, and consider the problem of optimizing the evaluation of SPARQL queries, showing that a natural fragment of this language has some good properties in this respect. We furthermore study the expressive power of SPARQL, by comparing it with some well-known query languages such as relational algebra. We conclude by considering the issue of querying RDF data in the presence of RDFS vocabulary. In particular, we present a recently proposed extension of SPARQL with navigational capabilities.

Recovery of plastic wastes from dumpsite as refuse-derived fuel and its utilization in small gasification system.

PubMed

Chiemchaisri, Chart; Charnnok, Boonya; Visvanathan, Chettiyappan

2010-03-01

An effort to utilize solid wastes at dumpsite as refuse-derived fuel (RDF) was carried out. The produced RDF briquette was then utilized in the gasification system. These wastes were initially examined for their physical composition and chemical characteristics. The wastes contained high plastic content of 24.6-44.8%, majority in polyethylene plastic bag form. The plastic wastes were purified by separating them from other components through manual separation and trommel screen after which their content increased to 82.9-89.7%. Subsequently, they were mixed with binding agent (cassava root) and transformed into RDF briquette. Maximum plastic content in RDF briquette was limit to 55% to maintain physical strength and maximum chlorine content. The RDF briquette was tested in a down-draft gasifier. The produced gas contained average energy content of 1.76 MJ/m(3), yielding cold gas efficiency of 66%. The energy production cost from this RDF process was estimated as USD0.05 perkWh. 2009 Elsevier Ltd. All rights reserved.

Molecular dynamics simulations of shock waves in oriented nitromethane single crystals: plane-specific effects.

PubMed

He, Lan; Sewell, Thomas D; Thompson, Donald L

2012-01-21

Molecular dynamics simulations of supported shock waves (shock pressure P(s) ∼ 15 GPa) propagating along the [110], [011], [101], and [111] directions in crystalline nitromethane initially at T = 200 K were performed using the nonreactive Sorescu-Rice-Thompson force field [D. C. Sorescu, B. M. Rice, and D. L. Thompson, J. Phys. Chem. B 104, 8406 (2000)]. These simulations, combined with those from a preceding study of shocks propagating along [100], [010], and [001] directions in nitromethane for similar conditions of temperature and shock pressure [L. He, T. D. Sewell, and D. L. Thompson, J. Chem. Phys. 134, 124506 (2011)], have been used to study the post-shock relaxation phenomena. Shocks along [010] and [101] lead to a crystal-crystal structure transformation. Shocks propagating along [011], [110], [111], [100], and [001] exhibit plane-specific disordering, which was characterized by calculating as functions of time the 1D mean square displacement (MSD), 2D radial distribution function (RDF), and 2D orientation order parameter P(2)(θ) in orthogonal planes mutually perpendicular to the shock plane; and by calculating as functions of distance behind the shock front the Cartesian components of intermolecular, intramolecular, and total kinetic energies. The 2D RDF results show that the structural disordering for shocks along [100], [110], and [111] is strongly plane-specific; whereas for shocks along [001] and [011], the loss of crystal structural order is almost equivalent in the orthogonal planes perpendicular to the shock plane. Based on the entire set of simulations, there is a trend for the most extensive disordering to occur in the (010) and (110) planes, less extensive disordering to occur in the (100) plane, and essentially no disordering to occur in the (001) plane. The 2D P(2)(θ) and 1D MSD profiles show, respectively, that the orientational and translational disordering is plane-specific, which results in the plane-specific structural disordering observed in the 2D RDF. By contrast, the kinetic energy partitioning and redistribution do not exhibit plane specificity, as shown by the similarity of spatial profiles of the Cartesian components of the intermolecular, intramolecular, and total kinetic energies in orthogonal planes perpendicular to the shock plane. © 2012 American Institute of Physics

Structural correlation of the chalcogenide Ge40Se60 glass

NASA Astrophysics Data System (ADS)

Moharram, A. H.

2017-01-01

Binary Ge40Se60 glass was prepared using the melt-quench technique. The total structure factors, S( K), are obtained using the X-ray diffraction in the wave vector interval 0.28 ≤ K ≤ 6.5 Å-1. The appearance of the first sharp diffraction peak (FSDP) in the structure factor indicates the presence of the intermediate range order. Radial distribution functions, RDF( r), have been obtained using either the conventional (Fourier) transformation or the Monte Carlo simulation of the experimental X-ray data. The short range order parameters deduced from the Monte Carlo total correlation, T( r), functions are better than those obtained from the conventional (Fourier) T( r) data. Gaussian analyses of the total correlation function show that Ge2(Se1/2)6 molecular units are the basic structural units for the investigated Ge40Se60 glass.

Labeling RDF Graphs for Linear Time and Space Querying

NASA Astrophysics Data System (ADS)

Furche, Tim; Weinzierl, Antonius; Bry, François

Indices and data structures for web querying have mostly considered tree shaped data, reflecting the view of XML documents as tree-shaped. However, for RDF (and when querying ID/IDREF constraints in XML) data is indisputably graph-shaped. In this chapter, we first study existing indexing and labeling schemes for RDF and other graph datawith focus on support for efficient adjacency and reachability queries. For XML, labeling schemes are an important part of the widespread adoption of XML, in particular for mapping XML to existing (relational) database technology. However, the existing indexing and labeling schemes for RDF (and graph data in general) sacrifice one of the most attractive properties of XML labeling schemes, the constant time (and per-node space) test for adjacency (child) and reachability (descendant). In the second part, we introduce the first labeling scheme for RDF data that retains this property and thus achieves linear time and space processing of acyclic RDF queries on a significantly larger class of graphs than previous approaches (which are mostly limited to tree-shaped data). Finally, we show how this labeling scheme can be applied to (acyclic) SPARQL queries to obtain an evaluation algorithm with time and space complexity linear in the number of resources in the queried RDF graph.

Querying clinical data in HL7 RIM based relational model with morph-RDB.

PubMed

Priyatna, Freddy; Alonso-Calvo, Raul; Paraiso-Medina, Sergio; Corcho, Oscar

2017-10-05

Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to heterogeneous data sources. One possible approach to accommodate this need is to use RDB2RDF systems that provide RDF datasets as the unified view. These RDF datasets may be materialized and stored in a triple store, or transformed into RDF in real time, as virtual RDF data sources. Our previous efforts involved materialized RDF datasets, hence losing data freshness. In this paper we present a solution that uses an ontology based on the HL7 v3 Reference Information Model and a set of R2RML mappings that relate this ontology to an underlying relational database implementation, and where morph-RDB is used to expose a virtual, non-materialized SPARQL endpoint over the data. By applying a set of optimization techniques on the SPARQL-to-SQL query translation algorithm, we can now issue SPARQL queries to the underlying relational data with generally acceptable performance.

Release of sulfur and chlorine during cofiring RDF and coal in an internally circulating fluidized bed

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

Xiaolin Wei; Yang Wang; Dianfu Liu

2009-03-15

An internally circulating fluidized bed (ICFB) was applied to investigate the behavior of chlorine and sulfur during cofiring RDF and coal. The pollutant emissions in the flue gas were measured by Fourier transform infrared (FTIR) spectrometry (Gasmet DX-3000). In the tests, the concentrations of the species CO, CO{sub 2}, HCl, and SO{sub 2} were measured online. Results indicated when cofiring RDF and char, due to the higher content of chlorine in RDF, the formation of HCl significantly increases. The concentration of SO{sub 2} is relatively low because alkaline metal in the fuel ash can absorb SO{sub 2}. The concentration ofmore » CO emission during firing pure RDF is relatively higher and fluctuates sharply. With the CaO addition, the sulfur absorption by calcium quickly increases, and the desulfurization ratio is bigger than the dechlorination ratio. The chemical equilibrium method is applied to predict the behavior of chlorine. Results show that gaseous HCl emission increases with increasing RDF fraction, and gaseous KCl and NaCl formation might occur. 35 refs., 18 figs., 2 tabs.« less

DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases.

PubMed

Queralt-Rosinach, Núria; Piñero, Janet; Bravo, Àlex; Sanz, Ferran; Furlong, Laura I

2016-07-15

DisGeNET-RDF makes available knowledge on the genetic basis of human diseases in the Semantic Web. Gene-disease associations (GDAs) and their provenance metadata are published as human-readable and machine-processable web resources. The information on GDAs included in DisGeNET-RDF is interlinked to other biomedical databases to support the development of bioinformatics approaches for translational research through evidence-based exploitation of a rich and fully interconnected linked open data. http://rdf.disgenet.org/ support@disgenet.org. © The Author 2016. Published by Oxford University Press.

SPARQLog: SPARQL with Rules and Quantification

NASA Astrophysics Data System (ADS)

Bry, François; Furche, Tim; Marnette, Bruno; Ley, Clemens; Linse, Benedikt; Poppe, Olga

SPARQL has become the gold-standard for RDF query languages. Nevertheless, we believe there is further room for improving RDF query languages. In this chapter, we investigate the addition of rules and quantifier alternation to SPARQL. That extension, called SPARQLog, extends previous RDF query languages by arbitrary quantifier alternation: blank nodes may occur in the scope of all, some, or none of the universal variables of a rule. In addition, SPARQLog is aware of important RDF features such as the distinction between blank nodes, literals and IRIs or the RDFS vocabulary. The semantics of SPARQLog is closed (every answer is an RDF graph), but lifts RDF's restrictions on literal and blank node occurrences for intermediary data. We show how to define a sound and complete operational semantics that can be implemented using existing logic programming techniques. While SPARQLog is Turing complete, we identify a decidable (in fact, polynomial time) fragment SwARQLog ensuring polynomial data-complexity inspired from the notion of super-weak acyclicity in data exchange. Furthermore, we prove that SPARQLog with no universal quantifiers in the scope of existential ones (∀ ∃ fragment) is equivalent to full SPARQLog in presence of graph projection. Thus, the convenience of arbitrary quantifier alternation comes, in fact, for free. These results, though here presented in the context of RDF querying, apply similarly also in the more general setting of data exchange.

Perspectives and limits for cement kilns as a destination for RDF.

PubMed

Genon, G; Brizio, E

2008-11-01

RDF, the high calorific value fraction of MSW obtained by conventional separation systems, can be employed in technological plants (mainly cement kilns) in order to obtain a useful energy recovery. It is interesting and important to evaluate this possibility within the general framework of waste-to-energy solutions. The solution must be assessed on the basis of different aspects, namely: technological features and clinker characteristics; local atmospheric pollution; the effects of RDF used in cement kilns on the generation of greenhouse gases; the economics of conventional solid fuels substitution and planning perspectives, from the point of view of the destination of RDF and optimal cement kiln policy. The different experiences of this issue throughout Europe are reviewed, and some applications within Italy are also been considered. The main findings of the study are that the use of RDF in cement kilns instead of coal or coke offers environmental benefits in terms of greenhouse gases, while the formation of conventional gaseous pollutants is not a critical aspect. Indeed, the generation of nitrogen oxides can probably be lower because of lower flame temperatures or lower air excess. The presence of chlorinated micro-pollutants is not influenced by the presence of RDF in fuel, whereas depending on the quality of the RDF, some problems could arise compared to the substituted fuel as far as heavy metals are concerned, chiefly the more volatile ones.

SP2Bench: A SPARQL Performance Benchmark

NASA Astrophysics Data System (ADS)

Schmidt, Michael; Hornung, Thomas; Meier, Michael; Pinkel, Christoph; Lausen, Georg

A meaningful analysis and comparison of both existing storage schemes for RDF data and evaluation approaches for SPARQL queries necessitates a comprehensive and universal benchmark platform. We present SP2Bench, a publicly available, language-specific performance benchmark for the SPARQL query language. SP2Bench is settled in the DBLP scenario and comprises a data generator for creating arbitrarily large DBLP-like documents and a set of carefully designed benchmark queries. The generated documents mirror vital key characteristics and social-world distributions encountered in the original DBLP data set, while the queries implement meaningful requests on top of this data, covering a variety of SPARQL operator constellations and RDF access patterns. In this chapter, we discuss requirements and desiderata for SPARQL benchmarks and present the SP2Bench framework, including its data generator, benchmark queries and performance metrics.

Analysis and interpretation of the leaching behaviour of waste thermal treatment bottom ash by batch and column tests.

PubMed

Di Gianfilippo, Martina; Costa, Giulia; Verginelli, Iason; Gavasci, Renato; Lombardi, Francesco

2016-10-01

This paper investigates the leaching behaviour of specific types of waste thermal treatment bottom ash (BA) as a function of both pH and the liquid-to-solid ratio (L/S). Specifically, column percolation tests and different types of batch tests (including pH-dependence) were applied to BA produced by hospital waste incineration (HW-I), Refuse Derived Fuel (RDF) gasification (RDF-G) and RDF incineration (RDF-I). The results of these tests were interpreted applying an integrated graphical and modelling approach aimed at identifying the main mechanisms (solubility, availability or time-controlled dissolution and diffusion) governing the release of specific constituents from each type of BA. The final aim of this work was in fact to gain insight on the information that can be provided by the leaching tests applied, and hence on which ones may be more suitable to apply for assessing the leaching concentrations expected in the field. The results of the leaching tests showed that the three samples of analysed BA presented differences of orders of magnitude in their leaching behaviour, especially as a function of pH, but also in terms of the L/S. These were mainly related to the differences in mineralogy of the samples. In addition, for the same type of bottom ash, the comparison between the results of batch and percolation column tests, expressed in terms of cumulative release, showed that for some constituents (e.g. Mg for HW-I BA and Cu for RDF-G BA) differences of over one order of magnitude were obtained due to variations in pH and DOC release. Similarly, the eluate concentrations observed in the percolation tests, for most of the investigated elements, were not directly comparable with the results of the pH-dependence tests. In particular, in some cases the percolation test results showed eluate concentrations of some constituents (e.g. K and Ca in HW-I BA) of up to one order of magnitude higher than the values obtained from the pH-dependence experiments at the same pH value. This was attributed to a rapid washout from the column of the soluble phases present in the BA. In contrast, for other constituents (e.g. Mg and Ba for the RDF-G BA), especially at high L/S ratios, the concentrations in the column tests were of up to one order of magnitude lower than the solubility value, indicating release under non-equilibrium conditions. In these cases, batch pH-dependence tests should be preferred, since column tests results could underestimate the concentrations expected in the field. Copyright © 2016 Elsevier Ltd. All rights reserved.

cMapper: gene-centric connectivity mapper for EBI-RDF platform.

PubMed

Shoaib, Muhammad; Ansari, Adnan Ahmad; Ahn, Sung-Min

2017-01-15

In this era of biological big data, data integration has become a common task and a challenge for biologists. The Resource Description Framework (RDF) was developed to enable interoperability of heterogeneous datasets. The EBI-RDF platform enables an efficient data integration of six independent biological databases using RDF technologies and shared ontologies. However, to take advantage of this platform, biologists need to be familiar with RDF technologies and SPARQL query language. To overcome this practical limitation of the EBI-RDF platform, we developed cMapper, a web-based tool that enables biologists to search the EBI-RDF databases in a gene-centric manner without a thorough knowledge of RDF and SPARQL. cMapper allows biologists to search data entities in the EBI-RDF platform that are connected to genes or small molecules of interest in multiple biological contexts. The input to cMapper consists of a set of genes or small molecules, and the output are data entities in six independent EBI-RDF databases connected with the given genes or small molecules in the user's query. cMapper provides output to users in the form of a graph in which nodes represent data entities and the edges represent connections between data entities and inputted set of genes or small molecules. Furthermore, users can apply filters based on database, taxonomy, organ and pathways in order to focus on a core connectivity graph of their interest. Data entities from multiple databases are differentiated based on background colors. cMapper also enables users to investigate shared connections between genes or small molecules of interest. Users can view the output graph on a web browser or download it in either GraphML or JSON formats. cMapper is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on Tomcat server. We developed the user interface using HTML5, JQuery and the Cytoscape Graph API. cMapper can be accessed at http://cmapper.ewostech.net Readers can download the development manual from the website http://cmapper.ewostech.net/docs/cMapperDocumentation.pdf. Source Code is available at https://github.com/muhammadshoaib/cmapperContact:smahn@gachon.ac.krSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

RDF SKETCH MAPS - KNOWLEDGE COMPLEXITY REDUCTION FOR PRECISION MEDICINE ANALYTICS.

PubMed

Thanintorn, Nattapon; Wang, Juexin; Ersoy, Ilker; Al-Taie, Zainab; Jiang, Yuexu; Wang, Duolin; Verma, Megha; Joshi, Trupti; Hammer, Richard; Xu, Dong; Shin, Dmitriy

2016-01-01

Realization of precision medicine ideas requires significant research effort to be able to spot subtle differences in complex diseases at the molecular level to develop personalized therapies. It is especially important in many cases of highly heterogeneous cancers. Precision diagnostics and therapeutics of such diseases demands interrogation of vast amounts of biological knowledge coupled with novel analytic methodologies. For instance, pathway-based approaches can shed light on the way tumorigenesis takes place in individual patient cases and pinpoint to novel drug targets. However, comprehensive analysis of hundreds of pathways and thousands of genes creates a combinatorial explosion, that is challenging for medical practitioners to handle at the point of care. Here we extend our previous work on mapping clinical omics data to curated Resource Description Framework (RDF) knowledge bases to derive influence diagrams of interrelationships of biomarker proteins, diseases and signal transduction pathways for personalized theranostics. We present RDF Sketch Maps - a computational method to reduce knowledge complexity for precision medicine analytics. The method of RDF Sketch Maps is inspired by the way a sketch artist conveys only important visual information and discards other unnecessary details. In our case, we compute and retain only so-called RDF Edges - places with highly important diagnostic and therapeutic information. To do this we utilize 35 maps of human signal transduction pathways by transforming 300 KEGG maps into highly processable RDF knowledge base. We have demonstrated potential clinical utility of RDF Sketch Maps in hematopoietic cancers, including analysis of pathways associated with Hairy Cell Leukemia (HCL) and Chronic Myeloid Leukemia (CML) where we achieved up to 20-fold reduction in the number of biological entities to be analyzed, while retaining most likely important entities. In experiments with pathways associated with HCL a generated RDF Sketch Map of the top 30% paths retained important information about signaling cascades leading to activation of proto-oncogene BRAF, which is usually associated with a different cancer, melanoma. Recent reports of successful treatments of HCL patients by the BRAF-targeted drug vemurafenib support the validity of the RDF Sketch Maps findings. We therefore believe that RDF Sketch Maps will be invaluable for hypothesis generation for precision diagnostics and therapeutics as well as drug repurposing studies.

A simple and effective solution to the constrained QM/MM simulations

NASA Astrophysics Data System (ADS)

Takahashi, Hideaki; Kambe, Hiroyuki; Morita, Akihiro

2018-04-01

It is a promising extension of the quantum mechanical/molecular mechanical (QM/MM) approach to incorporate the solvent molecules surrounding the QM solute into the QM region to ensure the adequate description of the electronic polarization of the solute. However, the solvent molecules in the QM region inevitably diffuse into the MM bulk during the QM/MM simulation. In this article, we developed a simple and efficient method, referred to as the "boundary constraint with correction (BCC)," to prevent the diffusion of the solvent water molecules by means of a constraint potential. The point of the BCC method is to compensate the error in a statistical property due to the bias potential by adding a correction term obtained through a set of QM/MM simulations. The BCC method is designed so that the effect of the bias potential completely vanishes when the QM solvent is identical with the MM solvent. Furthermore, the desirable conditions, that is, the continuities of energy and force and the conservations of energy and momentum, are fulfilled in principle. We applied the QM/MM-BCC method to a hydronium ion(H3O+) in aqueous solution to construct the radial distribution function (RDF) of the solvent around the solute. It was demonstrated that the correction term fairly compensated the error and led the RDF in good agreement with the result given by an ab initio molecular dynamics simulation.

Structural and dynamical properties of recombining ultracold neutral plasma

NASA Astrophysics Data System (ADS)

Tiwari, Sanat Kumar; Shaffer, Nathaniel R.; Baalrud, Scott D.

2017-10-01

An ultracold plasma (UCP) is an evolving collection of free charges and bound charges (Rydberg atoms). Over time, bound species concentration increases due to recombination. We present the structural and dynamical properties of an evolving UCP using classical molecular dynamics simulation. Coulomb collapse is avoided using a repulsive core with the attractive Coulomb potential. The repulsive core size controls the concentration of bound states, as it determines the depth of the potential well between opposite charges. We vary the repulsive core size to emulate the quasi-static state of plasma at different time during the evolution. Binary, chain and ring-like bound states are observed in the simulation carried out at different coupling strengths and repulsive core size. The effect of bound states can be seen as molecular peaks in the radial distribution function (RDF). The thermodynamic properties associated with the free charges can be analyzed from RDF by separating free from bound states. These bound states also change the dynamical properties of the plasma. The electron velocity auto-correlation displays oscillations due to the orbital motion in bound states. These bound states act like a neutral species, damping electron plasmon modes and broadening the ion acoustic mode. This work is supported by AFOSR Grant Number FA9550-16-1-0221. It used computational resources by XSEDE, which is supported by NSF Grant Number ACI-1053575.

How to establish a successful revolving drug fund: the experience of Khartoum state in the Sudan

PubMed Central

2009-01-01

Abstract Problem During the 1990s, the Sudan began several initiatives to establish new medicine-financing mechanisms as part of the health reform process. Initial seed stocks were provided to each hospital. Unfortunately these facility-based funds did not regenerate and the hospitals were left without funds for medicines. The Revolving Drug Fund (RDF) was established in 1989 to facilitate access to medicines in health facilities in Khartoum state. Approach This study used quantitative and qualitative research techniques to collect data from health-care providers and users to evaluate the experience of operating an RDF in Khartoum state. Data from personal observations and from archival and statistical records were also analysed. Seven health facilities were sampled for this research. Local setting The Ministry of Health has a policy to expand the RDF to the whole country and has already commenced roll-out to seven more states. This policy is based on the experience of the RDF within Khartoum state. Relevant changes Khartoum state has a high (97%) level of availability of essential medicines and this is attributed to the RDF. The RDF medicines were mostly considered affordable by users and very few (6%) patients failed to obtain the prescribed medicines for financial reasons. Lessons learned The RDF could be successfully replicated in other states of the Sudan and in low-income countries with similar contexts on condition that they meet success factors, such as gradual implementation, political commitment and availability of hard currency. PMID:19274366

A 3D-analysis of cluster formation and dynamics of the X(-)-benzene (X = F, Cl, Br, I) ionic dimer solvated by Ar atoms.

PubMed

Albertí, Margarita; Huarte-Larrañaga, Fermín; Aguilar, Antonio; Lucas, José M; Pirani, Fernando

2011-05-14

The specific influence of X(-) ions (X = F,Cl, Br, I) in the solvation process of halide-benzene (X(-)-Bz) ionic heterodimers by Ar atoms is investigated by means of molecular dynamic (MD) simulations. The gradual evolution from cluster rearrangement to solvation dynamics is discussed by considering ensembles of n (n = 1-15 and n = 30) Ar atoms around the X(-)-Bz stable ionic dimers. The potential energy surfaces employed are based on an atom/ion-atom and atom/ion-bond decomposition, which has been developed previously by some of the authors. The outcome of the dynamics is analyzed by employing radial distribution functions (RDF) and tridimensional (3D) probability densities.

Deformation behaviors of Cu29Zr32Ti15Al5Ni19 high entropy bulk metallic glass during nanoindentation

NASA Astrophysics Data System (ADS)

Fang, Qihong; Yi, Ming; Li, Jia; Liu, Bin; Huang, Zaiwang

2018-06-01

The deformation behaviors of Cu29Zr32Ti15Al5Ni19 high entropy bulk metallic glass (HE-BMG) during the nanoindentation are presented via the large-scale molecular dynamics (MD) simulations. The indentation tests are carried out using spherical rigid indenter to investigate the microstructural evolution on the mechanical properties of HE-BMGs in terms of shear strain, indentation force, and surface morphology as well as radial distribution function (RDF). Based on the Hertzian fitting the load-displacement curve, HE-BMG Cu29Zr32Ti15Al5Ni19 has the Young's modulus of 93.1 GPa and hardness of 8.8 GPa. The indentation force requiring for the continual increasing contacted area between the indenter and the substrate goes up with the increasing of indentation depth. In addition, the symmetrical distribution of atomic displacement reveals the isotropic of HE-BMG after the indentation treatment. In the deformation region, the Al element would lead to the serious fluctuation in the first peak of RDF, which is much stronger than the other elements. The severe distortion from the atomic size difference maybe reduce the activation energy to the occurrence of shear deformation in HE-BMG, leading to the transition from brittle to ductile observed by the whole sliding of the local atom group. Through the indentation load-displacement curves at various temperatures, the softening of HE-BMG at high temperatures is in qualitative agreement with the experimental findings. Moreover, this effective strategy is used to accelerate the discovery of excellent mechanical properties of HE-BMGs by means of MD simulation, as well as understand the fundamental nanoindentation response of HE-BMGs.

The structural, electronic and spectroscopic properties of 4FPBAPE molecule: Experimental and theoretical study

NASA Astrophysics Data System (ADS)

Tanış, Emine; Babur Sas, Emine; Kurban, Mustafa; Kurt, Mustafa

2018-02-01

The experimental and theoretical study of 4-Formyl Phenyl Boronic Acid Pinacol Ester (4FPBAPE) molecule were performed in this work. 1H, 13C NMR and UV-Vis spectra were tested in dimethyl sulfoxide (DMSO). The structural, spectroscopic properties and energies of 4FPBAPE were obtained for two potential conformers from density functional theory (DFT) with B3LYP/6-311G (d, p) and CAM-B3LYP/6-311G (d, p) basis sets. The optimal geometry of those structures was obtained according to the position of oxygen atom upon determining the scan coordinates for each conformation. The most stable conformer was found as the A2 form. The fundamental vibrations were determined based on optimized structure in terms of total energy distribution. Electronic properties such as oscillator strength, wavelength, excitation energy, HOMO, LUMO and molecular electrostatic potential and structural properties such as radial distribution functions (RDF) and probability density depending on coordination number are presented. Theoretical results of 4-FPBAPE spectra were found to be compatible with observed spectra.

Radial Distribution Functions of Strongly Coupled Two-Temperature Plasmas

NASA Astrophysics Data System (ADS)

Shaffer, Nathaniel R.; Tiwari, Sanat Kumar; Baalrud, Scott D.

2017-10-01

We present tests of three theoretical models for the radial distribution functions (RDFs) in two-temperature strongly coupled plasmas. RDFs are useful in extending plasma thermodynamics and kinetic theory to strong coupling, but they are usually known only for thermal equilibrium or for approximate one-component model plasmas. Accurate two-component modeling is necessary to understand the impact of strong coupling on inter-species transport, e.g., ambipolar diffusion and electron-ion temperature relaxation. We demonstrate that the Seuferling-Vogel-Toeppfer (SVT) extension of the hypernetted chain equations not only gives accurate RDFs (as compared with classical molecular dynamics simulations), but also has a simple connection with the Yukawa OCP model. This connection gives a practical means to recover the structure of the electron background from knowledge of the ion-ion RDF alone. Using the model RDFs in Effective Potential Theory, we report the first predictions of inter-species transport coefficients of strongly coupled plasmas far from equilibrium. This work is supported by NSF Grant No. PHY-1453736, AFSOR Award No. FA9550-16-1-0221, and used XSEDE computational resources.

owlcpp: a C++ library for working with OWL ontologies.

PubMed

Levin, Mikhail K; Cowell, Lindsay G

2015-01-01

The increasing use of ontologies highlights the need for a library for working with ontologies that is efficient, accessible from various programming languages, and compatible with common computational platforms. We developed owlcpp, a library for storing and searching RDF triples, parsing RDF/XML documents, converting triples into OWL axioms, and reasoning. The library is written in ISO-compliant C++ to facilitate efficiency, portability, and accessibility from other programming languages. Internally, owlcpp uses the Raptor RDF Syntax library for parsing RDF/XML and the FaCT++ library for reasoning. The current version of owlcpp is supported under Linux, OSX, and Windows platforms and provides an API for Python. The results of our evaluation show that, compared to other commonly used libraries, owlcpp is significantly more efficient in terms of memory usage and searching RDF triple stores. owlcpp performs strict parsing and detects errors ignored by other libraries, thus reducing the possibility of incorrect semantic interpretation of ontologies. owlcpp is available at http://owl-cpp.sf.net/ under the Boost Software License, Version 1.0.

Generation of Test Questions from RDF Files Using PYTHON and SPARQL

NASA Astrophysics Data System (ADS)

Omarbekova, Assel; Sharipbay, Altynbek; Barlybaev, Alibek

2017-02-01

This article describes the development of the system for the automatic generation of test questions based on the knowledge base. This work has an applicable nature and provides detailed examples of the development of ontology and implementation the SPARQL queries in RDF-documents. Also it describes implementation of the program generating questions in the Python programming language including the necessary libraries while working with RDF-files.

The Analysis of RDF Semantic Data Storage Optimization in Large Data Era

NASA Astrophysics Data System (ADS)

He, Dandan; Wang, Lijuan; Wang, Can

2018-03-01

With the continuous development of information technology and network technology in China, the Internet has also ushered in the era of large data. In order to obtain the effective acquisition of information in the era of large data, it is necessary to optimize the existing RDF semantic data storage and realize the effective query of various data. This paper discusses the storage optimization of RDF semantic data under large data.

Kirkwood-Buff integrals of finite systems: shape effects

NASA Astrophysics Data System (ADS)

Dawass, Noura; Krüger, Peter; Simon, Jean-Marc; Vlugt, Thijs J. H.

2018-06-01

The Kirkwood-Buff (KB) theory provides an important connection between microscopic density fluctuations in liquids and macroscopic properties. Recently, Krüger et al. derived equations for KB integrals for finite subvolumes embedded in a reservoir. Using molecular simulation of finite systems, KB integrals can be computed either from density fluctuations inside such subvolumes, or from integrals of radial distribution functions (RDFs). Here, based on the second approach, we establish a framework to compute KB integrals for subvolumes with arbitrary convex shapes. This requires a geometric function w(x) which depends on the shape of the subvolume, and the relative position inside the subvolume. We present a numerical method to compute w(x) based on Umbrella Sampling Monte Carlo (MC). We compute KB integrals of a liquid with a model RDF for subvolumes with different shapes. KB integrals approach the thermodynamic limit in the same way: for sufficiently large volumes, KB integrals are a linear function of area over volume, which is independent of the shape of the subvolume.

Synthesis, crystal structure analysis, molecular docking studies and density functional theory predictions of the local reactive properties and degradation properties of a novel halochalcone

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.

2017-09-01

In the present study, single crystals of E)-3-(3,5-dichlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one, were prepared and structurally characterized by single crystal X-ray diffraction analysis. The molecular structure crystallized in monoclinic crystal system with P21/c space group. Sensitivity of the title molecule towards electrophilic attacks has been examined by calculations of average localized ionization energies (ALIE) and their mapping to electron density surface. Further determination of atoms that could be important reactive centres has been performed by calculations of Fukui functions. Sensitivity of title molecule towards autoxidation and hydrolysis mechanisms has been assessed by calculations of bond dissociation energies and radial distribution functions (RDF), respectively. Also, in order to explore possible binding mode of the title compound towards Dihydrofolate reductase enzyme, we have utilized in silico molecular docking to explore possible binding modes of the title compound with the DHFR enzyme.

Characterization of the Iberian Y chromosome haplogroup R-DF27 in Northern Spain.

PubMed

Villaescusa, Patricia; Illescas, María José; Valverde, Laura; Baeta, Miriam; Nuñez, Carolina; Martínez-Jarreta, Begoña; Zarrabeitia, Maria Teresa; Calafell, Francesc; de Pancorbo, Marian M

2017-03-01

The European paternal lineage R-DF27 has been proposed as a haplogroup of Iberian origin due to its maximum frequencies in the Iberian Peninsula. In this study, the distribution and structure of DF27 were characterized in 591 unrelated male individuals from four key populations of the north area of the Iberian Peninsula through the analysis of 12 Y-SNPs that define DF27 main sublineages. Additionally, Y-SNP allele frequencies were also gathered from the reference populations in the 1000 Genomes Project to compare and obtain a better landscape of the distribution of DF27. Our results reveal frequencies over 35% of DF27 haplogroup in the four North Iberian populations analyzed and high frequencies for its subhaplogroups. Considering the low frequency of DF27 and its sublineages in most populations outside of the Iberian Peninsula, this haplogroup seems to have geographical significance; thus, indicating a possible Iberian patrilineal origin of vestiges bearing this haplogroup. The dataset presented here contributes with new data to better understand the complex genetic variability of the Y chromosome in the Iberian Peninsula, that can be applied in Forensic Genetics. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Don’t Like RDF Reification? Making Statements about Statements Using Singleton Property

PubMed Central

Nguyen, Vinh; Bodenreider, Olivier; Sheth, Amit

2015-01-01

Statements about RDF statements, or meta triples, provide additional information about individual triples, such as the source, the occurring time or place, or the certainty. Integrating such meta triples into semantic knowledge bases would enable the querying and reasoning mechanisms to be aware of provenance, time, location, or certainty of triples. However, an efficient RDF representation for such meta knowledge of triples remains challenging. The existing standard reification approach allows such meta knowledge of RDF triples to be expressed using RDF by two steps. The first step is representing the triple by a Statement instance which has subject, predicate, and object indicated separately in three different triples. The second step is creating assertions about that instance as if it is a statement. While reification is simple and intuitive, this approach does not have formal semantics and is not commonly used in practice as described in the RDF Primer. In this paper, we propose a novel approach called Singleton Property for representing statements about statements and provide a formal semantics for it. We explain how this singleton property approach fits well with the existing syntax and formal semantics of RDF, and the syntax of SPARQL query language. We also demonstrate the use of singleton property in the representation and querying of meta knowledge in two examples of Semantic Web knowledge bases: YAGO2 and BKR. Our experiments on the BKR show that the singleton property approach gives a decent performance in terms of number of triples, query length and query execution time compared to existing approaches. This approach, which is also simple and intuitive, can be easily adopted for representing and querying statements about statements in other knowledge bases. PMID:25750938

Democratization in Albania: The OSCE, NATO and the European Union

DTIC Science & Technology

2010-06-01

html? maca =en-rss-en-all-1573-rdf (accessed 4 March 2010). 263 Manuel Montobbio de Balanzo, Spanish Ambassador to Albania, http://www.dw- world.de/dw...article/0,,5259561,00.html? maca =en-rss-en-all-1573-rdf (accessed 4 March 2010). 264 Reinhard Priebe, The Western Balkan European Perspective, http...world.de/dw/article/0,,5259561,00.html? maca =en-rss-en-all-1573-rdf (accessed 4 March 2010). European Commission Enlargement, Albania – Questions

A Preliminary Investigation of Reversing RML: From an RDF dataset to its Column-Based data source

PubMed Central

Gougousis, Alexandros

2015-01-01

Abstract Background A large percentage of scientific data with tabular structure are published on the Web of Data as interlinked RDF datasets. When we come to the issue of long-term preservation of such RDF-based digital objects, it is important to provide full support for reusing them in the future. In particular, it should include means for both players who have no familiarity with RDF data model and, at the same time, who by working only with the native format of the data still provide sufficient information. To achieve this, we need mechanisms to bring the data back to their original format and structure. New information In this paper, we investigate how to perform the reverse process for column-based data sources. In particular, we devise an algorithm, RML2CSV, and exemplify its implementation in transforming an RDF dataset into its CSV tabular structure, through the use of the same RML mapping document that was used to generate the set of RDF triples. Through a set of content-based criteria, we attempt a comparative evaluation to measure the similarity between the rebuilt CSV and the original one. The results are promising and show that, under certain assumptions, RML2CSV reconstructs the same data with the same structure, offering more advanced digital preservation services. PMID:26312054

Perspectives and limits for cement kilns as a destination for RDF

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

Genon, G.; Brizio, E.

2008-11-15

RDF, the high calorific value fraction of MSW obtained by conventional separation systems, can be employed in technological plants (mainly cement kilns) in order to obtain a useful energy recovery. It is interesting and important to evaluate this possibility within the general framework of waste-to-energy solutions. The solution must be assessed on the basis of different aspects, namely: technological features and clinker characteristics; local atmospheric pollution; the effects of RDF used in cement kilns on the generation of greenhouse gases; the economics of conventional solid fuels substitution and planning perspectives, from the point of view of the destination of RDFmore » and optimal cement kiln policy. The different experiences of this issue throughout Europe are reviewed, and some applications within Italy are also been considered. The main findings of the study are that the use of RDF in cement kilns instead of coal or coke offers environmental benefits in terms of greenhouse gases, while the formation of conventional gaseous pollutants is not a critical aspect. Indeed, the generation of nitrogen oxides can probably be lower because of lower flame temperatures or lower air excess. The presence of chlorinated micro-pollutants is not influenced by the presence of RDF in fuel, whereas depending on the quality of the RDF, some problems could arise compared to the substituted fuel as far as heavy metals are concerned, chiefly the more volatile ones.« less

DOGMA: A Disk-Oriented Graph Matching Algorithm for RDF Databases

NASA Astrophysics Data System (ADS)

Bröcheler, Matthias; Pugliese, Andrea; Subrahmanian, V. S.

RDF is an increasingly important paradigm for the representation of information on the Web. As RDF databases increase in size to approach tens of millions of triples, and as sophisticated graph matching queries expressible in languages like SPARQL become increasingly important, scalability becomes an issue. To date, there is no graph-based indexing method for RDF data where the index was designed in a way that makes it disk-resident. There is therefore a growing need for indexes that can operate efficiently when the index itself resides on disk. In this paper, we first propose the DOGMA index for fast subgraph matching on disk and then develop a basic algorithm to answer queries over this index. This algorithm is then significantly sped up via an optimized algorithm that uses efficient (but correct) pruning strategies when combined with two different extensions of the index. We have implemented a preliminary system and tested it against four existing RDF database systems developed by others. Our experiments show that our algorithm performs very well compared to these systems, with orders of magnitude improvements for complex graph queries.

Using RDF to Model the Structure and Process of Systems

NASA Astrophysics Data System (ADS)

Rodriguez, Marko A.; Watkins, Jennifer H.; Bollen, Johan; Gershenson, Carlos

Many systems can be described in terms of networks of discrete elements and their various relationships to one another. A semantic network, or multi-relational network, is a directed labeled graph consisting of a heterogeneous set of entities connected by a heterogeneous set of relationships. Semantic networks serve as a promising general-purpose modeling substrate for complex systems. Various standardized formats and tools are now available to support practical, large-scale semantic network models. First, the Resource Description Framework (RDF) offers a standardized semantic network data model that can be further formalized by ontology modeling languages such as RDF Schema (RDFS) and the Web Ontology Language (OWL). Second, the recent introduction of highly performant triple-stores (i.e. semantic network databases) allows semantic network models on the order of 109 edges to be efficiently stored and manipulated. RDF and its related technologies are currently used extensively in the domains of computer science, digital library science, and the biological sciences. This article will provide an introduction to RDF/RDFS/OWL and an examination of its suitability to model discrete element complex systems.

Toward a view-oriented approach for aligning RDF-based biomedical repositories.

PubMed

Anguita, A; García-Remesal, M; de la Iglesia, D; Graf, N; Maojo, V

2015-01-01

This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While several approaches for RDF-based database integration have been proposed, those focused on schema alignment have become the most widely adopted. All state-of-the-art solutions for aligning RDF-based sources resort to a simple technique inherited from legacy relational database integration methods. This technique - known as element-to-element (e2e) mappings - is based on establishing 1:1 mappings between single primitive elements - e.g. concepts, attributes, relationships, etc. - belonging to the source and target schemas. However, due to the intrinsic nature of RDF - a representation language based on defining tuples < subject, predicate, object > -, one may find RDF elements whose semantics vary dramatically when combined into a view involving other RDF elements - i.e. they depend on their context. The latter cannot be adequately represented in the target schema by resorting to the traditional e2e approach. These approaches fail to properly address this issue without explicitly modifying the target ontology, thus lacking the required expressiveness for properly reflecting the intended semantics in the alignment information. To enhance existing RDF schema alignment techniques by providing a mechanism to properly represent elements with context-dependent semantics, thus enabling users to perform more expressive alignments, including scenarios that cannot be adequately addressed by the existing approaches. Instead of establishing 1:1 correspondences between single primitive elements of the schemas, we propose adopting a view-based approach. The latter is targeted at establishing mapping relationships between RDF subgraphs - that can be regarded as the equivalent of views in traditional databases -, rather than between single schema elements. This approach enables users to represent scenarios defined by context-dependent RDF elements that cannot be properly represented when adopting the currently existing approaches. We developed a software tool implementing our view-based strategy. Our tool is currently being used in the context of the European Commission funded p-medicine project, targeted at creating a technological framework to integrate clinical and genomic data to facilitate the development of personalized drugs and therapies for cancer, based on the genetic profile of the patient. We used our tool to integrate different RDF-based databases - including different repositories of clinical trials and DICOM images - using the Health Data Ontology Trunk (HDOT) ontology as the target schema. The importance of database integration methods and tools in the context of biomedical research has been widely recognized. Modern research in this area - e.g. identification of disease biomarkers, or design of personalized therapies - heavily relies on the availability of a technical framework to enable researchers to uniformly access disparate repositories. We present a method and a tool that implement a novel alignment method specifically designed to support and enhance the integration of RDF-based data sources at schema (metadata) level. This approach provides an increased level of expressiveness compared to other existing solutions, and allows solving heterogeneity scenarios that cannot be properly represented using other state-of-the-art techniques.

Semantic Integration for Marine Science Interoperability Using Web Technologies

NASA Astrophysics Data System (ADS)

Rueda, C.; Bermudez, L.; Graybeal, J.; Isenor, A. W.

2008-12-01

The Marine Metadata Interoperability Project, MMI (http://marinemetadata.org) promotes the exchange, integration, and use of marine data through enhanced data publishing, discovery, documentation, and accessibility. A key effort is the definition of an Architectural Framework and Operational Concept for Semantic Interoperability (http://marinemetadata.org/sfc), which is complemented with the development of tools that realize critical use cases in semantic interoperability. In this presentation, we describe a set of such Semantic Web tools that allow performing important interoperability tasks, ranging from the creation of controlled vocabularies and the mapping of terms across multiple ontologies, to the online registration, storage, and search services needed to work with the ontologies (http://mmisw.org). This set of services uses Web standards and technologies, including Resource Description Framework (RDF), Web Ontology language (OWL), Web services, and toolkits for Rich Internet Application development. We will describe the following components: MMI Ontology Registry: The MMI Ontology Registry and Repository provides registry and storage services for ontologies. Entries in the registry are associated with projects defined by the registered users. Also, sophisticated search functions, for example according to metadata items and vocabulary terms, are provided. Client applications can submit search requests using the WC3 SPARQL Query Language for RDF. Voc2RDF: This component converts an ASCII comma-delimited set of terms and definitions into an RDF file. Voc2RDF facilitates the creation of controlled vocabularies by using a simple form-based user interface. Created vocabularies and their descriptive metadata can be submitted to the MMI Ontology Registry for versioning and community access. VINE: The Vocabulary Integration Environment component allows the user to map vocabulary terms across multiple ontologies. Various relationships can be established, for example exactMatch, narrowerThan, and subClassOf. VINE can compute inferred mappings based on the given associations. Attributes about each mapping, like comments and a confidence level, can also be included. VINE also supports registering and storing resulting mapping files in the Ontology Registry. The presentation will describe the application of semantic technologies in general, and our planned applications in particular, to solve data management problems in the marine and environmental sciences.

The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

PubMed

Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Pocock, Matthew; Flanagan, Keith; Hallinan, Jennifer; Wipat, Anil

2016-06-17

Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users.

Defense Advanced Research Projects Agency (DARPA) Agent Markup Language Computer Aided Knowledge Acquisition

DTIC Science & Technology

2005-06-01

34> <rdfs:subClassOf rdf:resource="#Condition"/> <rdfs:label>Economic Self -Sufficiency Class</rdfs:label> <cnd:categoryCode>C</cnd:categoryCode...cnd:index>3.3.4.1</cnd:index> <cnd:title>Economic Self -Sufficiency</cnd:title> <cnd:definition>The ability of a nation to...34#International_Economic_Position"/> <cnd:subCategory rdf:resource="# Self -Sufficiency_In_Food"/> <cnd:subCategory rdf:resource="# Self

Mechanisms for the clustering of inertial particles in the inertial range of isotropic turbulence

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

Bragg, Andrew D.; Ireland, Peter J.; Collins, Lance R.

2015-08-27

In this study, we consider the physical mechanism for the clustering of inertial particles in the inertial range of isotropic turbulence. We analyze the exact, but unclosed, equation governing the radial distribution function (RDF) and compare the mechanisms it describes for clustering in the dissipation and inertial ranges. We demonstrate that in the limit St r <<1, where St r is the Stokes number based on the eddy turnover time scale at separation r, the clustering in the inertial range can be understood to be due to the preferential sampling of the coarse-grained fluid velocity gradient tensor at that scale.more » When St r≳O(1) this mechanism gives way to a nonlocal clustering mechanism. These findings reveal that the clustering mechanisms in the inertial range are analogous to the mechanisms that we identified for the dissipation regime. Further, we discuss the similarities and differences between the clustering mechanisms we identify in the inertial range and the “sweep-stick” mechanism developed by Coleman and Vassilicos. We show that the idea that initial particles are swept along with acceleration stagnation points is only approximately true because there always exists a finite difference between the velocity of the acceleration stagnation points and the local fluid velocity. This relative velocity is sufficient to allow particles to traverse the average distance between the stagnation points within the correlation time scale of the acceleration field. We also show that the stick part of the mechanism is only valid for St r<<1 in the inertial range. We emphasize that our clustering mechanism provides the more fundamental explanation since it, unlike the sweep-stick mechanism, is able to explain clustering in arbitrary spatially correlated velocity fields. We then consider the closed, model equation for the RDF given in Zaichik and Alipchenkov and use this, together with the results from our analysis, to predict the analytic form of the RDF in the inertial range for St r<<1, which, unlike that in the dissipation range, is not scale invariant. Finally, the results are in good agreement with direct numerical simulations, provided the separations are well within the inertial range.« less

Anharmonicity and atomic distribution of SnTe and PbTe thermoelectrics

DOE PAGES

Li, C. W.; Ma, J.; Cao, H. B.; ...

2014-12-29

The structure and lattice dynamics of rock-salt thermoelectric materials SnTe and PbTe are investigated with single crystal and powder neutron diffraction, inelastic neutron scattering (INS), and first-principles simulations. Our first-principles calculations of the radial distribution function (RDF) in both SnTe and PbTe show a clear asymmetry in the first nearest-neighbor (1NN) peak, which increases with temperature, in agreement with experimental reports (Ref. 1,2). We show that this peak asymmetry for the 1NN Sn–Te or Pb–Te bond results from large-amplitude anharmonic vibrations (phonons). No atomic off-centering is found in our simulations. In addition, the atomic mean square displacements derived from ourmore » diffraction data reveal stiffer bonding at the anion site, in good agreement with the partial phonon densities of states from INS, and first-principles calculations. In conclusion, these results provide clear evidence for large-amplitude anharmonic phonons associated with the resonant bonding leading to the ferroelectric instability.« less

Pathogenicity Island Cross Talk Mediated by Recombination Directionality Factors Facilitates Excision from the Chromosome.

PubMed

Carpenter, Megan R; Rozovsky, Sharon; Boyd, E Fidelma

2015-12-14

Pathogenicity islands (PAIs) are mobile integrated genetic elements (MIGEs) that contain a diverse range of virulence factors and are essential in the evolution of pathogenic bacteria. PAIs are widespread among bacteria and integrate into the host genome, commonly at a tRNA locus, via integrase-mediated site-specific recombination. The excision of PAIs is the first step in the horizontal transfer of these elements and is not well understood. In this study, we examined the role of recombination directionality factors (RDFs) and their relationship with integrases in the excision of two PAIs essential for Vibrio cholerae host colonization: Vibrio pathogenicity island 1 (VPI-1) and VPI-2. VPI-1 does not contain an RDF, which allowed us to answer the question of whether RDFs are an absolute requirement for excision. We found that an RDF was required for efficient excision of VPI-2 but not VPI-1 and that RDFs can induce excision of both islands. Expression data revealed that the RDFs act as transcriptional repressors to both VPI-1- and VPI-2-encoded integrases. We demonstrated that the RDFs Vibrio excision factor A (VefA) and VefB bind at the attachment sites (overlapping the int promoter region) of VPI-1 and VPI-2, thus supporting this mode of integrase repression. In addition, V. cholerae RDFs are promiscuous due to their dual functions of promoting excision of both VPI-1 and VPI-2 and acting as negative transcriptional regulators of the integrases. This is the first demonstration of cross talk between PAIs mediated via RDFs which reveals the complex interactions that occur between separately acquired MIGEs. Deciphering the mechanisms of pathogenicity island excision is necessary for understanding the evolution and spread of these elements to their nonpathogenic counterparts. Such mechanistic insight would assist in predicting the mobility of uncharacterized genetic elements. This study identified extensive RDF-mediated cross talk between two nonhomologous VPIs and demonstrated the dual functionality of RDF proteins: (i) inducing PAI excision and (ii) acting as transcriptional regulators. Findings from this study may be implicated in determining the mobilome contribution of other bacteria with multiple MIGEs. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

RCQ-GA: RDF Chain Query Optimization Using Genetic Algorithms

NASA Astrophysics Data System (ADS)

Hogenboom, Alexander; Milea, Viorel; Frasincar, Flavius; Kaymak, Uzay

The application of Semantic Web technologies in an Electronic Commerce environment implies a need for good support tools. Fast query engines are needed for efficient querying of large amounts of data, usually represented using RDF. We focus on optimizing a special class of SPARQL queries, the so-called RDF chain queries. For this purpose, we devise a genetic algorithm called RCQ-GA that determines the order in which joins need to be performed for an efficient evaluation of RDF chain queries. The approach is benchmarked against a two-phase optimization algorithm, previously proposed in literature. The more complex a query is, the more RCQ-GA outperforms the benchmark in solution quality, execution time needed, and consistency of solution quality. When the algorithms are constrained by a time limit, the overall performance of RCQ-GA compared to the benchmark further improves.

RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.

PubMed

Anguita, Alberto; Martin, Luis; Garcia-Remesal, Miguel; Maojo, Victor

2013-07-01

This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to execute SPARQL queries for retrieving microarray data, either from specific experiments or from more than one experiment at a time. Our system optimizes response times by caching and reusing information from previous queries. In this paper, we describe our methods for achieving this transformation. We show that our approach is complementary to other existing initiatives, such as Bio2RDF, for accessing and retrieving data from the ArrayExpress database. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Dynamic Querying of Mass-Storage RDF Data with Rule-Based Entailment Regimes

NASA Astrophysics Data System (ADS)

Ianni, Giovambattista; Krennwallner, Thomas; Martello, Alessandra; Polleres, Axel

RDF Schema (RDFS) as a lightweight ontology language is gaining popularity and, consequently, tools for scalable RDFS inference and querying are needed. SPARQL has become recently a W3C standard for querying RDF data, but it mostly provides means for querying simple RDF graphs only, whereas querying with respect to RDFS or other entailment regimes is left outside the current specification. In this paper, we show that SPARQL faces certain unwanted ramifications when querying ontologies in conjunction with RDF datasets that comprise multiple named graphs, and we provide an extension for SPARQL that remedies these effects. Moreover, since RDFS inference has a close relationship with logic rules, we generalize our approach to select a custom ruleset for specifying inferences to be taken into account in a SPARQL query. We show that our extensions are technically feasible by providing benchmark results for RDFS querying in our prototype system GiaBATA, which uses Datalog coupled with a persistent Relational Database as a back-end for implementing SPARQL with dynamic rule-based inference. By employing different optimization techniques like magic set rewriting our system remains competitive with state-of-the-art RDFS querying systems.

Emissions During Co-Firing of RDF-5 with Coal in a 22 t/h Steam Bubbling Fluidized Bed Boiler

NASA Astrophysics Data System (ADS)

Wan, Hou-Peng; Chen, Jia-Yuan; Juch, Ching-I.; Chang, Ying-Hsi; Lee, Hom-Ti

The co-firing of biomass and fossil fuel in the same power plant is one of the most important issues when promoting the utilization of renewable energy in the world. Recently, the co-firing of coal together with biomass fuel, such as "densified refuse derived fuel" (d-RDF or RDF-5) or RPF (refuse paper & plastic fuel) from waste, has been considered as an environmentally sound and economical approach to both waste remediation and energy production in the world. Because of itscomplex characteristics when compared to fossil fuel, potential problems, such as combustion system stability, the corrosion of heat transfer tubes, the qualities of the ash, and the emissionof pollutants, are major concerns when co-firing the biomass fuel with fossil fuel in a traditional boiler. In this study, co-firing of coal with RDF-5 was conducted in a 22t/h bubbling fluidized bed (BFB) steam boiler to investigate the feasibility of utilizing RDF-5 as a sustainable fuels in a commercial coal-fired steam BFB boiler. The properties of the fly ash, bottom ash, and the emission of pollutants are analyzed and discussed in this study.

Refuse derived fuel potential in DKI Jakarta

NASA Astrophysics Data System (ADS)

Widyatmoko, H.

2018-01-01

Combustible waste fractions of municipal solid waste (MSW) which can not be easily separated or sorted, reused or recycled, may have a high calorifiv value (CV) that can be used in a fuel for energy recovery. The objective of this study was to explore the Refuse Derived Fuel (RDF) potential of municipal solid waste from DKI Jakarta to produce electricity and to promote it to be socially and politically acceptable. For this purpose, 24 sampels of RDF were taken from Bantargebang, cabonized, molded and pressed to be briquette. All samples were analized for moisture, ash, and calorific value in the physical and chemistry Laboratory of ITB Bandung. The analysis of calorific value (CV) shows the CV difference of 1815.8 cal/g between the briquettes (8051.25 cal/g) and the RDF (9867.12 cal/g. The total waste DKI which can be used as briquettes 5253 ton / day or equivalent with 49154115 kWh / day. If the efficiency of electricity production from RDF was 25%, then Jakarta is able to generate electricity from RDF of 12288529 kWh / day or as much as energy needed by 573,480 middle-class households with energy needs of 642.84 kWh/month.

Streamlining geospatial metadata in the Semantic Web

NASA Astrophysics Data System (ADS)

Fugazza, Cristiano; Pepe, Monica; Oggioni, Alessandro; Tagliolato, Paolo; Carrara, Paola

2016-04-01

In the geospatial realm, data annotation and discovery rely on a number of ad-hoc formats and protocols. These have been created to enable domain-specific use cases generalized search is not feasible for. Metadata are at the heart of the discovery process and nevertheless they are often neglected or encoded in formats that either are not aimed at efficient retrieval of resources or are plainly outdated. Particularly, the quantum leap represented by the Linked Open Data (LOD) movement did not induce so far a consistent, interlinked baseline in the geospatial domain. In a nutshell, datasets, scientific literature related to them, and ultimately the researchers behind these products are only loosely connected; the corresponding metadata intelligible only to humans, duplicated on different systems, seldom consistently. Instead, our workflow for metadata management envisages i) editing via customizable web- based forms, ii) encoding of records in any XML application profile, iii) translation into RDF (involving the semantic lift of metadata records), and finally iv) storage of the metadata as RDF and back-translation into the original XML format with added semantics-aware features. Phase iii) hinges on relating resource metadata to RDF data structures that represent keywords from code lists and controlled vocabularies, toponyms, researchers, institutes, and virtually any description one can retrieve (or directly publish) in the LOD Cloud. In the context of a distributed Spatial Data Infrastructure (SDI) built on free and open-source software, we detail phases iii) and iv) of our workflow for the semantics-aware management of geospatial metadata.

Towards a Semantic Web of Community, Content and Interactions

DTIC Science & Technology

2005-09-01

importance of setting goals and deadlines as a means to achieving progress on the nebulous road to a dissertation. Jim Herbsleb sparked my interest in...RDF, such as Turtle [Bec04], a text syntax for RDF, and N-Triples [GDB04]. 45 </dc:creator> <dc:title>The Semantic Web: An Introduction</dc:title...2):22–41, 1990. 2.2.2 [Bec04] Dave Beckett. Turtle –terse rdf triple language. http://www.ilrt.bris.ac.uk/discovery/2004/01/ turtle /, January 2004. 4

Using RDF and Git to Realize a Collaborative Metadata Repository.

PubMed

Stöhr, Mark R; Majeed, Raphael W; Günther, Andreas

2018-01-01

The German Center for Lung Research (DZL) is a research network with the aim of researching respiratory diseases. The participating study sites' register data differs in terms of software and coding system as well as data field coverage. To perform meaningful consortium-wide queries through one single interface, a uniform conceptual structure is required covering the DZL common data elements. No single existing terminology includes all our concepts. Potential candidates such as LOINC and SNOMED only cover specific subject areas or are not granular enough for our needs. To achieve a broadly accepted and complete ontology, we developed a platform for collaborative metadata management. The DZL data management group formulated detailed requirements regarding the metadata repository and the user interfaces for metadata editing. Our solution builds upon existing standard technologies allowing us to meet those requirements. Its key parts are RDF and the distributed version control system Git. We developed a software system to publish updated metadata automatically and immediately after performing validation tests for completeness and consistency.

Publications - RDF 2015-14 | Alaska Division of Geological & Geophysical

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content DGGS RDF 2015-14 Publication Details Title: Jumbo Dome, interior Alaska: Whole-rock, major- and , 2015, Jumbo Dome, interior Alaska: Whole-rock, major- and trace-element analyses: Alaska Division of

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MUNICIPAL WASTE COMBUSTION ASSESSMENT: FOSSIL FUEL CO-FIRING

EPA Science Inventory

The report identifies refuse derived fuel (RDF) processing operations and various RDF types; describes such fossil fuel co-firing techniques as coal fired spreader stokers, pulverized coal wall fired boilers, pulverized coal tangentially fired boilers, and cyclone fired boilers; ...

A Querying Method over RDF-ized Health Level Seven v2.5 Messages Using Life Science Knowledge Resources.

PubMed

Kawazoe, Yoshimasa; Imai, Takeshi; Ohe, Kazuhiko

2016-04-05

Health level seven version 2.5 (HL7 v2.5) is a widespread messaging standard for information exchange between clinical information systems. By applying Semantic Web technologies for handling HL7 v2.5 messages, it is possible to integrate large-scale clinical data with life science knowledge resources. Showing feasibility of a querying method over large-scale resource description framework (RDF)-ized HL7 v2.5 messages using publicly available drug databases. We developed a method to convert HL7 v2.5 messages into the RDF. We also converted five kinds of drug databases into RDF and provided explicit links between the corresponding items among them. With those linked drug data, we then developed a method for query expansion to search the clinical data using semantic information on drug classes along with four types of temporal patterns. For evaluation purpose, medication orders and laboratory test results for a 3-year period at the University of Tokyo Hospital were used, and the query execution times were measured. Approximately 650 million RDF triples for medication orders and 790 million RDF triples for laboratory test results were converted. Taking three types of query in use cases for detecting adverse events of drugs as an example, we confirmed these queries were represented in SPARQL Protocol and RDF Query Language (SPARQL) using our methods and comparison with conventional query expressions were performed. The measurement results confirm that the query time is feasible and increases logarithmically or linearly with the amount of data and without diverging. The proposed methods enabled query expressions that separate knowledge resources and clinical data, thereby suggesting the feasibility for improving the usability of clinical data by enhancing the knowledge resources. We also demonstrate that when HL7 v2.5 messages are automatically converted into RDF, searches are still possible through SPARQL without modifying the structure. As such, the proposed method benefits not only our hospitals, but also numerous hospitals that handle HL7 v2.5 messages. Our approach highlights a potential of large-scale data federation techniques to retrieve clinical information, which could be applied as applications of clinical intelligence to improve clinical practices, such as adverse drug event monitoring and cohort selection for a clinical study as well as discovering new knowledge from clinical information.

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

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

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation.

PubMed

Shokuhfar, Ali; Arab, Behrouz

2013-09-01

Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA) with diethylenetriamine (DETA) curing agent, and to study the behavior of resulted epoxy polymer with different conversion rates. The constant-strain (static) approach was then applied to calculate the mechanical properties (Bulk, shear and Young's moduli, elastic stiffness constants, and Poisson's ratio) of the uncured and cross-linked systems. Estimated material properties were found to be in good agreement with experimental observations. Moreover, the dependency of mechanical properties on the cross linking density was investigated and revealed improvements in the mechanical properties with increasing the cross linking density. The radial distribution function (RDF) was also used to study the evolution of local structures of the simulated systems as a function of cross linking density.

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

DOE PAGES

Timoshenko, Janis; Frenkel, Anatoly I.; Cintins, Arturs; ...

2018-05-25

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic andmore » austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions« less

Neural Network Approach for Characterizing Structural Transformations by X-Ray Absorption Fine Structure Spectroscopy

NASA Astrophysics Data System (ADS)

Timoshenko, Janis; Anspoks, Andris; Cintins, Arturs; Kuzmin, Alexei; Purans, Juris; Frenkel, Anatoly I.

2018-06-01

The knowledge of the coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use an artificial neural network approach to extract the information on the local structure and its in situ changes directly from the x-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from a body-centered to a face-centered cubic arrangement of iron atoms. This method is attractive for a broad range of materials and experimental conditions.

A comprehensive comparison between thermodynamic perturbation theory and first-order mean spherical approximation: Based on discrete potentials with hard core

NASA Astrophysics Data System (ADS)

Zhou, Shiqi; Zhou, Run

2017-08-01

Using the TL (Tang and Lu, 1993) method, Ornstein-Zernike integral equation is solved perturbatively under the mean spherical approximation (MSA) for fluid with potential consisting of a hard sphere plus square-well plus square-shoulder (HS + SW + SS) to obtain first-order analytic expressions of radial distribution function (RDF), second-order direct correlation function, and semi-analytic expressions for common thermodynamic properties. A comprehensive comparison between the first-order MSA and high temperature series expansion (HTSE) to third-, fifth- and seventh-order is performed over a wide parameter range for both a HS + SW and the HS + SW + SS model fluids by using corresponding ;exact; Monte Carlo results as a reference; although the HTSE is carried out up to seventh-order, and not to the first order as the first-order MSA the comparison is considered fair from a calculation complexity perspective. It is found that the performance of the first-order MSA is dramatically model-dependent: as target potentials go from the HS + SW to the HS + SW + SS, (i) there is a dramatic dropping of performance of the first-order MSA expressions in calculating the thermodynamic properties, especially both the excess internal energy and constant volume excess heat capacity of the HS + SW + SS model cannot be predicted even qualitatively correctly. (ii) One tendency is noticed that the first-order MSA gets more reliable with increasing temperatures in dealing with the pressure, excess Helmholtz free energy, excess enthalpy and excess chemical potential. (iii) Concerning the RDF, the first-order MSA is not as disappointing as it displays in the cases of thermodynamics. (iv) In the case of the HS + SW model, the first-order MSA solution is shown to be quantitatively correct in calculating the pressure and excess chemical potential even if the reduced temperatures are as low as 0.8. On the other hand, the seventh-order HTSE is less model-dependent; in most cases of the HS + SW and the HS + SW + SS models, the seventh-order HTSE improves the fifth- and third-order HTSE in both thermodynamic properties and RDF, and the improvements are very demonstrable in both the excess internal energy and constant volume excess heat capacity; for very limited cases, the seventh-order HTSE improves the fifth-order HTSE only within lower density domain and even shows a bit of inadaptation over higher density domain.

Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases

PubMed Central

2011-01-01

Background Although many biological databases are applying semantic web technologies, meaningful biological hypothesis testing cannot be easily achieved. Database-driven high throughput genomic hypothesis testing requires both of the capabilities of obtaining semantically relevant experimental data and of performing relevant statistical testing for the retrieved data. Tissue Microarray (TMA) data are semantically rich and contains many biologically important hypotheses waiting for high throughput conclusions. Methods An application-specific ontology was developed for managing TMA and DNA microarray databases by semantic web technologies. Data were represented as Resource Description Framework (RDF) according to the framework of the ontology. Applications for hypothesis testing (Xperanto-RDF) for TMA data were designed and implemented by (1) formulating the syntactic and semantic structures of the hypotheses derived from TMA experiments, (2) formulating SPARQLs to reflect the semantic structures of the hypotheses, and (3) performing statistical test with the result sets returned by the SPARQLs. Results When a user designs a hypothesis in Xperanto-RDF and submits it, the hypothesis can be tested against TMA experimental data stored in Xperanto-RDF. When we evaluated four previously validated hypotheses as an illustration, all the hypotheses were supported by Xperanto-RDF. Conclusions We demonstrated the utility of high throughput biological hypothesis testing. We believe that preliminary investigation before performing highly controlled experiment can be benefited. PMID:21342584

Modeling the Residual Strength of a Fibrous Composite Using the Residual Daniels Function

NASA Astrophysics Data System (ADS)

Paramonov, Yu.; Cimanis, V.; Varickis, S.; Kleinhofs, M.

2016-09-01

The concept of a residual Daniels function (RDF) is introduced. Together with the concept of Daniels sequence, the RDF is used for estimating the residual (after some preliminary fatigue loading) static strength of a unidirectional fibrous composite (UFC) and its S-N curve on the bases of test data. Usually, the residual strength is analyzed on the basis of a known S-N curve. In our work, an inverse approach is used: the S-N curve is derived from an analysis of the residual strength. This approach gives a good qualitive description of the process of decreasing residual strength and explanes the existence of the fatigue limit. The estimates of parameters of the corresponding regression model can be interpreted as estimates of parameters of the local strength of components of the UFC. In order to approach the quantitative experimental estimates of the fatigue life, some ideas based on the mathematics of the semiMarkovian process are employed. Satisfactory results in processing experimental data on the fatigue life and residual strength of glass/epoxy laminates are obtained.

Using XML to encode TMA DES metadata.

PubMed

Lyttleton, Oliver; Wright, Alexander; Treanor, Darren; Lewis, Paul

2011-01-01

The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.

Using XML to encode TMA DES metadata

PubMed Central

Lyttleton, Oliver; Wright, Alexander; Treanor, Darren; Lewis, Paul

2011-01-01

Background: The Tissue Microarray Data Exchange Specification (TMA DES) is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs. PMID:21969921

Computational fluid dynamics analysis of balloon-expandable coronary stents: influence of stent and vessel deformation.

PubMed

Martin, David M; Murphy, Eoin A; Boyle, Fergal J

2014-08-01

In many computational fluid dynamics (CFD) studies of stented vessel haemodynamics, the geometry of the stented vessel is described using non-deformed (NDF) geometrical models. These NDF models neglect complex physical features, such as stent and vessel deformation, which may have a major impact on the haemodynamic environment in stented coronary arteries. In this study, CFD analyses were carried out to simulate pulsatile flow conditions in both NDF and realistically-deformed (RDF) models of three stented coronary arteries. While the NDF models were completely idealised, the RDF models were obtained from nonlinear structural analyses and accounted for both stent and vessel deformation. Following the completion of the CFD analyses, major differences were observed in the time-averaged wall shear stress (TAWSS), time-averaged wall shear stress gradient (TAWSSG) and oscillatory shear index (OSI) distributions predicted on the luminal surface of the artery for the NDF and RDF models. Specifically, the inclusion of stent and vessel deformation in the CFD analyses resulted in a 32%, 30% and 31% increase in the area-weighted mean TAWSS, a 3%, 7% and 16% increase in the area-weighted mean TAWSSG and a 21%, 13% and 21% decrease in the area-weighted mean OSI for Stents A, B and C, respectively. These results suggest that stent and vessel deformation are likely to have a major impact on the haemodynamic environment in stented coronary arteries. In light of this observation, it is recommended that these features are considered in future CFD studies of stented vessel haemodynamics. Copyright © 2014 IPEM. Published by Elsevier Ltd. All rights reserved.

Separation of harmful impurities from refuse derived fuels (RDF) by a fluidized bed.

PubMed

Krüger, B; Mrotzek, A; Wirtz, S

2014-02-01

In firing systems of cement production plants and coal-fired power plants, regular fossil fuels are increasingly substituted by alternative fuels. Rising energy prices and ambitious CO2-reduction goals promote the use of alternative fuels as a significant contribution to efficient energy recovery. One possibility to protect energy resources are refuse-derived fuels (RDF), which are produced during the treatment of municipal solid, commercial and industrial waste. The waste fractions suitable for RDF have a high calorific value and are often not suitable for material recycling. With current treatment processes, RDF still contains components which impede the utilization in firing systems or limit the degree of substitution. The content of these undesired components may amount to 4 wt%. These, in most cases incombustible particles which consist of mineral, ceramic and metallic materials can cause damages in the conveying systems (e. g. rotary feeder) or result in contaminations of the products (e. g. cement, chalk). Up-to-date separation processes (sieve machine, magnet separator or air classifier) have individual weaknesses that could hamper a secure separation of these particles. This article describes a new technology for the separation of impurities from refuse derived fuels based on a rotating fluidized bed. In this concept a rotating motion of the particle bed is obtained by the tangential injection of the fluidization gas in a static geometry. The RDF-particles experience a centrifugal force which fluidized the bed radially. The technical principle allows tearing up of particle clusters to single particles. Radially inwards the vertical velocity is much lower thus particles of every description can fall down there. For the subsequent separation of the particles by form and density an additionally cone shaped plate was installed in the centre. Impurities have a higher density and a compact form compared to combustible particles and can be separated with a high efficiency. The new technology was experimentally investigated and proven using model-RDF, actual-RDF and impurities of different densities. In addition, numerical simulations were also done. The fluidization chamber was operated in batch mode. The article describes experiences and difficulties in using rotating fluidized bed systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Inhalation health effects of fine particles from the co-combustion of coal and refuse derived fuel.

PubMed

Fernandez, Art; Wendt, Jost O L; Wolski, Natacha; Hein, Klaus R G; Wang, Shengjun; Witten, Mark L

2003-06-01

This paper is concerned with health effects from the inhalation of particulate matter (PM) emitted from the combustion of coal, and from the co-combustion of refuse derived fuel (RDF) and pulverized coal mixtures, under both normal and low NO(x) conditions. Specific issues focus on whether the addition of RDF to coal has an effect on PM toxicity, and whether the application of staged combustion (for low NO(x)) may also be a factor in this regard. Ash particles were sampled and collected from a pilot scale combustion unit and then re-suspended and diluted to concentrations of approximately 1000 microg/m(3). These particles were inhaled by mice, which were held in a nose-only exposure configuration. Exposure tests were for 1 h per day, and involved three sets (eight mice per set) of mice. These three sets were exposed over 8, 16, and 24 consecutive days, respectively. Pathological lung damage was measured in terms of increases in lung permeability. Results show that the re-suspended coal/RDF ash appeared to cause very different effects on lung permeability than did coal ash alone. In addition, it was also shown that a "snapshot" of lung properties after a fixed number of daily 1-h exposures, can be misleading, since apparent repair mechanisms cause lung properties to change over a period of time. For the coal/RDF, the greatest lung damage (in terms of lung permeability increase) occurred at the short exposure period of 8 days, and thereafter appeared to be gradually repaired. Ash from staged (low NO(x)) combustion of coal/RDF appeared to cause greater lung injury than that from unstaged (high NO(x)) coal/RDF combustion, although the temporal behavior and (apparent) repair processes in each case were similar. In contrast to this, coal ash alone showed a slight decrease of lung permeability after 1 and 3 days, and this disappeared after 12 days. These observations are interpreted in the light of mechanisms proposed in the literature. The results all suggest that the composition of particles actually inhaled is important in determining lung injury. Particle size segregated leachability measurements showed that water soluble sulfur, zinc, and vanadium, but not iron, were present in the coal/RDF ash particles, which caused lung permeabilities to increase. However, the differences in health effects between unstaged and staged coal/RDF combustion could not be attributed to variations in pH values of the leachate.

Potential of solid waste utilization as source of refuse derived fuel (RDF) energy (case study at temporary solid waste disposal site in West Jakarta)

NASA Astrophysics Data System (ADS)

Indrawati, D.; Lindu, M.; Denita, P.

2018-01-01

This study aims to measure the volume of solid waste generated as well asits density, composition, and characteristics, to analyze the potential of waste in TPS to become RDF materials and to analyze the best composition mixture of RDF materials. The results show that the average of solid waste generation in TPS reaches 40.80 m3/day, with the largest percentage of its share is the organic waste component of 77.9%, while the smallest amount of its share is metal and rubber of 0.1%. The average water content and ash content of solid waste at the TPS is 27.7% and 6.4% respectively, while the average calorific potential value is 728.71 kcal/kg. The results of solid waste characteristics comparison at three TPS indicate thatTPS Tanjung Duren has the greatest waste potential to be processed into RDF materials with a calorific value of 893.73 kcal/kg, water content level of 24.6%, andlow ash content of 6.11%. This research has also shown that the best composition for RDF composite materials is rubber, wood, and textile mixtureexposed to outdoor drying conditions because it produced low water content and low ash content of 10.8% and 9.6%, thus optimizedthe calorific value of 4,372.896 kcal/kg.

Response of nitrogen and potassium fertigation to "Waris" almond (Prunus dulcis) under northwestern Himalayan Region of India.

PubMed

Kumar, Dinesh; Ahmed, N

2014-01-01

A field experiment was conducted on almond (Prunus dulcis) to study the effect of N&K fertigation on growth, yields and leaf nutrient status over two seasons (2011 and 2012) in Srinagar, Jammu and Kashmir, India. There were six treatments, namely, T1--100% recommended dose of fertilizers as soil application, T2--100% RDF through fertigations, T3--75% RDF through fertigation, T4--75% RDF through fertigation (split application), T5--50% RDF through fertigation and T6--50% RDF through fertigation (split application) with three replications under randomized block design. The results indicated that the maximum tree height (3.21 m and 3.56 m), nut weight (2.73 g and 1.94 g), nut yield (2.41 kg/tree and 5.98 kg/tree; 2.67 t/ha and 6.64 t/ha), and leaf nutrient content (2.34 and 2.38% N; 0.14 and 0.17% P; 1.37 and 1.41% K) were recorded in T4 treatment, whereas the highest TCSA of main trunk, primary, secondary, and tertiary branches (72.67 and 90.28 cm(2); 16.75 and 24.26 cm(2); 3.83 and 7.49 cm(2); 0.47 and 1.23 cm(2)), canopy volume (7.15 and 8.11 m(3)), and fruit number (990 and 3083/tree) were recorded in T2 in almond variety Waris.

Comparison of iterative inverse coarse-graining methods

NASA Astrophysics Data System (ADS)

Rosenberger, David; Hanke, Martin; van der Vegt, Nico F. A.

2016-10-01

Deriving potentials for coarse-grained Molecular Dynamics (MD) simulations is frequently done by solving an inverse problem. Methods like Iterative Boltzmann Inversion (IBI) or Inverse Monte Carlo (IMC) have been widely used to solve this problem. The solution obtained by application of these methods guarantees a match in the radial distribution function (RDF) between the underlying fine-grained system and the derived coarse-grained system. However, these methods often fail in reproducing thermodynamic properties. To overcome this deficiency, additional thermodynamic constraints such as pressure or Kirkwood-Buff integrals (KBI) may be added to these methods. In this communication we test the ability of these methods to converge to a known solution of the inverse problem. With this goal in mind we have studied a binary mixture of two simple Lennard-Jones (LJ) fluids, in which no actual coarse-graining is performed. We further discuss whether full convergence is actually needed to achieve thermodynamic representability.

Speckle lithography for fabricating Gaussian, quasi-random 2D structures and black silicon structures.

PubMed

Bingi, Jayachandra; Murukeshan, Vadakke Matham

2015-12-18

Laser speckle pattern is a granular structure formed due to random coherent wavelet interference and generally considered as noise in optical systems including photolithography. Contrary to this, in this paper, we use the speckle pattern to generate predictable and controlled Gaussian random structures and quasi-random structures photo-lithographically. The random structures made using this proposed speckle lithography technique are quantified based on speckle statistics, radial distribution function (RDF) and fast Fourier transform (FFT). The control over the speckle size, density and speckle clustering facilitates the successful fabrication of black silicon with different surface structures. The controllability and tunability of randomness makes this technique a robust method for fabricating predictable 2D Gaussian random structures and black silicon structures. These structures can enhance the light trapping significantly in solar cells and hence enable improved energy harvesting. Further, this technique can enable efficient fabrication of disordered photonic structures and random media based devices.

Structure, thermal expansion coefficient and phase stability of La2(Zr0.7Ce0.3)2O7 studied by molecular dynamic simulation and experiment

NASA Astrophysics Data System (ADS)

Che, JunWei; Liu, XiangYang; Wang, XueZhi; Liang, GongYing

2018-04-01

This paper presents structure, thermal expansion coefficient and phase stability of La2(Zr0.7Ce0.3)2O7 (LZ7C3) ceramic by both theoretical and experimental results. It was found out that LZ7C3 powders had a pyrochlore structure after being heat-treated at temperatures higher than 1473 K or higher according to XRD and TEM results. The calculated average thermal expansion coefficient (TEC) was 7.12 × 10-6 K-1, which is a little smaller than experiment result, but changes of calculated average TECs of LZ, YSZ and LZ7C3 had the same trend with experimental results. Finally, the radial distribution function (RDF) was calculated to study the phase stability of LZ7C3.

Molecular dynamics simulation of membrane in room temperature ionic liquids

NASA Astrophysics Data System (ADS)

Theng, Soong Guan; Jumbri, Khairulazhar bin; Wirzal, Mohd Dzul Hakim

2017-10-01

The polyvinylidene difluoride (PVDF) membrane has been a popular material in membrane separation process. In this work, molecular dynamic simulation was done on the PVDF membrane with 100 wt% IL and 50 wt% IL in GROningen MAchine for Chemical Simulations (GROMACS). The results was evaluated based on potential energy, root mean square deviation (RMSD) and radial distribution function (RDF). The stability and interaction of PVDF were evaluated. Results reveal that PVDF has a stronger interaction to [C2bim]+ cation compared to water and bromine anion. Both potential energy and RMSD were lower when the weight percentage of IL is higher. This indicates that the IL is able to stabilize the PVDF structure. RMSD reveals that [C2bim]+ cation is dominant at short distance (less than 1 nm), indicating that strong interaction of cation to PVDF. This understanding of the behavior of PVDF-IL could be used as a reference for future development of stronger membrane.

Crystal Orientation Effect on the Subsurface Deformation of Monocrystalline Germanium in Nanometric Cutting.

PubMed

Lai, Min; Zhang, Xiaodong; Fang, Fengzhou

2017-12-01

Molecular dynamics simulations of nanometric cutting on monocrystalline germanium are conducted to investigate the subsurface deformation during and after nanometric cutting. The continuous random network model of amorphous germanium is established by molecular dynamics simulation, and its characteristic parameters are extracted to compare with those of the machined deformed layer. The coordination number distribution and radial distribution function (RDF) show that the machined surface presents the similar amorphous state. The anisotropic subsurface deformation is studied by nanometric cutting on the (010), (101), and (111) crystal planes of germanium, respectively. The deformed structures are prone to extend along the 110 slip system, which leads to the difference in the shape and thickness of the deformed layer on various directions and crystal planes. On machined surface, the greater thickness of subsurface deformed layer induces the greater surface recovery height. In order to get the critical thickness limit of deformed layer on machined surface of germanium, the optimized cutting direction on each crystal plane is suggested according to the relevance of the nanometric cutting to the nanoindentation.

SU-G-201-10: Experimental Determination of Modified TG-43 Dosimetry Parameters for the Xoft Axxent® Electronic Brachytherapy Source

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

Simiele, S; Palmer, B; DeWerd, L

Purpose: The establishment of an air kerma rate standard at NIST for the Xoft Axxent{sup ®} electronic brachytherapy source (Axxent{sup ®} source) motivated the establishment of a modified TG-43 dosimetry formalism. This work measures the modified dosimetry parameters for the Axxent{sup ®} source in the absence of a treatment applicator for implementation in Xoft’s treatment planning system. Methods: The dose-rate conversion coefficient (DRCC), radial dose function (RDF) values, and polar anisotropy (PA) were measured using TLD-100 microcubes with NIST-calibrated sources. The DRCC and RDF measurements were performed in liquid water using an annulus of Virtual Water™ designed to align themore » TLDs at the height of the anode at fixed radii from the source. The PA was measured at several distances from the source in a PMMA phantom. MCNP-determined absorbed dose energy dependence correction factors were used to convert from dose to TLD to dose to liquid water for the DRCC, RDF, and PA measurements. The intrinsic energy dependence correction factor from the work of Pike was used. The AKR was determined using a NIST-calibrated HDR1000 Plus well-type ionization chamber. Results: The DRCC was determined to be 8.6 (cGy/hr)/(µGy/min). The radial dose values were determined to be 1.00 (1cm), 0.60 (2cm), 0.42 (3cm), and 0.32 (4cm), with agreement ranging from (5.7% to 10.9%) from the work of Hiatt et al. 2015 and agreement from (2.8% to 6.8%) with internal MCNP simulations. Conclusion: This work presents a complete dataset of modified TG-43 dosimetry parameters for the Axxent{sup ®} source in the absence of an applicator. Prior to this study a DRCC had not been measured for the Axxent{sup ®} source. This data will be used for calculating dose distributions for patients receiving treatment with the Axxent{sup ®} source in Xoft’s breast balloon and vaginal applicators, and for intraoperative radiotherapy. Sources and partial funding for this work were provided by Xoft Inc. (a subsidiary of iCAD). This work was also supported by the Radiological Sciences T32 Training Grant through the University of Wisconsin-Madison Medical Physics department (5T32CA009206-37).« less

Knowledge Visualizations: A Tool to Achieve Optimized Operational Decision Making and Data Integration

DTIC Science & Technology

2015-06-01

Hadoop Distributed File System (HDFS) without any integration with Accumulo-based Knowledge Stores based on OWL/RDF. 4. Cloud Based The Apache Software...BTW, 7(12), pp. 227–241. Godin, A. & Akins, D. (2014). Extending DCGS-N naval tactical clouds from in-storage to in-memory for the integrated fires...VISUALIZATIONS: A TOOL TO ACHIEVE OPTIMIZED OPERATIONAL DECISION MAKING AND DATA INTEGRATION by Paul C. Hudson Jeffrey A. Rzasa June 2015 Thesis

The Effect of Fuel Quality on Carbon Dioxide and Nitrogen Oxide Emissions, While Burning Biomass and RDF

NASA Astrophysics Data System (ADS)

Kalnacs, J.; Bendere, R.; Murasovs, A.; Arina, D.; Antipovs, A.; Kalnacs, A.; Sprince, L.

2018-02-01

The article analyses the variations in carbon dioxide emission factor depending on parameters characterising biomass and RDF (refuse-derived fuel). The influence of moisture, ash content, heat of combustion, carbon and nitrogen content on the amount of emission factors has been reviewed, by determining their average values. The options for the improvement of the fuel to result in reduced emissions of carbon dioxide and nitrogen oxide have been analysed. Systematic measurements of biomass parameters have been performed, by determining their average values, seasonal limits of variations in these parameters and their mutual relations. Typical average values of RDF parameters and limits of variations have been determined.

Synthesis, characterization and computational study of the newly synthetized sulfonamide molecule

NASA Astrophysics Data System (ADS)

Murthy, P. Krishna; Suneetha, V.; Armaković, Stevan; Armaković, Sanja J.; Suchetan, P. A.; Giri, L.; Rao, R. Sreenivasa

2018-02-01

A new compound N-(2,5-dimethyl-4-nitrophenyl)-4-methylbenzenesulfonamide (NDMPMBS) has been derived from 2,5-dimethyl-4-nitroaniline and 4-methylbenzene-1-sulfonyl chloride. Structure was characterized by SCXRD studies and spectroscopic tools. Compound crystallized in the monoclinic crystal system with P21/c space group a = 10.0549, b = 18.967, c = 8.3087, β = 103.18 and Z = 4. Type and nature of intermolecular interaction in crystal state investigated by 3D-Hirshfeld surface and 2D-finger print plots revealed that title compound stabilized by several interactions. The structural and electronic properties of title compound have been calculated at DFT/B3LYP/6-311G++(d,p) level of theory. Computationally obtained spectral data was compared with experimental results, showing excellent mutual agreement. Assignment of each vibrational wave number was done on the basis of potential energy distribution (PED). Investigation of local reactivity descriptors encompassed visualization of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) surfaces, visualization of Fukui functions, natural bond order (NBO) analysis, bond dissociation energies for hydrogen abstraction (H-BDE) and radial distribution functions (RDF) after molecular dynamics (MD) simulations. MD simulations were also used in order to investigate interaction of NDMPMBS molecule with 1WKR and 3ETT proteins protein.

Application of Resource Description Framework to Personalise Learning: Systematic Review and Methodology

ERIC Educational Resources Information Center

Jevsikova, Tatjana; Berniukevicius, Andrius; Kurilovas, Eugenijus

2017-01-01

The paper is aimed to present a methodology of learning personalisation based on applying Resource Description Framework (RDF) standard model. Research results are two-fold: first, the results of systematic literature review on Linked Data, RDF "subject-predicate-object" triples, and Web Ontology Language (OWL) application in education…

Policy Compliance of Queries for Private Information Retrieval

DTIC Science & Technology

2010-11-01

SPARQL, unfortunately, is not in RDF and so we had to develop tools to translate SPARQL queries into RDF to be used by our policy compliance prototype...policy-assurance/sparql2n3.py) that accepts SPARQL queries and returns the translated query in our simplified ontology. An example of a translated

The Feasibility of Radio Direction Finding for Swarm Localization

DTIC Science & Technology

2017-09-01

First, basic RDF theory is presented. Next, a laboratory experiment to evaluate RDF using a SDR is developed. Finally, experimental data are presented...angle vs. the true angle (top) and the recovered angle error (bottom) for noisy phase measurements ............................................... 8...difference (middle), and corrected phase difference (bottom) ................................................... 19 Fig. 22 Experimental phase

Improving integrative searching of systems chemical biology data using semantic annotation.

PubMed

Chen, Bin; Ding, Ying; Wild, David J

2012-03-08

Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

Mashup of Geo and Space Science Data Provided via Relational Databases in the Semantic Web

NASA Astrophysics Data System (ADS)

Ritschel, B.; Seelus, C.; Neher, G.; Iyemori, T.; Koyama, Y.; Yatagai, A. I.; Murayama, Y.; King, T. A.; Hughes, J. S.; Fung, S. F.; Galkin, I. A.; Hapgood, M. A.; Belehaki, A.

2014-12-01

The use of RDBMS for the storage and management of geo and space science data and/or metadata is very common. Although the information stored in tables is based on a data model and therefore well organized and structured, a direct mashup with RDF based data stored in triple stores is not possible. One solution of the problem consists in the transformation of the whole content into RDF structures and storage in triple stores. Another interesting way is the use of a specific system/service, such as e.g. D2RQ, for the access to relational database content as virtual, read only RDF graphs. The Semantic Web based -proof of concept- GFZ ISDC uses the triple store Virtuoso for the storage of general context information/metadata to geo and space science satellite and ground station data. There is information about projects, platforms, instruments, persons, product types, etc. available but no detailed metadata about the data granuals itself. Such important information, as e.g. start or end time or the detailed spatial coverage of a single measurement is stored in RDBMS tables of the ISDC catalog system only. In order to provide a seamless access to all available information about the granuals/data products a mashup of the different data resources (triple store and RDBMS) is necessary. This paper describes the use of D2RQ for a Semantic Web/SPARQL based mashup of relational databases used for ISDC data server but also for the access to IUGONET and/or ESPAS and further geo and space science data resources. RDBMS Relational Database Management System RDF Resource Description Framework SPARQL SPARQL Protocol And RDF Query Language D2RQ Accessing Relational Databases as Virtual RDF Graphs GFZ ISDC German Research Centre for Geosciences Information System and Data Center IUGONET Inter-university Upper Atmosphere Global Observation Network (Japanese project) ESPAS Near earth space data infrastructure for e-science (European Union funded project)

Computing Information Value from RDF Graph Properties

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

al-Saffar, Sinan; Heileman, Gregory

2010-11-08

Information value has been implicitly utilized and mostly non-subjectively computed in information retrieval (IR) systems. We explicitly define and compute the value of an information piece as a function of two parameters, the first is the potential semantic impact the target information can subjectively have on its recipient's world-knowledge, and the second parameter is trust in the information source. We model these two parameters as properties of RDF graphs. Two graphs are constructed, a target graph representing the semantics of the target body of information and a context graph representing the context of the consumer of that information. We computemore » information value subjectively as a function of both potential change to the context graph (impact) and the overlap between the two graphs (trust). Graph change is computed as a graph edit distance measuring the dissimilarity between the context graph before and after the learning of the target graph. A particular application of this subjective information valuation is in the construction of a personalized ranking component in Web search engines. Based on our method, we construct a Web re-ranking system that personalizes the information experience for the information-consumer.« less

Isomorphic semantic mapping of variant call format (VCF2RDF).

PubMed

Penha, Emanuel Diego S; Iriabho, Egiebade; Dussaq, Alex; de Oliveira, Diana Magalhães; Almeida, Jonas S

2017-02-15

The move of computational genomics workflows to Cloud Computing platforms is associated with a new level of integration and interoperability that challenges existing data representation formats. The Variant Calling Format (VCF) is in a particularly sensitive position in that regard, with both clinical and consumer-facing analysis tools relying on this self-contained description of genomic variation in Next Generation Sequencing (NGS) results. In this report we identify an isomorphic map between VCF and the reference Resource Description Framework. RDF is advanced by the World Wide Web Consortium (W3C) to enable representations of linked data that are both distributed and discoverable. The resulting ability to decompose VCF reports of genomic variation without loss of context addresses the need to modularize and govern NGS pipelines for Precision Medicine. Specifically, it provides the flexibility (i.e. the indexing) needed to support the wide variety of clinical scenarios and patient-facing governance where only part of the VCF data is fitting. Software libraries with a claim to be both domain-facing and consumer-facing have to pass the test of portability across the variety of devices that those consumers in fact adopt. That is, ideally the implementation should itself take place within the space defined by web technologies. Consequently, the isomorphic mapping function was implemented in JavaScript, and was tested in a variety of environments and devices, client and server side alike. These range from web browsers in mobile phones to the most popular micro service platform, NodeJS. The code is publicly available at https://github.com/ibl/VCFr , with a live deployment at: http://ibl.github.io/VCFr/ . jonas.almeida@stonybrookmedicine.edu. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Publications - RDF 2009-1 v. 1.2 | Alaska Division of Geological &

Science.gov Websites

main content DGGS RDF 2009-1 v. 1.2 Publication Details Title: Geochemical, major-oxide, minor-oxide , M.B., Szumigala, D.J., Andrew, J.E., Newberry, R.J., and Athey, J.E., 2009, Geochemical, major-oxide prospect; Keevy Peak Formation; LEA Creek prospect; Major Oxides; Mississippian; Newman Creek; Newman Creek

Publications - RDF 2005-5 | Alaska Division of Geological & Geophysical

Science.gov Websites

content DGGS RDF 2005-5 Publication Details Title: Major-oxide, minor-oxide, and trace-element geochemical ., and Lessard, R.R., 2005, Major-oxide, minor-oxide, and trace-element geochemical data from rocks ; Zinc; Zirconium Top of Page Department of Natural Resources, Division of Geological & Geophysical

Publications - RDF 2012-1 | Alaska Division of Geological & Geophysical

Science.gov Websites

Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska content DGGS RDF 2012-1 Publication Details Title: Palynological analysis of 228 outcrop samples from the ., 2012, Palynological analysis of 228 outcrop samples from the Kenai, Seldovia, and Tyonek quadrangles

Final Design Report for the RH LLW Disposal Facility (RDF) Project

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

Austad, Stephanie Lee

2015-09-01

The RH LLW Disposal Facility (RDF) Project was designed by AREVA Federal Services (AFS) and the design process was managed by Battelle Energy Alliance (BEA) for the Department of Energy (DOE). The final design report for the RH LLW Disposal Facility Project is a compilation of the documents and deliverables included in the facility final design.

Final Design Report for the RH LLW Disposal Facility (RDF) Project

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

Austad, S. L.

2015-05-01

The RH LLW Disposal Facility (RDF) Project was designed by AREVA Federal Services (AFS) and the design process was managed by Battelle Energy Alliance (BEA) for the Department of Energy (DOE). The final design report for the RH LLW Disposal Facility Project is a compilation of the documents and deliverables included in the facility final design.

An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics.

PubMed

Samwald, Matthias; Freimuth, Robert; Luciano, Joanne S; Lin, Simon; Powers, Robert L; Marshall, M Scott; Adlassnig, Klaus-Peter; Dumontier, Michel; Boyce, Richard D

2013-01-01

Genetic testing for personalizing pharmacotherapy is bound to become an important part of clinical routine. To address associated issues with data management and quality, we are creating a semantic knowledge base for clinical pharmacogenetics. The knowledge base is made up of three components: an expressive ontology formalized in the Web Ontology Language (OWL 2 DL), a Resource Description Framework (RDF) model for capturing detailed results of manual annotation of pharmacogenomic information in drug product labels, and an RDF conversion of relevant biomedical datasets. Our work goes beyond the state of the art in that it makes both automated reasoning as well as query answering as simple as possible, and the reasoning capabilities go beyond the capabilities of previously described ontologies.

Response of Nitrogen and Potassium Fertigation to “Waris” Almond (Prunus dulcis) under Northwestern Himalayan Region of India

PubMed Central

Ahmed, N.

2014-01-01

A field experiment was conducted on almond (Prunus dulcis) to study the effect of N&K fertigation on growth, yields and leaf nutrient status over two seasons (2011 and 2012) in Srinagar, Jammu and Kashmir, India. There were six treatments, namely, T1—100% recommended dose of fertilizers as soil application, T2—100% RDF through fertigations, T3—75% RDF through fertigation, T4—75% RDF through fertigation (split application), T5—50% RDF through fertigation and T6—50% RDF through fertigation (split application) with three replications under randomized block design. The results indicated that the maximum tree height (3.21 m and 3.56 m), nut weight (2.73 g and 1.94 g), nut yield (2.41 kg/tree and 5.98 kg/tree; 2.67 t/ha and 6.64 t/ha), and leaf nutrient content (2.34 and 2.38% N; 0.14 and 0.17% P; 1.37 and 1.41% K) were recorded in T4 treatment, whereas the highest TCSA of main trunk, primary, secondary, and tertiary branches (72.67 and 90.28 cm2; 16.75 and 24.26 cm2; 3.83 and 7.49 cm2; 0.47 and 1.23 cm2), canopy volume (7.15 and 8.11 m3), and fruit number (990 and 3083/tree) were recorded in T2 in almond variety Waris. PMID:24587708

Parallel approach in RDF query processing

NASA Astrophysics Data System (ADS)

Vajgl, Marek; Parenica, Jan

2017-07-01

Parallel approach is nowadays a very cheap solution to increase computational power due to possibility of usage of multithreaded computational units. This hardware became typical part of nowadays personal computers or notebooks and is widely spread. This contribution deals with experiments how evaluation of computational complex algorithm of the inference over RDF data can be parallelized over graphical cards to decrease computational time.

Publications - RDF 2008-1 v. 1.0.1 | Alaska Division of Geological &

Science.gov Websites

main content DGGS RDF 2008-1 v. 1.0.1 Publication Details Title: Major-oxide, minor-oxide, and trace , S.E., and Jing, L., 2008, Major-oxide, minor-oxide, and trace-element geochemical data from rocks and Birch Creek; Hope Creek; Idaho Creek; Major Oxides; McManus Creek; Montana Creek; Polar Creek; Pool

Data summary of municipal solid waste management alternatives. Volume 4, Appendix B: RDF technologies

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

None

1992-10-01

This appendix contains background information, technical descriptions, economic data, mass and energy balances, and information on environmental releases for the refuse derived fuels (RDF) option in municipal solid waste management alternatives. Demonstration programs at St. Louis, Missouri; Franklin, Ohio; and Delaware are discussed. Information on pellet production and cofiring with coal is also presented.

An RDF version of the VO Registry Version 1.00

NASA Astrophysics Data System (ADS)

Gray, Norman; Gray, Norman

2007-09-01

We describe the initial implementation of an RDF version of the IVOA Resource Registry, serving the registry data via a SPARQL query endpoint, including the creation of the ontology analogues of an important subset of the relevant XML Schemas, and the mechanics of the conversion process. The result is an experimental service, and this is an interim document.

Graph Visualization for RDF Graphs with SPARQL-EndPoints

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

Sukumar, Sreenivas R; Bond, Nathaniel

2014-07-11

RDF graphs are hard to visualize as triples. This software module is a web interface that connects to a SPARQL endpoint and retrieves graph data that the user can explore interactively and seamlessly. The software written in python and JavaScript has been tested to work on screens as little as the smart phones to large screens such as EVEREST.

A Formal Theory for Modular ERDF Ontologies

NASA Astrophysics Data System (ADS)

Analyti, Anastasia; Antoniou, Grigoris; Damásio, Carlos Viegas

The success of the Semantic Web is impossible without any form of modularity, encapsulation, and access control. In an earlier paper, we extended RDF graphs with weak and strong negation, as well as derivation rules. The ERDF #n-stable model semantics of the extended RDF framework (ERDF) is defined, extending RDF(S) semantics. In this paper, we propose a framework for modular ERDF ontologies, called modular ERDF framework, which enables collaborative reasoning over a set of ERDF ontologies, while support for hidden knowledge is also provided. In particular, the modular ERDF stable model semantics of modular ERDF ontologies is defined, extending the ERDF #n-stable model semantics. Our proposed framework supports local semantics and different points of view, local closed-world and open-world assumptions, and scoped negation-as-failure. Several complexity results are provided.

iSMART: Ontology-based Semantic Query of CDA Documents

PubMed Central

Liu, Shengping; Ni, Yuan; Mei, Jing; Li, Hanyu; Xie, Guotong; Hu, Gang; Liu, Haifeng; Hou, Xueqiao; Pan, Yue

2009-01-01

The Health Level 7 Clinical Document Architecture (CDA) is widely accepted as the format for electronic clinical document. With the rich ontological references in CDA documents, the ontology-based semantic query could be performed to retrieve CDA documents. In this paper, we present iSMART (interactive Semantic MedicAl Record reTrieval), a prototype system designed for ontology-based semantic query of CDA documents. The clinical information in CDA documents will be extracted into RDF triples by a declarative XML to RDF transformer. An ontology reasoner is developed to infer additional information by combining the background knowledge from SNOMED CT ontology. Then an RDF query engine is leveraged to enable the semantic queries. This system has been evaluated using the real clinical documents collected from a large hospital in southern China. PMID:20351883

Ondansetron rapidly dissolving film for the prophylactic treatment of radiation-induced nausea and vomiting-a pilot study.

PubMed

Wong, E; Pulenzas, N; Bedard, G; DeAngelis, C; Zhang, L; Tsao, M; Danjoux, C; Thavarajah, N; Lechner, B; McDonald, R; Cheon, P M; Chow, E

2015-06-01

The purpose of the present study was to investigate the efficacy of an ondansetron rapidly dissolving film (rdf) in the prophylaxis of radiation-induced nausea and vomiting (rinv). Rapidly dissolving film formulations facilitate drug delivery in circumstances in which swallowing the medication might be difficult for the patient. Patients undergoing palliative radiotherapy at risk for rinv were prescribed ondansetron rdf 8 mg twice daily while on treatment and were asked to complete a nausea and vomiting-specific daily diary, the Functional Living Index-Emesis (flie), and the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire-C15 Palliative (qlq-C15-pal). Patients were categorized as receiving primary or secondary prophylaxis based on whether they had already experienced emetic episodes. "Overall control" was defined as a maximum increase of 2 episodes of nausea or vomiting from baseline. "Acute phase" was defined as the days during radiation until the first day after radiation; "delayed phase" was defined as days 2-10 after radiation. The study accrued 30 patients. Rates of overall control for nausea and for vomiting during the acute phase in the primary prophylaxis group were 88% and 93% respectively; during the delayed phase, they were 73% and 75%. Rates of overall control for nausea and for vomiting during the acute phase in the secondary prophylaxis group were both 100%; during the delayed phase, they were 50%. The number of nausea and vomiting episodes was found to be significantly correlated with the flie and qlq-C15-pal questionnaires. Ondansetron rdf is effective for the prophylaxis of rinv.

Designing the microturbine engine for waste-derived fuels.

PubMed

Seljak, Tine; Katrašnik, Tomaž

2016-01-01

Presented paper deals with adaptation procedure of a microturbine (MGT) for exploitation of refuse derived fuels (RDF). RDF often possess significantly different properties than conventional fuels and usually require at least some adaptations of internal combustion systems to obtain full functionality. With the methodology, developed in the paper it is possible to evaluate the extent of required adaptations by performing a thorough analysis of fuel combustion properties in a dedicated experimental rig suitable for testing of wide-variety of waste and biomass derived fuels. In the first part key turbine components are analyzed followed by cause and effect analysis of interaction between different fuel properties and design parameters of the components. The data are then used to build a dedicated test system where two fuels with diametric physical and chemical properties are tested - liquefied biomass waste (LW) and waste tire pyrolysis oil (TPO). The analysis suggests that exploitation of LW requires higher complexity of target MGT system as stable combustion can be achieved only with regenerative thermodynamic cycle, high fuel preheat temperatures and optimized fuel injection nozzle. Contrary, TPO requires less complex MGT design and sufficient operational stability is achieved already with simple cycle MGT and conventional fuel system. The presented approach of testing can significantly reduce the extent and cost of required adaptations of commercial system as pre-selection procedure of suitable MGT is done in developed test system. The obtained data can at the same time serve as an input for fine-tuning the processes for RDF production. Copyright © 2015. Published by Elsevier Ltd.

Executing SPARQL Queries over the Web of Linked Data

NASA Astrophysics Data System (ADS)

Hartig, Olaf; Bizer, Christian; Freytag, Johann-Christoph

The Web of Linked Data forms a single, globally distributed dataspace. Due to the openness of this dataspace, it is not possible to know in advance all data sources that might be relevant for query answering. This openness poses a new challenge that is not addressed by traditional research on federated query processing. In this paper we present an approach to execute SPARQL queries over the Web of Linked Data. The main idea of our approach is to discover data that might be relevant for answering a query during the query execution itself. This discovery is driven by following RDF links between data sources based on URIs in the query and in partial results. The URIs are resolved over the HTTP protocol into RDF data which is continuously added to the queried dataset. This paper describes concepts and algorithms to implement our approach using an iterator-based pipeline. We introduce a formalization of the pipelining approach and show that classical iterators may cause blocking due to the latency of HTTP requests. To avoid blocking, we propose an extension of the iterator paradigm. The evaluation of our approach shows its strengths as well as the still existing challenges.

Growth morphology of CL-20/HMX cocrystal explosive: insights from solvent behavior under different temperatures.

PubMed

Han, Gang; Li, Qi-Fa; Gou, Rui-Jun; Zhang, Shu-Hai; Ren, Fu-de; Wang, Li; Guan, Rong

2017-11-28

A 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) /1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX)-isopropanol (IPA) interfacial model was constructed to investigate the effect of temperature on cocrystal morphology. A constant volume and temperature molecular dynamics (NVT-MD) simulation was performed on the interfacial model at various temperatures (295-355 K, 20 K intervals). The surface electrostatic potential (ESP) of the CL-20/HMX cocrystal structure and IPA molecule were studied by the B3LYP method at 6-311++G (d, p) level. The surface energies, polarities, adsorption energy, mass density distribution, radial distribution function (RDF), mean square displacement (MSD) and relative changes of attachment energy were analyzed. The results show that polarities of (1 0 0) and (0 1 1) cocrystal surfaces may be more negative and affected by IPA solvent. The adsorption energy per area indicates that growth of the (1 0-2) face in IPA conditions may be more limited, while the (1 0 0) face tends to grow more freely. MSD and diffusion coefficient (D) analyses demonstrated that IPA molecules gather more easily on the cocrystal surface at lower temperatures, and hence have a larger effect on the growth of cocrystal faces. RDF analysis shows that, with the increasing of temperature, the strength of hydrogen bond interactions between cocrystal and solvent becomes stronger, being highest at 335 K for the (1 0 0) and (0 1 1) interfacial models. Results of relative changes of modified attachment energy show that (1 0 0) and (0 1 1) faces tends to be larger than other faces. Moreover, the predicted morphologies at 295 and 355 K are consistent with experimental values, proving that the CL-20/HMX-IPA interfacial model is a reasonable one for this study. Graphical Abstract Construction of 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) /1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX)-isopropanol (IPA) interfacial model, analysis, and morphology prediction of cocrystal.

Demonstration of an Environmentally Benign and Reduced Corrosion Runway Deicing Fluid

DTIC Science & Technology

2011-01-01

ADDRESS(ES) Enviromental Security Technology Certification Program: 901 North Stuart Street, Suite 303, Arlington, Virginia 22203 10. SPONSOR...IMPLEMENTATION ISSUES Users may express concern because the Battelle-RDF is new and they may have reservations because of its potential damage to...several drivers for implementing a new , more environmentally friendly RDF. 1.3.1 Water Pollution Reduction The Clean Water Act (CWA) and its

Semantic e-Science: From Microformats to Models

NASA Astrophysics Data System (ADS)

Lumb, L. I.; Freemantle, J. R.; Aldridge, K. D.

2009-05-01

A platform has been developed to transform semi-structured ASCII data into a representation based on the eXtensible Markup Language (XML). A subsequent transformation allows the XML-based representation to be rendered in the Resource Description Format (RDF). Editorial metadata, expressed as external annotations (via XML Pointer Language), also survives this transformation process (e.g., Lumb et al., http://dx.doi.org/10.1016/j.cageo.2008.03.009). Because the XML-to-RDF transformation uses XSLT (eXtensible Stylesheet Language Transformations), semantic microformats ultimately encode the scientific data (Lumb & Aldridge, http://dx.doi.org/10.1109/HPCS.2006.26). In building the relationship-centric representation in RDF, a Semantic Model of the scientific data is extracted. The systematic enhancement in the expressivity and richness of the scientific data results in representations of knowledge that are readily understood and manipulated by intelligent software agents. Thus scientists are able to draw upon various resources within and beyond their discipline to use in their scientific applications. Since the resulting Semantic Models are independent conceptualizations of the science itself, the representation of scientific knowledge and interaction with the same can stimulate insight from different perspectives. Using the Global Geodynamics Project (GGP) for the purpose of illustration, the introduction of GGP microformats enable a Semantic Model for the GGP that can be semantically queried (e.g., via SPARQL, http://www.w3.org/TR/rdf-sparql-query). Although the present implementation uses the Open Source Redland RDF Libraries (http://librdf.org/), the approach is generalizable to other platforms and to projects other than the GGP (e.g., Baker et al., Informatics and the 2007-2008 Electronic Geophysical Year, Eos Trans. Am. Geophys. Un., 89(48), 485-486, 2008).

Enabling Graph Appliance for Genome Assembly

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

Singh, Rina; Graves, Jeffrey A; Lee, Sangkeun

2015-01-01

In recent years, there has been a huge growth in the amount of genomic data available as reads generated from various genome sequencers. The number of reads generated can be huge, ranging from hundreds to billions of nucleotide, each varying in size. Assembling such large amounts of data is one of the challenging computational problems for both biomedical and data scientists. Most of the genome assemblers developed have used de Bruijn graph techniques. A de Bruijn graph represents a collection of read sequences by billions of vertices and edges, which require large amounts of memory and computational power to storemore » and process. This is the major drawback to de Bruijn graph assembly. Massively parallel, multi-threaded, shared memory systems can be leveraged to overcome some of these issues. The objective of our research is to investigate the feasibility and scalability issues of de Bruijn graph assembly on Cray s Urika-GD system; Urika-GD is a high performance graph appliance with a large shared memory and massively multithreaded custom processor designed for executing SPARQL queries over large-scale RDF data sets. However, to the best of our knowledge, there is no research on representing a de Bruijn graph as an RDF graph or finding Eulerian paths in RDF graphs using SPARQL for potential genome discovery. In this paper, we address the issues involved in representing a de Bruin graphs as RDF graphs and propose an iterative querying approach for finding Eulerian paths in large RDF graphs. We evaluate the performance of our implementation on real world ebola genome datasets and illustrate how genome assembly can be accomplished with Urika-GD using iterative SPARQL queries.« less

Graph Mining Meets the Semantic Web

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

Lee, Sangkeun; Sukumar, Sreenivas R; Lim, Seung-Hwan

The Resource Description Framework (RDF) and SPARQL Protocol and RDF Query Language (SPARQL) were introduced about a decade ago to enable flexible schema-free data interchange on the Semantic Web. Today, data scientists use the framework as a scalable graph representation for integrating, querying, exploring and analyzing data sets hosted at different sources. With increasing adoption, the need for graph mining capabilities for the Semantic Web has emerged. We address that need through implementation of three popular iterative Graph Mining algorithms (Triangle count, Connected component analysis, and PageRank). We implement these algorithms as SPARQL queries, wrapped within Python scripts. We evaluatemore » the performance of our implementation on 6 real world data sets and show graph mining algorithms (that have a linear-algebra formulation) can indeed be unleashed on data represented as RDF graphs using the SPARQL query interface.« less

An Approach to Information Management for AIR7000 with Metadata and Ontologies

DTIC Science & Technology

2009-10-01

metadata. We then propose an approach based on Semantic Technologies including the Resource Description Framework (RDF) and Upper Ontologies, for the...mandating specific metadata schemas can result in interoperability problems. For example, many standards within the ADO mandate the use of XML for metadata...such problems, we propose an archi- tecture in which different metadata schemes can inter operate. By using RDF (Resource Description Framework ) as a

SCALE TSUNAMI Analysis of Critical Experiments for Validation of 233U Systems

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

Mueller, Don; Rearden, Bradley T

2009-01-01

Oak Ridge National Laboratory (ORNL) staff used the SCALE TSUNAMI tools to provide a demonstration evaluation of critical experiments considered for use in validation of current and anticipated operations involving {sup 233}U at the Radiochemical Development Facility (RDF). This work was reported in ORNL/TM-2008/196 issued in January 2009. This paper presents the analysis of two representative safety analysis models provided by RDF staff.

Nanoscale Subsurface Imaging of Nanocomposites via Resonant Difference-Frequency Atomic Force Ultrasonic Microscopy

NASA Technical Reports Server (NTRS)

Cantrell, Sean A.; Cantrell, John H.; Lillehei, Peter T.

2007-01-01

A scanning probe microscope methodology, called resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), has been developed. The method employs an ultrasonic wave launched from the bottom of a sample while the cantilever of an atomic force microscope engages the sample top surface. The cantilever is driven at a frequency differing from the ultrasonic frequency by one of the contact resonance frequencies of the cantilever. The nonlinear mixing of the oscillating cantilever and the ultrasonic wave at the sample surface generates difference-frequency oscillations at the cantilever contact resonance. The resonance-enhanced difference-frequency signals are used to create amplitude and phase-generated images of nanoscale near-surface and subsurface features. RDF-AFUM phase images of LaRC-CP2 polyimide polymer containing embedded nanostructures are presented. A RDF-AFUM micrograph of a 12.7 micrometer thick film of LaRC-CP2 containing a monolayer of gold nanoparticles embedded 7 micrometers below the specimen surface reveals the occurrence of contiguous amorphous and crystalline phases within the bulk of the polymer and a preferential growth of the crystalline phase in the vicinity of the gold nanoparticles. A RDF-AFUM micrograph of LaRC-CP2 film containing randomly dispersed carbon nanotubes reveals the growth of an interphase region at certain nanotube-polymer interfaces.

Information integration from heterogeneous data sources: a Semantic Web approach.

PubMed

Kunapareddy, Narendra; Mirhaji, Parsa; Richards, David; Casscells, S Ward

2006-01-01

Although the decentralized and autonomous implementation of health information systems has made it possible to extend the reach of surveillance systems to a variety of contextually disparate domains, public health use of data from these systems is not primarily anticipated. The Semantic Web has been proposed to address both representational and semantic heterogeneity in distributed and collaborative environments. We introduce a semantic approach for the integration of health data using the Resource Definition Framework (RDF) and the Simple Knowledge Organization System (SKOS) developed by the Semantic Web community.

Speckle lithography for fabricating Gaussian, quasi-random 2D structures and black silicon structures

PubMed Central

Bingi, Jayachandra; Murukeshan, Vadakke Matham

2015-01-01

Laser speckle pattern is a granular structure formed due to random coherent wavelet interference and generally considered as noise in optical systems including photolithography. Contrary to this, in this paper, we use the speckle pattern to generate predictable and controlled Gaussian random structures and quasi-random structures photo-lithographically. The random structures made using this proposed speckle lithography technique are quantified based on speckle statistics, radial distribution function (RDF) and fast Fourier transform (FFT). The control over the speckle size, density and speckle clustering facilitates the successful fabrication of black silicon with different surface structures. The controllability and tunability of randomness makes this technique a robust method for fabricating predictable 2D Gaussian random structures and black silicon structures. These structures can enhance the light trapping significantly in solar cells and hence enable improved energy harvesting. Further, this technique can enable efficient fabrication of disordered photonic structures and random media based devices. PMID:26679513

Fe/starch nanoparticle - Pseudomonas aeruginosa: Bio-physiochemical and MD studies.

PubMed

Mofradnia, Soheil Rezazadeh; Tavakoli, Zahra; Yazdian, Fatemeh; Rashedi, Hamid; Rasekh, Behnam

2018-05-03

In this research, we attempt to study biosurfactant production by Pseudomonas aeruginosa using Fe/starch nanoparticles. Fe/starch showed no bacterial toxicity at 1 mg/ml and increased the growth rate and biosurfactant production up to 23.21 and 20.73%, respectively. Surface tension, dry weight cell, and emulsification indexes (E24) were measured. Biosurfactant production was considered via computational techniques and molecular dynamic (MD) simulation through flexible and periodic conditions (by material studio software) as well. The results of software predictions demonstrate by radial distribution function (RDF), density, energy and temperature graphs. According to the present experimental results, increased 30% growth of the bacterium has been observed and the subsequent production of biosurfactant. The difference between the experimental results and simulation data were achieved up to 0.17 g/cm 3 , which confirms the prediction of data by the software due to a difference of <14.5% (ideal error value is 20%). Copyright © 2017. Published by Elsevier B.V.

Minimal Information for Neural Electromagnetic Ontologies (MINEMO): A standards-compliant method for analysis and integration of event-related potentials (ERP) data

PubMed Central

Frishkoff, Gwen; Sydes, Jason; Mueller, Kurt; Frank, Robert; Curran, Tim; Connolly, John; Kilborn, Kerry; Molfese, Dennis; Perfetti, Charles; Malony, Allen

2011-01-01

We present MINEMO (Minimal Information for Neural ElectroMagnetic Ontologies), a checklist for the description of event-related potentials (ERP) studies. MINEMO extends MINI (Minimal Information for Neuroscience Investigations)to the ERP domain. Checklist terms are explicated in NEMO, a formal ontology that is designed to support ERP data sharing and integration. MINEMO is also linked to an ERP database and web application (the NEMO portal). Users upload their data and enter MINEMO information through the portal. The database then stores these entries in RDF (Resource Description Framework), along with summary metrics, i.e., spatial and temporal metadata. Together these spatial, temporal, and functional metadata provide a complete description of ERP data and the context in which these data were acquired. The RDF files then serve as inputs to ontology-based labeling and meta-analysis. Our ultimate goal is to represent ERPs using a rich semantic structure, so results can be queried at multiple levels, to stimulate novel hypotheses and to promote a high-level, integrative account of ERP results across diverse study methods and paradigms. PMID:22180824

RDF (Refuse Derived Fuel) Utilization in a Navy Stoker Coal-Fired Boiler.

DTIC Science & Technology

1984-10-01

the energy production in any coal-fired boiler conversion consideration. The selection of the actual RDF to be used in a converted boiler should be... industrial boilers by gathering information from the Navy Energy and Environmental Support Activity, engineering field divi- sions, and field...activities. Currently the Navy has 27 industrial size boilers firing coal as a primary fuel and 10 firing coal as a secondary fuel. The four principal factors

A Framework for Building and Reasoning with Adaptive and Interoperable PMESII Models

DTIC Science & Technology

2007-11-01

Description Logic SOA Service Oriented Architecture SPARQL Simple Protocol And RDF Query Language SQL Standard Query Language SROM Stability and...another by providing a more expressive ontological structure for one of the models, e.g., semantic networks can be mapped to first- order logical...Pellet is an open-source reasoner that works with OWL-DL. It accepts the SPARQL protocol and RDF query language ( SPARQL ) and provides a Java API to

A novel adaptive Cuckoo search for optimal query plan generation.

PubMed

Gomathi, Ramalingam; Sharmila, Dhandapani

2014-01-01

The emergence of multiple web pages day by day leads to the development of the semantic web technology. A World Wide Web Consortium (W3C) standard for storing semantic web data is the resource description framework (RDF). To enhance the efficiency in the execution time for querying large RDF graphs, the evolving metaheuristic algorithms become an alternate to the traditional query optimization methods. This paper focuses on the problem of query optimization of semantic web data. An efficient algorithm called adaptive Cuckoo search (ACS) for querying and generating optimal query plan for large RDF graphs is designed in this research. Experiments were conducted on different datasets with varying number of predicates. The experimental results have exposed that the proposed approach has provided significant results in terms of query execution time. The extent to which the algorithm is efficient is tested and the results are documented.

Semantics based approach for analyzing disease-target associations.

PubMed

Kaalia, Rama; Ghosh, Indira

2016-08-01

A complex disease is caused by heterogeneous biological interactions between genes and their products along with the influence of environmental factors. There have been many attempts for understanding the cause of these diseases using experimental, statistical and computational methods. In the present work the objective is to address the challenge of representation and integration of information from heterogeneous biomedical aspects of a complex disease using semantics based approach. Semantic web technology is used to design Disease Association Ontology (DAO-db) for representation and integration of disease associated information with diabetes as the case study. The functional associations of disease genes are integrated using RDF graphs of DAO-db. Three semantic web based scoring algorithms (PageRank, HITS (Hyperlink Induced Topic Search) and HITS with semantic weights) are used to score the gene nodes on the basis of their functional interactions in the graph. Disease Association Ontology for Diabetes (DAO-db) provides a standard ontology-driven platform for describing genes, proteins, pathways involved in diabetes and for integrating functional associations from various interaction levels (gene-disease, gene-pathway, gene-function, gene-cellular component and protein-protein interactions). An automatic instance loader module is also developed in present work that helps in adding instances to DAO-db on a large scale. Our ontology provides a framework for querying and analyzing the disease associated information in the form of RDF graphs. The above developed methodology is used to predict novel potential targets involved in diabetes disease from the long list of loose (statistically associated) gene-disease associations. Copyright © 2016 Elsevier Inc. All rights reserved.

The application of SRF vs. RDF classification and specifications to the material flows of two mechanical-biological treatment plants of Rome: Comparison and implications.

PubMed

Di Lonardo, Maria Chiara; Franzese, Maurizio; Costa, Giulia; Gavasci, Renato; Lombardi, Francesco

2016-01-01

This work assessed the quality in terms of solid recovered fuel (SRF) definitions of the dry light flow (until now indicated as refuse derived fuel, RDF), heavy rejects and stabilisation rejects, produced by two mechanical biological treatment plants of Rome (Italy). SRF classification and specifications were evaluated first on the basis of RDF historical characterisation methods and data and then applying the sampling and analytical methods laid down by the recently issued SRF standards. The results showed that the dry light flow presented a worst SRF class in terms of net calorific value applying the new methods compared to that obtained from RDF historical data (4 instead of 3). This lead to incompliance with end of waste criteria established by Italian legislation for SRF use as co-fuel in cement kilns and power plants. Furthermore, the metal contents of the dry light flow obtained applying SRF current methods proved to be considerably higher (although still meeting SRF specifications) compared to those resulting from historical data retrieved with RDF standard methods. These differences were not related to a decrease in the quality of the dry light flow produced in the mechanical-biological treatment plants but rather to the different sampling procedures set by the former RDF and current SRF standards. In particular, the shredding of the sample before quartering established by the latter methods ensures that also the finest waste fractions, characterised by higher moisture and metal contents, are included in the sample to be analysed, therefore affecting the composition and net calorific value of the waste. As for the reject flows, on the basis of their SRF classification and specification parameters, it was found that combined with the dry light flow they may present similar if not the same class codes as the latter alone, thus indicating that these material flows could be also treated in combustion plants instead of landfilled. In conclusion, the introduction of SRF definitions, classification and specification procedures, while not necessarily leading to an upgrade of the waste as co-fuel in cement kilns and power plants, may anyhow provide new possibilities for energy recovery from waste by increasing the types of mechanically treated waste flows that may be thermally treated. Copyright © 2015 Elsevier Ltd. All rights reserved.

Low power test architecture for dynamic read destructive fault detection in SRAM

NASA Astrophysics Data System (ADS)

Takher, Vikram Singh; Choudhary, Rahul Raj

2018-06-01

Dynamic Read Destructive Fault (dRDF) is the outcome of resistive open defects in the core cells of static random-access memories (SRAMs). The sensitisation of dRDF involves either performing multiple read operations or creation of number of read equivalent stress (RES), on the core cell under test. Though the creation of RES is preferred over the performing multiple read operation on the core cell, cell dissipates more power during RES than during the read or write operation. This paper focuses on the reduction in power dissipation by optimisation of number of RESs, which are required to sensitise the dRDF during test mode of operation of SRAM. The novel pre-charge architecture has been proposed in order to reduce the power dissipation by limiting the number of RESs to an optimised number of two. The proposed low power architecture is simulated and analysed which shows reduction in power dissipation by reducing the number of RESs up to 18.18%.

Towards a semantic PACS: Using Semantic Web technology to represent imaging data.

PubMed

Van Soest, Johan; Lustberg, Tim; Grittner, Detlef; Marshall, M Scott; Persoon, Lucas; Nijsten, Bas; Feltens, Peter; Dekker, Andre

2014-01-01

The DICOM standard is ubiquitous within medicine. However, improved DICOM semantics would significantly enhance search operations. Furthermore, databases of current PACS systems are not flexible enough for the demands within image analysis research. In this paper, we investigated if we can use Semantic Web technology, to store and represent metadata of DICOM image files, as well as linking additional computational results to image metadata. Therefore, we developed a proof of concept containing two applications: one to store commonly used DICOM metadata in an RDF repository, and one to calculate imaging biomarkers based on DICOM images, and store the biomarker values in an RDF repository. This enabled us to search for all patients with a gross tumor volume calculated to be larger than 50 cc. We have shown that we can successfully store the DICOM metadata in an RDF repository and are refining our proof of concept with regards to volume naming, value representation, and the applications themselves.

Knowledge Representation and Management: a Linked Data Perspective.

PubMed

Barros, M; Couto, F M

2016-11-10

Biomedical research is increasingly becoming a data-intensive science in several areas, where prodigious amounts of data is being generated that has to be stored, integrated, shared and analyzed. In an effort to improve the accessibility of data and knowledge, the Linked Data initiative proposed a well-defined set of recommendations for exposing, sharing and integrating data, information and knowledge, using semantic web technologies. The main goal of this paper is to identify the current status and future trends of knowledge representation and management in Life and Health Sciences, mostly with regard to linked data technologies. We selected three prominent linked data studies, namely Bio2RDF, Open PHACTS and EBI RDF platform, and selected 14 studies published after 2014 (inclusive) that cited any of the three studies. We manually analyzed these 14 papers in relation to how they use linked data techniques. The analyses show a tendency to use linked data techniques in Life and Health Sciences, and even if some studies do not follow all of the recommendations, many of them already represent and manage their knowledge using RDF and biomedical ontologies. These insights from RDF and biomedical ontologies are having a strong impact on how knowledge is generated from biomedical data, by making data elements increasingly connected and by providing a better description of their semantics. As health institutes become more data centric, we believe that the adoption of linked data techniques will continue to grow and be an effective solution to knowledge representation and management.

HyQue: evaluating hypotheses using Semantic Web technologies.

PubMed

Callahan, Alison; Dumontier, Michel; Shah, Nigam H

2011-05-17

Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF. HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque.

Providing Geographic Datasets as Linked Data in Sdi

NASA Astrophysics Data System (ADS)

Hietanen, E.; Lehto, L.; Latvala, P.

2016-06-01

In this study, a prototype service to provide data from Web Feature Service (WFS) as linked data is implemented. At first, persistent and unique Uniform Resource Identifiers (URI) are created to all spatial objects in the dataset. The objects are available from those URIs in Resource Description Framework (RDF) data format. Next, a Web Ontology Language (OWL) ontology is created to describe the dataset information content using the Open Geospatial Consortium's (OGC) GeoSPARQL vocabulary. The existing data model is modified in order to take into account the linked data principles. The implemented service produces an HTTP response dynamically. The data for the response is first fetched from existing WFS. Then the Geographic Markup Language (GML) format output of the WFS is transformed on-the-fly to the RDF format. Content Negotiation is used to serve the data in different RDF serialization formats. This solution facilitates the use of a dataset in different applications without replicating the whole dataset. In addition, individual spatial objects in the dataset can be referred with URIs. Furthermore, the needed information content of the objects can be easily extracted from the RDF serializations available from those URIs. A solution for linking data objects to the dataset URI is also introduced by using the Vocabulary of Interlinked Datasets (VoID). The dataset is divided to the subsets and each subset is given its persistent and unique URI. This enables the whole dataset to be explored with a web browser and all individual objects to be indexed by search engines.

Recombination directionality factor gp3 binds ϕC31 integrase via the zinc domain, potentially affecting the trajectory of the coiled-coil motif

PubMed Central

Younger, Ellen; Fernando, Booshini D; Khaleel, Thanafez; Stark, W Marshall; Smith, Margaret C M

2018-01-01

Abstract To establish a prophage state, the genomic DNA of temperate bacteriophages normally becomes integrated into the genome of their host bacterium by integrase-mediated, site-specific DNA recombination. Serine integrases catalyse a single crossover between an attachment site in the host (attB) and a phage attachment site (attP) on the circularized phage genome to generate the integrated prophage DNA flanked by recombinant attachment sites, attL and attR. Exiting the prophage state and entry into the lytic growth cycle requires an additional phage-encoded protein, the recombination directionality factor or RDF, to mediate recombination between attL and attR and excision of the phage genome. The RDF is known to bind integrase and switch its activity from integration (attP x attB) to excision (attL x attR) but its precise mechanism is unclear. Here, we identify amino acid residues in the RDF, gp3, encoded by the Streptomyces phage ϕC31 and within the ϕC31 integrase itself that affect the gp3:Int interaction. We show that residue substitutions in integrase that reduce gp3 binding adversely affect both excision and integration reactions. The mutant integrase phenotypes are consistent with a model in which the RDF binds to a hinge region at the base of the coiled-coil motif in ϕC31 integrase. PMID:29228292

Molecular Dynamics Simulation of Mahkota Dewa (Phaleria Macrocarpa) Extract in Subcritical Water Extraction Process

NASA Astrophysics Data System (ADS)

Hashim, N. A.; Mudalip, S. K. Abdul; Harun, N.; Che Man, R.; Sulaiman, S. Z.; Arshad, Z. I. M.; Shaarani, S. M.

2018-05-01

Mahkota Dewa (Phaleria Macrocarpa), a good source of saponin, flavanoid, polyphenol, alkaloid, and mangiferin has an extensive range of medicinal effects. The intermolecular interactions between solute and solvents such as hydrogen bonding considered as an important factor that affect the extraction of bioactive compounds. In this work, molecular dynamics simulation was performed to elucidate the hydrogen bonding exists between Mahkota Dewa extracts and water during subcritical extraction process. A bioactive compound in the Mahkota Dewa extract, namely mangiferin was selected as a model compound. The simulation was performed at 373 K and 4.0 MPa using COMPASS force field and Ewald summation method available in Material Studio 7.0 simulation package. The radial distribution functions (RDF) between mangiferin and water signify the presence of hydrogen bonding in the extraction process. The simulation of the binary mixture of mangiferin:water shows that strong hydrogen bonding was formed. It is suggested that, the intermolecular interaction between OH2O••HMR4(OH1) has been identified to be responsible for the mangiferin extraction process.

Synthesis and structural characterization of CdS nanoparticles

NASA Astrophysics Data System (ADS)

Kotkata, M. F.; Masoud, A. E.; Mohamed, M. B.; Mahmoud, E. A.

2009-08-01

Amorphous CdS nanoparticles capped with cetyltrimethyl ammonium bromide (CTAB) were synthesised under various conditions using a coprecipitation method. A blue shift in the band gap was observed in the UV-visible absorption spectra indicating the formation of nanoparticles of an approximate size of 8 nm. The recorded transmission electron micrographs confirmed this result. The phase-nature, phase transformation as well as the structure of the synthesised CdS nanoparticles have been extensively characterized using X-ray diffraction (XRD), radial distribution function (RDF), differential scanning calorimetry (DSC), Fourier transform infrared (FT-IR), Raman scattering (RS) and/or heat stage X-ray diffraction (HSXRD). Analysis of the obtained results revealed that the synthesised amorphous CdS nanoparticles could be transformed into CdS nanocrystals having a zinc blende or a wurtzite structure, relying on the applied heat treatment scheme. The rate of nanocrystal growth depends on the aging period, prior filtering the reacted materials, and its relation to the quality of the capping process. Five days aging period tends to enhance the stability of the grown phase with a remarkable surface stability.

Diffusion coefficients of nitric oxide in water: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Pokharel, Sunil; Pantha, Nurapati; Adhikari, N. P.

2016-09-01

Self-diffusion coefficients along with the mutual diffusion coefficients of nitric oxide (NO) and SPC/E water (H2O) as solute and solvent of the mixture, have been studied within the framework of classical molecular dynamics level of calculations using GROMACS package. The radial distribution function (RDF) of the constituent compounds are calculated to study solute-solute, solute-solvent and solvent-solvent molecular interactions as a function of temperature. A dilute solution of five NO molecules (mole fraction 0.018) and 280 H2O molecules (mole fraction 0.982) has been taken as the sample. The self-diffusion coefficient of the solvent is calculated by using mean square displacement (MSD) where as that for solute (NO) is calculated by using MSD and velocity auto-correlation function (VACF). The results are then compared with the available experimental values. The results from the present work for water come in good agreement, very precise at low temperatures, with the experimental values. The diffusion coefficients of NO, on the other hands, agree well with the available theoretical studies, and also with experiment at low temperatures (up to 310 K). The results at the higher temperatures (up to 333 K), however, deviate significantly with the experimental observations. Also, the mutual diffusion coefficients of NO in water have been calculated by using Darken’s relation. The temperature dependence of the calculated diffusion coefficients follow the Arrhenius behavior.

Understanding reactivity of two newly synthetized imidazole derivatives by spectroscopic characterization and computational study

NASA Astrophysics Data System (ADS)

Hossain, Mossaraf; Thomas, Renjith; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Vijayakumar, G.; Van Alsenoy, C.

2018-04-01

Two newly synthetized imidazole derivatives (1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (MPDIA) and 1-(4-bromophenyl)-4,5-dimethyl-1H-imidazole-2-yl acetate (BPDIA)) have been prepared by solvent-free synthesis pathway and their specific spectroscopic and reactive properties have been discussed based on combined experimental and computational approaches. Aside of synthesis, experimental part of this work included measurements of IR, FT-Raman and NMR spectra. All of the aforementioned spectra were also obtained computationally, within the framework of density functional theory (DFT) approach. Additionally, DFT calculations have been used in order to investigate local reactivity properties based on molecular orbital theory, molecular electrostatic potential (MEP), average local ionization energy (ALIE), Fukui functions and bond dissociation energy (BDE). Molecular dynamics (MD) simulations have been used in order to obtain radial distribution functions (RDF), which were used for identification of the atoms with pronounced interactions with water molecules. MEP showed negative regions are mainly localized over N28, O29, O35 atoms, it is represent with red colour in rainbow color scheme for MPDIA and BPDIA (which are most reactive sites for electrophilic attack). The first order hyperpolarizabilities of MPDIA and BPDIA are 20.15 and 6.10 times that of the standard NLO material urea. Potential interaction with antihypertensive protein hydrolase.

A future Outlook: Web based Simulation of Hydrodynamic models

NASA Astrophysics Data System (ADS)

Islam, A. S.; Piasecki, M.

2003-12-01

Despite recent advances to present simulation results as 3D graphs or animation contours, the modeling user community still faces some shortcomings when trying to move around and analyze data. Typical problems include the lack of common platforms with standard vocabulary to exchange simulation results from different numerical models, insufficient descriptions about data (metadata), lack of robust search and retrieval tools for data, and difficulties to reuse simulation domain knowledge. This research demonstrates how to create a shared simulation domain in the WWW and run a number of models through multi-user interfaces. Firstly, meta-datasets have been developed to describe hydrodynamic model data based on geographic metadata standard (ISO 19115) that has been extended to satisfy the need of the hydrodynamic modeling community. The Extended Markup Language (XML) is used to publish this metadata by the Resource Description Framework (RDF). Specific domain ontology for Web Based Simulation (WBS) has been developed to explicitly define vocabulary for the knowledge based simulation system. Subsequently, this knowledge based system is converted into an object model using Meta Object Family (MOF). The knowledge based system acts as a Meta model for the object oriented system, which aids in reusing the domain knowledge. Specific simulation software has been developed based on the object oriented model. Finally, all model data is stored in an object relational database. Database back-ends help store, retrieve and query information efficiently. This research uses open source software and technology such as Java Servlet and JSP, Apache web server, Tomcat Servlet Engine, PostgresSQL databases, Protégé ontology editor, RDQL and RQL for querying RDF in semantic level, Jena Java API for RDF. Also, we use international standards such as the ISO 19115 metadata standard, and specifications such as XML, RDF, OWL, XMI, and UML. The final web based simulation product is deployed as Web Archive (WAR) files which is platform and OS independent and can be used by Windows, UNIX, or Linux. Keywords: Apache, ISO 19115, Java Servlet, Jena, JSP, Metadata, MOF, Linux, Ontology, OWL, PostgresSQL, Protégé, RDF, RDQL, RQL, Tomcat, UML, UNIX, Windows, WAR, XML

HyQue: evaluating hypotheses using Semantic Web technologies

PubMed Central

2011-01-01

Background Key to the success of e-Science is the ability to computationally evaluate expert-composed hypotheses for validity against experimental data. Researchers face the challenge of collecting, evaluating and integrating large amounts of diverse information to compose and evaluate a hypothesis. Confronted with rapidly accumulating data, researchers currently do not have the software tools to undertake the required information integration tasks. Results We present HyQue, a Semantic Web tool for querying scientific knowledge bases with the purpose of evaluating user submitted hypotheses. HyQue features a knowledge model to accommodate diverse hypotheses structured as events and represented using Semantic Web languages (RDF/OWL). Hypothesis validity is evaluated against experimental and literature-sourced evidence through a combination of SPARQL queries and evaluation rules. Inference over OWL ontologies (for type specifications, subclass assertions and parthood relations) and retrieval of facts stored as Bio2RDF linked data provide support for a given hypothesis. We evaluate hypotheses of varying levels of detail about the genetic network controlling galactose metabolism in Saccharomyces cerevisiae to demonstrate the feasibility of deploying such semantic computing tools over a growing body of structured knowledge in Bio2RDF. Conclusions HyQue is a query-based hypothesis evaluation system that can currently evaluate hypotheses about the galactose metabolism in S. cerevisiae. Hypotheses as well as the supporting or refuting data are represented in RDF and directly linked to one another allowing scientists to browse from data to hypothesis and vice versa. HyQue hypotheses and data are available at http://semanticscience.org/projects/hyque. PMID:21624158

Fourier Transform Infrared (FT-IR) and Laser Ablation Inductively Coupled Plasma-Mass Spectrometry (LA-ICP-MS) Imaging of Cerebral Ischemia: Combined Analysis of Rat Brain Thin Cuts Toward Improved Tissue Classification.

PubMed

Balbekova, Anna; Lohninger, Hans; van Tilborg, Geralda A F; Dijkhuizen, Rick M; Bonta, Maximilian; Limbeck, Andreas; Lendl, Bernhard; Al-Saad, Khalid A; Ali, Mohamed; Celikic, Minja; Ofner, Johannes

2018-02-01

Microspectroscopic techniques are widely used to complement histological studies. Due to recent developments in the field of chemical imaging, combined chemical analysis has become attractive. This technique facilitates a deepened analysis compared to single techniques or side-by-side analysis. In this study, rat brains harvested one week after induction of photothrombotic stroke were investigated. Adjacent thin cuts from rats' brains were imaged using Fourier transform infrared (FT-IR) microspectroscopy and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). The LA-ICP-MS data were normalized using an internal standard (a thin gold layer). The acquired hyperspectral data cubes were fused and subjected to multivariate analysis. Brain regions affected by stroke as well as unaffected gray and white matter were identified and classified using a model based on either partial least squares discriminant analysis (PLS-DA) or random decision forest (RDF) algorithms. The RDF algorithm demonstrated the best results for classification. Improved classification was observed in the case of fused data in comparison to individual data sets (either FT-IR or LA-ICP-MS). Variable importance analysis demonstrated that both molecular and elemental content contribute to the improved RDF classification. Univariate spectral analysis identified biochemical properties of the assigned tissue types. Classification of multisensor hyperspectral data sets using an RDF algorithm allows access to a novel and in-depth understanding of biochemical processes and solid chemical allocation of different brain regions.

Knowledge Representation and Management: A Linked Data Perspective

PubMed Central

Barros, M.

2016-01-01

Summary Introduction Biomedical research is increasingly becoming a data-intensive science in several areas, where prodigious amounts of data is being generated that has to be stored, integrated, shared and analyzed. In an effort to improve the accessibility of data and knowledge, the Linked Data initiative proposed a well-defined set of recommendations for exposing, sharing and integrating data, information and knowledge, using semantic web technologies. Objective The main goal of this paper is to identify the current status and future trends of knowledge representation and management in Life and Health Sciences, mostly with regard to linked data technologies. Methods We selected three prominent linked data studies, namely Bio2RDF, Open PHACTS and EBI RDF platform, and selected 14 studies published after 2014 (inclusive) that cited any of the three studies. We manually analyzed these 14 papers in relation to how they use linked data techniques. Results The analyses show a tendency to use linked data techniques in Life and Health Sciences, and even if some studies do not follow all of the recommendations, many of them already represent and manage their knowledge using RDF and biomedical ontologies. Conclusion These insights from RDF and biomedical ontologies are having a strong impact on how knowledge is generated from biomedical data, by making data elements increasingly connected and by providing a better description of their semantics. As health institutes become more data centric, we believe that the adoption of linked data techniques will continue to grow and be an effective solution to knowledge representation and management. PMID:27830248

FT-IR and FT-Raman characterization and investigation of reactive properties of N-(3-iodo-4-methylphenyl)pyrazine-2-carboxamide by molecular dynamics simulations and DFT calculations

NASA Astrophysics Data System (ADS)

Ranjith, P. K.; Al-Abdullah, Ebtehal S.; Al-Omary, Fatmah A. M.; El-Emam, Ali A.; Anto, P. L.; Sheena, Mary Y.; Armaković, Stevan; Armaković, Sanja J.; Zitko, Jan; Dolezal, Martin; Van Alsenoy, C.

2017-05-01

The FT-IR and FT-Raman spectra of N-(3-iodo-4-methylphenyl)pyrazine-2-carboxamide were recorded and the experimentally observed wavenumbers are compared with the theoretically obtained wavenumbers. The redshift of the Nsbnd H stretching mode in the IR spectrum from the computed value indicated the weakening of the Nsbnd H bond. The ring breathing modes of the phenyl ring and pyrazine ring are assigned at 819 and 952 cm-1 theoretically. Using natural bond orbital analysis, the stability of the molecule arising from hyperconjugative interaction and charge delocalization has been analyzed. The most reactive sites in the molecule were identified by molecular electrostatic potential map. The calculations of the average local ionization energy (ALIE) were used for visualization and determination of molecule sites possibly prone to electrophilic attacks. Further information on possible reactive centers of title molecule has been obtained by calculations of Fukui functions. Vulnerability of title molecule towards autoxidation mechanism was investigated by calculations of bond dissociation energies (BDE), while vulnerability towards hydrolysis was investigated by calculations of radial distribution functions (RDF) as obtained after molecular dynamics (MD) simulations. Molecular docking studies suggest that the compound might exhibit inhibitory activity against mGluRs.

Refuse derived fuel (RDF) plasma torch gasification as a feasible route to produce low environmental impact syngas for the cement industry.

PubMed

López-Sabirón, Ana M; Fleiger, Kristina; Schäfer, Stefan; Antoñanzas, Javier; Irazustabarrena, Ane; Aranda-Usón, Alfonso; Ferreira, Germán A

2015-08-01

Plasma torch gasification (PTG) is currently researched as a technology for solid waste recovery. However, scientific studies based on evaluating its environmental implications considering the life cycle assessment (LCA) methodology are lacking. Therefore, this work is focused on comparing the environmental effect of the emissions of syngas combustion produced by refuse derived fuel (RDF) and PTG as alternative fuels, with that related to fossil fuel combustion in the cement industry. To obtain real data, a semi-industrial scale pilot plant was used to perform experimental trials on RDF-PTG.The results highlight that PTG for waste to energy recovery in the cement industry is environmentally feasible considering its current state of development. A reduction in every impact category was found when a total or partial substitution of alternative fuel for conventional fuel in the calciner firing (60 % of total thermal energy input) was performed. Furthermore, the results revealed that electrical energy consumption in PTG is also an important parameter from the LCA approach. © The Author(s) 2015.

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

Kara, Mustafa, E-mail: mustafa.kara@mam.gov.t; Guenay, Esin; Tabak, Yasemin

Municipal solid waste (MSW) is one of the most important environmental problems arising from rapid urbanization and industrialization. The use of alternative fuels in rotary kilns of cement plants is very important for reducing cost, saving fossil fuels and also eliminating waste materials, accumulated during production or after using these materials. Cement industries has an important potential for supplying preferable solutions to the waste management. Energy recovery from waste is also important for the reduction of CO{sub 2} emissions. This paper presents an investigation of the development of refuse derived fuel (RDF) materials from non-recycling wastes and the determination ofmore » its potential use as an alternative fuel in cement production in Istanbul, Turkey. RDF produced from MSW was analyzed and its effects on cement production process were examined. For this purpose, the produced RDF was mixed with the main fuel (LPG) in ratios of 0%, 5%, 10%, 15% and 20%. Then chemical and mineralogical analyses of the produced clinker were carried out. It is believed that successful results of this study will be a good example for municipalities and cement industries in order to achieve both economic and environmental benefits.« less

Rolling Deck to Repository (R2R): A "Linked Data" Approach for the U.S. Academic Research Fleet

NASA Astrophysics Data System (ADS)

Arko, R.; Chandler, C.; Clark, P.; Milan, A.; Mize, J.

2012-04-01

The Rolling Deck to Repository (R2R; http://rvdata.us/) program is developing infrastructure to routinely document, assess, and preserve the underway sensor data from U.S. academic research vessels. The R2R master catalog of vessels, instrument systems, operating institutions, cruises, personnel, data sets, event logs, and field reports has grown to over 2,200 cruises in less than two years, and is now accessible via Web services. This catalog is of great value to peer data systems, ranging from large inter/national data centers to small disciplinary data offices, as an aid in quality controlling their own collections and finding related data from authoritative sources. R2R breaks with the tradition of stovepipe portals built around complex search interfaces tightly bound to backend databases. Instead, we have adopted a Linked Data approach to publish our catalog content, based on the W3C Resource Description Framework (RDF) and Uniform Resource Identifiers (URIs). Our data model is published as a collection of W3C Simple Knowledge Organization System (SKOS) concepts, mapped to partner vocabularies such as those developed by the Global Change Master Directory (GCMD) and the pan-European SeaDataNet partnership, and our catalog content is published as collections of RDF resources with globally unique and persistent identifiers. The combination of exposing our data model, mapping local terms to community-wide vocabularies, and using reliable identifiers improves interoperability and reduces ambiguity. R2R's metric of success is the degree to which peer data systems harvest and reuse our content. R2R is working collaboratively with the NOAA National Data Centers and the NSF-funded Biological and Chemical Oceanography Data Management Office (BCO-DMO) on a range of Linked Data pilot applications, including production of ISO-compliant metadata and deployment of a RDF Query Language (SPARQL) interface. Our objective is to support a distributed, loosely federated network of complementary systems that collectively manage the vast body of ocean science data. We will present results and lessons learned.

A molecular dynamics study on the role of attractive and repulsive forces in internal energy, internal pressure and structure of dense fluids

NASA Astrophysics Data System (ADS)

Goharshadi, Elaheh K.; Morsali, Ali; Mansoori, G. Ali

2007-01-01

Isotherms of experimental data of internal pressure of dense fluids versus molar volume, Vm are shown to have each a maximum point at a Vmax below the critical molar volume. In this study, we investigated the role of attractive and repulsive intermolecular energies on this behavior using a molecular dynamics simulation technique. In the simulation, we choose the Lennard-Jones (LJ) intermolecular potential energy function. The LJ potential is known to be an effective potential representing a statistical average of the true pair and many-body interactions in simple molecular systems. The LJ potential function is divided into attractive and repulsive parts. MD calculations have produced internal energy, potential energy, transitional kinetic energy, and radial distribution function (RDF) for argon at 180 K and 450 K using LJ potential, LJ repulsive, and LJ attractive parts. It is shown that the LJ potential function is well capable of predicting the inflection point in the internal energy-molar volume curve as well as maximum point in the internal pressure-molar volume curve. It is also shown that at molar volumes higher than Vmax, the attractive forces have strong influence on determination of internal energy and internal pressure. At volumes lower than Vmax, neither repulsive nor attractive forces are dominating. Also, the coincidence between RDFs resulting from LJ potential and repulsive parts of LJ potential improves as molar volume approaches Vmax from high molar volumes. The coincidence becomes complete at Vmax ⩾ V.

Towards a semantics-based approach in the development of geographic portals

NASA Astrophysics Data System (ADS)

Athanasis, Nikolaos; Kalabokidis, Kostas; Vaitis, Michail; Soulakellis, Nikolaos

2009-02-01

As the demand for geospatial data increases, the lack of efficient ways to find suitable information becomes critical. In this paper, a new methodology for knowledge discovery in geographic portals is presented. Based on the Semantic Web, our approach exploits the Resource Description Framework (RDF) in order to describe the geoportal's information with ontology-based metadata. When users traverse from page to page in the portal, they take advantage of the metadata infrastructure to navigate easily through data of interest. New metadata descriptions are published in the geoportal according to the RDF schemas.

NASA Thesaurus Data File

NASA Technical Reports Server (NTRS)

2012-01-01

The NASA Thesaurus contains the authorized NASA subject terms used to index and retrieve materials in the NASA Aeronautics and Space Database (NA&SD) and NASA Technical Reports Server (NTRS). The scope of this controlled vocabulary includes not only aerospace engineering, but all supporting areas of engineering and physics, the natural space sciences (astronomy, astrophysics, planetary science), Earth sciences, and the biological sciences. The NASA Thesaurus Data File contains all valid terms and hierarchical relationships, USE references, and related terms in machine-readable form. The Data File is available in the following formats: RDF/SKOS, RDF/OWL, ZThes-1.0, and CSV/TXT.

Binder enhanced refuse derived fuel

DOEpatents

Daugherty, Kenneth E.; Venables, Barney J.; Ohlsson, Oscar O.

1996-01-01

A refuse derived fuel (RDF) pellet having about 11% or more particulate calcium hydroxide which is utilized in a combustionable mixture. The pellets are used in a particulate fuel bring a mixture of 10% or more, on a heat equivalent basis, of the RDF pellet which contains calcium hydroxide as a binder, with 50% or more, on a heat equivalent basis, of a sulphur containing coal. Combustion of the mixture is effective to produce an effluent gas from the combustion zone having a reduced SO.sub.2 and polycyclic aromatic hydrocarbon content of effluent gas from similar combustion materials not containing the calcium hydroxide.

Connecting geoscience systems and data using Linked Open Data in the Web of Data

NASA Astrophysics Data System (ADS)

Ritschel, Bernd; Neher, Günther; Iyemori, Toshihiko; Koyama, Yukinobu; Yatagai, Akiyo; Murayama, Yasuhiro; Galkin, Ivan; King, Todd; Fung, Shing F.; Hughes, Steve; Habermann, Ted; Hapgood, Mike; Belehaki, Anna

2014-05-01

Linked Data or Linked Open Data (LOD) in the realm of free and publically accessible data is one of the most promising and most used semantic Web frameworks connecting various types of data and vocabularies including geoscience and related domains. The semantic Web extension to the commonly existing and used World Wide Web is based on the meaning of entities and relationships or in different words classes and properties used for data in a global data and information space, the Web of Data. LOD data is referenced and mash-uped by URIs and is retrievable using simple parameter controlled HTTP-requests leading to a result which is human-understandable or machine-readable. Furthermore the publishing and mash-up of data in the semantic Web realm is realized by specific Web standards, such as RDF, RDFS, OWL and SPARQL defined for the Web of Data. Semantic Web based mash-up is the Web method to aggregate and reuse various contents from different sources, such as e.g. using FOAF as a model and vocabulary for the description of persons and organizations -in our case- related to geoscience projects, instruments, observations, data and so on. On the example of three different geoscience data and information management systems, such as ESPAS, IUGONET and GFZ ISDC and the associated science data and related metadata or better called context data, the concept of the mash-up of systems and data using the semantic Web approach and the Linked Open Data framework is described in this publication. Because the three systems are based on different data models, data storage structures and technical implementations an extra semantic Web layer upon the existing interfaces is used for mash-up solutions. In order to satisfy the semantic Web standards, data transition processes, such as the transfer of content stored in relational databases or mapped in XML documents into SPARQL capable databases or endpoints using D2R or XSLT is necessary. In addition, the use of mapped and/or merged domain specific and cross-domain vocabularies in the sense of terminological ontologies are the foundation for a virtually unified data retrieval and access in IUGONET, ESPAS and GFZ ISDC data management systems. SPARQL endpoints realized either by originally RDF databases, e.g. Virtuoso or by virtual SPARQL endpoints, e.g. D2R services enable an only upon Web standard-based mash-up of domain-specific systems and data, such as in this case the space weather and geomagnetic domain but also cross-domain connection to data and vocabularies, e.g. related to NASA's VxOs, particularly VWO or NASA's PDS data system within LOD. LOD - Linked Open Data RDF - Resource Description Framework RDFS - RDF Schema OWL - Ontology Web Language SPARQL - SPARQL Protocol and RDF Query Language FOAF - Friends of a Friend ontology ESPAS - Near Earth Space Data Infrastructure for e-Science (Project) IUGONET - Inter-university Upper Atmosphere Global Observation Network (Project) GFZ ISDC - German Research Centre for Geosciences Information System and Data Center XML - Extensible Mark-up Language D2R - (Relational) Database to RDF (Transformation) XSLT - Extensible Stylesheet Language Transformation Virtuoso - OpenLink Virtuoso Universal Server (including RDF data management) NASA - National Aeronautics and Space Administration VOx - Virtual Observatories VWO - Virtual Wave Observatory PDS - Planetary Data System

Enabling Graph Mining in RDF Triplestores using SPARQL for Holistic In-situ Graph Analysis

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

Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong

The graph analysis is now considered as a promising technique to discover useful knowledge in data with a new perspective. We envi- sion that there are two dimensions of graph analysis: OnLine Graph Analytic Processing (OLGAP) and Graph Mining (GM) where each respectively focuses on subgraph pattern matching and automatic knowledge discovery in graph. Moreover, as these two dimensions aim to complementarily solve complex problems, holistic in-situ graph analysis which covers both OLGAP and GM in a single system is critical for minimizing the burdens of operating multiple graph systems and transferring intermediate result-sets between those systems. Nevertheless, most existingmore » graph analysis systems are only capable of one dimension of graph analysis. In this work, we take an approach to enabling GM capabilities (e.g., PageRank, connected-component analysis, node eccentricity, etc.) in RDF triplestores, which are originally developed to store RDF datasets and provide OLGAP capability. More specifically, to achieve our goal, we implemented six representative graph mining algorithms using SPARQL. The approach allows a wide range of available RDF data sets directly applicable for holistic graph analysis within a system. For validation of our approach, we evaluate performance of our implementations with nine real-world datasets and three different computing environments - a laptop computer, an Amazon EC2 instance, and a shared-memory Cray XMT2 URIKA-GD graph-processing appliance. The experimen- tal results show that our implementation can provide promising and scalable performance for real world graph analysis in all tested environments. The developed software is publicly available in an open-source project that we initiated.« less

Palaeomagnetic time and space constraints of the Early Cretaceous Rhenodanubian Flysch zone (Eastern Alps)

NASA Astrophysics Data System (ADS)

Dallanave, Edoardo; Kirscher, Uwe; Hauck, Jürgen; Hesse, Reinhard; Bachtadse, Valerian; Wortmann, Ulrich Georg

2018-06-01

The Rhenodanubian Flysch zone (RDF) is a Lower Cretaceous-lower Palaeocene turbidite succession extending for ˜500 km from the Danube at Vienna to the Rhine Valley (Eastern Alps). It consists of calcareous and siliciclastic turbidite systems deposited in a trench abyssal plain. The age of deposition has been estimated through micropalaeontologic dating. However, palaeomagnetic studies constraining the age and the palaeolatitude of deposition of the RDF are still missing. Here, we present palaeomagnetic data from the Early Cretaceous Tristel and Rehbreingraben Formations of the RDF from two localities in the Bavarian Alps (Rehbrein Creek and Lainbach Valley, southern Germany), and from the stratigraphic equivalent of the Falknis Nappe (Liechtenstein). The quality of the palaeomagnetic signal has been assessed by either fold test (FT) or reversal test (RT). Sediments from the Falknis Nappe are characterized by a pervasive syntectonic magnetic overprint as tested by negative FT, and are thus excluded from the study. The sediments of the Rehbreingraben Formation at Rehbrein Creek, with positive RT, straddle magnetic polarity Chron M0r and the younger M΄-1r΄ reverse event, with an age of ˜127-123 Ma (late Barremian-early Aptian). At Lainbach Valley, no polarity reversals have been observed, but a positive FT gives confidence on the reliability of the data. The primary palaeomagnetic directions, after correction for inclination shallowing, allow to precisely constrain the depositional palaeolatitude of the Tristel and Rehbreingraben Formations around ˜28°N. In a palaeogeographic reconstruction of the Alpine Tethys at the Barremian/Aptian boundary, the RDF is located on the western margin of the Briançonnais terrain, which was separated from the European continent by the narrow Valais Ocean.

Gasification of Simplex briquets: briquet production. Vol. 1. Final report

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

Not Available

A 7-ton/hr briquetting plant was installed at International Briquetting in Baltimore, Maryland, and used to produce 360 tons of Simplex briquets from Pittsburgh No. 8 seam, Champion No. 1 mine caking coal and shredded, air-classified Baltimore County refuse. The production of these briquets was funded by the Department of Energy, through the US Bureau of Mines, and a consortium comprised of the New York State Energy Research and Development Authority and the Empire State Electric Energy Research Company. This report describes the briquetting plant and discusses the problems that were encountered in producing the briquets. The following modifications are recommendedmore » for future Simplex briquetting plants: drying equipment should be installed on the RDF feed system to ensure that the RDF moisture is below 18%; the crushed coal must be dried to less than 4% moisture to ensure its free flow in the bins; magnets should be installed above the coal and RDF feed conveyors to remove any tramp metal; a 3/4-inch screen should be installed over the coal feed bin to remove any oversize rocks or lump coal; the RDF handling system and turbulizer discharge to the press should all be enclosed for dust control (the enclosures should be vented to a baghouse); only heavy duty apron conveyors should be used where belt conveyors are needed; briquetts should be cured if they are going to be stored in containers where they might sweat; and a screen with 1 1/4-inch openings should be used to remove the fines from 2 1/4-inch briquets (this screen should be sufficiently large to prevent briquets from crowding together on the screen).« less

Towards a semantic medical Web: HealthCyberMap's tool for building an RDF metadata base of health information resources based on the Qualified Dublin Core Metadata Set.

PubMed

Boulos, Maged N; Roudsari, Abdul V; Carson, Ewart R

2002-07-01

HealthCyberMap (http://healthcybermap.semanticweb.org/) aims at mapping Internet health information resources in novel ways for enhanced retrieval and navigation. This is achieved by collecting appropriate resource metadata in an unambiguous form that preserves semantics. We modelled a qualified Dublin Core (DC) metadata set ontology with extra elements for resource quality and geographical provenance in Prot g -2000. A metadata collection form helps acquiring resource instance data within Prot g . The DC subject field is populated with UMLS terms directly imported from UMLS Knowledge Source Server using UMLS tab, a Prot g -2000 plug-in. The project is saved in RDFS/RDF. The ontology and associated form serve as a free tool for building and maintaining an RDF medical resource metadata base. The UMLS tab enables browsing and searching for concepts that best describe a resource, and importing them to DC subject fields. The resultant metadata base can be used with a search and inference engine, and have textual and/or visual navigation interface(s) applied to it, to ultimately build a medical Semantic Web portal. Different ways of exploiting Prot g -2000 RDF output are discussed. By making the context and semantics of resources, not merely their raw text and formatting, amenable to computer 'understanding,' we can build a Semantic Web that is more useful to humans than the current Web. This requires proper use of metadata and ontologies. Clinical codes can reliably describe the subjects of medical resources, establish the semantic relationships (as defined by underlying coding scheme) between related resources, and automate their topical categorisation.

The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web.

PubMed

Stucky, Brian J; Deck, John; Conlin, Tom; Ziemba, Lukasz; Cellinese, Nico; Guralnick, Robert

2014-07-29

Recent years have brought great progress in efforts to digitize the world's biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web technologies have been widely recognized by biodiversity scientists for their potential to help solve this problem, yet these technologies have so far seen little use for biodiversity data. Such slow uptake has been due, in part, to the relative complexity of Semantic Web technologies along with a lack of domain-specific software tools to help non-experts publish their data to the Semantic Web. The BiSciCol Triplifier is new software that greatly simplifies the process of converting biodiversity data in standard, tabular formats, such as Darwin Core-Archives, into Semantic Web-ready Resource Description Framework (RDF) representations. The Triplifier uses a vocabulary based on the popular Darwin Core standard, includes both Web-based and command-line interfaces, and is fully open-source software. Unlike most other RDF conversion tools, the Triplifier does not require detailed familiarity with core Semantic Web technologies, and it is tailored to a widely popular biodiversity data format and vocabulary standard. As a result, the Triplifier can often fully automate the conversion of biodiversity data to RDF, thereby making the Semantic Web much more accessible to biodiversity scientists who might otherwise have relatively little knowledge of Semantic Web technologies. Easy availability of biodiversity data as RDF will allow researchers to combine data from disparate sources and analyze them with powerful linked data querying tools. However, before software like the Triplifier, and Semantic Web technologies in general, can reach their full potential for biodiversity science, the biodiversity informatics community must address several critical challenges, such as the widespread failure to use robust, globally unique identifiers for biodiversity data.

Enabling Graph Mining in RDF Triplestores using SPARQL for Holistic In-situ Graph Analysis

DOE PAGES

Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong; ...

2016-01-01

The graph analysis is now considered as a promising technique to discover useful knowledge in data with a new perspective. We envi- sion that there are two dimensions of graph analysis: OnLine Graph Analytic Processing (OLGAP) and Graph Mining (GM) where each respectively focuses on subgraph pattern matching and automatic knowledge discovery in graph. Moreover, as these two dimensions aim to complementarily solve complex problems, holistic in-situ graph analysis which covers both OLGAP and GM in a single system is critical for minimizing the burdens of operating multiple graph systems and transferring intermediate result-sets between those systems. Nevertheless, most existingmore » graph analysis systems are only capable of one dimension of graph analysis. In this work, we take an approach to enabling GM capabilities (e.g., PageRank, connected-component analysis, node eccentricity, etc.) in RDF triplestores, which are originally developed to store RDF datasets and provide OLGAP capability. More specifically, to achieve our goal, we implemented six representative graph mining algorithms using SPARQL. The approach allows a wide range of available RDF data sets directly applicable for holistic graph analysis within a system. For validation of our approach, we evaluate performance of our implementations with nine real-world datasets and three different computing environments - a laptop computer, an Amazon EC2 instance, and a shared-memory Cray XMT2 URIKA-GD graph-processing appliance. The experimen- tal results show that our implementation can provide promising and scalable performance for real world graph analysis in all tested environments. The developed software is publicly available in an open-source project that we initiated.« less

Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing-activated transfer of a mobile genetic element.

PubMed

Ramsay, Joshua P; Tester, Laura G L; Major, Anthony S; Sullivan, John T; Edgar, Christina D; Kleffmann, Torsten; Patterson-House, Jackson R; Hall, Drew A; Tate, Warren P; Hynes, Michael F; Ronson, Clive W

2015-03-31

Symbiosis islands are integrative and conjugative mobile genetic elements that convert nonsymbiotic rhizobia into nitrogen-fixing symbionts of leguminous plants. Excision of the Mesorhizobium loti symbiosis island ICEMlSym(R7A) is indirectly activated by quorum sensing through TraR-dependent activation of the excisionase gene rdfS. Here we show that a +1 programmed ribosomal frameshift (PRF) fuses the coding sequences of two TraR-activated genes, msi172 and msi171, producing an activator of rdfS expression named Frameshifted excision activator (FseA). Mass-spectrometry and mutational analyses indicated that the PRF occurred through +1 slippage of the tRNA(phe) from UUU to UUC within a conserved msi172-encoded motif. FseA activated rdfS expression in the absence of ICEMlSym(R7A), suggesting that it directly activated rdfS transcription, despite being unrelated to any characterized DNA-binding proteins. Bacterial two-hybrid and gene-reporter assays demonstrated that FseA was also bound and inhibited by the ICEMlSym(R7A)-encoded quorum-sensing antiactivator QseM. Thus, activation of ICEMlSym(R7A) excision is counteracted by TraR antiactivation, ribosomal frameshifting, and FseA antiactivation. This robust suppression likely dampens the inherent biological noise present in the quorum-sensing autoinduction circuit and ensures that ICEMlSym(R7A) transfer only occurs in a subpopulation of cells in which both qseM expression is repressed and FseA is translated. The architecture of the ICEMlSym(R7A) transfer regulatory system provides an example of how a set of modular components have assembled through evolution to form a robust genetic toggle that regulates gene transcription and translation at both single-cell and cell-population levels.

Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing–activated transfer of a mobile genetic element

PubMed Central

Ramsay, Joshua P.; Tester, Laura G. L.; Major, Anthony S.; Sullivan, John T.; Edgar, Christina D.; Kleffmann, Torsten; Patterson-House, Jackson R.; Hall, Drew A.; Tate, Warren P.; Hynes, Michael F.; Ronson, Clive W.

2015-01-01

Symbiosis islands are integrative and conjugative mobile genetic elements that convert nonsymbiotic rhizobia into nitrogen-fixing symbionts of leguminous plants. Excision of the Mesorhizobium loti symbiosis island ICEMlSymR7A is indirectly activated by quorum sensing through TraR-dependent activation of the excisionase gene rdfS. Here we show that a +1 programmed ribosomal frameshift (PRF) fuses the coding sequences of two TraR-activated genes, msi172 and msi171, producing an activator of rdfS expression named Frameshifted excision activator (FseA). Mass-spectrometry and mutational analyses indicated that the PRF occurred through +1 slippage of the tRNAphe from UUU to UUC within a conserved msi172-encoded motif. FseA activated rdfS expression in the absence of ICEMlSymR7A, suggesting that it directly activated rdfS transcription, despite being unrelated to any characterized DNA-binding proteins. Bacterial two-hybrid and gene-reporter assays demonstrated that FseA was also bound and inhibited by the ICEMlSymR7A-encoded quorum-sensing antiactivator QseM. Thus, activation of ICEMlSymR7A excision is counteracted by TraR antiactivation, ribosomal frameshifting, and FseA antiactivation. This robust suppression likely dampens the inherent biological noise present in the quorum-sensing autoinduction circuit and ensures that ICEMlSymR7A transfer only occurs in a subpopulation of cells in which both qseM expression is repressed and FseA is translated. The architecture of the ICEMlSymR7A transfer regulatory system provides an example of how a set of modular components have assembled through evolution to form a robust genetic toggle that regulates gene transcription and translation at both single-cell and cell-population levels. PMID:25787256

Partial replacement of fossil fuel in a cement plant: risk assessment for the population living in the neighborhood.

PubMed

Rovira, Joaquim; Mari, Montse; Nadal, Martí; Schuhmacher, Marta; Domingo, José L

2010-10-15

In cement plants, the substitution of traditional fossil fuels not only allows a reduction of CO(2), but it also means to check-out residual materials, such as sewage sludge or municipal solid wastes (MSW), which should otherwise be disposed somehow/somewhere. In recent months, a cement plant placed in Alcanar (Catalonia, Spain) has been conducting tests to replace fossil fuel by refuse-derived fuel (RDF) from MSW. In July 2009, an operational test was progressively initiated by reaching a maximum of partial substitution of 20% of the required energy. In order to study the influence of the new process, environmental monitoring surveys were performed before and after the RDF implementation. Metals and polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs) were analyzed in soil, herbage, and air samples collected around the facility. In soils, significant decreases of PCDD/F levels, as well as in some metal concentrations were found, while no significant increases in the concentrations of these pollutants were observed. In turn, PM(10) levels remained constant, with a value of 16μgm(-3). In both surveys, the carcinogenic and non-carcinogenic risks derived from exposure to metals and PCDD/Fs for the population living in the vicinity of the facility were within the ranges considered as acceptable according to national and international standards. This means that RDF may be a successful choice in front of classical fossil fuels, being in accordance with the new EU environmental policies, which entail the reduction of CO(2) emissions and the energetic valorization of MSW. However, further long-term environmental studies are necessary to corroborate the harmlessness of RDF, in terms of human health risks. Copyright © 2010 Elsevier B.V. All rights reserved.

Stochastic Theory for the Clustering of Rapidly Settling, Low-Inertia Particle Pairs in Isotropic Turbulence - II

NASA Astrophysics Data System (ADS)

Rani, Sarma; Gupta, Vijay; Koch, Donald

2017-11-01

A stochastic theory is developed to predict the Radial Distribution Function (RDF) of monodisperse, rapidly settling, low-inertia particle pairs in isotropic turbulence. In the second version of the theory (T2), the dimensionless strain-rate and rotation-rate tensors ``seen'' by the primary particle are assumed to be Gaussian distributed, where the strain-rate and rotation-rate tensors are non-dimensionlized using the instantaneous dissipation rate and enstrophy, respectively. Accordingly, closure is again derived for the drift flux driving particle clustering, in the asympotic limits of Stokes number St =τp /τη << 1 , and settling paramater Sv = gτp /uη >> 1 . Only the drift flux differs for T1 and T2, while the diffusive flux remains the same. The RDFs for rapidly settling pairs again show an inverse power dependency on pair separation r with an exponent, c1, that is proportional to St2 . However, in contrast to T1, the c1 values predicted by T2 show good qualitative and resonable quantitative agreement with the c1 values obtained from DNS of settling particles in isotropic turbulence. Further, the T2-predicted c1 values are smaller than those obtained from DNS of non-settling particles in isotropic turbulence. Funding from the CBET Division of the National Science Foundation is gratefully acknowledged.

Suppression of threshold voltage variability in MOSFETs by adjustment of ion implantation parameters

NASA Astrophysics Data System (ADS)

Park, Jae Hyun; Chang, Tae-sig; Kim, Minsuk; Woo, Sola; Kim, Sangsig

2018-01-01

In this study, we investigate threshold voltage (VTH) variability of metal-oxide-semiconductor field-effect transistors induced by random dopant fluctuation (RDF). Our simulation work demonstrates not only the influence of the implantation parameters such as its dose, tilt angle, energy, and rotation angle on the RDF-induced VTH variability, but also the solution to reduce the effect of this variability. By adjusting the ion implantation parameters, the 3σ (VTH) is reduced from 43.8 mV to 28.9 mV. This 34% reduction is significant, considering that our technique is very cost effective and facilitates easy fabrication, increasing availability.

On the Semantics of SPARQL

NASA Astrophysics Data System (ADS)

Arenas, Marcelo; Gutierrez, Claudio; Pérez, Jorge

The Resource Description Framework (RDF) is the standard data model for representing information about World Wide Web resources. In January 2008, it was released the recommendation of the W3C for querying RDF data, a query language called SPARQL. In this chapter, we give a detailed description of the semantics of this language. We start by focusing on the definition of a formal semantics for the core part of SPARQL, and then move to the definition for the entire language, including all the features in the specification of SPARQL by the W3C such as blank nodes in graph patterns and bag semantics for solutions.

Produce and Consume Linked Data with Drupal!

NASA Astrophysics Data System (ADS)

Corlosquet, Stéphane; Delbru, Renaud; Clark, Tim; Polleres, Axel; Decker, Stefan

Currently a large number of Web sites are driven by Content Management Systems (CMS) which manage textual and multimedia content but also - inherently - carry valuable information about a site's structure and content model. Exposing this structured information to the Web of Data has so far required considerable expertise in RDF and OWL modelling and additional programming effort. In this paper we tackle one of the most popular CMS: Drupal. We enable site administrators to export their site content model and data to the Web of Data without requiring extensive knowledge on Semantic Web technologies. Our modules create RDFa annotations and - optionally - a SPARQL endpoint for any Drupal site out of the box. Likewise, we add the means to map the site data to existing ontologies on the Web with a search interface to find commonly used ontology terms. We also allow a Drupal site administrator to include existing RDF data from remote SPARQL endpoints on the Web in the site. When brought together, these features allow networked RDF Drupal sites that reuse and enrich Linked Data. We finally discuss the adoption of our modules and report on a use case in the biomedical field and the current status of its deployment.

M ξ, M αβ, M γ and M m X-ray production cross-sections for elements with 71⩽ z⩽92 at 5.96 keV photon energy

NASA Astrophysics Data System (ADS)

Sharma, Manju; Sharma, Veena; Kumar, Sanjeev; Puri, S.; Singh, Nirmal

2006-11-01

The M ξ, M αβ, M γ and M m X-ray production (XRP) cross-sections have been measured for the elements with 71⩽ Z⩽92 at 5.96 keV incident photon energy satisfying EM1< Einc< EL3, where EM1(L3) is the M 1(L 3) subshell binding energy. These XRP cross-sections have been calculated using photoionization cross-sections based on the relativistic Dirac-Hartree-Slater (RDHS) model with three sets of X-ray emission rates, fluorescence, Coster-Kronig and super Coster-Kronig yields based on (i) the non-relativistic Hartree-Slater (NRHS) potential model, (ii) the RDHS model and (iii) the relativistic Dirac-Fock (RDF) model. For the third set, the M i ( i=1-5) subshell fluorescence yields have been calculated using the RDF model-based X-ray emission rates and total widths reevaluated to incorporate the RDF model-based radiative widths. The measured cross-sections have been compared with the calculated values to check the applicability of the physical parameters based on different models.

Supramolecular architecture of 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole.3H2O: Synthesis, spectroscopic investigations, DFT computation, MD simulations and docking studies

NASA Astrophysics Data System (ADS)

Murthy, P. Krishna; Smitha, M.; Sheena Mary, Y.; Armaković, Stevan; Armaković, Sanja J.; Rao, R. Sreenivasa; Suchetan, P. A.; Giri, L.; Pavithran, Rani; Van Alsenoy, C.

2017-12-01

Crystal and molecular structure of newly synthesized compound 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole (BMMBI) has been authenticated by single crystal X-ray diffraction, FT-IR, FT-Raman, 1H NMR, 13C NMR and UV-Visible spectroscopic techniques; compile both experimental and theoretical results which are performed by DFT/B3LYP/6-311++G(d,p) method at ground state in gas phase. Visualize nature and type of intermolecular interactions and crucial role of these interactions in supra-molecular architecture has been investigated by use of a set of graphical tools 3D-Hirshfeld surfaces and 2D-fingerprint plots analysis. The title compound stabilized by strong intermolecular hydrogen bonds N⋯Hsbnd O and O⋯Hsbnd O, which are envisaged by dark red spots on dnorm mapped surfaces and weak Br⋯Br contacts envisaged by red spot on dnorm mapped surface. The detailed fundamental vibrational assignments of wavenumbers were aid by with help of Potential Energy distribution (PED) analysis by using GAR2PED program and shows good agreement with experimental values. Besides frontier orbitals analysis, global reactivity descriptors, natural bond orbitals and Mullikan charges analysis were performed by same basic set at ground state in gas phase. Potential reactive sites of the title compound have been identified by ALIE, Fukui functions and MEP, which are mapped to the electron density surfaces. Stability of BMMBI have been investigated from autoxidation process and pronounced interaction with water (hydrolysis) by using bond dissociation energies (BDE) and radial distribution functions (RDF), respectively after MD simulations. In order to identify molecule's most important reactive spots we have used a combination of DFT calculations and MD simulations. Reactivity study encompassed calculations of a set of quantities such as: HOMO-LUMO gap, MEP and ALIE surfaces, Fukui functions, bond dissociation energies and radial distribution functions. To confirm the potential of title molecule in the area of pharmaceutics, we have also calculated a series of drug likeness parameters. Possibly important biological activity of BMMBI molecule was also confirmed by molecular docking study.

Tunable gas adsorption in graphene oxide framework

NASA Astrophysics Data System (ADS)

Razmkhah, Mohammad; Moosavi, Fatemeh; Taghi Hamed Mosavian, Mohammad; Ahmadpour, Ali

2018-06-01

Effect of length of linker inter-space was studied on the adsorption capacity of CO2 by graphene oxide framework (GOF). Effect of linker inter-space of 14, 11, and 8 Å was studied here. The linker inter-space of 11 Å showed the highest CO2 adsorption capacity. A dual-site Langmuir model was observed for adsorption of CO2 and CH4 into the GOF. According to radial distribution function (RDF), facial and central atoms of linker are the dual-site predicted by Langmuir model. Two distinguishable sites of adsorption and parallel orientation of CO2 are the main reasons of high adsorption capacity in 11 Å linker inter-space. Gas-adsorbent affinity obtains the orientation of CO2 near the linker. The affinity in the 11 Å linker inter-space is the highest. Thus, it forces the CO2 to lay parallel and orient more localized than the other GOFs. In addition, CH4 resulted higher working capacity than CO2 in 14 Å. This occurs because of the change in gas-adsorbent affinity by changing pressure. An entrance adsorption occurs out of the pore of the GOF. This adsorption is not as stable as deep adsorption.

Molecular dynamic simulations on TKX-50/RDX cocrystal.

PubMed

Xiong, Shuling; Chen, Shusen; Jin, Shaohua

2017-06-01

Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) is a newly synthesized energetic material with excellent comprehensive properties. Cyclotrimethylenetrinitramine (RDX) is currently one of the most widely used energetic materials in the world. TKX-50 and RDX supercell models and TKX-50/RDX cocrystal model were constructed based on their crystal cell parameters and the formation mechanism of cocrystal, respectively, then they were simulated by molecular dynamics (MD) simulations. The maximum trigger bond (NNO 2 ) length(L max ), binding energy (E bind ), radial distribution function (RDF), cohesive energy density(CED) and mechanical properties were simulated at different temperatures based on the simulated equilibrium structures of the models. The simulated results indicate that hydrogen bond and van der Waals force interactions exist in the cocrystal system and the hydrogen bonds are mainly derived from the hydrogen atom of TKX-50 with the oxygen or nitrogen atom of RDX. Moreover, TKX-50/RDX cocrystal structure significantly reduces the sensitivity and improves the thermodynamic stability of RDX, and it also shows better mechanical properties than pure TKX-50 and RDX, indicating that it will vastly expand the application scope of the single compound explosives. Copyright © 2017 Elsevier Inc. All rights reserved.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100-x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-03-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

X-ray characterization of indium during melting

NASA Astrophysics Data System (ADS)

Gondi, P.; Montanari, R.; Costanza, G.

During melting of Indium the structure of solid and liquid phases have been investigated by X-ray diffractometry (XRD) in 1-g conditions. At the melting point T M a re-orientation of crystalline grains occurs in the solid phase. The texture change, unusually rapid for a thermally activated process, is attributed to an abnormal increase of vacancy concentration. This explanation is in agreement with the observed shifts of XRD peaks towards lower angles. As a consequence of the texture change, the lattice planes facing the first formed liquid are (002) and (101) planes, i.e. those planes allocating 1st and 2nd neighbours around a given atom with shell radii very close to the mean distance of nearest neighbours in liquid as obtained from the radial distribution function (RDF). Convective motions in the liquid can be eliminated by repeating the same XRD measurements in μ-g. To get the best experimental conditions it is discussed the possibility to use thin oxide films grown on the external surface of samples as containers during melting. This technique was already successfully tested by present investigators in the experiment ES 311 A-B carried out during the mission SPACELAB-1.

Atomic Scale Investigation of Structural Properties and Glass Forming Ability of Ti100- x Al x Metallic Glasses

NASA Astrophysics Data System (ADS)

Tahiri, M.; Hasnaoui, A.; Sbiaai, K.

2018-06-01

In this work, we employed molecular dynamics (MD) simulations to study Ti-Al metallic glasses (MGs) using the embedded atom method (EAM) potential to model the atomic interaction with different compositions. The results showed evidence of the metallic glass formation induced by the split occurring in the second peak of the radial distribution function (RDF) curves implying both Ti and Al atoms. The common neighbor analysis (CNA) method confirmed the presence of the icosahedral clusters with a maximum amount observed for an alloy with 75 pct of Al. Analysis of coordination numbers (CNs) indicated that the total CNs are nearly unchanged in these systems. Finally, Voronoi tessellation analyses (VTA) showed a higher value of the number of icosahedral units at Ti25Al75 composition. This specific composition represents a nearby peritectic point localized at a low melting point in the Ti-Al binary phase diagram. The glass forming ability (GFA) becomes important when the fraction of Al increases by forming and connecting "icosahedral-like" clusters (12-coordinated <0, 0, 12, 0> and 13-coordinated <0, 1, 10, 2>) and by playing a main role in the structure stability of the Ti-Al MGs.

Quantifying Dimer and Trimer Formation by Tri- n -butyl Phosphates in n -Dodecane: Molecular Dynamics Simulations

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

Vo, Quynh N.; Dang, Liem X.; Nilsson, Mikael

2016-07-21

Tri-n-butyl phosphate (TBP), a representative of neutral organophosphorous ligands, is an important extractant used in solvent extraction process for the recovery of uranium and plutonium from spent nuclear fuel. Microscopic pictures of TBP isomerism and its behavior in n-dodecane diluent were investigated utilizing MD simulations with previously optimized force field parameters for TBP and n-dodecane. Potential Mean Force (PMF) calculations on a single TBP molecule show seven probable TBP isomers. Radial Distribution Functions (RDF) of TBP suggests the existence of TBP trimers at high TBP concentrations in addition to dimers. 2D PMF calculations were performed to determine the angle andmore » distance criteria for TBP trimers. The dimerization and trimerization constants of TBP in n-dodecane were obtained and match our own experimental values using FTIR technique. The new insights into the conformational behaviors of TBP molecule as a monomer and as part of an aggregate could greatly aid the understanding of the complexation between TBP and metal ions in solvent extraction system. The U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences funded the work performed by LXD.« less

Beyond 10 Years of Evolving the IGSN Architecture: What's Next?

NASA Astrophysics Data System (ADS)

Lehnert, K.; Arko, R. A.

2016-12-01

The IGSN was developed as part of a US NSF-funded project, which started in 2004 to establish a registry for sample metadata, the System for Earth Sample Registration (SESAR). The initial version of the system provided a centralized solution for users to submit information about their samples and obtain IGSNs and bar codes. A new distributed architecture for the IGSN was designed at a workshop in 2011 that aimed to advance the global implementation of the IGSN. The workshop led to the founding of an international non-profit organization, the IGSN e.V., that adopted the governance model of the DataCite consortium as a non-profit membership organization and its architecture with a central registry and a network of distributed Allocating Agents that provide registration services to the users. Recent progress came at a workshop in 2015, where stakeholders from both geoscience and life science disciplines drafted a standard IGSN metadata schema for describing samples with an essential set of properties about the sample's origin and classification, creating a "birth certificate" for the sample. Consensus was reached that the IGSN should also be used to identify sampling features and collection of samples. The IGSN e.V. global network has steadily grown, with now members in 4 continents and 5 Allocating Agents operational in the US, Australia, and Europe. A Central Catalog has been established at the IGSN Management Office that harvests "birth certificate" metadata records from Allocating Agents via the Open Archives Initiative Protocol for Metadata Harvest (OAI-PMH), and publishes them as a Linked Open Data graph using the Resource Description Framework (RDF) and RDF Query Language (SPARQL) for reuse by Semantic Web clients. Next developments will include a web-based validation service that allows journal editors to check the validity of IGSNs and compliance with metadata requirements, and use of community-recommended vocabularies for specific disciplines.

Insight into the reactive properties of newly synthesized 1,2,4-triazole derivative by combined experimental (FT-IR and FR-Raman) and theoretical (DFT and MD) study

NASA Astrophysics Data System (ADS)

Mary, Y. Sheena; Al-Omary, Fatmah A. M.; Mostafa, Gamal A. E.; El-Emam, Ali A.; Manjula, P. S.; Sarojini, B. K.; Narayana, B.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.

2017-08-01

The vibrational spectral analysis has been carried out on 4-[(E)-(4-hydroxybenzylidene)amino]-3-methyl-1H-1,2,4-triazole-5(4H)-thione (HBAMTT) in order explore the chemical and pharmacological properties. The most important reactive sites have been identified employing molecular electrostatic potential map. Nonlinear optical properties are identified and the first hyperpolarizability is 80.35 times that of urea, which is standard NLO material. The molecular activity is studied from the dislocation of the frontier molecular orbitals and NBO analysis is carried to gain an insight into the charge transfer within the molecular system. Using molecular electrostatic potential map, the electrophilic and nucleophilic sites are identified. Title molecule was further investigated from the aspect of local reactivity properties by calculations of average local ionization energies (ALIE) and Fukui functions. Vulnerability towards autoxidation and hydrolysis mechanisms has been assessed thanks to the calculations of bond dissociation energies (BDE) and radial distribution functions (RDF), respectively. This information was also valuable for the initial investigation of degradation properties of the title molecule. Thanks to the molecular docking studies, it can be concluded that docked ligand forms a stable complex with AChE and could be used as a new drug for the Alzheimer's disease, myasthenia gravis and glaucoma.

Rapid Capability Fielding Toolbox Study

DTIC Science & Technology

2010-03-01

templates derived from best  practices.  The Object Management Group (OMG) is incorporating emerging standards for W3C, SysML, RDF, OWL,  and  BPMN ...capabilities to the  warfighter. 33  Glossary  Acronyms    BPMN   Business Process Modeling Notation  CAD  Computer‐Aided Design  CAE  Computer‐Aided...deployed  on  standards‐based  run‐time  environments.    The  trend  is  that  the  emerging  standards  for  W3C,  SysML,  RDF,  OWL,  and  BPMN   are

X ray absorption fine structure of systems in the anharmonic limit

NASA Astrophysics Data System (ADS)

Mustredeleon, J.; Conradson, S. D.; Batistic, I.; Bishop, A. R.; Raistrick, I.; Jackson, W. E.; Brown, G. E.

A new approach to the analysis of x-ray absorption fine structure (XAFS) data is presented. It is based on the use of radial distribution functions directly calculated from a single-particle ion Hamiltonian containing model potentials. The starting point of this approach is the statistical average of the XAFS for an atomic pair. This average can be computed using a radial distribution function (RDF), which can be expressed in terms of the eigenvalues and wavefunctions associated with the model potential. The pair potential describing the ionic motion is then expressed in terms of parameters that are determined by fitting this statistical average to the experimental XAFS spectrum. This approach allows the use of XAFS as a tool for mapping near-neighbor interatomic potentials, and allows the treatment of systems which exhibit strongly anharmonic potentials which can be treated by perturbative methods. Using this method we have analyzed the high temperature behavior of the oxygen contributions to the Fe K-edge XAFS in the ferrosilicate minerals andradite (Ca3Fe2Si3O12) and magnesiowustite (Mg(0.9)Fe(0.1)O). Using a temperature dependent anharmonic correction derived from these model compounds, we have found evidence for a local structural change in the Fe-O coordination environment upon melting of the geologically important mineral fayalite (Fe2SiO4). We have also employed this method to the study of the axial oxygen contributions to the polarized Cu K-edge XAFS on oriented samples of YBa2Cu3O7 and related compounds. From this study we find evidence for an axial oxygen-centered lattice distortion accompanying the superconducting phase transition and a correlation between this distortion and Tc. The relation of the observed lattice distortion to mechanisms of superconductivity is discussed.

Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe

PubMed Central

Haley, Joshua A.; Stark, W. Marshall

2016-01-01

ABSTRACT Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In Streptomyces, most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here, we present the genome of a new Streptomyces phage, ϕJoe, and investigate the conditions for integration and excision of the ϕJoe genome. ϕJoe belongs to the largest Streptomyces phage cluster (R4-like) and encodes a serine integrase. The attB site from Streptomyces venezuelae was used efficiently by an integrating plasmid, pCMF92, constructed using the ϕJoe int-attP locus. The attB site for ϕJoe integrase was occupied in several Streptomyces genomes, including that of S. coelicolor, by a mobile element that varies in gene content and size between host species. Serine integrases require a phage-encoded recombination directionality factor (RDF) to activate the excision reaction. The ϕJoe RDF was identified, and its function was confirmed in vivo. Both the integrase and RDF were active in in vitro recombination assays. The ϕJoe site-specific recombination system is likely to be an important addition to the synthetic biology and genome engineering toolbox. IMPORTANCE Streptomyces spp. are prolific producers of secondary metabolites, including many clinically useful antibiotics. Bacteriophage-derived integrases are important tools for genetic engineering, as they enable integration of heterologous DNA into the Streptomyces chromosome with ease and high efficiency. Recently, researchers have been applying phage integrases for a variety of applications in synthetic biology, including rapid assembly of novel combinations of genes, biosensors, and biocomputing. An important requirement for optimal experimental design and predictability when using integrases, however, is the need for multiple enzymes with different specificities for their integration sites. In order to provide a broad platform of integrases, we identified and validated the integrase from a newly isolated Streptomyces phage, ϕJoe. ϕJoe integrase is active in vitro and in vivo. The specific recognition site for integration is present in a wide range of different actinobacteria, including Streptomyces venezuelae, an emerging model bacterium in Streptomyces research. PMID:28003200

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

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

Hasan, S. M. Shamimul; Fox, Edward A.; Bisset, Keith

Computational epidemiology seeks to develop computational methods to study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. Recent advances in computing and data sciences have led to the development of innovative modeling environments to support this important goal. The datasets used to drive the dynamic models as well as the data produced by these models presents unique challenges owing to their size, heterogeneity and diversity. These datasets form the basis of effective and easy to use decision support and analytical environments. Asmore » a result, it is important to develop scalable data management systems to store, manage and integrate these datasets. In this paper, we develop EpiK—a knowledge base that facilitates the development of decision support and analytical environments to support epidemic science. An important goal is to develop a framework that links the input as well as output datasets to facilitate effective spatio-temporal and social reasoning that is critical in planning and intervention analysis before and during an epidemic. The data management framework links modeling workflow data and its metadata using a controlled vocabulary. The metadata captures information about storage, the mapping between the linked model and the physical layout, and relationships to support services. EpiK is designed to support agent-based modeling and analytics frameworks—aggregate models can be seen as special cases and are thus supported. We use semantic web technologies to create a representation of the datasets that encapsulates both the location and the schema heterogeneity. The choice of RDF as a representation language is motivated by the diversity and growth of the datasets that need to be integrated. A query bank is developed—the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks. The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK. EpiK can hide schema and location heterogeneity while efficiently supporting queries that span the computational epidemiology modeling pipeline: from model construction to simulation output. As a result, we show that the performance of benchmark queries varies significantly with respect to the choice of hardware underlying the database and resource description framework (RDF) engine.« less

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

DOE PAGES

Hasan, S. M. Shamimul; Fox, Edward A.; Bisset, Keith; ...

2017-11-06

Computational epidemiology seeks to develop computational methods to study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. Recent advances in computing and data sciences have led to the development of innovative modeling environments to support this important goal. The datasets used to drive the dynamic models as well as the data produced by these models presents unique challenges owing to their size, heterogeneity and diversity. These datasets form the basis of effective and easy to use decision support and analytical environments. Asmore » a result, it is important to develop scalable data management systems to store, manage and integrate these datasets. In this paper, we develop EpiK—a knowledge base that facilitates the development of decision support and analytical environments to support epidemic science. An important goal is to develop a framework that links the input as well as output datasets to facilitate effective spatio-temporal and social reasoning that is critical in planning and intervention analysis before and during an epidemic. The data management framework links modeling workflow data and its metadata using a controlled vocabulary. The metadata captures information about storage, the mapping between the linked model and the physical layout, and relationships to support services. EpiK is designed to support agent-based modeling and analytics frameworks—aggregate models can be seen as special cases and are thus supported. We use semantic web technologies to create a representation of the datasets that encapsulates both the location and the schema heterogeneity. The choice of RDF as a representation language is motivated by the diversity and growth of the datasets that need to be integrated. A query bank is developed—the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks. The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK. EpiK can hide schema and location heterogeneity while efficiently supporting queries that span the computational epidemiology modeling pipeline: from model construction to simulation output. As a result, we show that the performance of benchmark queries varies significantly with respect to the choice of hardware underlying the database and resource description framework (RDF) engine.« less

Semantic Web repositories for genomics data using the eXframe platform.

PubMed

Merrill, Emily; Corlosquet, Stéphane; Ciccarese, Paolo; Clark, Tim; Das, Sudeshna

2014-01-01

With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge.

Nonlinear Saturable and Polarization-induced Absorption of Rhenium Disulfide

PubMed Central

Cui, Yudong; Lu, Feifei; Liu, Xueming

2017-01-01

Monolayer of transition metal dichalcogenides (TMDs), with lamellar structure as that of graphene, has attracted significant attentions in optoelectronics and photonics. Here, we focus on the optical absorption response of a new member TMDs, rhenium disulphide (ReS2) whose monolayer and bulk forms have the nearly identical band structures. The nonlinear saturable and polarization-induced absorption of ReS2 are investigated at near-infrared communication band beyond its bandgap. It is found that the ReS2-covered D-shaped fiber (RDF) displays the remarkable polarization-induced absorption, which indicates the different responses for transverse electric (TE) and transverse magnetic (TM) polarizations relative to ReS2 plane. Nonlinear saturable absorption of RDF exhibits the similar saturable fluence of several tens of μJ/cm2 and modulation depth of about 1% for ultrafast pulses with two orthogonal polarizations. RDF is utilized as a saturable absorber to achieve self-started mode-locking operation in an Er-doped fiber laser. The results broaden the operation wavelength of ReS2 from visible light to around 1550 nm, and numerous applications may benefit from the anisotropic and nonlinear absorption characteristics of ReS2, such as in-line optical polarizers, high-power pulsed lasers, and optical communication system. PMID:28053313

Histological evaluation of direct pulp capping of rat pulp with experimentally developed low-viscosity adhesives containing reparative dentin-promoting agents.

PubMed

Suzuki, Masaya; Taira, Yoshihisa; Kato, Chikage; Shinkai, Koichi; Katoh, Yoshiroh

2016-01-01

This study examines the wound healing process in exposed rat pulp when capped with experimental adhesive resin systems. Experimental adhesive resin system for direct pulp capping was composed of primer-I (PI), -II (PII), and -III (PIII) and an experimental bonding agent (EBA). PI was Clearfil(®) SE Bond(®)/Primer (CSP) containing 5.0 wt% CaCl2, PII was PI containing 10 wt% nanofiller (Aerosil(®) 380), and PIII was CSP containing 5.0 wt% of compounds of equal moles of synthetic peptides (pA and pB) derived from dentin matrix protein 1. EBA was Clearfil(®) SE Bond(®)/Bond (CSB) containing 10 wt% hydroxyapatite powders. Three experimental groups were designed. PI was assigned to experimental Groups 1 and 3. PII was assigned to experimental Groups 2 and 3. PIII and EBA were assigned to all experimental adhesive groups. Control teeth were capped with calcium hydroxide preparation (Dycal(®)), and CSP and CSB were applied to the cavity. The rats were sacrificed after each observation period (14, 28, 56, and 112 days). The following parameters were evaluated: pulp tissue disorganization, inflammatory cell infiltration, reparative dentin formation (RDF), and bacterial penetration. There were no significant differences among all the groups for all parameters and all observation periods (p>0.05, Kruskal-Wallis test). All groups showed initial RDF at 14 days postoperatively and extensive RDF until 112 days postoperatively. Groups 2 and 3 demonstrated higher quantity of mineralized dentin bridge formation compared with Group 1. Addition of nanofillers to the primer was effective in promoting high-density RDF. Experimentally developed adhesive resin systems induce the exposed pulp to produce almost the same quantity of reparative dentin as calcium hydroxide. However, we need further studies to elucidate whether the same results could be obtained in humans. Copyright © 2015 Elsevier Ltd. All rights reserved.

Publishing Data on Physical Samples Using the GeoLink Ontology and Linked Data Platforms

NASA Astrophysics Data System (ADS)

Ji, P.; Arko, R. A.; Lehnert, K. A.; Song, L.; Carter, M. R.; Hsu, L.

2015-12-01

Interdisciplinary Earth Data Alliance (IEDA), one of partners in EarthCube GeoLink project, seeks to explore the extent to which the use of GeoLink reusable Ontology Design Patterns (ODPs) and linked data platforms in IEDA data infrastructure can make research data more easily accessible and valuable. Linked data for the System for Earth Sample Registration (SESAR) is the first effort of IEDA to show how linked data enhance the presentation of IEDA data system architecture. SESAR Linked Data maps each table and column in SESAR database to RDF class and property based on GeoLink view, which build on the top of GeoLink ODPs. Then, uses D2RQ dumping the contents of SESAR database into RDF triples on the basis of mapping results. And, the dumped RDF triples is loaded into GRAPHDB, an RDF graph database, as permanent data in the form of atomic facts expressed as subjects, predicates and objects which provide support for semantic interoperability between IEDA and other GeoLink partners. Finally, an integrated browsing and searching interface build on Callimachus, a highly scalable platform for publishing linked data, is introduced to make sense of data stored in triplestore. Drill down and through features are built in the interface to help users locating content efficiently. The drill down feature enables users to explore beyond the summary information in the instance list of a specific class and into the detail from the specific instance page. The drill through feature enables users to jump from one instance to another one by simply clicking the link of the latter nested in the former region. Additionally, OpenLayers map is embedded into the interface to enhance the attractiveness of the presentation of instance which has geospatial information. Furthermore, by linking instances in the SESAR datasets to matching or corresponding instances in external sets, the presentation has been enriched with additional information about related classes like person, cruise, etc.

Design and validation of a German version of the GSRS-IBS - an analysis of its psychometric quality and factorial structure.

PubMed

Schäfer, Sarah K; Weidner, Kathrin Julia; Hoppner, Jorge; Becker, Nicolas; Friedrich, Dana; Stokes, Caroline S; Lammert, Frank; Köllner, Volker

2017-12-04

Currently, a suitable questionnaire in German language is not available to monitor the progression and evaluate the severity of irritable bowel syndrome (IBS). Therefore, this study aimed to translate the Gastrointestinal Symptom Rating Scale for Irritable Bowel Syndrome (GSRS-IBS) into German and to evaluate its psychometric qualities and factorial structure. This study is based on a total sample of 372 participants [62.6% female, mean age = 41 years (SD = 17 years)]. 17.5% of the participants had a diagnosis of IBS, 19.9% were receiving treatment for chronic inflammatory bowel disease, 12.1% of the participants were recruited from a psychosomatic clinic, and 50.5% belonged to a control group. All participants completed the German version of GSRS-IBS (called Reizdarm-Fragebogen, RDF), as well as the Gießen Subjective Complaints List (GBB-24) and the Hospital Anxiety and Depression Scale - German version (HADS-D). The internal consistency of the RDF total scale was at least satisfactory in all subsamples (Cronbach's Alpha between .77 and .92), and for all subscales (Cronbach's Alpha between .79 and .91). The item difficulties (between .25 and .73) and the item-total correlations (between .48 and .83) were equally satisfactory. Principal axis analysis revealed a four-factorial structure of the RDF items, which mainly resembled the structure of the English original. Convergent validity was established based on substantial and significant correlations with the stomach-complaint scale of the GBB-24 (r = .71; p < .01) and the anxiety (r = .42; p < .01) and depression scales (r = .43; p < .01) of the HADS-D. The German version of the GSRS-IBS RDF proves to be an effective, reliable, and valid questionnaire for the assessment of symptom severity in IBS, which can be used in clinical practice as well as in clinical studies.

Macromolecule simulation and CH4 adsorption mechanism of coal vitrinite

NASA Astrophysics Data System (ADS)

Yu, Song; Yan-ming, Zhu; Wu, Li

2017-02-01

The microscopic mechanism of interactions between CH4 and coal macromolecules is of significant practical and theoretical importance in CBM development and methane storage. Under periodic boundary conditions, the optimal energy configuration of coal vitrinite, which has a higher torsion degree and tighter arrangement, can be determined by the calculation of molecular mechanics (MM) and molecular dynamics (MD), and annealing kinetics simulation based on ultimate analysis, 13C NMR, FT IR and HRTEM. Macromolecular stabilization is primarily due to the van der Waals energy and covalent bond energy, mainly consisting of bond torsion energy and bond angle energy. Using the optimal configuration as the adsorbent, GCMC simulation of vitrinite adsorption of CH4 is conducted. A saturated state is reached after absorbing 17 CH4s per coal vitrinite molecule. CH4 is preferentially adsorbed on the edge, and inclined to gathering around the branched chains of the inner vitrinite sites. Finally, the adsorption parameters are calculated through first principle DFT. The adsorbability order is as follows: aromatic structure> heteroatom rings > oxygen functional groups. The adsorption energy order is as follows: Top < Bond < Center, Up < Down. The order of average RDF better reflects the adsorption ability and that of [-COOH] is lower than those of [sbnd Cdbnd O] and [Csbnd Osbnd C]. CH4 distributed in the distance of 0.99-16 Å to functional groups in the type of monolayer adsorption and the average distance order manifest as [sbnd Cdbnd O] (1.64 Å) < [Csbnd Osbnd C] (1.89 Å) < [sbnd COOH] (3.78 Å) < [-CH3] (4.11 Å) according to the average RDF curves. CH4 enriches around [sbnd Cdbnd O] and [Csbnd O-C] whereas is rather dispersed about [-COOH] and [CH3]. Simulation and experiment data are both in strong agreement with the Langmuir and D-A isothermal adsorption model and the D-A model fit better than Langmuir model. Preferential adsorption sites and orientations in vitrinite are identical to those of graphite/graphene. However, the energy of the most preferential location is much lower than that of graphite/graphene. CH4 is more easily absorbed on the surface of vitrinite. Adsorbability varies considerably at different adsorption locations and sites on the surface of vitrinite. Crystal parameter of vitrinite is a = b = c = 15.8 Å and majority of its micropores are blow 15.8 Å, indicating that the vitrinite have the optimum adsorption aperture. It can explain its higher observed adsorption capacities for CH4 compared with graphite/graphene.

Synthesis and quantitative structure-activity relationship (QSAR) study of novel isoxazoline and oxime derivatives of podophyllotoxin as insecticidal agents.

PubMed

Wang, Yi; Shao, Yonghua; Wang, Yangyang; Fan, Lingling; Yu, Xiang; Zhi, Xiaoyan; Yang, Chun; Qu, Huan; Yao, Xiaojun; Xu, Hui

2012-08-29

In continuation of our program aimed at the discovery and development of natural-product-based insecticidal agents, 33 isoxazoline and oxime derivatives of podophyllotoxin modified in the C and D rings were synthesized and their structures were characterized by Proton nuclear magnetic resonance ((1)H NMR), high-resolution mass spectrometry (HRMS), electrospray ionization-mass spectrometry (ESI-MS), optical rotation, melting point (mp), and infrared (IR) spectroscopy. The stereochemical configurations of compounds 5e, 5f, and 9f were unambiguously determined by X-ray crystallography. Their insecticidal activity was evaluated against the pre-third-instar larvae of northern armyworm, Mythimna separata (Walker), in vivo. Compounds 5e, 9c, 11g, and 11h especially exhibited more promising insecticidal activity than toosendanin, a commercial botanical insecticide extracted from Melia azedarach . A genetic algorithm combined with multiple linear regression (GA-MLR) calculation is performed by the MOBY DIGS package. Five selected descriptors are as follows: one two-dimensional (2D) autocorrelation descriptor (GATS4e), one edge adjacency indice (EEig06x), one RDF descriptor (RDF080v), one three-dimensional (3D) MoRSE descriptor (Mor09v), and one atom-centered fragment (H-052) descriptor. Quantitative structure-activity relationship studies demonstrated that the insecticidal activity of these compounds was mainly influenced by many factors, such as electronic distribution, steric factors, etc. For this model, the standard deviation error in prediction (SDEP) is 0.0592, the correlation coefficient (R(2)) is 0.861, and the leave-one-out cross-validation correlation coefficient (Q(2)loo) is 0.797.

Information Model Translation to Support a Wider Science Community

NASA Astrophysics Data System (ADS)

Hughes, John S.; Crichton, Daniel; Ritschel, Bernd; Hardman, Sean; Joyner, Ronald

2014-05-01

The Planetary Data System (PDS), NASA's long-term archive for solar system exploration data, has just released PDS4, a modernization of the PDS architecture, data standards, and technical infrastructure. This next generation system positions the PDS to meet the demands of the coming decade, including big data, international cooperation, distributed nodes, and multiple ways of analysing and interpreting data. It also addresses three fundamental project goals: providing more efficient data delivery by data providers to the PDS, enabling a stable, long-term usable planetary science data archive, and enabling services for the data consumer to find, access, and use the data they require in contemporary data formats. The PDS4 information architecture is used to describe all PDS data using a common model. Captured in an ontology modeling tool it supports a hierarchy of data dictionaries built to the ISO/IEC 11179 standard and is designed to increase flexibility, enable complex searches at the product level, and to promote interoperability that facilitates data sharing both nationally and internationally. A PDS4 information architecture design requirement stipulates that the content of the information model must be translatable to external data definition languages such as XML Schema, XMI/XML, and RDF/XML. To support the semantic Web standards we are now in the process of mapping the contents into RDF/XML to support SPARQL capable databases. We are also building a terminological ontology to support virtually unified data retrieval and access. This paper will provide an overview of the PDS4 information architecture focusing on its domain information model and how the translation and mapping are being accomplished.

PharmARTS: terminology web services for drug safety data coding and retrieval.

PubMed

Alecu, Iulian; Bousquet, Cédric; Degoulet, Patrice; Jaulent, Marie-Christine

2007-01-01

MedDRA and WHO-ART are the terminologies used to encode drug safety reports. The standardisation achieved with these terminologies facilitates: 1) The sharing of safety databases; 2) Data mining for the continuous reassessment of benefit-risk ratio at national or international level or in the pharmaceutical industry. There is some debate about the capacity of these terminologies for retrieving case reports related to similar medical conditions. We have developed a resource that allows grouping similar medical conditions more effectively than WHO-ART and MedDRA. We describe here a software tool facilitating the use of this terminological resource thanks to an RDF framework with support for RDF Schema inferencing and querying. This tool eases coding and data retrieval in drug safety.

A linked GeoData map for enabling information access

USGS Publications Warehouse

Powell, Logan J.; Varanka, Dalia E.

2018-01-10

OverviewThe Geospatial Semantic Web (GSW) is an emerging technology that uses the Internet for more effective knowledge engineering and information extraction. Among the aims of the GSW are to structure the semantic specifications of data to reduce ambiguity and to link those data more efficiently. The data are stored as triples, the basic data unit in graph databases, which are similar to the vector data model of geographic information systems (GIS); that is, a node-edge-node model that forms a graph of semantically related information. The GSW is supported by emerging technologies such as linked geospatial data, described below, that enable it to store and manage geographical data that require new cartographic methods for visualization. This report describes a map that can interact with linked geospatial data using a simulation of a data query approach called the browsable graph to find information that is semantically related to a subject of interest, visualized using the Data Driven Documents (D3) library. Such a semantically enabled map functions as a map knowledge base (MKB) (Varanka and Usery, 2017).A MKB differs from a database in an important way. The central element of a triple, alternatively called the edge or property, is composed of a logic formalization that structures the relation between the first and third parts, the nodes or objects. Node-edge-node represents the graphic form of the triple, and the subject-property-object terms represent the data structure. Object classes connect to build a federated graph, similar to a network in visual form. Because the triple property is a logical statement (a predicate), the data graph represents logical propositions or assertions accepted to be true about the subject matter. These logical formalizations can be manipulated to calculate new triples, representing inferred logical assertions, from the existing data.To demonstrate a MKB system, a technical proof-of-concept is developed that uses geographically attributed Resource Description Framework (RDF) serializations of linked data for mapping. The proof-of-concept focuses on accessing triple data from visual elements of a geographic map as the interface to the MKB. The map interface is embedded with other essential functions such as SPARQL Protocol and RDF Query Language (SPARQL) data query endpoint services and reasoning capabilities of Apache Marmotta (Apache Software Foundation, 2017). An RDF database of the Geographic Names Information System (GNIS), which contains official names of domestic feature in the United States, was linked to a county data layer from The National Map of the U.S. Geological Survey. The county data are part of a broader Government Units theme offered to the public as Esri shapefiles. The shapefile used to draw the map itself was converted to a geographic-oriented JavaScript Object Notation (JSON) (GeoJSON) format and linked through various properties with a linked geodata version of the GNIS database called “GNIS–LD” (Butler and others, 2016; B. Regalia and others, University of California-Santa Barbara, written commun., 2017). The GNIS–LD files originated in Terse RDF Triple Language (Turtle) format but were converted to a JSON format specialized in linked data, “JSON–LD” (Beckett and Berners-Lee, 2011; Sorny and others, 2014). The GNIS–LD database is composed of roughly three predominant triple data graphs: Features, Names, and History. The graphs include a set of namespace prefixes used by each of the attributes. Predefining the prefixes made the conversion to the JSON–LD format simple to complete because Turtle and JSON–LD are variant specifications of the basic RDF concept.To convert a shapefile into GeoJSON format to capture the geospatial coordinate geometry objects, an online converter, Mapshaper, was used (Bloch, 2013). To convert the Turtle files, a custom converter written in Java reconstructs the files by parsing each grouping of attributes belonging to one subject and pasting the data into a new file that follows the syntax of JSON–LD. Additionally, the Features file contained its own set of geometries, which was exported into a separate JSON–LD file along with its elevation value to form a fourth file, named “features-geo.json.” Extracted data from external files can be represented in HyperText Markup Language (HTML) path objects. The goal was to import multiple JSON–LD files using this approach.

Production, quality and quality assurance of Refuse Derived Fuels (RDFs).

PubMed

Sarc, R; Lorber, K E

2013-09-01

This contribution describes characterization, classification, production, application and quality assurance of Refuse Derived Fuels (RDFs) that are increasingly used in a wide range of co-incineration plants. It is shown in this paper, that the fuel-parameter, i.e. net calorific value [MJ/kg(OS)], particle size d(90) or d(95) [mm], impurities [w%], chlorine content [w%], sulfur content [w%], fluorine content [w%], ash content [w%], moisture [w%] and heavy metals content [mg/kg(DM)], can be preferentially used for the classification of different types of RDF applied for co-incineration and substitution of fossil-fuel in different industial sectors. Describing the external production of RDF by processing and confectioning of wastes as well as internal processing of waste at the incineration plant, a case study is reported on the application of RDF made out of different household waste fractions in a 120,000t/yr Waste to Energy (WtE) circulating fluidized bed (CFB) incinerator. For that purpose, delivered wastes, as well as incinerator feedstock material (i.e. after internal waste processing) are extensively investigated. Starting with elaboration of sampling plan in accordance with the relevant guidelines and standards, waste from different suppliers was sampled. Moreover, manual sorting analyses and chemical analyses were carried out. Finally, results of investigations are presented and discussed in the paper. Copyright © 2013 Elsevier Ltd. All rights reserved.

Semantic Web repositories for genomics data using the eXframe platform

PubMed Central

2014-01-01

Background With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. Methods To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Conclusions Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge. PMID:25093072

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

Ekmekcioglu, Mehmet, E-mail: meceng3584@yahoo.co; Kaya, Tolga; Kahraman, Cengiz

The use of fuzzy multiple criteria analysis (MCA) in solid waste management has the advantage of rendering subjective and implicit decision making more objective and analytical, with its ability to accommodate both quantitative and qualitative data. In this paper a modified fuzzy TOPSIS methodology is proposed for the selection of appropriate disposal method and site for municipal solid waste (MSW). Our method is superior to existing methods since it has capability of representing vague qualitative data and presenting all possible results with different degrees of membership. In the first stage of the proposed methodology, a set of criteria of cost,more » reliability, feasibility, pollution and emission levels, waste and energy recovery is optimized to determine the best MSW disposal method. Landfilling, composting, conventional incineration, and refuse-derived fuel (RDF) combustion are the alternatives considered. The weights of the selection criteria are determined by fuzzy pairwise comparison matrices of Analytic Hierarchy Process (AHP). It is found that RDF combustion is the best disposal method alternative for Istanbul. In the second stage, the same methodology is used to determine the optimum RDF combustion plant location using adjacent land use, climate, road access and cost as the criteria. The results of this study illustrate the importance of the weights on the various factors in deciding the optimized location, with the best site located in Catalca. A sensitivity analysis is also conducted to monitor how sensitive our model is to changes in the various criteria weights.« less

Generating and Executing Complex Natural Language Queries across Linked Data.

PubMed

Hamon, Thierry; Mougin, Fleur; Grabar, Natalia

2015-01-01

With the recent and intensive research in the biomedical area, the knowledge accumulated is disseminated through various knowledge bases. Links between these knowledge bases are needed in order to use them jointly. Linked Data, SPARQL language, and interfaces in Natural Language question-answering provide interesting solutions for querying such knowledge bases. We propose a method for translating natural language questions in SPARQL queries. We use Natural Language Processing tools, semantic resources, and the RDF triples description. The method is designed on 50 questions over 3 biomedical knowledge bases, and evaluated on 27 questions. It achieves 0.78 F-measure on the test set. The method for translating natural language questions into SPARQL queries is implemented as Perl module available at http://search.cpan.org/ thhamon/RDF-NLP-SPARQLQuery.

Introducing glycomics data into the Semantic Web

PubMed Central

2013-01-01

Background Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. Results In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as “proofs-of-concept” to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. Conclusions We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains. PMID:24280648

Introducing glycomics data into the Semantic Web.

PubMed

Aoki-Kinoshita, Kiyoko F; Bolleman, Jerven; Campbell, Matthew P; Kawano, Shin; Kim, Jin-Dong; Lütteke, Thomas; Matsubara, Masaaki; Okuda, Shujiro; Ranzinger, Rene; Sawaki, Hiromichi; Shikanai, Toshihide; Shinmachi, Daisuke; Suzuki, Yoshinori; Toukach, Philip; Yamada, Issaku; Packer, Nicolle H; Narimatsu, Hisashi

2013-11-26

Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as "switches" that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as "proofs-of-concept" to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains.

Analysis and Comparison with DNS of a Stochastic Model for the Relative Motion of High-Stokes-Number Particles in Isotropic Turbulence

NASA Astrophysics Data System (ADS)

Dhariwal, Rohit; Rani, Sarma; Koch, Donald

2015-11-01

In an earlier work, Rani, Dhariwal, and Koch (JFM, Vol. 756, 2014) developed an analytical closure for the diffusion current in the PDF transport equation describing the relative motion of high-Stokes-number particle pairs in isotropic turbulence. In this study, an improved closure was developed for the diffusion coefficient, such that the motion of the particle-pair center of mass is taken into account. Using the earlier and the new analytical closures, Langevin simulations of pair relative motion were performed for four particle Stokes numbers, Stη = 10 , 20 , 40 , 80 and at two Taylor micro-scale Reynolds numbers Reλ = 76 , 131 . Detailed comparisons of the analytical model predictions with those of DNS were undertaken. It is seen that the pair relative motion statistics obtained from the improved theory show excellent agreement with the DNS statistics. The radial distribution functions (RDFs), and relative velocity PDFs obtained from the improved-closure-based Langevin simulations are found to be in very good agreement with those from DNS. It was found that the RDFs and relative velocity RMS increased with Reλ for all Stη . The collision kernel also increased strongly with Reλ , since it depended on the RDF and the radial relative velocities.

Effect of total and pair configurational entropy in determining dynamics of supercooled liquids over a range of densities

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

Banerjee, Atreyee; Nandi, Manoj Kumar; Bhattacharyya, Sarika Maitra, E-mail: mb.sarika@ncl.res.in

2016-07-21

In this paper, we present a study of supercooled liquids interacting with the Lennard Jones potential and the corresponding purely repulsive (Weeks-Chandler-Andersen) potential, over a range of densities and temperatures, in order to understand the origin of their different dynamics in spite of their structures being similar. Using the configurational entropy as the thermodynamic marker via the Adam Gibbs relation, we show that the difference in the dynamics of these two systems at low temperatures can be explained from thermodynamics. At higher densities both the thermodynamical and dynamical difference between these model systems decrease, which is quantitatively demonstrated in thismore » paper by calculating different parameters. The study also reveals the origin of the difference in pair entropy despite the similarity in the structure. Although the maximum difference in structure is obtained in the partial radial distribution function of the B type of particles, the rdf of AA pairs and AB pairs gives rise to the differences in the entropy and dynamics. This work supports the observation made in an earlier study [A. Banerjee et al., Phys. Rev. Lett. 113, 225701 (2014)] and shows that they are generic in nature, independent of density.« less

Static and dynamic properties of smoothed dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Alizadehrad, Davod; Fedosov, Dmitry A.

2018-03-01

In this paper, static and dynamic properties of the smoothed dissipative particle dynamics (SDPD) method are investigated. We study the effect of method parameters on SDPD fluid properties, such as structure, speed of sound, and transport coefficients, and show that a proper choice of parameters leads to a well-behaved and accurate fluid model. In particular, the speed of sound, the radial distribution function (RDF), shear-thinning of viscosity, the mean-squared displacement (〈R2 〉 ∝ t), and the Schmidt number (Sc ∼ O (103) - O (104)) can be controlled, such that the model exhibits a fluid-like behavior for a wide range of temperatures in simulations. Furthermore, in addition to the consideration of fluid density variations for fluid compressibility, a more challenging test of incompressibility is performed by considering the Poisson ratio and divergence of velocity field in an elongational flow. Finally, as an example of complex-fluid flow, we present the applicability and validity of the SDPD method with an appropriate choice of parameters for the simulation of cellular blood flow in irregular geometries. In conclusion, the results demonstrate that the SDPD method is able to approximate well a nearly incompressible fluid behavior, which includes hydrodynamic interactions and consistent thermal fluctuations, thereby providing, a powerful approach for simulations of complex mesoscopic systems.

S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

PubMed Central

2010-01-01

Background Biomedical research is set to greatly benefit from the use of semantic web technologies in the design of computational infrastructure. However, beyond well defined research initiatives, substantial issues of data heterogeneity, source distribution, and privacy currently stand in the way towards the personalization of Medicine. Results A computational framework for bioinformatic infrastructure was designed to deal with the heterogeneous data sources and the sensitive mixture of public and private data that characterizes the biomedical domain. This framework consists of a logical model build with semantic web tools, coupled with a Markov process that propagates user operator states. An accompanying open source prototype was developed to meet a series of applications that range from collaborative multi-institution data acquisition efforts to data analysis applications that need to quickly traverse complex data structures. This report describes the two abstractions underlying the S3DB-based infrastructure, logical and numerical, and discusses its generality beyond the immediate confines of existing implementations. Conclusions The emergence of the "web as a computer" requires a formal model for the different functionalities involved in reading and writing to it. The S3DB core model proposed was found to address the design criteria of biomedical computational infrastructure, such as those supporting large scale multi-investigator research, clinical trials, and molecular epidemiology. PMID:20646315

Control of Recombination Directionality by the Listeria Phage A118 Protein Gp44 and the Coiled-Coil Motif of Its Serine Integrase.

PubMed

Mandali, Sridhar; Gupta, Kushol; Dawson, Anthony R; Van Duyne, Gregory D; Johnson, Reid C

2017-06-01

The serine integrase of phage A118 catalyzes integrative recombination between attP on the phage and a specific attB locus on the chromosome of Listeria monocytogenes , but it is unable to promote excisive recombination between the hybrid attL and attR sites found on the integrated prophage without assistance by a recombination directionality factor (RDF). We have identified and characterized the phage-encoded RDF Gp44, which activates the A118 integrase for excision and inhibits integration. Gp44 binds to the C-terminal DNA binding domain of integrase, and we have localized the primary binding site to be within the mobile coiled-coil (CC) motif but distinct from the distal tip of the CC that is required for recombination. This interaction is sufficient to inhibit integration, but a second interaction involving the N-terminal end of Gp44 is also required to activate excision. We provide evidence that these two contacts modulate the trajectory of the CC motifs as they extend out from the integrase core in a manner dependent upon the identities of the four att sites. Our results support a model whereby Gp44 shapes the Int-bound complexes to control which att sites can synapse and recombine. IMPORTANCE Serine integrases mediate directional recombination between bacteriophage and bacterial chromosomes. These highly regulated site-specific recombination reactions are integral to the life cycle of temperate phage and, in the case of Listeria monocytogenes lysogenized by A118 family phage, are an essential virulence determinant. Serine integrases are also utilized as tools for genetic engineering and synthetic biology because of their exquisite unidirectional control of the DNA exchange reaction. Here, we identify and characterize the recombination directionality factor (RDF) that activates excision and inhibits integration reactions by the phage A118 integrase. We provide evidence that the A118 RDF binds to and modulates the trajectory of the long coiled-coil motif that extends from the large carboxyl-terminal DNA binding domain and is postulated to control the early steps of recombination site synapsis. Copyright © 2017 American Society for Microbiology.

Towards linked open gene mutations data

PubMed Central

2012-01-01

Background With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework. In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data. Methods A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest. Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite. Results We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application. Conclusions This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development. The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine. PMID:22536974

Towards linked open gene mutations data.

PubMed

Zappa, Achille; Splendiani, Andrea; Romano, Paolo

2012-03-28

With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework. In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data. A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest. Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite. We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application. This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development.The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine.

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

Plasma gasification of refuse derived fuel in a single-stage system using different gasifying agents.

PubMed

Agon, N; Hrabovský, M; Chumak, O; Hlína, M; Kopecký, V; Masláni, A; Bosmans, A; Helsen, L; Skoblja, S; Van Oost, G; Vierendeels, J

2016-01-01

The renewable evolution in the energy industry and the depletion of natural resources are putting pressure on the waste industry to shift towards flexible treatment technologies with efficient materials and/or energy recovery. In this context, a thermochemical conversion method of recent interest is plasma gasification, which is capable of producing syngas from a wide variety of waste streams. The produced syngas can be valorized for both energetic (heat and/or electricity) and chemical (ammonia, hydrogen or liquid hydrocarbons) end-purposes. This paper evaluates the performance of experiments on a single-stage plasma gasification system for the treatment of refuse-derived fuel (RDF) from excavated waste. A comparative analysis of the syngas characteristics and process yields was done for seven cases with different types of gasifying agents (CO2+O2, H2O, CO2+H2O and O2+H2O). The syngas compositions were compared to the thermodynamic equilibrium compositions and the performance of the single-stage plasma gasification of RDF was compared to that of similar experiments with biomass and to the performance of a two-stage plasma gasification process with RDF. The temperature range of the experiment was from 1400 to 1600 K and for all cases, a medium calorific value syngas was produced with lower heating values up to 10.9 MJ/Nm(3), low levels of tar, high levels of CO and H2 and which composition was in good agreement to the equilibrium composition. The carbon conversion efficiency ranged from 80% to 100% and maximum cold gas efficiency and mechanical gasification efficiency of respectively 56% and 95%, were registered. Overall, the treatment of RDF proved to be less performant than that of biomass in the same system. Compared to a two-stage plasma gasification system, the produced syngas from the single-stage reactor showed more favourable characteristics, while the recovery of the solid residue as a vitrified slag is an advantage of the two-stage set-up. Copyright © 2015 Elsevier Ltd. All rights reserved.

AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services.

PubMed

Correa, Miria C; Deus, Helena F; Vasconcelos, Ana T; Hayashi, Yuki; Ajani, Jaffer A; Patnana, Srikrishna V; Almeida, Jonas S

2010-10-26

AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application. The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces automatically assembled for multiple and volatile views of a domain. By coding AGUIA in JavaScript, for which all browsers include a native interpreter, a solution was found that assembles interfaces that are meaningful to the particular user, and which are also ubiquitous and lightweight, allowing the computational load to be carried by the client's machine.

Behavior of cesium in municipal solid waste incineration.

PubMed

Oshita, Kazuyuki; Aoki, Hiroshi; Fukutani, Satoshi; Shiota, Kenji; Fujimori, Takashi; Takaoka, Masaki

2015-05-01

As a result of the Fukushima Daiichi Nuclear Power Plant accident on March 11, 2011 in Japan radioactive nuclides, primarily (134)Cs and (137)Cs were released, contaminating municipal solid waste and sewage sludge in the area. Although stabilizing the waste and reducing its volume is an important issue differing from Chernobyl nuclear power plant accident, secondary emission of radioactive nuclides as a result of any intermediate remediation process is of concern. Unfortunately, there is little research on the behavior of radioactive nuclides during waste treatment. This study focuses on waste incineration in an effort to clarify the behavior of radioactive nuclides, specifically, refuse-derived fuel (RDF) with added (133)Cs (stable nuclide) or (134)Cs (radioactive nuclide) was incinerated in laboratory- and pilot-scale experiments. Next, thermogravimetric (TG) and differential thermal analysis (DTA) of stable Cs compounds, as well as an X-ray absorption fine structure (XAFS) analysis of Cs concentrated in the ashes were performed to validate the behavior and chemical forms of Cs during the combustion. Our results showed that at higher temperatures and at larger equivalence ratios, (133)Cs was distributed to the bottom ash at lower concentration, and the influence of the equivalence ratio was more significant at lower temperatures. (134)Cs behaved in a similar fashion as (133)Cs. We found through TG-DTA and XAFS analysis that a portion of Cs in RDF vaporizes and is transferred to fly ash where it exists as CsCl in the MSW incinerator. We conclude that Cs-contaminated municipal solid wastes could be incinerated at high temperatures resulting in a small amount of fly ash with a high concentration of radioactive Cs, and a bottom ash with low concentrations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genome Integration and Excision by a New Streptomyces Bacteriophage, ϕJoe.

PubMed

Fogg, Paul C M; Haley, Joshua A; Stark, W Marshall; Smith, Margaret C M

2017-03-01

Bacteriophages are the source of many valuable tools for molecular biology and genetic manipulation. In Streptomyces , most DNA cloning vectors are based on serine integrase site-specific DNA recombination systems derived from phage. Because of their efficiency and simplicity, serine integrases are also used for diverse synthetic biology applications. Here, we present the genome of a new Streptomyces phage, ϕJoe, and investigate the conditions for integration and excision of the ϕJoe genome. ϕJoe belongs to the largest Streptomyces phage cluster (R4-like) and encodes a serine integrase. The attB site from Streptomyces venezuelae was used efficiently by an integrating plasmid, pCMF92, constructed using the ϕJoe int-attP locus. The attB site for ϕJoe integrase was occupied in several Streptomyces genomes, including that of S. coelicolor , by a mobile element that varies in gene content and size between host species. Serine integrases require a phage-encoded recombination directionality factor (RDF) to activate the excision reaction. The ϕJoe RDF was identified, and its function was confirmed in vivo Both the integrase and RDF were active in in vitro recombination assays. The ϕJoe site-specific recombination system is likely to be an important addition to the synthetic biology and genome engineering toolbox. IMPORTANCE Streptomyces spp. are prolific producers of secondary metabolites, including many clinically useful antibiotics. Bacteriophage-derived integrases are important tools for genetic engineering, as they enable integration of heterologous DNA into the Streptomyces chromosome with ease and high efficiency. Recently, researchers have been applying phage integrases for a variety of applications in synthetic biology, including rapid assembly of novel combinations of genes, biosensors, and biocomputing. An important requirement for optimal experimental design and predictability when using integrases, however, is the need for multiple enzymes with different specificities for their integration sites. In order to provide a broad platform of integrases, we identified and validated the integrase from a newly isolated Streptomyces phage, ϕJoe. ϕJoe integrase is active in vitro and in vivo The specific recognition site for integration is present in a wide range of different actinobacteria, including Streptomyces venezuelae , an emerging model bacterium in Streptomyces research. Copyright © 2017 Fogg et al.

The effects of dication symmetry on ionic liquid electrolytes in supercapacitors.

PubMed

Li, Song; Zhu, Mengyang; Feng, Guang

2016-11-23

The effects of dication symmetry on the structure and capacitance of the electrical double layers (EDLs) of dicationic ionic liquids (DILs) near graphene electrodes were investigated by molecular dynamics (MD) simulation in this work. Symmetrical 1-hexyl-3-dimethylimidazolium di[bis(trifluoromethyl)imide]([C6(mim)2](Tf2N)2) and asymmetrical 1-(1-trimethylammonium-yl-hexyl)-3-methylimidazolium di[bis(trifluoro-methanesulfonyl)-imide] ([C6(tma)(mim)](Tf2N)2) were both employed. Radial distribution function (RDF) analysis of the two DILs revealed a shorter distance between the cation-anion pairs in symmetrical [C6(mim)2](Tf2N)2), which was attributed to the closely packed imidazolium ring-anion pairs. In contrast, the trimethylammonium head groups and anions exhibit a relatively longer distance, but a stronger correlation in asymmetrical [C6(tma)(mim)](Tf2N)2. In addition, it was illustrated that more symmetrical DIL ions in EDLs are distributed near graphite electrodes and exhibit closer distances to the electrode, which is most probably due to the parallel orientation of imidazolium rings, reducing the distance between the cation and the graphene. In contrast, asymmetrical DILs, with one trimethylammonium head group and one imidazolium ring in the dications, are loosely packed due to their tilting orientation near graphene surfaces. However, the capacitance-potential (C-V) curves of the two DILs are almost the same, regardless of the opposite sign of potential of zero charge (PZC), indicating the insignificant influence of dication symmetry on the capacitance of DIL-based supercapacitors.

The effects of dication symmetry on ionic liquid electrolytes in supercapacitors

NASA Astrophysics Data System (ADS)

Li, Song; Zhu, Mengyang; Feng, Guang

2016-11-01

The effects of dication symmetry on the structure and capacitance of the electrical double layers (EDLs) of dicationic ionic liquids (DILs) near graphene electrodes were investigated by molecular dynamics (MD) simulation in this work. Symmetrical 1-hexyl-3-dimethylimidazolium di[bis(trifluoromethyl)imide]([C6(mim)2](Tf2N)2) and asymmetrical 1-(1-trimethylammonium-yl-hexyl)-3-methylimidazolium di[bis(trifluoro-methanesulfonyl)-imide] ([C6(tma)(mim)](Tf2N)2) were both employed. Radial distribution function (RDF) analysis of the two DILs revealed a shorter distance between the cation-anion pairs in symmetrical [C6(mim)2](Tf2N)2), which was attributed to the closely packed imidazolium ring-anion pairs. In contrast, the trimethylammonium head groups and anions exhibit a relatively longer distance, but a stronger correlation in asymmetrical [C6(tma)(mim)](Tf2N)2. In addition, it was illustrated that more symmetrical DIL ions in EDLs are distributed near graphite electrodes and exhibit closer distances to the electrode, which is most probably due to the parallel orientation of imidazolium rings, reducing the distance between the cation and the graphene. In contrast, asymmetrical DILs, with one trimethylammonium head group and one imidazolium ring in the dications, are loosely packed due to their tilting orientation near graphene surfaces. However, the capacitance-potential (C-V) curves of the two DILs are almost the same, regardless of the opposite sign of potential of zero charge (PZC), indicating the insignificant influence of dication symmetry on the capacitance of DIL-based supercapacitors.

Publications - RDF 2015-10 | Alaska Division of Geological & Geophysical

Science.gov Websites

Keywords 40Ar/39Ar; Age Dates; Analyses; Analyses and Sampling; Analytical Lab Results; Analytical Results ; Ar-Ar; Bedrock; Bedrock Geology; Cretaceous; Early Jurassic; Eocene; Geochronology; Geology; Lab

Climate Change, Disaster and Sentiment Analysis over Social Media Mining

NASA Astrophysics Data System (ADS)

Lee, J.; McCusker, J. P.; McGuinness, D. L.

2012-12-01

Accelerated climate change causes disasters and disrupts people living all over the globe. Disruptive climate events are often reflected in expressed sentiments of the people affected. Monitoring changes in these sentiments during and after disasters can reveal relationships between climate change and mental health. We developed a semantic web tool that uses linked data principles and semantic web technologies to integrate data from multiple sources and analyze them together. We are converting statistical data on climate change and disaster records obtained from the World Bank data catalog and the International Disaster Database into a Resource Description Framework (RDF) representation that was annotated with the RDF Data Cube vocabulary. We compare these data with a dataset of tweets that mention terms from the Emotion Ontology to get a sense of how disasters can impact the affected populations. This dataset is being gathered using an infrastructure we developed that extracts term uses in Twitter with controlled vocabularies. This data was also converted to RDF structure so that statistical data on the climate change and disasters is analyzed together with sentiment data. To visualize and explore relationship of the multiple data across the dimensions of time and location, we use the qb.js framework. We are using this approach to investigate the social and emotional impact of climate change. We hope that this will demonstrate the use of social media data as a valuable source of understanding on global climate change.

Fuzzy multicriteria disposal method and site selection for municipal solid waste.

PubMed

Ekmekçioğlu, Mehmet; Kaya, Tolga; Kahraman, Cengiz

2010-01-01

The use of fuzzy multiple criteria analysis (MCA) in solid waste management has the advantage of rendering subjective and implicit decision making more objective and analytical, with its ability to accommodate both quantitative and qualitative data. In this paper a modified fuzzy TOPSIS methodology is proposed for the selection of appropriate disposal method and site for municipal solid waste (MSW). Our method is superior to existing methods since it has capability of representing vague qualitative data and presenting all possible results with different degrees of membership. In the first stage of the proposed methodology, a set of criteria of cost, reliability, feasibility, pollution and emission levels, waste and energy recovery is optimized to determine the best MSW disposal method. Landfilling, composting, conventional incineration, and refuse-derived fuel (RDF) combustion are the alternatives considered. The weights of the selection criteria are determined by fuzzy pairwise comparison matrices of Analytic Hierarchy Process (AHP). It is found that RDF combustion is the best disposal method alternative for Istanbul. In the second stage, the same methodology is used to determine the optimum RDF combustion plant location using adjacent land use, climate, road access and cost as the criteria. The results of this study illustrate the importance of the weights on the various factors in deciding the optimized location, with the best site located in Catalca. A sensitivity analysis is also conducted to monitor how sensitive our model is to changes in the various criteria weights. 2010 Elsevier Ltd. All rights reserved.

Digital Workflows for a 3d Semantic Representation of AN Ancient Mining Landscape

NASA Astrophysics Data System (ADS)

Hiebel, G.; Hanke, K.

2017-08-01

The ancient mining landscape of Schwaz/Brixlegg in the Tyrol, Austria witnessed mining from prehistoric times to modern times creating a first order cultural landscape when it comes to one of the most important inventions in human history: the production of metal. In 1991 a part of this landscape was lost due to an enormous landslide that reshaped part of the mountain. With our work we want to propose a digital workflow to create a 3D semantic representation of this ancient mining landscape with its mining structures to preserve it for posterity. First, we define a conceptual model to integrate the data. It is based on the CIDOC CRM ontology and CRMgeo for geometric data. To transform our information sources to a formal representation of the classes and properties of the ontology we applied semantic web technologies and created a knowledge graph in RDF (Resource Description Framework). Through the CRMgeo extension coordinate information of mining features can be integrated into the RDF graph and thus related to the detailed digital elevation model that may be visualized together with the mining structures using Geoinformation systems or 3D visualization tools. The RDF network of the triple store can be queried using the SPARQL query language. We created a snapshot of mining, settlement and burial sites in the Bronze Age. The results of the query were loaded into a Geoinformation system and a visualization of known bronze age sites related to mining, settlement and burial activities was created.

Property Graph vs RDF Triple Store: A Comparison on Glycan Substructure Search

PubMed Central

Alocci, Davide; Mariethoz, Julien; Horlacher, Oliver; Bolleman, Jerven T.; Campbell, Matthew P.; Lisacek, Frederique

2015-01-01

Resource description framework (RDF) and Property Graph databases are emerging technologies that are used for storing graph-structured data. We compare these technologies through a molecular biology use case: glycan substructure search. Glycans are branched tree-like molecules composed of building blocks linked together by chemical bonds. The molecular structure of a glycan can be encoded into a direct acyclic graph where each node represents a building block and each edge serves as a chemical linkage between two building blocks. In this context, Graph databases are possible software solutions for storing glycan structures and Graph query languages, such as SPARQL and Cypher, can be used to perform a substructure search. Glycan substructure searching is an important feature for querying structure and experimental glycan databases and retrieving biologically meaningful data. This applies for example to identifying a region of the glycan recognised by a glycan binding protein (GBP). In this study, 19,404 glycan structures were selected from GlycomeDB (www.glycome-db.org) and modelled for being stored into a RDF triple store and a Property Graph. We then performed two different sets of searches and compared the query response times and the results from both technologies to assess performance and accuracy. The two implementations produced the same results, but interestingly we noted a difference in the query response times. Qualitative measures such as portability were also used to define further criteria for choosing the technology adapted to solving glycan substructure search and other comparable issues. PMID:26656740

Analytical Model of the Nonlinear Dynamics of Cantilever Tip-Sample Surface Interactions for Various Acoustic-Atomic Force Microscopies

NASA Technical Reports Server (NTRS)

Cantrell, John H., Jr.; Cantrell, Sean A.

2008-01-01

A comprehensive analytical model of the interaction of the cantilever tip of the atomic force microscope (AFM) with the sample surface is developed that accounts for the nonlinearity of the tip-surface interaction force. The interaction is modeled as a nonlinear spring coupled at opposite ends to linear springs representing cantilever and sample surface oscillators. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a standard iteration procedure. Solutions are obtained for the phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) techniques including force modulation microscopy, atomic force acoustic microscopy, ultrasonic force microscopy, heterodyne force microscopy, resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM), and the commonly used intermittent contact mode (TappingMode) generally available on AFMs. The solutions are used to obtain a quantitative measure of image contrast resulting from variations in the Young modulus of the sample for the amplitude and phase images generated by the A-AFM techniques. Application of the model to RDF-AFUM and intermittent soft contact phase images of LaRC-cp2 polyimide polymer is discussed. The model predicts variations in the Young modulus of the material of 24 percent from the RDF-AFUM image and 18 percent from the intermittent soft contact image. Both predictions are in good agreement with the literature value of 21 percent obtained from independent, macroscopic measurements of sheet polymer material.

40 CFR 260.11 - References.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Hydrocarbon Fuels by Bomb Calorimeter (High-Precision Method),” IBR approved for §§ 264.1033, 265.1033. (5... Methods for Preparing Refuse-Derived Fuel (RDF) Samples for Analyses of Metals,” Test Method C—Bomb, Acid...

OpenFlyData: an exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster.

PubMed

Miles, Alistair; Zhao, Jun; Klyne, Graham; White-Cooper, Helen; Shotton, David

2010-10-01

Integrating heterogeneous data across distributed sources is a major requirement for in silico bioinformatics supporting translational research. For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection and validate experimental results. However, current data integration solutions tend to be heavy weight, and require significant initial and ongoing investment of effort. Development of a common Web-based data integration infrastructure (a.k.a. data web), using Semantic Web standards, promises to alleviate these difficulties, but little is known about the feasibility, costs, risks or practical means of migrating to such an infrastructure. We describe the development of OpenFlyData, a proof-of-concept system integrating gene expression data on D. melanogaster, combining Semantic Web standards with light-weight approaches to Web programming based on Web 2.0 design patterns. To support researchers designing and validating functional genomic studies, OpenFlyData includes user-facing search applications providing intuitive access to and comparison of gene expression data from FlyAtlas, the BDGP in situ database, and FlyTED, using data from FlyBase to expand and disambiguate gene names. OpenFlyData's services are also openly accessible, and are available for reuse by other bioinformaticians and application developers. Semi-automated methods and tools were developed to support labour- and knowledge-intensive tasks involved in deploying SPARQL services. These include methods for generating ontologies and relational-to-RDF mappings for relational databases, which we illustrate using the FlyBase Chado database schema; and methods for mapping gene identifiers between databases. The advantages of using Semantic Web standards for biomedical data integration are discussed, as are open issues. In particular, although the performance of open source SPARQL implementations is sufficient to query gene expression data directly from user-facing applications such as Web-based data fusions (a.k.a. mashups), we found open SPARQL endpoints to be vulnerable to denial-of-service-type problems, which must be mitigated to ensure reliability of services based on this standard. These results are relevant to data integration activities in translational bioinformatics. The gene expression search applications and SPARQL endpoints developed for OpenFlyData are deployed at http://openflydata.org. FlyUI, a library of JavaScript widgets providing re-usable user-interface components for Drosophila gene expression data, is available at http://flyui.googlecode.com. Software and ontologies to support transformation of data from FlyBase, FlyAtlas, BDGP and FlyTED to RDF are available at http://openflydata.googlecode.com. SPARQLite, an implementation of the SPARQL protocol, is available at http://sparqlite.googlecode.com. All software is provided under the GPL version 3 open source license.

Technologies and practices for maintaining and publishing earth science vocabularies

NASA Astrophysics Data System (ADS)

Cox, Simon; Yu, Jonathan; Williams, Megan; Giabardo, Fabrizio; Lowe, Dominic

2015-04-01

Shared vocabularies are a key element in geoscience data interoperability. Many organizations curate vocabularies, with most Geologic Surveys having a long history of development of lexicons and authority tables. However, their mode of publication is heterogeneous, ranging from PDFs and HTML web pages, spreadsheets and CSV, through various user-interfaces, and public and private APIs. Content maintenance ranges from tightly-governed and externally opaque, through various community processes, all the way to crowd-sourcing ('folksonomies'). Meanwhile, there is an increasing expectation of greater harmonization and vocabulary re-use, which create requirements for standardized content formalization and APIs, along with transparent content maintenance and versioning. We have been trialling a combination of processes and software dealing with vocabulary formalization, registration, search and linking. We use the Simplified Knowledge Organization System (SKOS) to provide a generic interface to content. SKOS is an RDF technology for multi-lingual, hierarchical vocabularies, oriented around 'concepts' denoted by URIs, and thus consistent with Linked Open Data. SKOS may be mixed in with classes and properties from specialized ontologies which provide a more specific interface when required. We have developed a suite of practices and techniques for conversion of content from the source technologies and styles into SKOS, largely based on spreadsheet manipulation before RDF conversion, and SPARQL afterwards. The workflow for each vocabulary must be adapted to match the specific inputs. In linked data applications, two requirements are paramount for user confidence: (i) the URI that denotes a vocabulary item is persistent, and should be dereferenceable indefinitely; (ii) the history and status of the resource denoted by a URI must be available. This is implemented by the Linked Data Registry (LDR), originally developed for the World Meteorological Organization and the UK Environment Agency, and now adapted and enhanced for deployment by CSIRO and the Australian Bureau of Meteorology. The LDR applies a standard content registration paradigm to RDF data, also including a delegation mode that enables a system to register (endorse) externally managed content. The locally managed RDF is exposed on a SPARQL endpoint. The registry implementation enables a flexible interaction pattern to support various specific content publication workflows, with the key feature of making the content externally accessible through a standard interface alongside its history, previous versions, and status. SPARQL is the standard low-level API for RDF including SKOS. On top of this we have developed SISSvoc, a SKOS-based RESTful API. This has been used it to deploy a number of vocabularies on behalf of the IUGS, ICS, NERC, OGC, the Australian Government, and CSIRO projects. Applications like SISSvoc Search provide a simple search UI on top of one or more SISSvoc sources. Together, these components provide a powerful and flexible system for providing earth science vocabularies for the community, consistent with semantic web and linked-data principles.

SemantGeo: Powering Ecological and Environment Data Discovery and Search with Standards-Based Geospatial Reasoning

NASA Astrophysics Data System (ADS)

Seyed, P.; Ashby, B.; Khan, I.; Patton, E. W.; McGuinness, D. L.

2013-12-01

Recent efforts to create and leverage standards for geospatial data specification and inference include the GeoSPARQL standard, Geospatial OWL ontologies (e.g., GAZ, Geonames), and RDF triple stores that support GeoSPARQL (e.g., AllegroGraph, Parliament) that use RDF instance data for geospatial features of interest. However, there remains a gap on how best to fuse software engineering best practices and GeoSPARQL within semantic web applications to enable flexible search driven by geospatial reasoning. In this abstract we introduce the SemantGeo module for the SemantEco framework that helps fill this gap, enabling scientists find data using geospatial semantics and reasoning. SemantGeo provides multiple types of geospatial reasoning for SemantEco modules. The server side implementation uses the Parliament SPARQL Endpoint accessed via a Tomcat servlet. SemantGeo uses the Google Maps API for user-specified polygon construction and JsTree for providing containment and categorical hierarchies for search. SemantGeo uses GeoSPARQL for spatial reasoning alone and in concert with RDFS/OWL reasoning capabilities to determine, e.g., what geofeatures are within, partially overlap with, or within a certain distance from, a given polygon. We also leverage qualitative relationships defined by the Gazetteer ontology that are composites of spatial relationships as well as administrative designations or geophysical phenomena. We provide multiple mechanisms for exploring data, such as polygon (map-based) and named-feature (hierarchy-based) selection, that enable flexible search constraints using boolean combination of selections. JsTree-based hierarchical search facets present named features and include a 'part of' hierarchy (e.g., measurement-site-01, Lake George, Adirondack Region, NY State) and type hierarchies (e.g., nodes in the hierarchy for WaterBody, Park, MeasurementSite), depending on the ';axis of choice' option selected. Using GeoSPARQL and aforementioned ontology, these hierarchies are constrained based on polygon selection, where the corresponding polygons of the contained features are visually rendered to assist exploration. Once measurement sites are plotted based on initial search, subsequent searches using JsTree selections can extend the previous based on nearby waterbodies in some semantic relationship of interest. For example, ';tributary of' captures water bodies that flow into the current one, and extending the original search to include tributaries of the observed water body is useful to environmental scientists for isolating the source of characteristic levels, including pollutants. Ultimately any SemantEco module can leverage SemantGeo's underlying APIs, leveraged in a deployment of SemantEco that combines EPA and USGS water quality data, and one customized for searching data available from the Darrin Freshwater Institute. Future work will address generating RDF geometry data from shape files, aligning RDF data sources to better leverage qualitative and spatial relationships, and validating newly generated RDF data adhering to the GeoSPARQL standard.

Towards the new heterocycle based molecule: Synthesis, characterization and reactivity study

NASA Astrophysics Data System (ADS)

Murthy, P. Krishna; Sheena Mary, Y.; Suneetha, V.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Giri, L.; Suchetan, P. A.; Van Alsenoy, C.

2017-06-01

4-Chloro-2-(3-fluorophenyl)-2,3-dihydro-1H-pyrrolo[3,4-c]pyridin-1-one (CFPDPPO) have been synthesized by hydride transfer from Et3SiH to carbenium ions(reduction reaction), which is formed by reaction between 4-chloro-2-(3-fluorophenyl)-3-hydroxy-2,3-dihydro-1H-pyrrolo[3,4-c]pyridin-1-one with TFA, the single crystals were grown in acetonitrile by slow evaporation technique at room temperature and characterized by single crystal X-ray diffraction, FT-IR, FT-Raman, 1H NMR, 13C NMR and ESI-MS. The experimental vibrational spectra were compared with the calculated spectra and each vibrational wavenumber was assigned on the basis of potential energy distribution (PED). Gauge-including atomic orbital 1H NMR and 13C NMR chemical shifts calculations were carried out and compared with experimental data. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analysed using NBO analysis. First hyperpolarizability is calculated in order to find its role in non-linear optics. Besides molecular electrostatic potential (MEP), global reactivity descriptors, thermodynamic properties, and Mullikan charge analysis of the title compound were computed with the same method in gas phase, theoretically. Further, employing combination of DFT calculations and molecular dynamics (MD) simulations, we have investigated in detail reactive properties of the title molecule. Investigation of local reactive properties encompassed calculations of average local ionization energies (ALIE) and Fukui functions. Stability in water has been investigated by calculations of radial distribution functions (RDF), while sensitivity towards the mechanism of autoxidation has been investigated by calculations of bond dissociation energies (BDE). The docked ligand forms a stable complex with human alpha9 nicotinic acetylcholine receptor antagonist and can be a lead compound for developing new anti-cancerous drug.

Evaluation of the topological characteristics of the turbulent flow in a `box of turbulence' through 2D time-resolved particle image velocimetry

NASA Astrophysics Data System (ADS)

Lian, Huan; Soulopoulos, Nikolaos; Hardalupas, Yannis

2017-09-01

The experimental evaluation of the topological characteristics of the turbulent flow in a `box' of homogeneous and isotropic turbulence (HIT) with zero mean velocity is presented. This requires an initial evaluation of the effect of signal noise on measurement of velocity invariants. The joint probability distribution functions (pdfs) of experimentally evaluated, noise contaminated, velocity invariants have a different shape than the corresponding noise-free joint pdfs obtained from the DNS data of the Johns Hopkins University (JHU) open resource HIT database. A noise model, based on Gaussian and impulsive Salt and Pepper noise, is established and added artificially to the DNS velocity vector field of the JHU database. Digital filtering methods, based on Median and Wiener Filters, are chosen to eliminate the modeled noise source and their capacity to restore the joint pdfs of velocity invariants to that of the noise-free DNS data is examined. The remaining errors after filtering are quantified by evaluating the global mean velocity, turbulent kinetic energy and global turbulent homogeneity, assessed through the behavior of the ratio of the standard deviation of the velocity fluctuations in two directions, the energy spectrum of the velocity fluctuations and the eigenvalues of the rate-of-strain tensor. A method of data filtering, based on median filtered velocity using different median filter window size, is used to quantify the clustering of zero velocity points of the turbulent field using the radial distribution function (RDF) and Voronoï analysis to analyze the 2D time-resolved particle image velocimetry (TR-PIV) velocity measurements. It was found that a median filter with window size 3 × 3 vector spacing is the effective and efficient approach to eliminate the experimental noise from PIV measured velocity images to a satisfactory level and extract the statistical two-dimensional topological turbulent flow patterns.

An Evaluation of shore-based radio direction finding

DOT National Transportation Integrated Search

1978-09-30

This report describes an evaluation of Radio Direction Finding (RDF) techniques for shore-based position location performed by the Transportation Systems Center (TSC). The evaluation consisted of the following three phases: (1) A preliminary survey t...

Publications - RDF 2015-2 | Alaska Division of Geological & Geophysical

Science.gov Websites

Tidal Datum Portal Climate and Cryosphere Hazards Coastal Hazards Program Guide to Geologic Hazards in -bay Shapefile 24.5 M Metadata - Read me Keywords Bathymetry; Bering Sea; Chukchi Sea; Coastal; Gambell

Descriptive Metadata: Emerging Standards.

ERIC Educational Resources Information Center

Ahronheim, Judith R.

1998-01-01

Discusses metadata, digital resources, cross-disciplinary activity, and standards. Highlights include Standard Generalized Markup Language (SGML); Extensible Markup Language (XML); Dublin Core; Resource Description Framework (RDF); Text Encoding Initiative (TEI); Encoded Archival Description (EAD); art and cultural-heritage metadata initiatives;…

Publications - RDF 2016-6 v. 1.1 | Alaska Division of Geological &

Science.gov Websites

Alaska's Mineral Industry Reports AKGeology.info Rare Earth Elements WebGeochem Engineering Geology Alaska 345.0 K Metadata - Read me Keywords Alaska Range; Analyses; Analyses and Sampling; Analytical Lab

Regular paths in SparQL: querying the NCI Thesaurus.

PubMed

Detwiler, Landon T; Suciu, Dan; Brinkley, James F

2008-11-06

OWL, the Web Ontology Language, provides syntax and semantics for representing knowledge for the semantic web. Many of the constructs of OWL have a basis in the field of description logics. While the formal underpinnings of description logics have lead to a highly computable language, it has come at a cognitive cost. OWL ontologies are often unintuitive to readers lacking a strong logic background. In this work we describe GLEEN, a regular path expression library, which extends the RDF query language SparQL to support complex path expressions over OWL and other RDF-based ontologies. We illustrate the utility of GLEEN by showing how it can be used in a query-based approach to defining simpler, more intuitive views of OWL ontologies. In particular we show how relatively simple GLEEN-enhanced SparQL queries can create views of the OWL version of the NCI Thesaurus that match the views generated by the web-based NCI browser.

Evaluation of the performance of open-source RDBMS and triplestores for storing medical data over a web service.

PubMed

Kilintzis, Vassilis; Beredimas, Nikolaos; Chouvarda, Ioanna

2014-01-01

An integral part of a system that manages medical data is the persistent storage engine. For almost twenty five years Relational Database Management Systems(RDBMS) were considered the obvious decision, yet today new technologies have emerged that require our attention as possible alternatives. Triplestores store information in terms of RDF triples without necessarily binding to a specific predefined structural model. In this paper we present an attempt to compare the performance of Apache JENA-Fuseki and the Virtuoso Universal Server 6 triplestores with that of MySQL 5.6 RDBMS for storing and retrieving medical information that it is communicated as RDF/XML ontology instances over a RESTful web service. The results show that the performance, calculated as average time of storing and retrieving instances, is significantly better using Virtuoso Server while MySQL performed better than Fuseki.

Meeting report: advancing practical applications of biodiversity ontologies

PubMed Central

2014-01-01

We describe the outcomes of three recent workshops aimed at advancing development of the Biological Collections Ontology (BCO), the Population and Community Ontology (PCO), and tools to annotate data using those and other ontologies. The first workshop gathered use cases to help grow the PCO, agreed upon a format for modeling challenging concepts such as ecological niche, and developed ontology design patterns for defining collections of organisms and population-level phenotypes. The second focused on mapping datasets to ontology terms and converting them to Resource Description Framework (RDF), using the BCO. To follow-up, a BCO hackathon was held concurrently with the 16th Genomics Standards Consortium Meeting, during which we converted additional datasets to RDF, developed a Material Sample Core for the Global Biodiversity Information Framework, created a Web Ontology Language (OWL) file for importing Darwin Core classes and properties into BCO, and developed a workflow for converting biodiversity data among formats.

Effects of introducing energy recovery processes to the municipal solid waste management system in Ulaanbaatar, Mongolia.

PubMed

Toshiki, Kosuke; Giang, Pham Quy; Serrona, Kevin Roy B; Sekikawa, Takahiro; Yu, Jeoung-soo; Choijil, Baasandash; Kunikane, Shoichi

2015-02-01

Currently, most developing countries have not set up municipal solid waste management systems with a view of recovering energy from waste or reducing greenhouse gas emissions. In this article, we have studied the possible effects of introducing three energy recovery processes either as a single or combination approach, refuse derived fuel production, incineration and waste power generation, and methane gas recovery from landfill and power generation in Ulaanbaatar, Mongolia, as a case study. We concluded that incineration process is the most suitable as first introduction of energy recovery. To operate it efficiently, 3Rs strategies need to be promoted. And then, RDF production which is made of waste papers and plastics in high level of sorting may be considered as the second step of energy recovery. However, safety control and marketability of RDF will be required at that moment. Copyright © 2014. Published by Elsevier B.V.

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

NONE

Circulating fluidized-bed (CFB) boilers have ben used for years in Scandinavia to burn refuse-derived fuel (RDF). Now, Foster Wheeler Power Systems, Inc., (Clinton, N.J.) is bringing the technology to the US. Touted as the world`s largest waste-to-energy plant to use CFB technology, the Robbins (III.) Resource Recovery Facility will have the capacity to process 1,600 tons/d of municipal solid waste (MSW) when it begins operation in early 1997. The facility will have two materials-separation and RDF-processing trains, each with dual trommel screens, magnetic and eddy current separators, and shredders. About 25% of the incoming MSW will be sorted and removedmore » for recycling, while 75% of it will be turned into fuel, with a heat value of roughly 6,170 btu/lb. Once burned in the twin CFB boilers the resulting steam will be routed through a single turbine generator to produce 50,000 mW of electric power.« less

Measuring the order in ordered porous arrays: can bees outperform humans?

NASA Astrophysics Data System (ADS)

Kaatz, F. H.

2006-08-01

A method that explains how to quantify the amount of order in “ordered” and “highly ordered” porous arrays is derived. Ordered arrays from bee honeycomb and several from the general field of nanoscience are compared. Accurate measures of the order in porous arrays are made using the discrete radial distribution function (RDF). Nanoporous anodized aluminum oxide (AAO), hexagonal arrays from functional materials, hexagonal arrays from nanosphere lithography, and square arrays defined by interference lithography (all taken from the literature) are compared to two-dimensional model systems. These arrays have a range of pore diameters from ˜60 to 180 nm. An order parameter, OP 3 , is defined to evaluate the total order in a given array such that an ideal network has the value of 1. When we compare RDFs of man-made arrays with that of our honeycomb (pore diameter ˜5.89 mm), a locally grown version made by Apis mellifera without the use of foundation comb, we find OP 3 =0.399 for the honeycomb and OP 3 =0.572 for man’s best hexagonal array. The nearest neighbor peaks range from 4.65 for the honeycomb to 5.77 for man’s best hexagonal array, while the ideal hexagonal array has an average of 5.93 nearest neighbors. Ordered arrays are now becoming quite common in nanostructured science, while bee honeycombs were studied for millennia. This paper describes the first method to quantify the order found in these arrays with a simple yet elegant procedure that provides a precise measurement of the order in one array compared to other arrays.

Electron tomography and fractal aspects of MoS2 and MoS2/Co spheres.

PubMed

Ramos, Manuel; Galindo-Hernández, Félix; Arslan, Ilke; Sanders, Toby; Domínguez, José Manuel

2017-09-26

A study was made by a combination of 3D electron tomography reconstruction methods and N 2 adsorption for determining the fractal dimension for nanometric MoS 2 and MoS 2 /Co catalyst particles. DFT methods including Neimarke-Kiselev's method allowed to determine the particle porosity and fractal arrays at the atomic scale for the S-Mo-S(Co) 2D- layers that conform the spherically shaped catalyst particles. A structural and textural correlation was sought by further characterization performed by x-ray Rietveld refinement and Radial Distribution Function (RDF) methods, electron density maps, computational density functional theory methods and nitrogen adsorption methods altogether, for studying the structural and textural features of spherical MoS 2 and MoS 2 /Co particles. Neimark-Kiselev's equations afforded the evaluation of a pore volume variation from 10 to 110 cm 3 /g by cobalt insertion in the MoS 2 crystallographic lattice, which induces the formation of cavities and throats in between of less than 29 nm, with a curvature radius r k  < 14.4 nm; typical large needle-like arrays having 20 2D layers units correspond to a model consisting of smooth surfaces within these cavities. Decreasing D P , D B , D I and D M values occur when Co atoms are present in the MoS 2 laminates, which promote the formation of smoother edges and denser surfaces that have an influence on the catalytic properties of the S-Mo-S(Co) system.

Compatibility analysis of material and energy recovery in a regional solid waste management system.

PubMed

Chang, Ying-Hsi; Chang, Ni-Bin

2003-01-01

The rising prices of raw materials and concerns about energy conservation have resulted in an increasing interest in the simultaneous recovery of materials and energy from waste streams. Compatibility exists for several economic, environmental, and managerial reasons. Installing an on-site or off-site presorting facility before an incinerator could be a feasible alternative to achieve both goals if household recycling programs cannot succeed in local communities. However, the regional impacts of presorting solid waste on a waste-to-energy facility remain unclear because of the inherent complexity of solid waste compositions and properties over different areas. This paper applies a system-based approach to assess the impact of installing a refuse-derived fuel (RDF) process before an incinerator. Such an RDF process, consisting of standard unit operations of shredding, magnetic separation, trommel screening, and air classification, might be useful for integrating the recycling and presorting efforts for a large-scale municipal incinerator from a regional sense. An optimization modeling analysis is performed to characterize such integration potential so that the optimal size of the RDF process and associated shipping patterns for flow control can be foreseen. It aims at exploring how the waste inflows with different rates of generation, physical and chemical compositions, and heating values collected from differing administrative districts can be processed by either a centralized presorting facility or an incinerator to meet both the energy recovery and throughput requirements. A case study conducted in Taipei County, which is one of the most densely populated metropolitan areas in Taiwan, further confirms the application potential of such a cost-benefit analysis.

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

Yan, Rui; Praggastis, Brenda L.; Smith, William P.

While streaming data have become increasingly more popular in business and research communities, semantic models and processing software for streaming data have not kept pace. Traditional semantic solutions have not addressed transient data streams. Semantic web languages (e.g., RDF, OWL) have typically addressed static data settings and linked data approaches have predominantly addressed static or growing data repositories. Streaming data settings have some fundamental differences; in particular, data are consumed on the fly and data may expire. Stream reasoning, a combination of stream processing and semantic reasoning, has emerged with the vision of providing "smart" processing of streaming data. C-SPARQLmore » is a prominent stream reasoning system that handles semantic (RDF) data streams. Many stream reasoning systems including C-SPARQL use a sliding window and use data arrival time to evict data. For data streams that include expiration times, a simple arrival time scheme is inadequate if the window size does not match the expiration period. In this paper, we propose a cache-enabled, order-aware, ontology-based stream reasoning framework. This framework consumes RDF streams with expiration timestamps assigned by the streaming source. Our framework utilizes both arrival and expiration timestamps in its cache eviction policies. In addition, we introduce the notion of "semantic importance" which aims to address the relevance of data to the expected reasoning, thus enabling the eviction algorithms to be more context- and reasoning-aware when choosing what data to maintain for question answering. We evaluate this framework by implementing three different prototypes and utilizing five metrics. The trade-offs of deploying the proposed framework are also discussed.« less

Publications - RDF 2014-20 | Alaska Division of Geological & Geophysical

Science.gov Websites

Tidal Datum Portal Climate and Cryosphere Hazards Coastal Hazards Program Guide to Geologic Hazards in Download golovin-lidar-las-index Shapefile 71.0 K Metadata - Read me Keywords Coastal; Coastal and River

Publications - RDF 2015-3 | Alaska Division of Geological & Geophysical

Science.gov Websites

Surveys Home About Us Director's Office Alaska Statutes Annual Reports Employment Staff Directory Microsoft Excel 358.0 K Metadata - Read me Keywords 40Ar/39Ar; Age Dates; Ar-Ar; Bendeleben Mountains; Big

AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services

PubMed Central

2010-01-01

Background AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. Methods The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. Results We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application. Conclusions The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces automatically assembled for multiple and volatile views of a domain. By coding AGUIA in JavaScript, for which all browsers include a native interpreter, a solution was found that assembles interfaces that are meaningful to the particular user, and which are also ubiquitous and lightweight, allowing the computational load to be carried by the client's machine. PMID:20977768

Linked data and provenance in biological data webs.

PubMed

Zhao, Jun; Miles, Alistair; Klyne, Graham; Shotton, David

2009-03-01

The Web is now being used as a platform for publishing and linking life science data. The Web's linking architecture can be exploited to join heterogeneous data from multiple sources. However, as data are frequently being updated in a decentralized environment, provenance information becomes critical to providing reliable and trustworthy services to scientists. This article presents design patterns for representing and querying provenance information relating to mapping links between heterogeneous data from sources in the domain of functional genomics. We illustrate the use of named resource description framework (RDF) graphs at different levels of granularity to make provenance assertions about linked data, and demonstrate that these assertions are sufficient to support requirements including data currency, integrity, evidential support and historical queries.

Synthesis and characterization of Mg-Al-layered double hydroxides intercalated with cubane-1,4-dicarboxylate anions.

PubMed

Rezvani, Zolfaghar; Arjomandi Rad, Farzad; Khodam, Fatemeh

2015-01-21

In the present work, Mg2Al-layered double hydroxide (LDH) intercalated with cubane-1,4-dicarboxylate anions was prepared from the reaction of solutions of Mg(ii) and Al(iii) nitrate salts with an alkaline solution of cubane-1,4-dicarboxylic acid by using the coprecipitation method. The successful preparation of a nanohybrid of cubane-1,4-dicarboxylate(cubane-dc) anions with LDH was confirmed by powder X-ray diffraction, FTIR spectroscopy and thermal gravimetric analysis (TGA). The increase in the basal spacing of LDHs from 8.67 Å to 13.40 Å shows that cubane-dc anions were successfully incorporated into the interlayer space. Thermogravimetric analyses confirm that the thermal stability of the intercalated cubane-dc anions is greater than that of the pure form before intercalation because of host-guest interactions involving hydrogen bonds. The interlayer structure, hydrogen bonding, and subsequent distension of LDH compounds containing cubane-dc anions were shown by molecular simulation. The RDF (radial distribution function), mean square displacement (MSD), and self-diffusion coefficient were calculated using the trajectory files on the basis of molecular dynamics (MD) simulations, and the results indicated that the cubane-dc anions were more stable when intercalated into the LDH layers. A good agreement was obtained between calculated and measured X-ray diffraction patterns and between experimental and calculated basal spacings.

Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii.

PubMed

Ahmad, Sajjad; Raza, Saad; Uddin, Reaz; Azam, Syed Sikander

2017-10-01

MurF ligase catalyzes the final cytoplasmic step of bacterial peptidoglycan biosynthesis and, as such, is a validated target for therapeutic intervention. Herein, we performed molecular docking to identify putative inhibitors of Acinetobacter baumannii MurF (AbMurF). Based on comparative docking analysis, compound 114 (ethyl pyridine substituted 3-cyanothiophene) was predicted to potentially be the most active ligand. Computational pharmacokinetic characterization of drug-likeness of the compound showed it to fulfil all the parameters of Muegge and the MDDR rule. A molecular dynamic simulation of 114 indicated the complex to be stable on the basis of an average root mean square deviation (RMSD) value of 2.09Å for the ligand. The stability of the complex was further supported by root mean square fluctuation (RMSF), beta factor and radius of gyration values. Analyzing the complex using radial distribution function (RDF) and a novel analytical tool termed the axial frequency distribution (AFD) illustrated that after simulation the ligand is positioned in close vicinity of the protein active site where Thr42 and Asp43 participate in hydrogen bonding and stabilization of the complex. Binding free energy calculations based on the Poisson-Boltzmann or Generalized-Born Surface Area Continuum Solvation (MM(PB/GB)SA) method indicated the van der Waals contribution to the overall binding energy of the complex to be dominant along with electrostatic contributions involving the hot spot amino acids from the protein active site. The present results indicate that the screened compound 114 may act as a parent structure for designing potent derivatives against AbMurF in specific and MurF of other bacterial pathogens in general. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular dynamics simulation studies of novel β-lactamase inhibitor.

PubMed

Ul Haq, Farhan; Abro, Asma; Raza, Saad; Liedl, Klaus R; Azam, Syed Sikander

2017-06-01

New Delhi Metallo-β-Lactamase-1 (NDM-1) has drawn great attention due to its diverse antibiotic resistant activity. It can hydrolyze almost all clinically available β-lactam antibiotics. To inhibit the activity of NDM-1 a new strategy is proposed using computational methods. Molecular dynamics (MD) simulations are used to analyze the molecular interactions between selected inhibitor candidates and NDM-1 structure. The enzyme-ligand complex is subject to binding free energy calculations using MM(PB/GB)SA methods. The role of each residue of the active site contributing in ligand binding affinity is explored using energy decomposition analysis. Furthermore, a hydrogen bonding network between ligand and enzyme active site is observed and key residues are identified ensuring that the ligand stays inside the active site and maintains its movement towards the active site pocket. A production run of 150ns is carried out and results are analyzed using root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) to explain the stability of enzyme ligand complex. Important active site residue e.g. PHE70, VAL73, TRP93, HIS122, GLN123, ASP124, HIS189, LYS216, CYS208, LYS211, ALA215, HIS250, and SER251 were observed to be involved in ligand attachemet inside the active site pocket, hence depicting its inhibitor potential. Hydrogen bonds involved in structural stability are analyzed through radial distribution function (RDF) and contribution of important residues involved in ligand movement is explained using a novel analytical tool, axial frequency distribution (AFD) to observe the role of important hydrogen bonding partners between ligand atoms and active site residues. Copyright © 2017 Elsevier Inc. All rights reserved.

Oil Contact Angles in a Water-Decane-Silicon Dioxide System: Effects of Surface Charge

NASA Astrophysics Data System (ADS)

Xu, Shijing; Wang, Jingyao; Wu, Jiazhong; Liu, Qingjie; Sun, Chengzhen; Bai, Bofeng

2018-04-01

Oil wettability in the water-oil-rock systems is very sensitive to the evolution of surface charges on the rock surfaces induced by the adsorption of ions and other chemical agents in water flooding. Through a set of large-scale molecular dynamics simulations, we reveal the effects of surface charge on the oil contact angles in an ideal water-decane-silicon dioxide system. The results show that the contact angles of oil nano-droplets have a great dependence on the surface charges. As the surface charge density exceeds a critical value of 0.992 e/nm2, the contact angle reaches up to 78.8° and the water-wet state is very apparent. The variation of contact angles can be confirmed from the number density distributions of oil molecules. With increasing the surface charge density, the adsorption of oil molecules weakens and the contact areas between nano-droplets and silicon dioxide surface are reduced. In addition, the number density distributions, RDF distributions, and molecular orientations indicate that the oil molecules are adsorbed on the silicon dioxide surface layer-by-layer with an orientation parallel to the surface. However, the layered structure of oil molecules near the silicon dioxide surface becomes more and more obscure at higher surface charge densities.

Oil Contact Angles in a Water-Decane-Silicon Dioxide System: Effects of Surface Charge.

PubMed

Xu, Shijing; Wang, Jingyao; Wu, Jiazhong; Liu, Qingjie; Sun, Chengzhen; Bai, Bofeng

2018-04-19

Oil wettability in the water-oil-rock systems is very sensitive to the evolution of surface charges on the rock surfaces induced by the adsorption of ions and other chemical agents in water flooding. Through a set of large-scale molecular dynamics simulations, we reveal the effects of surface charge on the oil contact angles in an ideal water-decane-silicon dioxide system. The results show that the contact angles of oil nano-droplets have a great dependence on the surface charges. As the surface charge density exceeds a critical value of 0.992 e/nm 2 , the contact angle reaches up to 78.8° and the water-wet state is very apparent. The variation of contact angles can be confirmed from the number density distributions of oil molecules. With increasing the surface charge density, the adsorption of oil molecules weakens and the contact areas between nano-droplets and silicon dioxide surface are reduced. In addition, the number density distributions, RDF distributions, and molecular orientations indicate that the oil molecules are adsorbed on the silicon dioxide surface layer-by-layer with an orientation parallel to the surface. However, the layered structure of oil molecules near the silicon dioxide surface becomes more and more obscure at higher surface charge densities.

Browsing and Visualization of Linked Environmental Data

NASA Astrophysics Data System (ADS)

Nikolaou, Charalampos; Kyzirakos, Kostis; Bereta, Konstantina; Dogani, Kallirroi; Koubarakis, Manolis

2014-05-01

Linked environmental data has started to appear on the Web as environmental researchers make use of technologies such as ontologies, RDF, and SPARQL. Many of these datasets have an important geospatial and temporal dimension. The same is true also for the Web of data that is being rapidly populated not only with geospatial information, but also with temporal information. As the real-world entities represented in linked geospatial datasets evolve over time, the datasets themselves get updated and both the spatial and the temporal dimension of data become significant for users. For example, in the Earth Observation and Environment domains, data is constantly produced by satellite sensors and is associated with metadata containing, among others, temporal attributes, such as the time that an image was acquired. In addition, the acquisitions are considered to be valid for specific periods of time, for example until they get updated by new acquisitions. Satellite acquisitions might be utilized in applications such as the CORINE Land Cover programme operated by the European Environment Agency that makes available as a cartographic product the land cover of European areas. Periodically CORINE publishes the changes in the land cover of these areas in the form of changesets. Tools for exploiting the abundance of geospatial information have also started to emerge. However, these tools are designed for browsing a single data source, while in addition they cannot represent the temporal dimension. This is for two reasons: a) the lack of an implementation of a data model and a query language with temporal features covering the various semantics associated with the representation of time (e.g., valid and user-defined), and b) the lack of a standard temporal extension of RDF that would allow practitioners to utilize when publishing RDF data. Recently, we presented the temporal features of the data model stRDF, the query language stSPARQL, and their implementation in the geospatial RDF store Strabon (http://www.strabon.di.uoa.gr/) which, apart from querying geospatial information, can also be used to query both the valid time of a triple and user-defined time. With the aim of filling the aforementioned gaps and going beyond data exploration to map creation and sharing, we have designed and developed SexTant (http://sextant.di.uoa.gr/). SexTant can be used to produce thematic maps by layering spatiotemporal information which exists in a number of data sources ranging from standard SPARQL endpoints, to SPARQL endpoints following the standard GeoSPARQL defined by the Open Geospatial Consortium (OGC) for the modelling and querying of geospatial information, and other well-adopted geospatial file formats, such as KML and GeoJSON. In this work, we pick some real use cases from the environment domain to showcase the usefulness of SexTant to the environmental studies of a domain expert by presenting its browsing and visualization capabilities using a number of environmental datasets that we have published as linked data and also other geospatial data sources publicly available on the Web, such as KML files.

46 CFR 148.245 - Direct reduced iron (DRI); lumps, pellets, and cold-molded briquettes.

Code of Federal Regulations, 2013 CFR

2013-10-01

... the concentration of fines (pieces less than 6.35mm in size) in any one location in the cargo hold. (h) Radar and RDF scanners must be protected against the dust generated during cargo transfer operations of...

46 CFR 148.245 - Direct reduced iron (DRI); lumps, pellets, and cold-molded briquettes.

Code of Federal Regulations, 2014 CFR

2014-10-01

... the concentration of fines (pieces less than 6.35mm in size) in any one location in the cargo hold. (h) Radar and RDF scanners must be protected against the dust generated during cargo transfer operations of...

46 CFR 148.245 - Direct reduced iron (DRI); lumps, pellets, and cold-molded briquettes.

Code of Federal Regulations, 2012 CFR

2012-10-01

... the concentration of fines (pieces less than 6.35mm in size) in any one location in the cargo hold. (h) Radar and RDF scanners must be protected against the dust generated during cargo transfer operations of...

Approaches to Linked Open Data at data.oceandrilling.org

NASA Astrophysics Data System (ADS)

Fils, D.

2012-12-01

The data.oceandrilling.org web application applies Linked Open Data (LOD) patterns to expose Deep Sea Drilling Project (DSDP), Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) data. Ocean drilling data is represented in a rich range of data formats: high resolution images, file based data sets and sample based data. This richness of data types has been well met by semantic approaches and will be demonstrated. Data has been extracted from CSV, HTML and RDBMS through custom software and existing packages for loading into a SPARQL 1.1 compliant triple store. Practices have been developed to streamline the maintenance of the RDF graphs and properly expose them using LOD approaches like VoID and HTML embedded structured data. Custom and existing vocabularies are used to allow semantic relations between resources. Use of the W3c draft RDF Data Cube Vocabulary and other approaches for encoding time scales, taxonomic fossil data and other graphs will be shown. A software layer written in Google Go mediates the RDF to web pipeline. The approach used is general and can be applied to other similar environments like node.js or Python Twisted. To facilitate communication user interface software libraries such as D3 and packages such as S2S and LodLive have been used. Additionally OpenSearch API's, structured data in HTML and SPARQL endpoints provide various access methods for applications. The data.oceandrilling.org is not viewed as a web site but as an application that communicate with a range of clients. This approach helps guide the development more along software practices than along web site authoring approaches.

Geoscience Australia Publishes Sample Descriptions using W3C standards

NASA Astrophysics Data System (ADS)

Car, N. J.; Cox, S. J. D.; Bastrakova, I.; Wyborn, L. A.

2017-12-01

The recent revision of the W3C Semantic Sensor Network Ontology (SSN) has focused on three key concerns: Extending the scope of the ontology to include sampling and actuation as well as observation and sensing Modularizing the ontology into a simple core with few classes and properties and little formal axiomatization, supplemented by additional modules that formalize the semantics and extend the scope Alignments with several existing applications and upper ontologies These enhancements mean that SSN can now be used as the basis for publishing descriptions of geologic samples as Linked Data. Geoscience Australia maintains a database of about three million samples, collected over 50 years through projects from ocean core, terrestrial rock and hydrochemistry borehole projects, almost all of which are held in in the special-purpose GA samples repository. Access to descriptions of these samples as Linked Data has recently been enabled. The sample descriptions can be viewed in various machine-readable formalizations, including IGSN (XML & RDF), Dublin Core (XML & RDF) and SSN (RDF), as well as web landing-pages for people. Of particular importance is the support for encoding relationships between samples, and between samples and surveys, boreholes, and traverses which they are related to, as well as between samples processed for analytical purposes and their parents, siblings, and back to the original field samples. The SSN extension for Sample Relationships provides an extensible, semantically rich mechanism to capture any relationship necessary to explain the provenance of observation results obtained from samples. Sample citation is facilitated through the use of URI-based persistent identifiers which resolve to samples' landing pages. The sample system also allows PROV pingbacks to be received for samples when users of them record provenance for their actions.

Characterization of products obtained from pyrolysis and steam gasification of wood waste, RDF, and RPF.

PubMed

Hwang, In-Hee; Kobayashi, Jun; Kawamoto, Katsuya

2014-02-01

Pyrolysis and steam gasification of woody biomass chip (WBC) obtained from construction and demolition wastes, refuse-derived fuel (RDF), and refuse paper and plastic fuel (RPF) were performed at various temperatures using a lab-scale instrument. The gas, liquid, and solid products were examined to determine their generation amounts, properties, and the carbon balance between raw material and products. The amount of product gas and its hydrogen concentration showed a considerable difference depending on pyrolysis and steam gasification at higher temperature. The reaction of steam and solid product, char, contributed to an increase in gas amount and hydrogen concentration. The amount of liquid products generated greatly depended on temperature rather than pyrolysis or steam gasification. The compositions of liquid product varied relying on raw materials used at 500°C but the polycyclic aromatic hydrocarbons became the major compounds at 900°C irrespective of the raw materials used. Almost fixed carbon (FC) of raw materials remained as solid products under pyrolysis condition whereas FC started to decompose at 700°C under steam gasification condition. For WBC, both char utilization by pyrolysis at low temperature (500°C) and syngas recovery by steam gasification at higher temperature (900°C) might be practical options. From the results of carbon balance of RDF and RPF, it was confirmed that the carbon conversion to liquid products conspicuously increased as the amount of plastic increased in the raw material. To recover feedstock from RPF, pyrolysis for oil recovery at low temperature (500°C) might be one of viable options. Steam gasification at 900°C could be an option but the method of tar reforming (e.g. catalyst utilization) should be considered. Copyright © 2013 Elsevier Ltd. All rights reserved.

Self-organizing maps of molecular descriptors for sesquiterpene lactones and their application to the chemotaxonomy of the Asteraceae family.

PubMed

Scotti, Marcus T; Emerenciano, Vicente; Ferreira, Marcelo J P; Scotti, Luciana; Stefani, Ricardo; da Silva, Marcelo S; Mendonça Junior, Francisco Jaime B

2012-04-20

The Asteraceae, one of the largest families among angiosperms, is chemically characterised by the production of sesquiterpene lactones (SLs). A total of 1,111 SLs, which were extracted from 658 species, 161 genera, 63 subtribes and 15 tribes of Asteraceae, were represented and registered in two dimensions in the SISTEMATX, an in-house software system, and were associated with their botanical sources. The respective 11 block of descriptors: Constitutional, Functional groups, BCUT, Atom-centred, 2D autocorrelations, Topological, Geometrical, RDF, 3D-MoRSE, GETAWAY and WHIM were used as input data to separate the botanical occurrences through self-organising maps. Maps that were generated with each descriptor divided the Asteraceae tribes, with total index values between 66.7% and 83.6%. The analysis of the results shows evident similarities among the Heliantheae, Helenieae and Eupatorieae tribes as well as between the Anthemideae and Inuleae tribes. Those observations are in agreement with systematic classifications that were proposed by Bremer, which use mainly morphological and molecular data, therefore chemical markers partially corroborate with these classifications. The results demonstrate that the atom-centred and RDF descriptors can be used as a tool for taxonomic classification in low hierarchical levels, such as tribes. Descriptors obtained through fragments or by the two-dimensional representation of the SL structures were sufficient to obtain significant results, and better results were not achieved by using descriptors derived from three-dimensional representations of SLs. Such models based on physico-chemical properties can project new design SLs, similar structures from literature or even unreported structures in two-dimensional chemical space. Therefore, the generated SOMs can predict the most probable tribe where a biologically active molecule can be found according Bremer classification.

Quality Management, Certification and Rating of Health Information on the Net with MedCERTAIN: Using a medPICS/RDF/XML metadata structure for implementing eHealth ethics and creating trust globally

PubMed Central

Eysenbach, Gunther; Yihune, Gabriel; Lampe, Kristian; Cross, Phil; Brickley, Dan

2000-01-01

MedCERTAIN (MedPICS Certification and Rating of Trustworthy Health Information on the Net, http://www.medcertain.org/) is a recently launched international project funded under the European Union's (EU) "Action Plan for safer use of the Internet". It provides a technical infrastructure and a conceptual basis for an international system of "quality seals", ratings and self-labelling of Internet health information, with the final aim to establish a global "trustmark" for networked health information. Digital "quality seals" are evaluative metadata (using standards such as PICS=Platform for Internet Content Selection, now being replaced by RDF/XML) assigned by trusted third-party raters. The project also enables and encourages self-labelling with descriptive metainformation by web authors. Together these measures will help consumers as well as professionals to identify high-quality information on the Internet. MedCERTAIN establishes a fully functional demonstrator for a self- and third-party rating system enabling consumers and professionals to filter harmful health information and to positively identify and select high quality information. We aim to provide a trustmark system which allows citizens to place greater confidence in networked information, to encourage health information providers to follow best practices guidelines such as the Washington eHealth Code of Ethics, to provide effective feedback and law enforcement channels to handle user complaints, and to stimulate medical societies to develop standard for patient information. The project further proposes and identifies standards for interoperability of rating and description services (such as libraries or national health portals) and fosters a worldwide collaboration to guide consumers to high-quality information on the web.

Publications - RDF 2015-4 | Alaska Division of Geological & Geophysical

Science.gov Websites

, and the northern Darby Mountains, Bendeleben, Candle, Kotzebue, and Solomon quadrangles, Alaska publication sales page for more information. Quadrangle(s): Bendeleben; Candle; Kotzebue; Solomon drainages, Granite Mountain, and the northern Darby Mountains, Bendeleben, Candle, Kotzebue, and Solomon

Publications - RDF 2004-1 | Alaska Division of Geological & Geophysical

Science.gov Websites

, C-4, and B-5 quadrangles, Alaska Authors: Athey, J.E., Layer, P.W., and Drake, Jeff Publication Date ): Livengood Bibliographic Reference Athey, J.E., Layer, P.W., and Drake, Jeff, 2004, 40Ar/39Ar ages of rocks

Publications - RDF 2002-1 | Alaska Division of Geological & Geophysical

Science.gov Websites

., Clautice, K.H., Flynn, R.L., Grady, J.C., Munly, W.C., and Johnson, M.R. Publication Date: Aug 2002 ., Flynn, R.L., Grady, J.C., Munly, W.C., and Johnson, M.R., 2002, Major-oxide, minor-oxide, trace-element

Assignment of EC Numbers to Enzymatic Reactions with Reaction Difference Fingerprints

PubMed Central

Hu, Qian-Nan; Zhu, Hui; Li, Xiaobing; Zhang, Manman; Deng, Zhe; Yang, Xiaoyan; Deng, Zixin

2012-01-01

The EC numbers represent enzymes and enzyme genes (genomic information), but they are also utilized as identifiers of enzymatic reactions (chemical information). In the present work (ECAssigner), our newly proposed reaction difference fingerprints (RDF) are applied to assign EC numbers to enzymatic reactions. The fingerprints of reactant molecules minus the fingerprints of product molecules will generate reaction difference fingerprints, which are then used to calculate reaction Euclidean distance, a reaction similarity measurement, of two reactions. The EC number of the most similar training reaction will be assigned to an input reaction. For 5120 balanced enzymatic reactions, the RDF with a fingerprint length at 3 obtained at the sub-subclass, subclass, and main class level with cross-validation accuracies of 83.1%, 86.7%, and 92.6% respectively. Compared with three published methods, ECAssigner is the first fully automatic server for EC number assignment. The EC assignment system (ECAssigner) is freely available via: http://cadd.whu.edu.cn/ecassigner/. PMID:23285222

Fly ash in landfill top covers - a review.

PubMed

Brännvall, E; Kumpiene, J

2016-01-01

Increase of energy recovery from municipal solid waste by incineration results in the increased amounts of incineration residues, such as fly ash, that have to be taken care of. Material properties should define whether fly ash is a waste or a viable resource to be used for various applications. Here, two areas of potential fly ash application are reviewed: the use of fly ash in a landfill top cover either as a liner material or as a soil amendment in vegetation layer. Fly ashes from incineration of three types of fuel are considered: refuse derived fuel (RDF), municipal solid waste incineration (MSWI) and biofuel. Based on the observations, RDF and MSWI fly ash is considered as suitable materials to be used in a landfill top cover liner. Whereas MSWI and biofuel fly ashes based on element availability for plant studies, could be considered suitable for the vegetation layer of the top cover. Responsible application of MSWI ashes is, however, warranted in order to avoid element accumulation in soil and elevation of background values over time.

Composing Data Parallel Code for a SPARQL Graph Engine

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

Castellana, Vito G.; Tumeo, Antonino; Villa, Oreste

Big data analytics process large amount of data to extract knowledge from them. Semantic databases are big data applications that adopt the Resource Description Framework (RDF) to structure metadata through a graph-based representation. The graph based representation provides several benefits, such as the possibility to perform in memory processing with large amounts of parallelism. SPARQL is a language used to perform queries on RDF-structured data through graph matching. In this paper we present a tool that automatically translates SPARQL queries to parallel graph crawling and graph matching operations. The tool also supports complex SPARQL constructs, which requires more than basicmore » graph matching for their implementation. The tool generates parallel code annotated with OpenMP pragmas for x86 Shared-memory Multiprocessors (SMPs). With respect to commercial database systems such as Virtuoso, our approach reduces memory occupation due to join operations and provides higher performance. We show the scaling of the automatically generated graph-matching code on a 48-core SMP.« less

ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology.

PubMed

Jiang, Guoqian; Solbrig, Harold R; Chute, Christopher G

2011-01-01

A source of semantically coded Adverse Drug Event (ADE) data can be useful for identifying common phenotypes related to ADEs. We proposed a comprehensive framework for building a standardized ADE knowledge base (called ADEpedia) through combining ontology-based approach with semantic web technology. The framework comprises four primary modules: 1) an XML2RDF transformation module; 2) a data normalization module based on NCBO Open Biomedical Annotator; 3) a RDF store based persistence module; and 4) a front-end module based on a Semantic Wiki for the review and curation. A prototype is successfully implemented to demonstrate the capability of the system to integrate multiple drug data and ontology resources and open web services for the ADE data standardization. A preliminary evaluation is performed to demonstrate the usefulness of the system, including the performance of the NCBO annotator. In conclusion, the semantic web technology provides a highly scalable framework for ADE data source integration and standard query service.

Scenario driven data modelling: a method for integrating diverse sources of data and data streams

PubMed Central

2011-01-01

Background Biology is rapidly becoming a data intensive, data-driven science. It is essential that data is represented and connected in ways that best represent its full conceptual content and allows both automated integration and data driven decision-making. Recent advancements in distributed multi-relational directed graphs, implemented in the form of the Semantic Web make it possible to deal with complicated heterogeneous data in new and interesting ways. Results This paper presents a new approach, scenario driven data modelling (SDDM), that integrates multi-relational directed graphs with data streams. SDDM can be applied to virtually any data integration challenge with widely divergent types of data and data streams. In this work, we explored integrating genetics data with reports from traditional media. SDDM was applied to the New Delhi metallo-beta-lactamase gene (NDM-1), an emerging global health threat. The SDDM process constructed a scenario, created a RDF multi-relational directed graph that linked diverse types of data to the Semantic Web, implemented RDF conversion tools (RDFizers) to bring content into the Sematic Web, identified data streams and analytical routines to analyse those streams, and identified user requirements and graph traversals to meet end-user requirements. Conclusions We provided an example where SDDM was applied to a complex data integration challenge. The process created a model of the emerging NDM-1 health threat, identified and filled gaps in that model, and constructed reliable software that monitored data streams based on the scenario derived multi-relational directed graph. The SDDM process significantly reduced the software requirements phase by letting the scenario and resulting multi-relational directed graph define what is possible and then set the scope of the user requirements. Approaches like SDDM will be critical to the future of data intensive, data-driven science because they automate the process of converting massive data streams into usable knowledge. PMID:22165854

Spatial Knowledge Infrastructures - Creating Value for Policy Makers and Benefits the Community

NASA Astrophysics Data System (ADS)

Arnold, L. M.

2016-12-01

The spatial data infrastructure is arguably one of the most significant advancements in the spatial sector. It's been a game changer for governments, providing for the coordination and sharing of spatial data across organisations and the provision of accessible information to the broader community of users. Today however, end-users such as policy-makers require far more from these spatial data infrastructures. They want more than just data; they want the knowledge that can be extracted from data and they don't want to have to download, manipulate and process data in order to get the knowledge they seek. It's time for the spatial sector to reduce its focus on data in spatial data infrastructures and take a more proactive step in emphasising and delivering the knowledge value. Nowadays, decision-makers want to be able to query at will the data to meet their immediate need for knowledge. This is a new value proposal for the decision-making consumer and will require a shift in thinking. This paper presents a model for a Spatial Knowledge Infrastructure and underpinning methods that will realise a new real-time approach to delivering knowledge. The methods embrace the new capabilities afforded through the sematic web, domain and process ontologies and natural query language processing. Semantic Web technologies today have the potential to transform the spatial industry into more than just a distribution channel for data. The Semantic Web RDF (Resource Description Framework) enables meaning to be drawn from data automatically. While pushing data out to end-users will remain a central role for data producers, the power of the semantic web is that end-users have the ability to marshal a broad range of spatial resources via a query to extract knowledge from available data. This can be done without actually having to configure systems specifically for the end-user. All data producers need do is make data accessible in RDF and the spatial analytics does the rest.

A program for the conversion of The National Map data from proprietary format to resource description framework (RDF)

USGS Publications Warehouse

Bulen, Andrew; Carter, Jonathan J.; Varanka, Dalia E.

2011-01-01

To expand data functionality and capabilities for users of The National Map of the U.S. Geological Survey, data sets for six watersheds and three urban areas were converted from the Best Practices vector data model formats to Semantic Web data formats. This report describes and documents the conver-sion process. The report begins with an introduction to basic Semantic Web standards and the background of The National Map. Data were converted from a proprietary format to Geog-raphy Markup Language to capture the geometric footprint of topographic data features. Configuration files were designed to eliminate redundancy and make the conversion more efficient. A SPARQL endpoint was established for data validation and queries. The report concludes by describing the results of the conversion.

The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery

PubMed Central

2014-01-01

The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description of arbitrary (real, hypothesized, virtual, fictional) objects, processes and their attributes. SIO specifies simple design patterns to describe and associate qualities, capabilities, functions, quantities, and informational entities including textual, geometrical, and mathematical entities, and provides specific extensions in the domains of chemistry, biology, biochemistry, and bioinformatics. SIO provides an ontological foundation for the Bio2RDF linked data for the life sciences project and is used for semantic integration and discovery for SADI-based semantic web services. SIO is freely available to all users under a creative commons by attribution license. See website for further information: http://sio.semanticscience.org. PMID:24602174

User-Centric Approach for Benchmark RDF Data Generator in Big Data Performance Analysis

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

Purohit, Sumit; Paulson, Patrick R.; Rodriguez, Luke R.

This research focuses on user-centric approach of building such tools and proposes a flexible, extensible, and easy to use framework to support performance analysis of Big Data systems. Finally, case studies from two different domains are presented to validate the framework.

Ontology Matching Across Domains

DTIC Science & Technology

2010-05-01

matching include GMO [1], Anchor-Prompt [2], and Similarity Flooding [3]. GMO is an iterative structural matcher, which uses RDF bipartite graphs to...AFRL under contract# FA8750-09-C-0058. References [1] Hu, W., Jian, N., Qu, Y., Wang, Y., “ GMO : a graph matching for ontologies”, in: Proceedings of

A FIELD TEST USING COAL:DRDF BLENDS IN SPREADER STOKER-FIRED BOILERS

EPA Science Inventory

This program was conducted to characterize and demonstrate the technical, economic, and environmental feasibility of combustion densified forms of refuse derived fuel (dRDF) blended with coal in spreader stoker-fired boilers. A total of 258.5 Mg (285 tons) of pelletized 1/2-inch-...

Publications - RDF 2005-2 | Alaska Division of Geological & Geophysical

Science.gov Websites

, and non-carbonate carbon data from rocks collected in the Solomon, Bendeleben, and Nome quadrangles for more information. Quadrangle(s): Bendeleben; Nome; Solomon Bibliographic Reference Werdon, M.B , geochemical, and non-carbonate carbon data from rocks collected in the Solomon, Bendeleben, and Nome

Publications - RDF 2011-1 | Alaska Division of Geological & Geophysical

Science.gov Websites

Solomon Quadrangle, Seward Peninsula, Alaska Authors: Werdon, M.B. Publication Date: Mar 2011 Publisher or please see our publication sales page for more information. Quadrangle(s): Solomon Bibliographic Reference Werdon, M.B., 2011, Outcrop structural data collected in 2006 in the Solomon Quadrangle, Seward

Multi-INT Complex Event Processing using Approximate, Incremental Graph Pattern Search

DTIC Science & Technology

2012-06-01

graph pattern search and SPARQL queries . Total execution time for 10 executions each of 5 random pattern searches in synthetic data sets...01/11 1000 10000 100000 RDF triples Time (secs) 10 20 Graph pattern algorithm SPARQL queries Initial Performance Comparisons 09/18/11 2011 Thrust Area

12 CFR 1292.1 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Investment Cash Advance program means: (1) A Bank's AHP; (2) A Bank's CIP; (3) A Bank's RDF program or UDF...) through (1)(iv), and (2)(i) and (2)(ii) of this definition are eligible for CIP advances. Targeted...; (3) For advances provided under CIP: (i) For economic development projects, incomes at or below 80...

12 CFR 952.1 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CIP; (3) A Bank's RDF program or UDF program using any combination of the targeted beneficiaries and... paragraphs (1)(i) through (1)(iv), and (2)(i) and (2)(ii) of this definition are eligible for CIP advances..., for a family of four; (3) For advances provided under CIP: (i) For economic development projects...

12 CFR 952.1 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CIP; (3) A Bank's RDF program or UDF program using any combination of the targeted beneficiaries and... paragraphs (1)(i) through (1)(iv), and (2)(i) and (2)(ii) of this definition are eligible for CIP advances..., for a family of four; (3) For advances provided under CIP: (i) For economic development projects...

12 CFR 952.1 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CIP; (3) A Bank's RDF program or UDF program using any combination of the targeted beneficiaries and... paragraphs (1)(i) through (1)(iv), and (2)(i) and (2)(ii) of this definition are eligible for CIP advances..., for a family of four; (3) For advances provided under CIP: (i) For economic development projects...

The semantic planetary data system

NASA Technical Reports Server (NTRS)

Hughes, J. Steven; Crichton, Daniel; Kelly, Sean; Mattmann, Chris

2005-01-01

This paper will provide a brief overview of the PDS data model and the PDS catalog. It will then describe the implentation of the Semantic PDS including the development of the formal ontology, the generation of RDFS/XML and RDF/XML data sets, and the buiding of the semantic search application.

Social Networking on the Semantic Web

ERIC Educational Resources Information Center

Finin, Tim; Ding, Li; Zhou, Lina; Joshi, Anupam

2005-01-01

Purpose: Aims to investigate the way that the semantic web is being used to represent and process social network information. Design/methodology/approach: The Swoogle semantic web search engine was used to construct several large data sets of Resource Description Framework (RDF) documents with social network information that were encoded using the…

An Introduction to the Resource Description Framework.

ERIC Educational Resources Information Center

Miller, Eric

1998-01-01

Explains the Resource Description Framework (RDF), an infrastructure developed under the World Wide Web Consortium that enables the encoding, exchange, and reuse of structured metadata. It is an application of Extended Markup Language (XML), which is a subset of Standard Generalized Markup Language (SGML), and helps with expressing semantics.…

SU-E-T-354: Efficient and Enhanced QA Testing of Linear Accelerators Using a Real-Time Beam Monitor

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

Jung, J; Farrokhkish, M; Norrlinger, B

2015-06-15

Purpose: To investigate the feasibility of performing routine QA tests of linear accelerators (Linac) using the Integral Quality Monitoring (IQM) system. The system, consisting of a 1-D sensitivity gradient large area ion-chamber mounted at the collimator, allows automatic collection and analysis of beam data. Methods: The IQM was investigated to perform several QA constancy tests, similar to those recommended by AAPM TG142, of a Linac including: beam output, MLC calibration, beam symmetry, relative dose factor (RDF), dose linearity, output as a function of gantry angle and dose rate. All measurements by the IQM system accompanied a reference measurement using amore » conventional dosimetry system and were performed on an Elekta Infinity Linac with Agility MLC. The MLC calibration check is done using a Picket-Fence type 2×10cm{sup 2} field positioned at different off-axis locations along the chamber gradient. Beam symmetry constancy values are established by signals from an 4×4cm{sup 2} aperture located at various off-axis positions; the sensitivity of the test was determined by the changes in the signals in response to a tilt in the beam. The data for various square field sizes were used to develop a functional relationship with RDF. Results: The IQM tracked the beam output well within 1% of the reference ion-chamber readings. The Picket-Fence type field test detected a 1mm shift error of one MLC bank. The system was able to detect 2.5% or greater beam asymmetry. The IQM results for all other QA tests were found to agree with the reference values to within 0.5%. Conclusion: It was demonstrated that the IQM system can effectively monitor the Linac performance parameters for the purpose of routine QA constancy tests. With minimum user interactions a comprehensive set of tests can be performed efficiently, allowing frequent monitoring of the Linac. The presenting author’s salary is funded by the manufacturer of the QA device. All the other authors have financial interests with the commercialization of this QA device.« less

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

Cao, Siqin; Department of Chemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon; Sheong, Fu Kit

Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achievemore » this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute.« less

Publications - RDF 2007-4 | Alaska Division of Geological & Geophysical

Science.gov Websites

, and non-carbonate carbon data from rocks collected in the Solomon and Nome quadrangles, Seward information. Quadrangle(s): Nome; Solomon Bibliographic Reference Werdon, M.B., Newberry, R.J., Szumigala, D.J -carbonate carbon data from rocks collected in the Solomon and Nome quadrangles, Seward Peninsula, Alaska in

Digital Rights Management Implemented by RDF Graph Approach

ERIC Educational Resources Information Center

Yang, Jin Tan; Horng, Huai-Chien

2006-01-01

This paper proposes a design framework for constructing Digital Rights Management (DRM) that enables learning objects in legal usage. The central theme of this framework is that any design of a DRM must have theories as foundations to make the maintenance, extension or interoperability easy. While a learning objective consists of learning…

Map Metadata: Essential Elements for Search and Storage

ERIC Educational Resources Information Center

Beamer, Ashley

2009-01-01

Purpose: The purpose of this paper is to develop an understanding of the issues surrounding the cataloguing of maps in archives and libraries. An investigation into appropriate metadata formats, such as MARC21, EAD and Dublin Core with RDF, shows how particular map data can be stored. Mathematical map elements, specifically co-ordinates, are…

46 CFR 148.250 - Direct reduced iron (DRI); hot-molded briquettes.

Code of Federal Regulations, 2011 CFR

2011-10-01

... concentration of fines (pieces less than 6.35mm in size) in any one location in the cargo hold. (f) Adequate... hot-molded briquettes. (h) Radar and RDF scanners must be adequately protected against dust generated during cargo transfer operations of DRI hot-molded briquettes. (i) During final discharge only, a fine...

46 CFR 148.250 - Direct reduced iron (DRI); hot-molded briquettes.

Code of Federal Regulations, 2012 CFR

2012-10-01

... concentration of fines (pieces less than 6.35mm in size) in any one location in the cargo hold. (f) Adequate... hot-molded briquettes. (h) Radar and RDF scanners must be adequately protected against dust generated during cargo transfer operations of DRI hot-molded briquettes. (i) During final discharge only, a fine...

46 CFR 148.250 - Direct reduced iron (DRI); hot-molded briquettes.

Code of Federal Regulations, 2014 CFR

2014-10-01

... concentration of fines (pieces less than 6.35mm in size) in any one location in the cargo hold. (f) Adequate... hot-molded briquettes. (h) Radar and RDF scanners must be adequately protected against dust generated during cargo transfer operations of DRI hot-molded briquettes. (i) During final discharge only, a fine...

46 CFR 148.250 - Direct reduced iron (DRI); hot-molded briquettes.

Code of Federal Regulations, 2013 CFR

2013-10-01

... concentration of fines (pieces less than 6.35mm in size) in any one location in the cargo hold. (f) Adequate... hot-molded briquettes. (h) Radar and RDF scanners must be adequately protected against dust generated during cargo transfer operations of DRI hot-molded briquettes. (i) During final discharge only, a fine...

Publications - RDF 2015-7 | Alaska Division of Geological & Geophysical

Science.gov Websites

, Geochemical reanalysis of historical U.S. Geological Survey sediment samples from the northeastern Alaska Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

Publications - RDF 2015-5 | Alaska Division of Geological & Geophysical

Science.gov Websites

Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical Alaska's Mineral Industry Reports AKGeology.info Rare Earth Elements WebGeochem Engineering Geology Alaska

Publications - RDF 2016-3 | Alaska Division of Geological & Geophysical

Science.gov Websites

Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical Alaska's Mineral Industry Reports AKGeology.info Rare Earth Elements WebGeochem Engineering Geology Alaska

Publications - RDF 2005-4 | Alaska Division of Geological & Geophysical

Science.gov Websites

District; Trace Elements; Trace Metals; Tungsten; Uranium; Vanadium; Yttrium; Zinc; Zirconium Top of Page Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

Publications - RDF 2016-5 | Alaska Division of Geological & Geophysical

Science.gov Websites

Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical Alaska's Mineral Industry Reports AKGeology.info Rare Earth Elements WebGeochem Engineering Geology Alaska

Publications - RDF 2010-2 | Alaska Division of Geological & Geophysical

Science.gov Websites

Prospect; Trace Elements; Trace Metals; Triassic; Wrangellia Terrane; geoscientificInformation Top of Page Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

Publications - RDF 2014-22 | Alaska Division of Geological & Geophysical

Science.gov Websites

Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical Alaska's Mineral Industry Reports AKGeology.info Rare Earth Elements WebGeochem Engineering Geology Alaska

Publications - RDF 2000-4 | Alaska Division of Geological & Geophysical

Science.gov Websites

Oxides; Palladium; Platinum; Rare Earth Elements; STATEMAP Project; Trace Metals Top of Page Department Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

Publications - RDF 2015-6 | Alaska Division of Geological & Geophysical

Science.gov Websites

Sediments; Trace Elements; Trace Geochemical; Trace Metals; geoscientificInformation Top of Page Department Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

Publications - RDF 2015-8 | Alaska Division of Geological & Geophysical

Science.gov Websites

from the Tonsina area, Valdez Quadrangle, Alaska: Alaska Division of Geological & Geophysical Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

An Ontology Infrastructure for an E-Learning Scenario

ERIC Educational Resources Information Center

Guo, Wen-Ying; Chen, De-Ren

2007-01-01

Selecting appropriate learning services for a learner from a large number of heterogeneous knowledge sources is a complex and challenging task. This article illustrates and discusses how Semantic Web technologies such as RDF [resource description framework] and ontology can be applied to e-learning systems to help the learner in selecting an…

NATIONAL INCINERATOR TESTING AND EVALUATION PROGRAM: THE ENVIRONMENTAL CHARACTERIZATION OF REFUSE-DERIVED FUEL (RDF) COMBUSTION TECHNOLOGY - MID-CONNECTICUT FACILITY,

EPA Science Inventory

The report gives results of an environmental characterization of refuse-derived, semi-suspension burning technology at a facility in Hartford, CT, that represents state-of-the-art technology, including a spray dryer/fabric filter flue gas cleaning (FGC) system for each unit. The ...

BioSWR – Semantic Web Services Registry for Bioinformatics

PubMed Central

Repchevsky, Dmitry; Gelpi, Josep Ll.

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license. PMID:25233118

BioSWR--semantic web services registry for bioinformatics.

PubMed

Repchevsky, Dmitry; Gelpi, Josep Ll

2014-01-01

Despite of the variety of available Web services registries specially aimed at Life Sciences, their scope is usually restricted to a limited set of well-defined types of services. While dedicated registries are generally tied to a particular format, general-purpose ones are more adherent to standards and usually rely on Web Service Definition Language (WSDL). Although WSDL is quite flexible to support common Web services types, its lack of semantic expressiveness led to various initiatives to describe Web services via ontology languages. Nevertheless, WSDL 2.0 descriptions gained a standard representation based on Web Ontology Language (OWL). BioSWR is a novel Web services registry that provides standard Resource Description Framework (RDF) based Web services descriptions along with the traditional WSDL based ones. The registry provides Web-based interface for Web services registration, querying and annotation, and is also accessible programmatically via Representational State Transfer (REST) API or using a SPARQL Protocol and RDF Query Language. BioSWR server is located at http://inb.bsc.es/BioSWR/and its code is available at https://sourceforge.net/projects/bioswr/under the LGPL license.

Linking netCDF Data with the Semantic Web - Enhancing Data Discovery Across Domains

NASA Astrophysics Data System (ADS)

Biard, J. C.; Yu, J.; Hedley, M.; Cox, S. J. D.; Leadbetter, A.; Car, N. J.; Druken, K. A.; Nativi, S.; Davis, E.

2016-12-01

Geophysical data communities are publishing large quantities of data across a wide variety of scientific domains which are overlapping more and more. Whilst netCDF is a common format for many of these communities, it is only one of a large number of data storage and transfer formats. One of the major challenges ahead is finding ways to leverage these diverse data sets to advance our understanding of complex problems. We describe a methodology for incorporating Resource Description Framework (RDF) triples into netCDF files called netCDF-LD (netCDF Linked Data). NetCDF-LD explicitly connects the contents of netCDF files - both data and metadata, with external web-based resources, including vocabularies, standards definitions, and data collections, and through them, a whole host of related information. This approach also preserves and enhances the self describing essence of the netCDF format and its metadata, whilst addressing the challenge of integrating various conventions into files. We present a case study illustrating how reasoning over RDF graphs can empower researchers to discover datasets across domain boundaries.

An introduction to the Semantic Web for health sciences librarians.

PubMed

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-04-01

The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. The paper is structured into two main parts. "Semantic Web Technology" provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. "Semantic Web Applications and Research Projects in the Biomedical Field" is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects.

Terminology representation guidelines for biomedical ontologies in the semantic web notations.

PubMed

Tao, Cui; Pathak, Jyotishman; Solbrig, Harold R; Wei, Wei-Qi; Chute, Christopher G

2013-02-01

Terminologies and ontologies are increasingly prevalent in healthcare and biomedicine. However they suffer from inconsistent renderings, distribution formats, and syntax that make applications through common terminologies services challenging. To address the problem, one could posit a shared representation syntax, associated schema, and tags. We identified a set of commonly-used elements in biomedical ontologies and terminologies based on our experience with the Common Terminology Services 2 (CTS2) Specification as well as the Lexical Grid (LexGrid) project. We propose guidelines for precisely such a shared terminology model, and recommend tags assembled from SKOS, OWL, Dublin Core, RDF Schema, and DCMI meta-terms. We divide these guidelines into lexical information (e.g. synonyms, and definitions) and semantic information (e.g. hierarchies). The latter we distinguish for use by informal terminologies vs. formal ontologies. We then evaluate the guidelines with a spectrum of widely used terminologies and ontologies to examine how the lexical guidelines are implemented, and whether our proposed guidelines would enhance interoperability. Copyright © 2012 Elsevier Inc. All rights reserved.

Disease Compass- a navigation system for disease knowledge based on ontology and linked data techniques.

PubMed

Kozaki, Kouji; Yamagata, Yuki; Mizoguchi, Riichiro; Imai, Takeshi; Ohe, Kazuhiko

2017-06-19

Medical ontologies are expected to contribute to the effective use of medical information resources that store considerable amount of data. In this study, we focused on disease ontology because the complicated mechanisms of diseases are related to concepts across various medical domains. The authors developed a River Flow Model (RFM) of diseases, which captures diseases as the causal chains of abnormal states. It represents causes of diseases, disease progression, and downstream consequences of diseases, which is compliant with the intuition of medical experts. In this paper, we discuss a fact repository for causal chains of disease based on the disease ontology. It could be a valuable knowledge base for advanced medical information systems. We developed the fact repository for causal chains of diseases based on our disease ontology and abnormality ontology. This section summarizes these two ontologies. It is developed as linked data so that information scientists can access it using SPARQL queries through an Resource Description Framework (RDF) model for causal chain of diseases. We designed the RDF model as an implementation of the RFM for the fact repository based on the ontological definitions of the RFM. 1554 diseases and 7080 abnormal states in six major clinical areas, which are extracted from the disease ontology, are published as linked data (RDF) with SPARQL endpoint (accessible API). Furthermore, the authors developed Disease Compass, a navigation system for disease knowledge. Disease Compass can browse the causal chains of a disease and obtain related information, including abnormal states, through two web services that provide general information from linked data, such as DBpedia, and 3D anatomical images. Disease Compass can provide a complete picture of disease-associated processes in such a way that fits with a clinician's understanding of diseases. Therefore, it supports user exploration of disease knowledge with access to pertinent information from a variety of sources.

Physical Samples Linked Data in Action

NASA Astrophysics Data System (ADS)

Ji, P.; Arko, R. A.; Lehnert, K.; Bristol, S.

2017-12-01

Most data and metadata related to physical samples currently reside in isolated relational databases driven by diverse data models. How to approach the challenge for sharing, interchanging and integrating data from these difference relational databases motivated us to publish Linked Open Data for collections of physical samples, using Semantic Web technologies including the Resource Description Framework (RDF), RDF Query Language (SPARQL), and Web Ontology Language (OWL). In last few years, we have released four knowledge graphs concentrated on physical samples, including System for Earth Sample Registration (SESAR), USGS National Geochemical Database (NGDC), Ocean Biogeographic Information System (OBIS), and Earthchem Database. Currently the four knowledge graphs contain over 12 million facets (triples) about objects of interest to the geoscience domain. Choosing appropriate domain ontologies for representing context of data is the core of the whole work. Geolink ontology developed by Earthcube Geolink project was used as top level to represent common concepts like person, organization, cruise, etc. Physical sample ontology developed by Interdisciplinary Earth Data Alliance (IEDA) and Darwin Core vocabulary were used as second level to describe details about geological samples and biological diversity. We also focused on finding and building best tool chains to support the whole life cycle of publishing linked data we have, including information retrieval, linked data browsing and data visualization. Currently, Morph, Virtuoso Server, LodView, LodLive, and YASGUI were employed for converting, storing, representing, and querying data in a knowledge base (RDF triplestore). Persistent digital identifier is another main point we concentrated on. Open Researcher & Contributor IDs (ORCIDs), International Geo Sample Numbers (IGSNs), Global Research Identifier Database (GRID) and other persistent identifiers were used to link different resources from various graphs with person, sample, organization, cruise, etc. This work is supported by the EarthCube "GeoLink" project (NSF# ICER14-40221 and others) and the "USGS-IEDA Partnership to Support a Data Lifecycle Framework and Tools" project (USGS# G13AC00381).

Publishing Linked Open Data for Physical Samples - Lessons Learned

NASA Astrophysics Data System (ADS)

Ji, P.; Arko, R. A.; Lehnert, K.; Bristol, S.

2016-12-01

Most data and information about physical samples and associated sampling features currently reside in relational databases. Integrating common concepts from various databases has motivated us to publish Linked Open Data for collections of physical samples, using Semantic Web technologies including the Resource Description Framework (RDF), RDF Query Language (SPARQL), and Web Ontology Language (OWL). The goal of our work is threefold: To evaluate and select ontologies in different granularities for common concepts; to establish best practices and develop a generic methodology for publishing physical sample data stored in relational database as Linked Open Data; and to reuse standard community vocabularies from the International Commission on Stratigraphy (ICS), Global Volcanism Program (GVP), General Bathymetric Chart of the Oceans (GEBCO), and others. Our work leverages developments in the EarthCube GeoLink project and the Interdisciplinary Earth Data Alliance (IEDA) facility for modeling and extracting physical sample data stored in relational databases. Reusing ontologies developed by GeoLink and IEDA has facilitated discovery and integration of data and information across multiple collections including the USGS National Geochemical Database (NGDB), System for Earth Sample Registration (SESAR), and Index to Marine & Lacustrine Geological Samples (IMLGS). We have evaluated, tested, and deployed Linked Open Data tools including Morph, Virtuoso Server, LodView, LodLive, and YASGUI for converting, storing, representing, and querying data in a knowledge base (RDF triplestore). Using persistent identifiers such as Open Researcher & Contributor IDs (ORCIDs) and International Geo Sample Numbers (IGSNs) at the record level makes it possible for other repositories to link related resources such as persons, datasets, documents, expeditions, awards, etc. to samples, features, and collections. This work is supported by the EarthCube "GeoLink" project (NSF# ICER14-40221 and others) and the "USGS-IEDA Partnership to Support a Data Lifecycle Framework and Tools" project (USGS# G13AC00381).

Life Cycle Assessment of the MBT plant in Ano Liossia, Athens, Greece

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

Abeliotis, Konstadinos, E-mail: kabeli@hua.gr; Kalogeropoulos, Alexandros; Lasaridi, Katia

2012-01-15

Highlights: Black-Right-Pointing-Pointer We model the operation of an MBT plant in Greece based on LCA. Black-Right-Pointing-Pointer We compare four different MBT operating scenarios (among them and with landfilling). Black-Right-Pointing-Pointer Even the current operation of the MBT plant is preferable to landfilling. Black-Right-Pointing-Pointer Utilization of the MBT compost and metals generates the most environmental gains. Black-Right-Pointing-Pointer Thermal exploitation of RDF improves further the environmental performance of the plant. - Abstract: The aim of this paper is the application of Life Cycle Assessment to the operation of the MBT facility of Ano Liossia in the region of Attica in Greece. The regionmore » of Attica is home to almost half the population of Greece and the management of its waste is a major issue. In order to explicitly analyze the operation of the MBT plant, five scenarios were generated. Actual operation data of the MBT plant for the year 2008 were provided by the region of Attica and the LCA modeling was performed via the SimaPro 5.1 software while impact assessment was performed utilizing the Eco-indicator'99 method. The results of our analysis indicate that even the current operation of the MBT plant is preferable to landfilling. Among the scenarios of MBT operation, the one with complete utilization of the MBT outputs, i.e. compost, RDF, ferrous and non-ferrous metals, is the one that generates the most environmental gains. Our analysis indicates that the exploitation of RDF via incineration is the key factor towards improving the environmental performance of the MBT plant. Our findings provide a quantitative understanding of the MBT plant. Interpretation of results showed that proper operation of the modern waste management systems can lead to substantial reduction of environmental impacts and savings of resources.« less

Publication and Retrieval of Computational Chemical-Physical Data Via the Semantic Web. Final Technical Report

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

Ostlund, Neil

This research showed the feasibility of applying the concepts of the Semantic Web to Computation Chemistry. We have created the first web portal (www.chemsem.com) that allows data created in the calculations of quantum chemistry, and other such chemistry calculations to be placed on the web in a way that makes the data accessible to scientists in a semantic form never before possible. The semantic web nature of the portal allows data to be searched, found, and used as an advance over the usual approach of a relational database. The semantic data on our portal has the nature of a Giantmore » Global Graph (GGG) that can be easily merged with related data and searched globally via a SPARQL Protocol and RDF Query Language (SPARQL) that makes global searches for data easier than with traditional methods. Our Semantic Web Portal requires that the data be understood by a computer and hence defined by an ontology (vocabulary). This ontology is used by the computer in understanding the data. We have created such an ontology for computational chemistry (purl.org/gc) that encapsulates a broad knowledge of the field of computational chemistry. We refer to this ontology as the Gainesville Core. While it is perhaps the first ontology for computational chemistry and is used by our portal, it is only a start of what must be a long multi-partner effort to define computational chemistry. In conjunction with the above efforts we have defined a new potential file standard (Common Standard for eXchange – CSX for computational chemistry data). This CSX file is the precursor of data in the Resource Description Framework (RDF) form that the semantic web requires. Our portal translates CSX files (as well as other computational chemistry data files) into RDF files that are part of the graph database that the semantic web employs. We propose a CSX file as a convenient way to encapsulate computational chemistry data.« less

ODISEES: A New Paradigm in Data Access

NASA Astrophysics Data System (ADS)

Huffer, E.; Little, M. M.; Kusterer, J.

2013-12-01

As part of its ongoing efforts to improve access to data, the Atmospheric Science Data Center has developed a high-precision Earth Science domain ontology (the 'ES Ontology') implemented in a graph database ('the Semantic Metadata Repository') that is used to store detailed, semantically-enhanced, parameter-level metadata for ASDC data products. The ES Ontology provides the semantic infrastructure needed to drive the ASDC's Ontology-Driven Interactive Search Environment for Earth Science ('ODISEES'), a data discovery and access tool, and will support additional data services such as analytics and visualization. The ES ontology is designed on the premise that naming conventions alone are not adequate to provide the information needed by prospective data consumers to assess the suitability of a given dataset for their research requirements; nor are current metadata conventions adequate to support seamless machine-to-machine interactions between file servers and end-user applications. Data consumers need information not only about what two data elements have in common, but also about how they are different. End-user applications need consistent, detailed metadata to support real-time data interoperability. The ES ontology is a highly precise, bottom-up, queriable model of the Earth Science domain that focuses on critical details about the measurable phenomena, instrument techniques, data processing methods, and data file structures. Earth Science parameters are described in detail in the ES Ontology and mapped to the corresponding variables that occur in ASDC datasets. Variables are in turn mapped to well-annotated representations of the datasets that they occur in, the instrument(s) used to create them, the instrument platforms, the processing methods, etc., creating a linked-data structure that allows both human and machine users to access a wealth of information critical to understanding and manipulating the data. The mappings are recorded in the Semantic Metadata Repository as RDF-triples. An off-the-shelf Ontology Development Environment and a custom Metadata Conversion Tool comprise a human-machine/machine-machine hybrid tool that partially automates the creation of metadata as RDF-triples by interfacing with existing metadata repositories and providing a user interface that solicits input from a human user, when needed. RDF-triples are pushed to the Ontology Development Environment, where a reasoning engine executes a series of inference rules whose antecedent conditions can be satisfied by the initial set of RDF-triples, thereby generating the additional detailed metadata that is missing in existing repositories. A SPARQL Endpoint, a web-based query service and a Graphical User Interface allow prospective data consumers - even those with no familiarity with NASA data products - to search the metadata repository to find and order data products that meet their exact specifications. A web-based API will provide an interface for machine-to-machine transactions.

Ontology-Based Approaches to Improve RDF Triple Store

ERIC Educational Resources Information Center

Albahli, Saleh M.

2016-01-01

The World Wide Web enables an easy, instant access to a huge quantity of information. Over the last few decades, a number of improvements have been achieved that helped the web reach its current state. However, the current Internet links documents together without understanding them, and thus, makes the content of web only human-readable rather…

Data summary of municipal solid waste management alternatives. Volume 12, Numerically indexed bibliography

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

None

1992-10-01

This appendix contains the numerically indexed bibliography for the complete group of reports on municipal solid waste management alternatives. The list references information on the following topics: mass burn technologies, RDF technologies, fluidized bed combustion, pyrolysis and gasification of MSW, materials recovery- recycling technologies, sanitary landfills, composting and anaerobic digestion of MSW.

Data summary of municipal solid waste management alternatives. Volume 11, Alphabetically indexed bibliography

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

None

1992-10-01

This appendix contains the alphabetically indexed bibliography for the complete group of reports on municipal waste management alternatives. The references are listed for each of the following topics: mass burn technologies, RDF technologies, fluidized-bed combustion, pyrolysis and gasification of MSW, materials recovery- recycling technologies, sanitary landfills, composting, and anaerobic digestion of MSW.

Provenance Store Evaluation

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

Paulson, Patrick R.; Gibson, Tara D.; Schuchardt, Karen L.

2008-03-01

Requirements for the provenance store and access API are developed. Existing RDF stores and APIs are evaluated against the requirements and performance benchmarks. The team’s conclusion is to use MySQL as a database backend, with a possible move to Oracle in the near-term future. Both Jena and Sesame’s APIs will be supported, but new code will use the Jena API

Publications - RDF 2002-3 | Alaska Division of Geological & Geophysical

Science.gov Websites

geochemical data from the rocks collected in the Big Delta Quadrangle, Alaska in 2001 Authors: Athey, J.E or please see our publication sales page for more information. Quadrangle(s): Big Delta Bibliographic , minor-oxide, trace-element, and geochemical data from the rocks collected in the Big Delta Quadrangle

Publications - RDF 2001-1 | Alaska Division of Geological & Geophysical

Science.gov Websites

geochemical data from rocks collected in the Salcha River-Pogo area in 2000, Big Delta and northwestern Eagle more information. Quadrangle(s): Big Delta; Eagle Bibliographic Reference Werdon, M.B., Athey, J.E , and geochemical data from rocks collected in the Salcha River-Pogo area in 2000, Big Delta and

Publications - RDF 2003-2 | Alaska Division of Geological & Geophysical

Science.gov Websites

geochemical data from rocks collected in the Big Delta Quadrangle, Alaska in 2002 Authors: Werdon, M.B . Quadrangle(s): Big Delta Bibliographic Reference Werdon, M.B., Newberry, R.J., Athey, J.E., Szumigala, D.J -element, and geochemical data from rocks collected in the Big Delta Quadrangle, Alaska in 2002: Alaska

Improved vortex reactor system

DOEpatents

Diebold, James P.; Scahill, John W.

1995-01-01

An improved vortex reactor system for affecting fast pyrolysis of biomass and Refuse Derived Fuel (RDF) feed materials comprising: a vortex reactor having its axis vertically disposed in relation to a jet of a horizontally disposed steam ejector that impels feed materials from a feeder and solids from a recycle loop along with a motive gas into a top part of said reactor.

EFFECTS OF COMBUSTION PARAMETERS ON POLYCHLORINATED DIBENZODIOXIN AND DIBENZOFURAN HOMOLOGUE PROFILES FROM MUNICIPAL WASTE AND COAL CO-COMBUSTION

EPA Science Inventory

Variation in polychlorinated dibenzo-p-dioxin and polychlorinated dibenzofuran (PCDD and PCDF) homologue profiles from a pilot scale (0.6 MWt, 2x106 Btu/hr), co-fired-fuel [densified refuse derived fuel (dRDF) and high-sulfur Illinois coal] combustion system was used to provide i...

Publications - RDF 2015-16 | Alaska Division of Geological & Geophysical

Science.gov Websites

rocks collected in 2015 in the Wrangellia mineral assessment area, Alaska: Alaska Division of Geological Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

Publications - RDF 2008-2 v. 1.0.1 | Alaska Division of Geological &

Science.gov Websites

Geophysical Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Alaska's Mineral Industry Reports AKGeology.info Rare Earth Elements WebGeochem Engineering Geology Alaska

Publications - RDF 2012-3 | Alaska Division of Geological & Geophysical

Science.gov Websites

Assessment Project; Trace Elements; geoscientificInformation Top of Page Department of Natural Resources Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

Publications - RDF 2015-9 | Alaska Division of Geological & Geophysical

Science.gov Websites

samples from the Zane Hills, Hughes and Shungnak quadrangles, Alaska: Alaska Division of Geological & Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

Publications - RDF 2016-2 | Alaska Division of Geological & Geophysical

Science.gov Websites

, Major-oxide and trace-element geochemistry of mafic rocks in the Carboniferous Lisburne Group, Ivishak Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

Publications - RDF 2004-2 | Alaska Division of Geological & Geophysical

Science.gov Websites

; Trace Elements; Trace Metals; Tungsten; Vanadium; Yttrium; Zinc; Zirconium Top of Page Department of Surveys Skip to content State of Alaska myAlaska My Government Resident Business in Alaska Visiting Alaska State Employees DGGS State of Alaska search Alaska Division of Geological & Geophysical

THE EFFECT OF COFIRING HIGH-SULFUR COAL WITH MUNICIPAL WASTE ON FORMATION OF POLYCHLORINATED DIBENZODIOXIN AND POLYCHLORINATED DIBENZOFURAN

EPA Science Inventory

The effect of co-firing minor amounts (5-10 wt%) of high sulfur coal with municipal refuse-derived fuel (RDF) on emissions of polychlorinated dibenzo-p-dioxin (PCDD) and polychlorinated dibenzofuran (PCDF) was studied under a range of operating conditions. Through use of 2x facto...

Next Generation Models for Storage and Representation of Microbial Biological Annotation

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

Quest, Daniel J; Land, Miriam L; Brettin, Thomas S

2010-01-01

Background Traditional genome annotation systems were developed in a very different computing era, one where the World Wide Web was just emerging. Consequently, these systems are built as centralized black boxes focused on generating high quality annotation submissions to GenBank/EMBL supported by expert manual curation. The exponential growth of sequence data drives a growing need for increasingly higher quality and automatically generated annotation. Typical annotation pipelines utilize traditional database technologies, clustered computing resources, Perl, C, and UNIX file systems to process raw sequence data, identify genes, and predict and categorize gene function. These technologies tightly couple the annotation software systemmore » to hardware and third party software (e.g. relational database systems and schemas). This makes annotation systems hard to reproduce, inflexible to modification over time, difficult to assess, difficult to partition across multiple geographic sites, and difficult to understand for those who are not domain experts. These systems are not readily open to scrutiny and therefore not scientifically tractable. The advent of Semantic Web standards such as Resource Description Framework (RDF) and OWL Web Ontology Language (OWL) enables us to construct systems that address these challenges in a new comprehensive way. Results Here, we develop a framework for linking traditional data to OWL-based ontologies in genome annotation. We show how data standards can decouple hardware and third party software tools from annotation pipelines, thereby making annotation pipelines easier to reproduce and assess. An illustrative example shows how TURTLE (Terse RDF Triple Language) can be used as a human readable, but also semantically-aware, equivalent to GenBank/EMBL files. Conclusions The power of this approach lies in its ability to assemble annotation data from multiple databases across multiple locations into a representation that is understandable to researchers. In this way, all researchers, experimental and computational, will more easily understand the informatics processes constructing genome annotation and ultimately be able to help improve the systems that produce them.« less

Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study.

PubMed

Bandyopadhyay, Dibyendu; Bhanja, K; Mohan, Sadhana; Ghosh, Swapan K; Choudhury, Niharendu

2015-08-27

Like-charge ion-pair formation in an aqueous solution of guanidinium chloride (GdmCl) has two important facets. On one hand, it describes the role of the arginine (ARG) side chain in aggregation and dimer formation in proteins, and on the other hand, it lends support for the direct mechanism of protein denaturation by GdmCl. We employ all-atom molecular dynamics simulations to investigate the effect of GdmCl concentration on the like-charge ion-pair formation of guanidinium ions (Gdm(+)). From analyses of the radial distribution function (RDF) between the carbon atoms of two guanidinium moieties, the existence of both contact pairs and solvent-separated pairs has been observed. Although the peak height corresponding to the contact-pair state decreases, the number of Gdm(+) ions in the contact-pair state actually increases with increasing GdmCl concentration. We have also investigated the effect of the concentration of Gdm(+) on the structure of water. The effect of GdmCl concentration on the radial and tetrahedral structures of water is found to be negligibly small; however, GdmCl concentration has a considerable effect on the hydrogen-bonding structure of water. It is demonstrated that the presence of chloride ions, not Gdm(+), in the first solvation shell of water causes the distortion in the hydrogen-bonding network of water. In order to establish that Gdm(+) not only stacks against another Gdm(+) but also directly attacks the ARG residue of a protein or peptide, simulation of an ARG-rich peptide in 6 M aqueous solution of GdmCl has been performed. The analyses of RDFs and orientation distributions reveal that the Gdm(+) moiety of the GdmCl attacks the same moiety in the ARG side chain with a parallel stacking orientation.

A self-updating road map of The Cancer Genome Atlas.

PubMed

Robbins, David E; Grüneberg, Alexander; Deus, Helena F; Tanik, Murat M; Almeida, Jonas S

2013-05-15

Since 2011, The Cancer Genome Atlas' (TCGA) files have been accessible through HTTP from a public site, creating entirely new possibilities for cancer informatics by enhancing data discovery and retrieval. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data. However, to realize this possibility, a continually updated road map of files in the TCGA is required. Creation of such a road map represents a significant data modeling challenge, due to the size and fluidity of this resource: each of the 33 cancer types is instantiated in only partially overlapping sets of analytical platforms, while the number of data files available doubles approximately every 7 months. We developed an engine to index and annotate the TCGA files, relying exclusively on third-generation web technologies (Web 3.0). Specifically, this engine uses JavaScript in conjunction with the World Wide Web Consortium's (W3C) Resource Description Framework (RDF), and SPARQL, the query language for RDF, to capture metadata of files in the TCGA open-access HTTP directory. The resulting index may be queried using SPARQL, and enables file-level provenance annotations as well as discovery of arbitrary subsets of files, based on their metadata, using web standard languages. In turn, these abilities enhance the reproducibility and distribution of novel results delivered as elements of a web-based computational ecosystem. The development of the TCGA Roadmap engine was found to provide specific clues about how biomedical big data initiatives should be exposed as public resources for exploratory analysis, data mining and reproducible research. These specific design elements align with the concept of knowledge reengineering and represent a sharp departure from top-down approaches in grid initiatives such as CaBIG. They also present a much more interoperable and reproducible alternative to the still pervasive use of data portals. A prepared dashboard, including links to source code and a SPARQL endpoint, is available at http://bit.ly/TCGARoadmap. A video tutorial is available at http://bit.ly/TCGARoadmapTutorial. robbinsd@uab.edu.

A self-updating road map of The Cancer Genome Atlas

PubMed Central

Robbins, David E.; Grüneberg, Alexander; Deus, Helena F.; Tanik, Murat M.; Almeida, Jonas S.

2013-01-01

Motivation: Since 2011, The Cancer Genome Atlas’ (TCGA) files have been accessible through HTTP from a public site, creating entirely new possibilities for cancer informatics by enhancing data discovery and retrieval. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data. However, to realize this possibility, a continually updated road map of files in the TCGA is required. Creation of such a road map represents a significant data modeling challenge, due to the size and fluidity of this resource: each of the 33 cancer types is instantiated in only partially overlapping sets of analytical platforms, while the number of data files available doubles approximately every 7 months. Results: We developed an engine to index and annotate the TCGA files, relying exclusively on third-generation web technologies (Web 3.0). Specifically, this engine uses JavaScript in conjunction with the World Wide Web Consortium’s (W3C) Resource Description Framework (RDF), and SPARQL, the query language for RDF, to capture metadata of files in the TCGA open-access HTTP directory. The resulting index may be queried using SPARQL, and enables file-level provenance annotations as well as discovery of arbitrary subsets of files, based on their metadata, using web standard languages. In turn, these abilities enhance the reproducibility and distribution of novel results delivered as elements of a web-based computational ecosystem. The development of the TCGA Roadmap engine was found to provide specific clues about how biomedical big data initiatives should be exposed as public resources for exploratory analysis, data mining and reproducible research. These specific design elements align with the concept of knowledge reengineering and represent a sharp departure from top-down approaches in grid initiatives such as CaBIG. They also present a much more interoperable and reproducible alternative to the still pervasive use of data portals. Availability: A prepared dashboard, including links to source code and a SPARQL endpoint, is available at http://bit.ly/TCGARoadmap. A video tutorial is available at http://bit.ly/TCGARoadmapTutorial. Contact: robbinsd@uab.edu PMID:23595662

Network of Research Infrastructures for European Seismology (NERIES)-Web Portal Developments for Interactive Access to Earthquake Data on a European Scale

NASA Astrophysics Data System (ADS)

Spinuso, A.; Trani, L.; Rives, S.; Thomy, P.; Euchner, F.; Schorlemmer, D.; Saul, J.; Heinloo, A.; Bossu, R.; van Eck, T.

2009-04-01

The Network of Research Infrastructures for European Seismology (NERIES) is European Commission (EC) project whose focus is networking together seismological observatories and research institutes into one integrated European infrastructure that provides access to data and data products for research. Seismological institutes and organizations in European and Mediterranean countries maintain large, geographically distributed data archives, therefore this scenario suggested a design approach based on the concept of an internet service oriented architecture (SOA) to establish a cyberinfrastructure for distributed and heterogeneous data streams and services. Moreover, one of the goals of NERIES is to design and develop a Web portal that acts as the uppermost layer of the infrastructure and provides rendering capabilities for the underlying sets of data The Web services that are currently being designed and implemented will deliver data that has been adopted to appropriate formats. The parametric information about a seismic event is delivered using a seismology-specific Extensible mark-up Language(XML) format called QuakeML (https://quake.ethz.ch/quakeml), which has been formalized and implemented in coordination with global earthquake-information agencies. Uniform Resource Identifiers (URIs) are used to assign identifiers to (1) seismic-event parameters described by QuakeML, and (2) generic resources, for example, authorities, locations providers, location methods, software adopted, and so on, described by use of a data model constructed with the resource description framework (RDF) and accessible as a service. The European-Mediterranean Seismological Center (EMSC) has implemented a unique event identifier (UNID) that will create the seismic event URI used by the QuakeML data model. Access to data such as broadband waveform, accelerometric data and stations inventories will be also provided through a set of Web services that will wrap the middleware used by the seismological observatory or institute that is supplying the data. Each single application of the portal consists of a Java-based JSR-168-standard portlet (often provided with interactive maps for data discovery). In specific cases, it will be possible to distribute the deployment of the portlets among the data providers, such as seismological agencies, because of the adoption, within the distributed architecture of the NERIES portal of the Web Services for Remote Portlets (WSRP) standard for presentation-oriented web services The purpose of the portal is to provide to the user his own environment where he can surf and retrieve the data of interest, offering a set of shopping carts with storage and management facilities. This approach involves having the user interact with dedicated tools in order to compose personalized datasets that can be downloaded or combined with other information available either through the NERIES network of Web services or through the user`s own carts. Administrative applications also are provided to perform monitoring tasks such as retrieving service statistics or scheduling submitted data requests. An administrative tool is included that allows the RDF model to be extended, within certain constraints, with new classes and properties.

Network of Research Infrastructures for European Seismology (NERIES) - Web Portal Developments for Interactive Access to Earthquake Data on a European Scale

NASA Astrophysics Data System (ADS)

Spinuso, A.; Trani, L.; Rives, S.; Thomy, P.; Euchner, F.; Schorlemmer, D.; Saul, J.; Heinloo, A.; Bossu, R.; van Eck, T.

2008-12-01

The Network of Research Infrastructures for European Seismology (NERIES) is European Commission (EC) project whose focus is networking together seismological observatories and research institutes into one integrated European infrastructure that provides access to data and data products for research. Seismological institutes and organizations in European and Mediterranean countries maintain large, geographically distributed data archives, therefore this scenario suggested a design approach based on the concept of an internet service oriented architecture (SOA) to establish a cyberinfrastructure for distributed and heterogeneous data streams and services. Moreover, one of the goals of NERIES is to design and develop a Web portal that acts as the uppermost layer of the infrastructure and provides rendering capabilities for the underlying sets of data The Web services that are currently being designed and implemented will deliver data that has been adopted to appropriate formats. The parametric information about a seismic event is delivered using a seismology- specific Extensible mark-up Language(XML) format called QuakeML (https://quake.ethz.ch/quakeml), which has been formalized and implemented in coordination with global earthquake-information agencies. Uniform Resource Identifiers (URIs) are used to assign identifiers to (1) seismic-event parameters described by QuakeML, and (2) generic resources, for example, authorities, locations providers, location methods, software adopted, and so on, described by use of a data model constructed with the resource description framework (RDF) and accessible as a service. The European-Mediterranean Seismological Center (EMSC) has implemented a unique event identifier (UNID) that will create the seismic event URI used by the QuakeML data model. Access to data such as broadband waveform, accelerometric data and stations inventories will be also provided through a set of Web services that will wrap the middleware used by the seismological observatory or institute that is supplying the data. Each single application of the portal consists of a Java-based JSR-168-standard portlet (often provided with interactive maps for data discovery). In specific cases, it will be possible to distribute the deployment of the portlets among the data providers, such as seismological agencies, because of the adoption, within the distributed architecture of the NERIES portal of the Web Services for Remote Portlets (WSRP) standard for presentation-oriented web services The purpose of the portal is to provide to the user his own environment where he can surf and retrieve the data of interest, offering a set of shopping carts with storage and management facilities. This approach involves having the user interact with dedicated tools in order to compose personalized datasets that can be downloaded or combined with other information available either through the NERIES network of Web services or through the user's own carts. Administrative applications also are provided to perform monitoring tasks such as retrieving service statistics or scheduling submitted data requests. An administrative tool is included that allows the RDF model to be extended, within certain constraints, with new classes and properties.

Predict the glass transition temperature of glycerol-water binary cryoprotectant by molecular dynamic simulation.

PubMed

Li, Dai-Xi; Liu, Bao-Lin; Liu, Yi-shu; Chen, Cheng-lung

2008-04-01

Vitrification is proposed to be the best way for the cryopreservation of organs. The glass transition temperature (T(g)) of vitrification solutions is a critical parameter of fundamental importance for cryopreservation by vitrification. The instruments that can detect the thermodynamic, mechanical and dielectric changes of a substance may be used to determine the glass transition temperature. T(g) is usually measured by using differential scanning calorimetry (DSC). In this study, the T(g) of the glycerol-aqueous solution (60%, wt/%) was determined by isothermal-isobaric molecular dynamic simulation (NPT-MD). The software package Discover in Material Studio with the Polymer Consortium Force Field (PCFF) was used for the simulation. The state parameters of heat capacity at constant pressure (C(p)), density (rho), amorphous cell volume (V(cell)) and specific volume (V(specific)) and radial distribution function (rdf) were obtained by NPT-MD in the temperature range of 90-270K. These parameters showed a discontinuity at a specific temperature in the plot of state parameter versus temperature. The temperature at the discontinuity is taken as the simulated T(g) value for glycerol-water binary solution. The T(g) values determined by simulation method were compared with the values in the literatures. The simulation values of T(g) (160.06-167.51K) agree well with the DSC results (163.60-167.10K) and the DMA results (159.00K). We drew the conclusion that molecular dynamic simulation (MDS) is a potential method for investigating the glass transition temperature (T(g)) of glycerol-water binary cryoprotectants and may be used for other vitrification solutions.

Reference interaction site model with hydrophobicity induced density inhomogeneity: An analytical theory to compute solvation properties of large hydrophobic solutes in the mixture of polyatomic solvent molecules.

PubMed

Cao, Siqin; Sheong, Fu Kit; Huang, Xuhui

2015-08-07

Reference interaction site model (RISM) has recently become a popular approach in the study of thermodynamical and structural properties of the solvent around macromolecules. On the other hand, it was widely suggested that there exists water density depletion around large hydrophobic solutes (>1 nm), and this may pose a great challenge to the RISM theory. In this paper, we develop a new analytical theory, the Reference Interaction Site Model with Hydrophobicity induced density Inhomogeneity (RISM-HI), to compute solvent radial distribution function (RDF) around large hydrophobic solute in water as well as its mixture with other polyatomic organic solvents. To achieve this, we have explicitly considered the density inhomogeneity at the solute-solvent interface using the framework of the Yvon-Born-Green hierarchy, and the RISM theory is used to obtain the solute-solvent pair correlation. In order to efficiently solve the relevant equations while maintaining reasonable accuracy, we have also developed a new closure called the D2 closure. With this new theory, the solvent RDFs around a large hydrophobic particle in water and different water-acetonitrile mixtures could be computed, which agree well with the results of the molecular dynamics simulations. Furthermore, we show that our RISM-HI theory can also efficiently compute the solvation free energy of solute with a wide range of hydrophobicity in various water-acetonitrile solvent mixtures with a reasonable accuracy. We anticipate that our theory could be widely applied to compute the thermodynamic and structural properties for the solvation of hydrophobic solute.

An Educational Tool for Browsing the Semantic Web

ERIC Educational Resources Information Center

Yoo, Sujin; Kim, Younghwan; Park, Seongbin

2013-01-01

The Semantic Web is an extension of the current Web where information is represented in a machine processable way. It is not separate from the current Web and one of the confusions that novice users might have is where the Semantic Web is. In fact, users can easily encounter RDF documents that are components of the Semantic Web while they navigate…

Improved vortex reactor system

DOEpatents

Diebold, J.P.; Scahill, J.W.

1995-05-09

An improved vortex reactor system is described for affecting fast pyrolysis of biomass and Refuse Derived Fuel (RDF) feed materials comprising: a vortex reactor having its axis vertically disposed in relation to a jet of a horizontally disposed steam ejector that impels feed materials from a feeder and solids from a recycle loop along with a motive gas into a top part of said reactor. 12 figs.

Life cycle assessment of the use of alternative fuels in cement kilns: A case study.

PubMed

Georgiopoulou, Martha; Lyberatos, Gerasimos

2018-06-15

The benefits of using alternative fuels (AFs) in the cement industry include reduction of the use of non-renewable fossil fuels and lower emissions of greenhouse gases, since fossil fuels are replaced with materials that would otherwise be degraded or incinerated with corresponding emissions and final residues. Furthermore, the use of alternative fuels maximizes the recovery of energy. Seven different scenaria were developed for the production of 1 ton of clinker in a rotary cement kiln. Each of these scenaria includes the use of alternative fuels such as RDF (Refuse derived fuel), TDF (Tire derived fuel) and BS (Biological sludge) or a mixture of them, in partial replacement of conventional fuels such as coal and pet coke. The purpose of this study is to evaluate the environmental impacts of the use of alternative fuels in relation to conventional fuels in the kiln operation. The Life Cycle Assessment (LCA) methodology is used to quantify the potential environmental impacts in each scenario. The interpretation of the results provides the conclusion that the most environmentally friendly prospect is the scenario based on RDF while the less preferable scenario is the scenario based on BS. Copyright © 2017 Elsevier Ltd. All rights reserved.

Towards Linked Open Services and Processes

NASA Astrophysics Data System (ADS)

Krummenacher, Reto; Norton, Barry; Marte, Adrian

The combination of semantic technology and Web services in form of 'Semantic Web Services' has until now been oriented towards extension of the WS-* stack with ontology-based descriptions. The same time, there is a strong movement away from this stack - for which the 'Web' part is little more than branding - towards RESTful services. The Linked Open Data initiative is a keen adopter of this approach and exposes many datasets via SPARQL endpoints and RESTful services. Our developing approach of 'Linked Open Services', whose current state is described in this paper, accommodates such Linked Data endpoints and general RESTful services alongside WS-* stack-based services with descriptions based on RDF and SPARQL. This capitalises on the Linked Data Cloud and makes service description and comprehension more easy and direct to the growing Linked Data community. Along the way, we show how the existing link between service messaging and the semantic viewpoint, commonly called 'lifting and lowering', is usually unduly restricted to ontology-based classification and misses how the effect of a service contributes to the knowledge of its consumer. Our SPARQL-based approach helps also in the composition of services as knowledge-centric processes, and encourages the development and exposure of services that communicate RDF.

Flow analysis of metals in a municipal solid waste management system.

PubMed

Jung, C H; Matsuto, T; Tanaka, N

2006-01-01

This study aimed to identify the metal flow in a municipal solid waste (MSW) management system. Outputs of a resource recovery facility, refuse derived fuel (RDF) production facility, carbonization facility, plastics liquefaction facility, composting facility, and bio-gasification facility were analyzed for metal content and leaching concentration. In terms of metal content, bulky and incombustible waste had the highest values. Char from a carbonization facility, which treats household waste, had a higher metal content than MSW incinerator bottom ash. A leaching test revealed that Cd and Pb in char and Pb in RDF production residue exceeded the Japanese regulatory criteria for landfilling, so special attention should be paid to final disposal of these substances. By multiplying metal content and the generation rate of outputs, the metal content of input waste to each facility was estimated. For most metals except Cr, the total contribution ratio of paper/textile/plastics, bulky waste, and incombustible waste was over 80%. Approximately 30% of Cr originated from plastic packaging. Finally, several MSW management scenarios showed that most metals are transferred to landfills and the leaching potential of metals to the environment is quite small.

An introduction to the Semantic Web for health sciences librarians*

PubMed Central

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-01-01

Objectives: The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. Methodology: The paper is structured into two main parts. “Semantic Web Technology” provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. “Semantic Web Applications and Research Projects in the Biomedical Field” is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Discussion and Conclusions: Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects. PMID:16636713

HodDB: Design and Analysis of a Query Processor for Brick.

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

Fierro, Gabriel; Culler, David

Brick is a recently proposed metadata schema and ontology for describing building components and the relationships between them. It represents buildings as directed labeled graphs using the RDF data model. Using the SPARQL query language, building-agnostic applications query a Brick graph to discover the set of resources and relationships they require to operate. Latency-sensitive applications, such as user interfaces, demand response and modelpredictive control, require fast queries — conventionally less than 100ms. We benchmark a set of popular open-source and commercial SPARQL databases against three real Brick models using seven application queries and find that none of them meet thismore » performance target. This lack of performance can be attributed to design decisions that optimize for queries over large graphs consisting of billions of triples, but give poor spatial locality and join performance on the small dense graphs typical of Brick. We present the design and evaluation of HodDB, a RDF/SPARQL database for Brick built over a node-based index structure. HodDB performs Brick queries 3-700x faster than leading SPARQL databases and consistently meets the 100ms threshold, enabling the portability of important latency-sensitive building applications.« less

A semantic web ontology for small molecules and their biological targets.

PubMed

Choi, Jooyoung; Davis, Melissa J; Newman, Andrew F; Ragan, Mark A

2010-05-24

A wide range of data on sequences, structures, pathways, and networks of genes and gene products is available for hypothesis testing and discovery in biological and biomedical research. However, data describing the physical, chemical, and biological properties of small molecules have not been well-integrated with these resources. Semantically rich representations of chemical data, combined with Semantic Web technologies, have the potential to enable the integration of small molecule and biomolecular data resources, expanding the scope and power of biomedical and pharmacological research. We employed the Semantic Web technologies Resource Description Framework (RDF) and Web Ontology Language (OWL) to generate a Small Molecule Ontology (SMO) that represents concepts and provides unique identifiers for biologically relevant properties of small molecules and their interactions with biomolecules, such as proteins. We instanced SMO using data from three public data sources, i.e., DrugBank, PubChem and UniProt, and converted to RDF triples. Evaluation of SMO by use of predetermined competency questions implemented as SPARQL queries demonstrated that data from chemical and biomolecular data sources were effectively represented and that useful knowledge can be extracted. These results illustrate the potential of Semantic Web technologies in chemical, biological, and pharmacological research and in drug discovery.

Executing SADI services in Galaxy.

PubMed

Aranguren, Mikel Egaña; González, Alejandro Rodríguez; Wilkinson, Mark D

2014-01-01

In recent years Galaxy has become a popular workflow management system in bioinformatics, due to its ease of installation, use and extension. The availability of Semantic Web-oriented tools in Galaxy, however, is limited. This is also the case for Semantic Web Services such as those provided by the SADI project, i.e. services that consume and produce RDF. Here we present SADI-Galaxy, a tool generator that deploys selected SADI Services as typical Galaxy tools. SADI-Galaxy is a Galaxy tool generator: through SADI-Galaxy, any SADI-compliant service becomes a Galaxy tool that can participate in other out-standing features of Galaxy such as data storage, history, workflow creation, and publication. Galaxy can also be used to execute and combine SADI services as it does with other Galaxy tools. Finally, we have semi-automated the packing and unpacking of data into RDF such that other Galaxy tools can easily be combined with SADI services, plugging the rich SADI Semantic Web Service environment into the popular Galaxy ecosystem. SADI-Galaxy bridges the gap between Galaxy, an easy to use but "static" workflow system with a wide user-base, and SADI, a sophisticated, semantic, discovery-based framework for Web Services, thus benefiting both user communities.

Flow analysis of metals in a municipal solid waste management system

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

Jung, C.H.; Matsuto, T.; Tanaka, N.

2006-07-01

This study aimed to identify the metal flow in a municipal solid waste (MSW) management system. Outputs of a resource recovery facility, refuse derived fuel (RDF) production facility, carbonization facility, plastics liquefaction facility, composting facility, and bio-gasification facility were analyzed for metal content and leaching concentration. In terms of metal content, bulky and incombustible waste had the highest values. Char from a carbonization facility, which treats household waste, had a higher metal content than MSW incinerator bottom ash. A leaching test revealed that Cd and Pb in char and Pb in RDF production residue exceeded the Japanese regulatory criteria formore » landfilling, so special attention should be paid to final disposal of these substances. By multiplying metal content and the generation rate of outputs, the metal content of input waste to each facility was estimated. For most metals except Cr, the total contribution ratio of paper/textile/plastics, bulky waste, and incombustible waste was over 80%. Approximately 30% of Cr originated from plastic packaging. Finally, several MSW management scenarios showed that most metals are transferred to landfills and the leaching potential of metals to the environment is quite small.« less

Linked Data: what does it offer Earth Sciences?

NASA Astrophysics Data System (ADS)

Cox, Simon; Schade, Sven

2010-05-01

'Linked Data' is a current buzz-phrase promoting access to various forms of data on the internet. It starts from the two principles that have underpinned the architecture and scalability of the World Wide Web: 1. Universal Resource Identifiers - using the http protocol which is supported by the DNS system. 2. Hypertext - in which URIs of related resources are embedded within a document. Browsing is the key mode of interaction, with traversal of links between resources under control of the client. Linked Data also adds, or re-emphasizes: • Content negotiation - whereby the client uses http headers to tell the service what representation of a resource is acceptable, • Semantic Web principles - formal semantics for links, following the RDF data model and encoding, and • The 'mashup' effect - in which original and unexpected value may emerge from reuse of data, even if published in raw or unpolished form. Linked Data promotes typed links to all kinds of data, so is where the semantic web meets the 'deep web', i.e. resources which may be accessed using web protocols, but are in representations not indexed by search engines. Earth sciences are data rich, but with a strong legacy of specialized formats managed and processed by disconnected applications. However, most contemporary research problems require a cross-disciplinary approach, in which the heterogeneity resulting from that legacy is a significant challenge. In this context, Linked Data clearly has much to offer the earth sciences. But, there are some important questions to answer. What is a resource? Most earth science data is organized in arrays and databases. A subset useful for a particular study is usually identified by a parameterized query. The Linked Data paradigm emerged from the world of documents, and will often only resolve data-sets. It is impractical to create even nested navigation resources containing links to all potentially useful objects or subsets. From the viewpoint of human user interfaces, the browse metaphor, which has been such an important part of the success of the web, must be augmented with other interaction mechanisms, including query. What are the impacts on search and metadata? Hypertext provides links selected by the page provider. However, science should endeavor to be exhaustive in its use of data. Resource discovery through links must be supplemented by more systematic data discovery through search. Conversely, the crawlers that generate search indexes must be fed by resource providers (a) serving navigation pages with links to every dataset (b) adding enough 'metadata' (semantics) on each link to effectively populate the indexes. Linked Data makes this easier due to its integration with semantic web technologies, including structured vocabularies. What is the relation between structured data and Linked Data? Linked Data has focused on web-pages (primarily HTML) for human browsing, and RDF for semantics, assuming that other representations are opaque. However, this overlooks the wealth of XML data on the web, some of which is structured according to XML Schemas that provide semantics. Technical applications can use content-negotiation to get a structured representation, and exploit its semantics. Particularly relevant for earth sciences are data representations based on OGC Geography Markup Language (GML), such as GeoSciML, O&M and MOLES. GML was strongly influenced by RDF, and typed links are intrinsic: xlink:href plays the role that rdf:resource does in RDF representations. Services which expose GML-formatted resources (such as OGC Web Feature Service) are a prototype of Linked Data. Giving credit where it is due. Organizations investing in data collection may be reluctant to publish the raw data prior to completing an initial analysis. To encourage early data publication the system must provide suitable incentives, and citation analysis must recognize the increasing diversity of publication routes and forms. Linked Data makes it easier to include rich citation information when data is both published and used.

Addressing the Challenges of Multi-Domain Data Integration with the SemantEco Framework

NASA Astrophysics Data System (ADS)

Patton, E. W.; Seyed, P.; McGuinness, D. L.

2013-12-01

Data integration across multiple domains will continue to be a challenge with the proliferation of big data in the sciences. Data origination issues and how data are manipulated are critical to enable scientists to understand and consume disparate datasets as research becomes more multidisciplinary. We present the SemantEco framework as an exemplar for designing an integrative portal for data discovery, exploration, and interpretation that uses best practice W3C Recommendations. We use the Resource Description Framework (RDF) with extensible ontologies described in the Web Ontology Language (OWL) to provide graph-based data representation. Furthermore, SemantEco ingests data via the software package csv2rdf4lod, which generates data provenance using the W3C provenance recommendation (PROV). Our presentation will discuss benefits and challenges of semantic integration, their effect on runtime performance, and how the SemantEco framework assisted in identifying performance issues and improved query performance across multiple domains by an order of magnitude. SemantEco benefits from a semantic approach that provides an 'open world', which allows data to incrementally change just as it does in the real world. SemantEco modules may load new ontologies and data using the W3C's SPARQL Protocol and RDF Query Language via HTTP. Modules may also provide user interface elements for applications and query capabilities to support new use cases. Modules can associate with domains, which are first-class objects in SemantEco. This enables SemantEco to perform integration and reasoning both within and across domains on module-provided data. The SemantEco framework has been used to construct a web portal for environmental and ecological data. The portal includes water and air quality data from the U.S. Geological Survey (USGS) and Environmental Protection Agency (EPA) and species observation counts for birds and fish from the Avian Knowledge Network and the Santa Barbara Long Term Ecological Research, respectively. We provide regulation ontologies using OWL2 datatype facets to detect out-of-range measurements for environmental standards set by the EPA, i.a. Users adjust queries using module-defined facets and a map presents the resulting measurement sites. Custom icons identify sites that violate regulations, making them easy to locate. Selecting a site gives the option of charting spatially proximate data from different domains over time. Our portal currently provides 1.6 billion triples of scientific data in RDF. We segment data by ZIP code and reasoning over 2157 measurements with our EPA regulation ontology that contains 131 regulations takes 2.5 seconds on a 2.4 GHz Intel Core 2 Quad with 8 GB of RAM. SemantEco's modular design and reasoning capabilities make it an exemplar for building multidisciplinary data integration tools that provide data access to scientists and the general population alike. Its provenance tracking provides accountability and its reasoning services can assist users in interpreting data. Future work includes support for geographical queries using the Open Geospatial Consortium's GeoSPARQL standard.

Linked Ocean Data

NASA Astrophysics Data System (ADS)

Leadbetter, Adam; Arko, Robert; Chandler, Cynthia; Shepherd, Adam

2014-05-01

"Linked Data" is a term used in Computer Science to encapsulate a methodology for publishing data and metadata in a structured format so that links may be created and exploited between objects. Berners-Lee (2006) outlines the following four design principles of a Linked Data system: Use Uniform Resource Identifiers (URIs) as names for things. Use HyperText Transfer Protocol (HTTP) URIs so that people can look up those names. When someone looks up a URI, provide useful information, using the standards (Resource Description Framework [RDF] and the RDF query language [SPARQL]). Include links to other URIs so that they can discover more things. In 2010, Berners-Lee revisited his original design plan for Linked Data to encourage data owners along a path to "good Linked Data". This revision involved the creation of a five star rating system for Linked Data outlined below. One star: Available on the web (in any format). Two stars: Available as machine-readable structured data (e.g. An Excel spreadsheet instead of an image scan of a table). Three stars: As two stars plus the use of a non-proprietary format (e.g. Comma Separated Values instead of Excel). Four stars: As three stars plus the use of open standards from the World Wide Web Commission (W3C) (i.e. RDF and SPARQL) to identify things, so that people can point to your data and metadata. Five stars: All the above plus link your data to other people's data to provide context Here we present work building on the SeaDataNet common vocabularies served by the NERC Vocabulary Server, connecting projects such as the Rolling Deck to Repository (R2R) and the Biological and Chemical Oceanography Data Management Office (BCO-DMO) and other vocabularies such as the Marine Metadata Interoperability Ontology Register and Repository and the NASA Global Change Master Directory to create a Linked Ocean Data cloud. Publishing the vocabularies and metadata in standard RDF XML and exposing SPARQL endpoints renders them five-star Linked Data repositories. The benefits of this approach include: increased interoperability between the metadata created by projects; improved data discovery as users of SeaDataNet, R2R and BCO-DMO terms can find data using labels with which they are familiar both standard tools and newly developed custom tools may be used to explore the data; and using standards means the custom tools are easier to develop Linked Data is a concept which has been in existence for nearly a decade, and has a simple set of formal best practices associated with it. Linked Data is increasingly being seen as a driver of the next generation of "community science" activities. While many data providers in the oceanographic domain may be unaware of Linked Data, they may also be providing it at one of its lower levels. Here we have shown that it is possible to deliver the highest standard of Linked Oceanographic Data, and some of the benefits of the approach.

Domain knowledge patterns in pedagogical diagnostics

NASA Astrophysics Data System (ADS)

Miarka, Rostislav

2017-07-01

This paper shows a proposal of representation of knowledge patterns in RDF(S) language. Knowledge patterns are used for reuse of knowledge. They can be divided into two groups - Top-level knowledge patterns and Domain knowledge patterns. Pedagogical diagnostics is aimed at testing of knowledge of students at primary and secondary school. An example of domain knowledge pattern from pedagogical diagnostics is part of this paper.

Active Wiki Knowledge Repository

DTIC Science & Technology

2012-10-01

data using SPARQL queries or RESTful web-services; ‘gardening’ tools for examining the semantically tagged content in the wiki; high-level language tool...Tagging & RDF triple-store Fusion and inferences for collaboration Tools for Consuming Data SPARQL queries or RESTful WS Inference & Gardening tools...other stores using AW SPARQL queries and rendering templates; and 4) Interactively share maps and other content using annotation tools to post notes

Agent-Based Computing Integration and Testing

DTIC Science & Technology

2006-12-01

Query Language (DQL). Regrettably, DQL never became a W3C Member Submission itself, but likely had some influence on the SPARQL Protocol And RDF... Query Language ( SPARQL ) subsequently produced by the W3C Data Access Working Group (DAWG) as that working group also contained members from the DAML...Sponsored by Defense Advanced Research Projects Agency DARPA Order No. K536 APPROVED FOR PUBLIC RELEASE

From Guerillas to Peacekeepers: The Evolution of the Rwandan Defense Forces

DTIC Science & Technology

2008-04-01

examined much of its history fron: a culturally appropriate, military perspective, the RDF’s record clearly demonstrates a professional military...warrior culture no doubt form the foundation of modern military consciousness in Rwanda, and those foundations are fittingly credited before analyzing any...foreign meddling and capable of independent growth and development. 6 The collectivist \\ ideology of the NRA, which emphasized general solidarity over

BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data

PubMed Central

2014-01-01

Background Biological databases vary enormously in size and data complexity, from small databases that contain a few million Resource Description Framework (RDF) triples to large databases that contain billions of triples. In this paper, we evaluate whether RDF native stores can be used to meet the needs of a biological database provider. Prior evaluations have used synthetic data with a limited database size. For example, the largest BSBM benchmark uses 1 billion synthetic e-commerce knowledge RDF triples on a single node. However, real world biological data differs from the simple synthetic data much. It is difficult to determine whether the synthetic e-commerce data is efficient enough to represent biological databases. Therefore, for this evaluation, we used five real data sets from biological databases. Results We evaluated five triple stores, 4store, Bigdata, Mulgara, Virtuoso, and OWLIM-SE, with five biological data sets, Cell Cycle Ontology, Allie, PDBj, UniProt, and DDBJ, ranging in size from approximately 10 million to 8 billion triples. For each database, we loaded all the data into our single node and prepared the database for use in a classical data warehouse scenario. Then, we ran a series of SPARQL queries against each endpoint and recorded the execution time and the accuracy of the query response. Conclusions Our paper shows that with appropriate configuration Virtuoso and OWLIM-SE can satisfy the basic requirements to load and query biological data less than 8 billion or so on a single node, for the simultaneous access of 64 clients. OWLIM-SE performs best for databases with approximately 11 million triples; For data sets that contain 94 million and 590 million triples, OWLIM-SE and Virtuoso perform best. They do not show overwhelming advantage over each other; For data over 4 billion Virtuoso works best. 4store performs well on small data sets with limited features when the number of triples is less than 100 million, and our test shows its scalability is poor; Bigdata demonstrates average performance and is a good open source triple store for middle-sized (500 million or so) data set; Mulgara shows a little of fragility. PMID:25089180

PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets.

PubMed

Djokic-Petrovic, Marija; Cvjetkovic, Vladimir; Yang, Jeremy; Zivanovic, Marko; Wild, David J

2017-09-20

There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources. PIBAS FedSPARQL is a web-based query builder and result set visualizer of bioinformatics data. As an advanced feature, our system can detect similar data items identified by different Uniform Resource Identifiers (URIs), using a text-mining algorithm based on the processing of named entities to be used in Vector Space Model and Cosine Similarity Measures. According to our knowledge, PIBAS FedSPARQL was unique among the systems that we found in that it allows detecting of similar data items. As a query builder, our system allows researchers to intuitively construct and run Federated SPARQL queries across multiple data sources, including global initiatives, such as Bio2RDF, Chem2Bio2RDF, EMBL-EBI, and one local initiative called CPCTAS, as well as additional user-specified data source. From the input topic, subtopic, template and keyword, a corresponding initial Federated SPARQL query is created and executed. Based on the data obtained, end users have the ability to choose the most appropriate data sources in their area of interest and exploit their Resource Description Framework (RDF) structure, which allows users to select certain properties of data to enhance query results. The developed system is flexible and allows intuitive creation and execution of queries for an extensive range of bioinformatics topics. Also, the novel "similar data items detection" algorithm can be particularly useful for suggesting new data sources and cost optimization for new experiments. PIBAS FedSPARQL can be expanded with new topics, subtopics and templates on demand, rendering information retrieval more robust.

Facilitating Semantic Interoperability Among Ocean Data Systems: ODIP-R2R Student Outcomes

NASA Astrophysics Data System (ADS)

Stocks, K. I.; Chen, Y.; Shepherd, A.; Chandler, C. L.; Dockery, N.; Elya, J. L.; Smith, S. R.; Ferreira, R.; Fu, L.; Arko, R. A.

2014-12-01

With informatics providing an increasingly important set of tools for geoscientists, it is critical to train the next generation of scientists in information and data techniques. The NSF-supported Rolling Deck to Repository (R2R) Program works with the academic fleet community to routinely document, assess, and preserve the underway sensor data from U.S. research vessels. The Ocean Data Interoperability Platform (ODIP) is an EU-US-Australian collaboration fostering interoperability among regional e-infrastructures through workshops and joint prototype development. The need to align terminology between systems is a common challenge across all of the ODIP prototypes. Five R2R students were supported to address aspects of semantic interoperability within ODIP. Developing a vocabulary matching service that links terms from different vocabularies with similar concept. The service implements Google Refine reconciliation service interface such that users can leverage Google Refine application as a friendly user interface while linking different vocabulary terms. Developing Resource Description Framework (RDF) resources that map Shipboard Automated Meteorological Oceanographic System (SAMOS) vocabularies to internationally served vocabularies. Each SAMOS vocabulary term (data parameter and quality control flag) will be described as an RDF resource page. These RDF resources allow for enhanced discoverability and retrieval of SAMOS data by enabling data searches based on parameter. Improving data retrieval and interoperability by exposing data and mapped vocabularies using Semantic Web technologies. We have collaborated with ODIP participating organizations in order to build a generalized data model that will be used to populate a SPARQL endpoint in order to provide expressive querying over our data files. Mapping local and regional vocabularies used by R2R to those used by ODIP partners. This work is described more fully in a companion poster. Making published Linked Data Web developer-friendly with a RESTful service. This goal was achieved by defining a proxy layer on top of the existing SPARQL endpoint that 1) translates HTTP requests into SPARQL queries, and 2) renders the returned results as required by the request sender using content negotiation, suffixes and parameters.

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease.

PubMed

Iyappan, Anandhi; Kawalia, Shweta Bagewadi; Raschka, Tamara; Hofmann-Apitius, Martin; Senger, Philipp

2016-07-08

Neurodegenerative diseases are incurable and debilitating indications with huge social and economic impact, where much is still to be learnt about the underlying molecular events. Mechanistic disease models could offer a knowledge framework to help decipher the complex interactions that occur at molecular and cellular levels. This motivates the need for the development of an approach integrating highly curated and heterogeneous data into a disease model of different regulatory data layers. Although several disease models exist, they often do not consider the quality of underlying data. Moreover, even with the current advancements in semantic web technology, we still do not have cure for complex diseases like Alzheimer's disease. One of the key reasons accountable for this could be the increasing gap between generated data and the derived knowledge. In this paper, we describe an approach, called as NeuroRDF, to develop an integrative framework for modeling curated knowledge in the area of complex neurodegenerative diseases. The core of this strategy lies in the usage of well curated and context specific data for integration into one single semantic web-based framework, RDF. This increases the probability of the derived knowledge to be novel and reliable in a specific disease context. This infrastructure integrates highly curated data from databases (Bind, IntAct, etc.), literature (PubMed), and gene expression resources (such as GEO and ArrayExpress). We illustrate the effectiveness of our approach by asking real-world biomedical questions that link these resources to prioritize the plausible biomarker candidates. Among the 13 prioritized candidate genes, we identified MIF to be a potential emerging candidate due to its role as a pro-inflammatory cytokine. We additionally report on the effort and challenges faced during generation of such an indication-specific knowledge base comprising of curated and quality-controlled data. Although many alternative approaches have been proposed and practiced for modeling diseases, the semantic web technology is a flexible and well established solution for harmonized aggregation. The benefit of this work, to use high quality and context specific data, becomes apparent in speculating previously unattended biomarker candidates around a well-known mechanism, further leveraged for experimental investigations.

Micropublications: a semantic model for claims, evidence, arguments and annotations in biomedical communications

PubMed Central

2014-01-01

Background Scientific publications are documentary representations of defeasible arguments, supported by data and repeatable methods. They are the essential mediating artifacts in the ecosystem of scientific communications. The institutional “goal” of science is publishing results. The linear document publication format, dating from 1665, has survived transition to the Web. Intractable publication volumes; the difficulty of verifying evidence; and observed problems in evidence and citation chains suggest a need for a web-friendly and machine-tractable model of scientific publications. This model should support: digital summarization, evidence examination, challenge, verification and remix, and incremental adoption. Such a model must be capable of expressing a broad spectrum of representational complexity, ranging from minimal to maximal forms. Results The micropublications semantic model of scientific argument and evidence provides these features. Micropublications support natural language statements; data; methods and materials specifications; discussion and commentary; challenge and disagreement; as well as allowing many kinds of statement formalization. The minimal form of a micropublication is a statement with its attribution. The maximal form is a statement with its complete supporting argument, consisting of all relevant evidence, interpretations, discussion and challenges brought forward in support of or opposition to it. Micropublications may be formalized and serialized in multiple ways, including in RDF. They may be added to publications as stand-off metadata. An OWL 2 vocabulary for micropublications is available at http://purl.org/mp. A discussion of this vocabulary along with RDF examples from the case studies, appears as OWL Vocabulary and RDF Examples in Additional file 1. Conclusion Micropublications, because they model evidence and allow qualified, nuanced assertions, can play essential roles in the scientific communications ecosystem in places where simpler, formalized and purely statement-based models, such as the nanopublications model, will not be sufficient. At the same time they will add significant value to, and are intentionally compatible with, statement-based formalizations. We suggest that micropublications, generated by useful software tools supporting such activities as writing, editing, reviewing, and discussion, will be of great value in improving the quality and tractability of biomedical communications. PMID:26261718

BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data.

PubMed

Wu, Hongyan; Fujiwara, Toyofumi; Yamamoto, Yasunori; Bolleman, Jerven; Yamaguchi, Atsuko

2014-01-01

Biological databases vary enormously in size and data complexity, from small databases that contain a few million Resource Description Framework (RDF) triples to large databases that contain billions of triples. In this paper, we evaluate whether RDF native stores can be used to meet the needs of a biological database provider. Prior evaluations have used synthetic data with a limited database size. For example, the largest BSBM benchmark uses 1 billion synthetic e-commerce knowledge RDF triples on a single node. However, real world biological data differs from the simple synthetic data much. It is difficult to determine whether the synthetic e-commerce data is efficient enough to represent biological databases. Therefore, for this evaluation, we used five real data sets from biological databases. We evaluated five triple stores, 4store, Bigdata, Mulgara, Virtuoso, and OWLIM-SE, with five biological data sets, Cell Cycle Ontology, Allie, PDBj, UniProt, and DDBJ, ranging in size from approximately 10 million to 8 billion triples. For each database, we loaded all the data into our single node and prepared the database for use in a classical data warehouse scenario. Then, we ran a series of SPARQL queries against each endpoint and recorded the execution time and the accuracy of the query response. Our paper shows that with appropriate configuration Virtuoso and OWLIM-SE can satisfy the basic requirements to load and query biological data less than 8 billion or so on a single node, for the simultaneous access of 64 clients. OWLIM-SE performs best for databases with approximately 11 million triples; For data sets that contain 94 million and 590 million triples, OWLIM-SE and Virtuoso perform best. They do not show overwhelming advantage over each other; For data over 4 billion Virtuoso works best. 4store performs well on small data sets with limited features when the number of triples is less than 100 million, and our test shows its scalability is poor; Bigdata demonstrates average performance and is a good open source triple store for middle-sized (500 million or so) data set; Mulgara shows a little of fragility.

Mining relational paths in integrated biomedical data.

PubMed

He, Bing; Tang, Jie; Ding, Ying; Wang, Huijun; Sun, Yuyin; Shin, Jae Hong; Chen, Bin; Moorthy, Ganesh; Qiu, Judy; Desai, Pankaj; Wild, David J

2011-01-01

Much life science and biology research requires an understanding of complex relationships between biological entities (genes, compounds, pathways, diseases, and so on). There is a wealth of data on such relationships in publicly available datasets and publications, but these sources are overlapped and distributed so that finding pertinent relational data is increasingly difficult. Whilst most public datasets have associated tools for searching, there is a lack of searching methods that can cross data sources and that in particular search not only based on the biological entities themselves but also on the relationships between them. In this paper, we demonstrate how graph-theoretic algorithms for mining relational paths can be used together with a previous integrative data resource we developed called Chem2Bio2RDF to extract new biological insights about the relationships between such entities. In particular, we use these methods to investigate the genetic basis of side-effects of thiazolinedione drugs, and in particular make a hypothesis for the recently discovered cardiac side-effects of Rosiglitazone (Avandia) and a prediction for Pioglitazone which is backed up by recent clinical studies.

BioSearch: a semantic search engine for Bio2RDF

PubMed Central

Qiu, Honglei; Huang, Jiacheng

2017-01-01

Abstract Biomedical data are growing at an incredible pace and require substantial expertise to organize data in a manner that makes them easily findable, accessible, interoperable and reusable. Massive effort has been devoted to using Semantic Web standards and technologies to create a network of Linked Data for the life sciences, among others. However, while these data are accessible through programmatic means, effective user interfaces for non-experts to SPARQL endpoints are few and far between. Contributing to user frustrations is that data are not necessarily described using common vocabularies, thereby making it difficult to aggregate results, especially when distributed across multiple SPARQL endpoints. We propose BioSearch — a semantic search engine that uses ontologies to enhance federated query construction and organize search results. BioSearch also features a simplified query interface that allows users to optionally filter their keywords according to classes, properties and datasets. User evaluation demonstrated that BioSearch is more effective and usable than two state of the art search and browsing solutions. Database URL: http://ws.nju.edu.cn/biosearch/ PMID:29220451

Standard biological parts knowledgebase.

PubMed

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

2011-02-24

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

Transformation of OODT CAS to Perform Larger Tasks

NASA Technical Reports Server (NTRS)

Mattmann, Chris; Freeborn, Dana; Crichton, Daniel; Hughes, John; Ramirez, Paul; Hardman, Sean; Woollard, David; Kelly, Sean

2008-01-01

A computer program denoted OODT CAS has been transformed to enable performance of larger tasks that involve greatly increased data volumes and increasingly intensive processing of data on heterogeneous, geographically dispersed computers. Prior to the transformation, OODT CAS (also alternatively denoted, simply, 'CAS') [wherein 'OODT' signifies 'Object-Oriented Data Technology' and 'CAS' signifies 'Catalog and Archive Service'] was a proven software component used to manage scientific data from spaceflight missions. In the transformation, CAS was split into two separate components representing its canonical capabilities: file management and workflow management. In addition, CAS was augmented by addition of a resource-management component. This third component enables CAS to manage heterogeneous computing by use of diverse resources, including high-performance clusters of computers, commodity computing hardware, and grid computing infrastructures. CAS is now more easily maintainable, evolvable, and reusable. These components can be used separately or, taking advantage of synergies, can be used together. Other elements of the transformation included addition of a separate Web presentation layer that supports distribution of data products via Really Simple Syndication (RSS) feeds, and provision for full Resource Description Framework (RDF) exports of metadata.

Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation.

PubMed

Cen, Min; Fan, Jian Fen; Liu, Dong Yan; Song, Xue Zeng; Liu, Jian; Zhou, Wei Qun; Xiao, He Ming

2013-02-01

Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the "horse-saddle" conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones' structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O(C) atoms of the CHPs' backbones and H(w) atoms of water molecules. N atoms of the CHPs' backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D ( xy )) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

Molecular dynamics simulations of lithium silicate/vanadium pentoxide interfacial lithium ion diffusion in thin film lithium ion-conducting devices

NASA Astrophysics Data System (ADS)

Li, Weiqun

The lithium ion diffusion behavior and mechanism in the glassy electrolyte and the electrolyte/cathode interface during the initial stage of lithium ion diffusing from electrolyte into cathode were investigated using Molecular Dynamics simulation technique. Lithium aluminosilicate glass electrolytes with different R (ratio of the concentration of Al to Li) were simulated. The structural features of the simulated glasses are analyzed using Radial Distribution Function (RDF) and Pair Distribution Function (PDF). The diffusion coefficient and activation energy of lithium ion diffusion in simulated lithium aluminosilicate glasses were calculated and the values are consistent with those in experimental glasses. The behavior of lithium ion diffusion from the glassy electrolyte into a polycrystalline layered intercalation cathode has been studied. The solid electrolyte was a model lithium silicate glass while the cathode was a nanocrystalline vanadia with amorphous V2O5 intergranular films (IGF) between the V2O5 crystals. Two different orientations between the V2O5 crystal planes are presented for lithium ion intercalation via the amorphous vanadia IGF. A series of polycrystalline vanadia cathodes with 1.3, 1.9, 2.9 and 4.4 nm thickness IGFs were simulated to examine the effects of the IGF thickness on lithium ion transport in the polycrystalline vanadia cathodes. The simulated results showed that the lithium ions diffused from the glassy electrolyte into the IGF of the polycrystalline vanadia cathode and then part of those lithium ions diffused into the crystalline V2O5 from the IGF. The simulated results also showed an ordering of the vanadium ion structure in the IGF near the IGF/V2 O5 interface. The ordering structure still existed with glass former silica additive in IGF. Additionally, 2.9 run is suggested to be the optimal thickness of the IGF, which is neither too thick to decrease the capacity of the cathode nor too thin to impede the transport of lithium from glassy electrolyte into the cathode. Parallel molecular dynamic simulation technique was also used for a larger electrolyte/cathode interface system, which include more atoms and more complicated microstructures. Simulation results from larger electrolyte/cathode interface system prove that there is no size effect on simulation of smaller electrolyte/cathode interface system from statistical point of view.

Publishing and Editing of Semantically-Enabled Scientific Metadata Across Multiple Web Platforms: Challenges and Experiences

NASA Astrophysics Data System (ADS)

Patton, E. W.; West, P.; Greer, R.; Jin, B.

2011-12-01

Following on work presented at the 2010 AGU Fall Meeting, we present a number of real-world collections of semantically-enabled scientific metadata ingested into the Tetherless World RDF2HTML system as structured data and presented and edited using that system. Two separate datasets from two different domains (oceanography and solar sciences) are made available using existing web standards and services, e.g. encoded using ontologies represented with the Web Ontology Language (OWL) and stored in a SPARQL endpoint for querying. These datasets are deployed for use in three different web environments, i.e. Drupal, MediaWiki, and a custom web portal written in Java, to highlight the cross-platform nature of the data presentation. Stylesheets used to transform concepts in each domain as well as shared terms into HTML will be presented to show the power of using common ontologies to publish data and support reuse of existing terminologies. In addition, a single domain dataset is shared between two separate portal instances to demonstrate the ability for this system to offer distributed access and modification of content across the Internet. Lastly, we will highlight challenges that arose in the software engineering process, outline the design choices we made in solving those issues, and discuss how future improvements to this and other systems will enable the evolution of distributed, decentralized collaborations for scientific data sharing across multiple research groups.

Development of Environmentally Benign and Reduced Corrosion Runway Deicing Fluid

DTIC Science & Technology

2009-08-01

PCNA Peter Cremer North America PG Propylene glycol P&G Proctor and Gamble Inc. PNNL Pacific Northwest National Laboratory RDF Runway Deicing...Navy/NAVAIR Defining Navy needs Mack Findley Peter Cremer North America (PCNA) Bio-based raw materials selection Pat Viani SMI AMS 1435 testing...SMI), and other laboratories under the leadership of SAE G-12 Fluids Subcommittee, and is expected to provide a better indication of compatibility with

Context and Domain Knowledge Enhanced Entity Spotting in Informal Text

NASA Astrophysics Data System (ADS)

Gruhl, Daniel; Nagarajan, Meena; Pieper, Jan; Robson, Christine; Sheth, Amit

This paper explores the application of restricted relationship graphs (RDF) and statistical NLP techniques to improve named entity annotation in challenging Informal English domains. We validate our approach using on-line forums discussing popular music. Named entity annotation is particularly difficult in this domain because it is characterized by a large number of ambiguous entities, such as the Madonna album "Music" or Lilly Allen's pop hit "Smile".

Publications - RDF 2015-15 v. 1.1 | Alaska Division of Geological &

Science.gov Websites

geochemical data from rocks collected in 2015 in the Tok area, Tanacross A-5, A-6, and parts of adjacent rocks collected in 2015 in the Tok area, Tanacross A-5, A-6, and parts of adjacent quadrangles, Alaska Geophysical Surveys Skip to content State of Alaska myAlaska My Government Resident Business in

Applying Semantic Web Concepts to Support Net-Centric Warfare Using the Tactical Assessment Markup Language (TAML)

DTIC Science & Technology

2006-06-01

SPARQL SPARQL Protocol and RDF Query Language SQL Structured Query Language SUMO Suggested Upper Merged Ontology SW... Query optimization algorithms are implemented in the Pellet reasoner in order to ensure querying a knowledge base is efficient . These algorithms...memory as a treelike structure in order for the data to be queried . XML Query (XQuery) is the standard language used when querying XML

An Ebola virus-centered knowledge base

PubMed Central

Kamdar, Maulik R.; Dumontier, Michel

2015-01-01

Ebola virus (EBOV), of the family Filoviridae viruses, is a NIAID category A, lethal human pathogen. It is responsible for causing Ebola virus disease (EVD) that is a severe hemorrhagic fever and has a cumulative death rate of 41% in the ongoing epidemic in West Africa. There is an ever-increasing need to consolidate and make available all the knowledge that we possess on EBOV, even if it is conflicting or incomplete. This would enable biomedical researchers to understand the molecular mechanisms underlying this disease and help develop tools for efficient diagnosis and effective treatment. In this article, we present our approach for the development of an Ebola virus-centered Knowledge Base (Ebola-KB) using Linked Data and Semantic Web Technologies. We retrieve and aggregate knowledge from several open data sources, web services and biomedical ontologies. This knowledge is transformed to RDF, linked to the Bio2RDF datasets and made available through a SPARQL 1.1 Endpoint. Ebola-KB can also be explored using an interactive Dashboard visualizing the different perspectives of this integrated knowledge. We showcase how different competency questions, asked by domain users researching the druggability of EBOV, can be formulated as SPARQL Queries or answered using the Ebola-KB Dashboard. Database URL: http://ebola.semanticscience.org. PMID:26055098

Using Linked Open Data and Semantic Integration to Search Across Geoscience Repositories

NASA Astrophysics Data System (ADS)

Mickle, A.; Raymond, L. M.; Shepherd, A.; Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Cheatham, M.; Fils, D.; Hitzler, P.; Janowicz, K.; Jones, M.; Krisnadhi, A.; Lehnert, K. A.; Narock, T.; Schildhauer, M.; Wiebe, P. H.

2014-12-01

The MBLWHOI Library is a partner in the OceanLink project, an NSF EarthCube Building Block, applying semantic technologies to enable knowledge discovery, sharing and integration. OceanLink is testing ontology design patterns that link together: two data repositories, Rolling Deck to Repository (R2R), Biological and Chemical Oceanography Data Management Office (BCO-DMO); the MBLWHOI Library Institutional Repository (IR) Woods Hole Open Access Server (WHOAS); National Science Foundation (NSF) funded awards; and American Geophysical Union (AGU) conference presentations. The Library is collaborating with scientific users, data managers, DSpace engineers, experts in ontology design patterns, and user interface developers to make WHOAS, a DSpace repository, linked open data enabled. The goal is to allow searching across repositories without any of the information providers having to change how they manage their collections. The tools developed for DSpace will be made available to the community of users. There are 257 registered DSpace repositories in the United Stated and over 1700 worldwide. Outcomes include: Integration of DSpace with OpenRDF Sesame triple store to provide SPARQL endpoint for the storage and query of RDF representation of DSpace resources, Mapping of DSpace resources to OceanLink ontology, and DSpace "data" add on to provide resolvable linked open data representation of DSpace resources.

An Ebola virus-centered knowledge base.

PubMed

Kamdar, Maulik R; Dumontier, Michel

2015-01-01

Ebola virus (EBOV), of the family Filoviridae viruses, is a NIAID category A, lethal human pathogen. It is responsible for causing Ebola virus disease (EVD) that is a severe hemorrhagic fever and has a cumulative death rate of 41% in the ongoing epidemic in West Africa. There is an ever-increasing need to consolidate and make available all the knowledge that we possess on EBOV, even if it is conflicting or incomplete. This would enable biomedical researchers to understand the molecular mechanisms underlying this disease and help develop tools for efficient diagnosis and effective treatment. In this article, we present our approach for the development of an Ebola virus-centered Knowledge Base (Ebola-KB) using Linked Data and Semantic Web Technologies. We retrieve and aggregate knowledge from several open data sources, web services and biomedical ontologies. This knowledge is transformed to RDF, linked to the Bio2RDF datasets and made available through a SPARQL 1.1 Endpoint. Ebola-KB can also be explored using an interactive Dashboard visualizing the different perspectives of this integrated knowledge. We showcase how different competency questions, asked by domain users researching the druggability of EBOV, can be formulated as SPARQL Queries or answered using the Ebola-KB Dashboard. © The Author(s) 2015. Published by Oxford University Press.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

PubMed Central

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-01

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

Benchmarking infrastructure for mutation text mining

PubMed Central

2014-01-01

Background Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation text mining systems. Results We propose a community-oriented annotation and benchmarking infrastructure to support development, testing, benchmarking, and comparison of mutation text mining systems. The design is based on semantic standards, where RDF is used to represent annotations, an OWL ontology provides an extensible schema for the data and SPARQL is used to compute various performance metrics, so that in many cases no programming is needed to analyze results from a text mining system. While large benchmark corpora for biological entity and relation extraction are focused mostly on genes, proteins, diseases, and species, our benchmarking infrastructure fills the gap for mutation information. The core infrastructure comprises (1) an ontology for modelling annotations, (2) SPARQL queries for computing performance metrics, and (3) a sizeable collection of manually curated documents, that can support mutation grounding and mutation impact extraction experiments. Conclusion We have developed the principal infrastructure for the benchmarking of mutation text mining tasks. The use of RDF and OWL as the representation for corpora ensures extensibility. The infrastructure is suitable for out-of-the-box use in several important scenarios and is ready, in its current state, for initial community adoption. PMID:24568600

Voluntary Medical Male Circumcision among Rwanda Defense Force Members.

PubMed

Grillo, Michael P; Djibo, Djeneba Audrey; Macera, Caroline A; Murego, Charles; Zimulinda, Eugene; Sebagabo, Marcellin; Gatsinzi, Valentin

2017-01-01

Strong scientific evidence supports voluntary medical male circumcision as part of an overall HIV prevention strategy, but self-report information on circumcision status may be inaccurate. The study objectives were to obtain estimates of male circumcision within the Rwanda Defense Force (RDF), to assess the ability of soldiers to correctly report their own circumcision status, and to document the uptake of voluntary medical male circumcision (VMMC) in the RDF. Data were collected from members of the Rwandan military during their annual physical examination. A self-administered questionnaire collected demographic and circumcision characteristics. Self-reported circumcision status was compared with the medical exam evaluation. Using questionnaires with complete data (n = 579), 69% of the study participants were circumcised by physical examination and there was a strong agreement with self-reported circumcision status (κ = 0.97). Almost half (44%) of all circumcisions had been performed within the past 2 years. These results suggest that self-report is an appropriate method to collect information on circumcision status in the Rwandan military. Many of the circumcisions occurred within the last 2 years, possibly as an effect of the successful scale-up of voluntary medical male circumcision in the Rwandan military utilizing effective messaging, demand creation, and positive news reported by the media. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

WebMedSA: a web-based framework for segmenting and annotating medical images using biomedical ontologies

NASA Astrophysics Data System (ADS)

Vega, Francisco; Pérez, Wilson; Tello, Andrés.; Saquicela, Victor; Espinoza, Mauricio; Solano-Quinde, Lizandro; Vidal, Maria-Esther; La Cruz, Alexandra

2015-12-01

Advances in medical imaging have fostered medical diagnosis based on digital images. Consequently, the number of studies by medical images diagnosis increases, thus, collaborative work and tele-radiology systems are required to effectively scale up to this diagnosis trend. We tackle the problem of the collaborative access of medical images, and present WebMedSA, a framework to manage large datasets of medical images. WebMedSA relies on a PACS and supports the ontological annotation, as well as segmentation and visualization of the images based on their semantic description. Ontological annotations can be performed directly on the volumetric image or at different image planes (e.g., axial, coronal, or sagittal); furthermore, annotations can be complemented after applying a segmentation technique. WebMedSA is based on three main steps: (1) RDF-ization process for extracting, anonymizing, and serializing metadata comprised in DICOM medical images into RDF/XML; (2) Integration of different biomedical ontologies (using L-MOM library), making this approach ontology independent; and (3) segmentation and visualization of annotated data which is further used to generate new annotations according to expert knowledge, and validation. Initial user evaluations suggest that WebMedSA facilitates the exchange of knowledge between radiologists, and provides the basis for collaborative work among them.

Benchmarking infrastructure for mutation text mining.

PubMed

Klein, Artjom; Riazanov, Alexandre; Hindle, Matthew M; Baker, Christopher Jo

2014-02-25

Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation text mining systems. We propose a community-oriented annotation and benchmarking infrastructure to support development, testing, benchmarking, and comparison of mutation text mining systems. The design is based on semantic standards, where RDF is used to represent annotations, an OWL ontology provides an extensible schema for the data and SPARQL is used to compute various performance metrics, so that in many cases no programming is needed to analyze results from a text mining system. While large benchmark corpora for biological entity and relation extraction are focused mostly on genes, proteins, diseases, and species, our benchmarking infrastructure fills the gap for mutation information. The core infrastructure comprises (1) an ontology for modelling annotations, (2) SPARQL queries for computing performance metrics, and (3) a sizeable collection of manually curated documents, that can support mutation grounding and mutation impact extraction experiments. We have developed the principal infrastructure for the benchmarking of mutation text mining tasks. The use of RDF and OWL as the representation for corpora ensures extensibility. The infrastructure is suitable for out-of-the-box use in several important scenarios and is ready, in its current state, for initial community adoption.

High-Performance Data Analytics Beyond the Relational and Graph Data Models with GEMS

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

Castellana, Vito G.; Minutoli, Marco; Bhatt, Shreyansh

Graphs represent an increasingly popular data model for data-analytics, since they can naturally represent relationships and interactions between entities. Relational databases and their pure table-based data model are not well suitable to store and process sparse data. Consequently, graph databases have gained interest in the last few years and the Resource Description Framework (RDF) became the standard data model for graph data. Nevertheless, while RDF is well suited to analyze the relationships between the entities, it is not efficient in representing their attributes and properties. In this work we propose the adoption of a new hybrid data model, based onmore » attributed graphs, that aims at overcoming the limitations of the pure relational and graph data models. We present how we have re-designed the GEMS data-analytics framework to fully take advantage of the proposed hybrid data model. To improve analysts productivity, in addition to a C++ API for applications development, we adopt GraQL as input query language. We validate our approach implementing a set of queries on net-flow data and we compare our framework performance against Neo4j. Experimental results show significant performance improvement over Neo4j, up to several orders of magnitude when increasing the size of the input data.« less

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

PubMed

Yokochi, Masashi; Kobayashi, Naohiro; Ulrich, Eldon L; Kinjo, Akira R; Iwata, Takeshi; Ioannidis, Yannis E; Livny, Miron; Markley, John L; Nakamura, Haruki; Kojima, Chojiro; Fujiwara, Toshimichi

2016-05-05

The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources.

Ontology Design of Influential People Identification Using Centrality

NASA Astrophysics Data System (ADS)

Maulana Awangga, Rolly; Yusril, Muhammad; Setyawan, Helmi

2018-04-01

Identifying influential people as a node in a graph theory commonly calculated by social network analysis. The social network data has the user as node and edge as relation forming a friend relation graph. This research is conducting different meaning of every nodes relation in the social network. Ontology was perfect match science to describe the social network data as conceptual and domain. Ontology gives essential relationship in a social network more than a current graph. Ontology proposed as a standard for knowledge representation for the semantic web by World Wide Web Consortium. The formal data representation use Resource Description Framework (RDF) and Web Ontology Language (OWL) which is strategic for Open Knowledge-Based website data. Ontology used in the semantic description for a relationship in the social network, it is open to developing semantic based relationship ontology by adding and modifying various and different relationship to have influential people as a conclusion. This research proposes a model using OWL and RDF for influential people identification in the social network. The study use degree centrality, between ness centrality, and closeness centrality measurement for data validation. As a conclusion, influential people identification in Facebook can use proposed Ontology model in the Group, Photos, Photo Tag, Friends, Events and Works data.

Validating EHR clinical models using ontology patterns.

PubMed

Martínez-Costa, Catalina; Schulz, Stefan

2017-12-01

Clinical models are artefacts that specify how information is structured in electronic health records (EHRs). However, the makeup of clinical models is not guided by any formal constraint beyond a semantically vague information model. We address this gap by advocating ontology design patterns as a mechanism that makes the semantics of clinical models explicit. This paper demonstrates how ontology design patterns can validate existing clinical models using SHACL. Based on the Clinical Information Modelling Initiative (CIMI), we show how ontology patterns detect both modeling and terminology binding errors in CIMI models. SHACL, a W3C constraint language for the validation of RDF graphs, builds on the concept of "Shape", a description of data in terms of expected cardinalities, datatypes and other restrictions. SHACL, as opposed to OWL, subscribes to the Closed World Assumption (CWA) and is therefore more suitable for the validation of clinical models. We have demonstrated the feasibility of the approach by manually describing the correspondences between six CIMI clinical models represented in RDF and two SHACL ontology design patterns. Using a Java-based SHACL implementation, we found at least eleven modeling and binding errors within these CIMI models. This demonstrates the usefulness of ontology design patterns not only as a modeling tool but also as a tool for validation. Copyright © 2017 Elsevier Inc. All rights reserved.

Novel integrated mechanical biological chemical treatment (MBCT) systems for the production of levulinic acid from fraction of municipal solid waste: A comprehensive techno-economic analysis.

PubMed

Sadhukhan, Jhuma; Ng, Kok Siew; Martinez-Hernandez, Elias

2016-09-01

This paper, for the first time, reports integrated conceptual MBCT/biorefinery systems for unlocking the value of organics in municipal solid waste (MSW) through the production of levulinic acid (LA by 5wt%) that increases the economic margin by 110-150%. After mechanical separation recovering recyclables, metals (iron, aluminium, copper) and refuse derived fuel (RDF), lignocelluloses from remaining MSW are extracted by supercritical-water for chemical valorisation, comprising hydrolysis in 2wt% dilute H2SO4 catalyst producing LA, furfural, formic acid (FA), via C5/C6 sugar extraction, in plug flow (210-230°C, 25bar, 12s) and continuous stirred tank (195-215°C, 14bar, 20min) reactors; char separation and LA extraction/purification by methyl isobutyl ketone solvent; acid/solvent and by-product recovery. The by-product and pulping effluents are anaerobically digested into biogas and fertiliser. Produced biogas (6.4MWh/t), RDF (5.4MWh/t), char (4.5MWh/t) are combusted, heat recovered into steam generation in boiler (efficiency: 80%); on-site heat/steam demand is met; balance of steam is expanded into electricity in steam turbines (efficiency: 35%). Copyright © 2016 Elsevier Ltd. All rights reserved.

Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data

PubMed Central

2013-01-01

Background The World Wide Web has become a dissemination platform for scientific and non-scientific publications. However, most of the information remains locked up in discrete documents that are not always interconnected or machine-readable. The connectivity tissue provided by RDF technology has not yet been widely used to support the generation of self-describing, machine-readable documents. Results In this paper, we present our approach to the generation of self-describing machine-readable scholarly documents. We understand the scientific document as an entry point and interface to the Web of Data. We have semantically processed the full-text, open-access subset of PubMed Central. Our RDF model and resulting dataset make extensive use of existing ontologies and semantic enrichment services. We expose our model, services, prototype, and datasets at http://biotea.idiginfo.org/ Conclusions The semantic processing of biomedical literature presented in this paper embeds documents within the Web of Data and facilitates the execution of concept-based queries against the entire digital library. Our approach delivers a flexible and adaptable set of tools for metadata enrichment and semantic processing of biomedical documents. Our model delivers a semantically rich and highly interconnected dataset with self-describing content so that software can make effective use of it. PMID:23734622

The health care and life sciences community profile for dataset descriptions

PubMed Central

Alexiev, Vladimir; Ansell, Peter; Bader, Gary; Baran, Joachim; Bolleman, Jerven T.; Callahan, Alison; Cruz-Toledo, José; Gaudet, Pascale; Gombocz, Erich A.; Gonzalez-Beltran, Alejandra N.; Groth, Paul; Haendel, Melissa; Ito, Maori; Jupp, Simon; Juty, Nick; Katayama, Toshiaki; Kobayashi, Norio; Krishnaswami, Kalpana; Laibe, Camille; Le Novère, Nicolas; Lin, Simon; Malone, James; Miller, Michael; Mungall, Christopher J.; Rietveld, Laurens; Wimalaratne, Sarala M.; Yamaguchi, Atsuko

2016-01-01

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets. PMID:27602295

Utility of the Personality Assessment Inventory for Detecting Malingered ADHD in College Students.

PubMed

Musso, Mandi W; Hill, Benjamin D; Barker, Alyse A; Pella, Russell D; Gouvier, Wm Drew

2016-09-01

The purpose of the current study is to examine the utility of the Personality Assessment Inventory (PAI) for detecting feigned ADHD in college students. A sample of 238 undergraduate students was recruited and asked to simulate ADHD (ADHD simulators) or respond honestly (controls) on the PAI. Archival data (n = 541) from individuals diagnosed with clinical ADHD, no diagnosis, learning disorder, mood/anxiety, comorbid ADHD-mood/anxiety, or suspect effort were used. Few individuals scored above the cutoffs on PAI validity scales. When alternative cutoff scores were examined, cutoffs of ≥77 on the Negative Impression Management (NIM) scale, ≥3 on the Malingering Index (MAL), and ≥1 on the Rogers Discriminant Function (RDF) yielded excellent specificity in all groups and sensitivities of .33, .30, and .20, respectively. Individuals who were asked to simulate ADHD easily manipulate the PAI; however, alternative cutoff scores proposed for PAI validity indices may improve the detection of feigned ADHD symptoms. © The Author(s) 2014.

The neuron classification problem

PubMed Central

Bota, Mihail; Swanson, Larry W.

2007-01-01

A systematic account of neuron cell types is a basic prerequisite for determining the vertebrate nervous system global wiring diagram. With comprehensive lineage and phylogenetic information unavailable, a general ontology based on structure-function taxonomy is proposed and implemented in a knowledge management system, and a prototype analysis of select regions (including retina, cerebellum, and hypothalamus) presented. The supporting Brain Architecture Knowledge Management System (BAMS) Neuron ontology is online and its user interface allows queries about terms and their definitions, classification criteria based on the original literature and “Petilla Convention” guidelines, hierarchies, and relations—with annotations documenting each ontology entry. Combined with three BAMS modules for neural regions, connections between regions and neuron types, and molecules, the Neuron ontology provides a general framework for physical descriptions and computational modeling of neural systems. The knowledge management system interacts with other web resources, is accessible in both XML and RDF/OWL, is extendible to the whole body, and awaits large-scale data population requiring community participation for timely implementation. PMID:17582506

SEEK: a systems biology data and model management platform.

PubMed

Wolstencroft, Katherine; Owen, Stuart; Krebs, Olga; Nguyen, Quyen; Stanford, Natalie J; Golebiewski, Martin; Weidemann, Andreas; Bittkowski, Meik; An, Lihua; Shockley, David; Snoep, Jacky L; Mueller, Wolfgang; Goble, Carole

2015-07-11

Systems biology research typically involves the integration and analysis of heterogeneous data types in order to model and predict biological processes. Researchers therefore require tools and resources to facilitate the sharing and integration of data, and for linking of data to systems biology models. There are a large number of public repositories for storing biological data of a particular type, for example transcriptomics or proteomics, and there are several model repositories. However, this silo-type storage of data and models is not conducive to systems biology investigations. Interdependencies between multiple omics datasets and between datasets and models are essential. Researchers require an environment that will allow the management and sharing of heterogeneous data and models in the context of the experiments which created them. The SEEK is a suite of tools to support the management, sharing and exploration of data and models in systems biology. The SEEK platform provides an access-controlled, web-based environment for scientists to share and exchange data and models for day-to-day collaboration and for public dissemination. A plug-in architecture allows the linking of experiments, their protocols, data, models and results in a configurable system that is available 'off the shelf'. Tools to run model simulations, plot experimental data and assist with data annotation and standardisation combine to produce a collection of resources that support analysis as well as sharing. Underlying semantic web resources additionally extract and serve SEEK metadata in RDF (Resource Description Format). SEEK RDF enables rich semantic queries, both within SEEK and between related resources in the web of Linked Open Data. The SEEK platform has been adopted by many systems biology consortia across Europe. It is a data management environment that has a low barrier of uptake and provides rich resources for collaboration. This paper provides an update on the functions and features of the SEEK software, and describes the use of the SEEK in the SysMO consortium (Systems biology for Micro-organisms), and the VLN (virtual Liver Network), two large systems biology initiatives with different research aims and different scientific communities.

GGDonto ontology as a knowledge-base for genetic diseases and disorders of glycan metabolism and their causative genes.

PubMed

Solovieva, Elena; Shikanai, Toshihide; Fujita, Noriaki; Narimatsu, Hisashi

2018-04-18

Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. The Glyco-Disease Genes Database (GDGDB), which provides information about these diseases and disorders as well as their causative genes, has been developed by the Research Center for Medical Glycoscience (RCMG) and released in April 2010. GDGDB currently provides information on about 80 genetic diseases and disorders caused by single-gene mutations in glyco-related genes. Many biomedical resources provide information about genetic disorders and genes involved in their pathogenesis, but resources focused on genetic disorders known to be related to glycan metabolism are lacking. With the aim of providing more comprehensive knowledge on genetic diseases and disorders of glycan biosynthesis and degradation, we enriched the content of the GDGDB database and improved the methods for data representation. We developed the Genetic Glyco-Diseases Ontology (GGDonto) and a RDF/SPARQL-based user interface using Semantic Web technologies. In particular, we represented the GGDonto content using Semantic Web languages, such as RDF, RDFS, SKOS, and OWL, and created an interactive user interface based on SPARQL queries. This user interface provides features to browse the hierarchy of the ontology, view detailed information on diseases and related genes, and find relevant background information. Moreover, it provides the ability to filter and search information by faceted and keyword searches. Focused on the molecular etiology, pathogenesis, and clinical manifestations of genetic diseases and disorders of glycan metabolism and developed as a knowledge-base for this scientific field, GGDonto provides comprehensive information on various topics, including links to aid the integration with other scientific resources. The availability and accessibility of this knowledge will help users better understand how genetic defects impact the metabolism of glycans as well as how this impaired metabolism affects various biological functions and human health. In this way, GGDonto will be useful in fields related to glycoscience, including cell biology, biotechnology, and biomedical, and pharmaceutical research.

Rolling Deck to Repository (R2R): A "Linked Data" Approach for the U.S. Academic Research Fleet

NASA Astrophysics Data System (ADS)

Arko, R. A.; Chandler, C. L.; Clark, P. D.; Milan, A.; Mize, J.

2011-12-01

The U.S. academic research fleet is an essential mobile observing platform for ocean science. The NSF-funded Rolling Deck to Repository (R2R) program is working with the fleet community to routinely document, assess, and preserve data from the underway sensor systems on each vessel.
The R2R facility maintains a master catalog of vessels, instrument systems, operating institutions, cruises, personnel, and data sets. In less than two years, the catalog has grown to over 2,000 cruises including unique identifiers for vessel deployments, project titles, chief scientists, dates, ports, survey targets, and navigation tracks. This master catalog is of great value to peer data systems, ranging from large national data centers to small disciplinary data offices, as an aid in organizing, extending, and quality controlling their own collections and finding related data from authoritative sources.
R2R breaks with the tradition of stovepipe portals built around complex search interfaces tightly bound to backend databases. Instead, we have adopted a Linked Data approach to publish our catalog content, based on the W3C Resource Description Framework (RDF) and Uniform Resource Identifiers (URIs). Our data model is published as a collection of W3C Simple Knowledge Organization System (SKOS) concepts, mapped to partner vocabularies such as those developed by the Global Change Master Directory (GCMD) and the pan-European SeaDataNet partnership, and our catalog content is published as collections of RDF resources with globally unique and persistent identifiers. The combination of exposing our data model, mapping local terms to community-wide vocabularies, and using reliable identifiers improves interoperability and reduces ambiguity. R2R's metric of success is the degree to which peer data systems routinely harvest and reuse our content.
R2R is working collaboratively with the NOAA National Data Centers and the NSF-funded Biological and Chemical Oceanography Data Management Office (BCO-DMO) on a range of Linked Data pilot applications, including production of ISO-compliant metadata and deployment of a SPARQL search interface. Our objective is to support a distributed, loosely federated network of complementary systems that collectively manage the vast body of ocean science data. We will present results and lessons learned.

Publishing high-quality climate data on the semantic web

NASA Astrophysics Data System (ADS)

Woolf, Andrew; Haller, Armin; Lefort, Laurent; Taylor, Kerry

2013-04-01

The effort over more than a decade to establish the semantic web [Berners-Lee et. al., 2001] has received a major boost in recent years through the Open Government movement. Governments around the world are seeking technical solutions to enable more open and transparent access to Public Sector Information (PSI) they hold. Existing technical protocols and data standards tend to be domain specific, and so limit the ability to publish and integrate data across domains (health, environment, statistics, education, etc.). The web provides a domain-neutral platform for information publishing, and has proven itself beyond expectations for publishing and linking human-readable electronic documents. Extending the web pattern to data (often called Web 3.0) offers enormous potential. The semantic web applies the basic web principles to data [Berners-Lee, 2006]: using URIs as identifiers (for data objects and real-world 'things', instead of documents) making the URIs actionable by providing useful information via HTTP using a common exchange standard (serialised RDF for data instead of HTML for documents) establishing typed links between information objects to enable linking and integration Leading examples of 'linked data' for publishing PSI may be found in both the UK (http://data.gov.uk/linked-data) and US (http://www.data.gov/page/semantic-web). The Bureau of Meteorology (BoM) is Australia's national meteorological agency, and has a new mandate to establish a national environmental information infrastructure (under the National Plan for Environmental Information, NPEI [BoM, 2012a]). While the initial approach is based on the existing best practice Spatial Data Infrastructure (SDI) architecture, linked-data is being explored as a technological alternative that shows great promise for the future. We report here the first trial of government linked-data in Australia under data.gov.au. In this initial pilot study, we have taken BoM's new high-quality reference surface temperature dataset, Australian Climate Observations Reference Network - Surface Air Temperature (ACORN-SAT) [BoM, 2012b]. This dataset contains daily homogenised surface temperature observations for 112 locations around Australia, dating back to 1910. An ontology for the dataset was developed [Lefort et. al., 2012], based on the existing Semantic Sensor Network ontology [Compton et. al., 2012] and the W3C RDF Data Cube vocabulary [W3C, 2012]. Additional vocabularies were developed, e.g. for BoM weather stations and rainfall districts. The dataset was converted to RDF and loaded into an RDF triplestore. The Linked-Data API (http://code.google.com/p/linked-data-api) was used to configure specific URI query patterns (e.g. for observation timeseries slices by station), and a SPARQL endpoint was provided for direct querying. In addition, some demonstration 'mash-ups' were developed, providing an interactive browser-based interface to the temperature timeseries. References [Berners-Lee et. al., 2001] Tim Berners-Lee, James Hendler and Ora Lassila (2001), "The Semantic Web", Scientific American, May 2001. [Berners-Lee, 2006] Tim Berners-Lee (2006), "Linked Data - Design Issues", W3C [http://www.w3.org/DesignIssues/LinkedData.html] [BoM, 2012a] Bureau of Meteorology (2012), "Environmental information" [http://www.bom.gov.au/environment/] [BoM, 2012b] Bureau of Meteorology (2012), "Australian Climate Observations Reference Network - Surface Air Temperature" [http://www.bom.gov.au/climate/change/acorn-sat/] [Compton et. al., 2012] Michael Compton, Payam Barnaghi, Luis Bermudez, Raul Garcia-Castro, Oscar Corcho, Simon Cox, John Graybeal, Manfred Hauswirth, Cory Henson, Arthur Herzog, Vincent Huang, Krzysztof Janowicz, W. David Kelsey, Danh Le Phuoc, Laurent Lefort, Myriam Leggieri, Holger Neuhaus, Andriy Nikolov, Kevin Page, Alexandre Passant, Amit Sheth, Kerry Taylor (2012), "The SSN Ontology of the W3C Semantic Sensor Network Incubator Group", J. Web Semantics, 17 (2012) [http://dx.doi.org/10.1016/j.websem.2012.05.003] [Lefort et. al., 2012] Laurent Lefort, Josh Bobruk, Armin Haller, Kerry Taylor and Andrew Woolf (2012), "A Linked Sensor Data Cube for a 100 Year Homogenised daily temperature dataset", Proc. Semantic Sensor Networks 2012 [http://ceur-ws.org/Vol-904/paper10.pdf] [W3C, 2012] W3C (2012), "The RDF Data Cube Vocabulary", [http://www.w3.org/TR/vocab-data-cube/

linkedISA: semantic representation of ISA-Tab experimental metadata.

PubMed

González-Beltrán, Alejandra; Maguire, Eamonn; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2014-01-01

Reporting and sharing experimental metadata- such as the experimental design, characteristics of the samples, and procedures applied, along with the analysis results, in a standardised manner ensures that datasets are comprehensible and, in principle, reproducible, comparable and reusable. Furthermore, sharing datasets in formats designed for consumption by humans and machines will also maximize their use. The Investigation/Study/Assay (ISA) open source metadata tracking framework facilitates standards-compliant collection, curation, visualization, storage and sharing of datasets, leveraging on other platforms to enable analysis and publication. The ISA software suite includes several components used in increasingly diverse set of life science and biomedical domains; it is underpinned by a general-purpose format, ISA-Tab, and conversions exist into formats required by public repositories. While ISA-Tab works well mainly as a human readable format, we have also implemented a linked data approach to semantically define the ISA-Tab syntax. We present a semantic web representation of the ISA-Tab syntax that complements ISA-Tab's syntactic interoperability with semantic interoperability. We introduce the linkedISA conversion tool from ISA-Tab to the Resource Description Framework (RDF), supporting mappings from the ISA syntax to multiple community-defined, open ontologies and capitalising on user-provided ontology annotations in the experimental metadata. We describe insights of the implementation and how annotations can be expanded driven by the metadata. We applied the conversion tool as part of Bio-GraphIIn, a web-based application supporting integration of the semantically-rich experimental descriptions. Designed in a user-friendly manner, the Bio-GraphIIn interface hides most of the complexities to the users, exposing a familiar tabular view of the experimental description to allow seamless interaction with the RDF representation, and visualising descriptors to drive the query over the semantic representation of the experimental design. In addition, we defined queries over the linkedISA RDF representation and demonstrated its use over the linkedISA conversion of datasets from Nature' Scientific Data online publication. Our linked data approach has allowed us to: 1) make the ISA-Tab semantics explicit and machine-processable, 2) exploit the existing ontology-based annotations in the ISA-Tab experimental descriptions, 3) augment the ISA-Tab syntax with new descriptive elements, 4) visualise and query elements related to the experimental design. Reasoning over ISA-Tab metadata and associated data will facilitate data integration and knowledge discovery.

Publishing NASA Metadata as Linked Open Data for Semantic Mashups

NASA Astrophysics Data System (ADS)

Wilson, Brian; Manipon, Gerald; Hua, Hook

2014-05-01

Data providers are now publishing more metadata in more interoperable forms, e.g. Atom or RSS 'casts', as Linked Open Data (LOD), or as ISO Metadata records. A major effort on the part of the NASA's Earth Science Data and Information System (ESDIS) project is the aggregation of metadata that enables greater data interoperability among scientific data sets regardless of source or application. Both the Earth Observing System (EOS) ClearingHOuse (ECHO) and the Global Change Master Directory (GCMD) repositories contain metadata records for NASA (and other) datasets and provided services. These records contain typical fields for each dataset (or software service) such as the source, creation date, cognizant institution, related access URL's, and domain and variable keywords to enable discovery. Under a NASA ACCESS grant, we demonstrated how to publish the ECHO and GCMD dataset and services metadata as LOD in the RDF format. Both sets of metadata are now queryable at SPARQL endpoints and available for integration into "semantic mashups" in the browser. It is straightforward to reformat sets of XML metadata, including ISO, into simple RDF and then later refine and improve the RDF predicates by reusing known namespaces such as Dublin core, georss, etc. All scientific metadata should be part of the LOD world. In addition, we developed an "instant" drill-down and browse interface that provides faceted navigation so that the user can discover and explore the 25,000 datasets and 3000 services. The available facets and the free-text search box appear in the left panel, and the instantly updated results for the dataset search appear in the right panel. The user can constrain the value of a metadata facet simply by clicking on a word (or phrase) in the "word cloud" of values for each facet. The display section for each dataset includes the important metadata fields, a full description of the dataset, potentially some related URL's, and a "search" button that points to an OpenSearch GUI that is pre-configured to search for granules within the dataset. We will present our experiences with converting NASA metadata into LOD, discuss the challenges, illustrate some of the enabled mashups, and demonstrate the latest version of the "instant browse" interface for navigating multiple metadata collections.

Semantic Web-based Vocabulary Broker for Open Science

NASA Astrophysics Data System (ADS)

Ritschel, B.; Neher, G.; Iyemori, T.; Murayama, Y.; Kondo, Y.; Koyama, Y.; King, T. A.; Galkin, I. A.; Fung, S. F.; Wharton, S.; Cecconi, B.

2016-12-01

Keyword vocabularies are used to tag and to identify data of science data repositories. Such vocabularies consist of controlled terms and the appropriate concepts, such as GCMD1 keywords or the ESPAS2 keyword ontology. The Semantic Web-based mash-up of domain-specific, cross- or even trans-domain vocabularies provides unique capabilities in the network of appropriate data resources. Based on a collaboration between GFZ3, the FHP4, the WDC for Geomagnetism5 and the NICT6 we developed the concept of a vocabulary broker for inter- and trans-disciplinary data detection and integration. Our prototype of the Semantic Web-based vocabulary broker uses OSF7 for the mash-up of geo and space research vocabularies, such as GCMD keywords, ESPAS keyword ontology and SPASE8 keyword vocabulary. The vocabulary broker starts the search with "free" keywords or terms of a specific vocabulary scheme. The vocabulary broker almost automatically connects the different science data repositories which are tagged by terms of the aforementioned vocabularies. Therefore the mash-up of the SKOS9 based vocabularies with appropriate metadata from different domains can be realized by addressing LOD10 resources or virtual SPARQL11 endpoints which maps relational structures into the RDF format12. In order to demonstrate such a mash-up approach in real life, we installed and use a D2RQ13 server for the integration of IUGONET14 data which are managed by a relational database. The OSF based vocabulary broker and the D2RQ platform are installed at virtual LINUX machines at the Kyoto University. The vocabulary broker meets the standard of a main component of the WDS15 knowledge network. The Web address of the vocabulary broker is http://wdcosf.kugi.kyoto-u.ac.jp 1 Global Change Master Directory2 Near earth space data infrastructure for e-science3 German Research Centre for Geosciences4 University of Applied Sciences Potsdam5 World Data Center for Geomagnetism Kyoto6 National Institute of Information and Communications Technology Tokyo7 Open Semantic Framework8 Space Physics Archive Search and Extract9 Simple Knowledge Organization System10 Linked Open Data11 SPARQL Protocol And RDF Query12 Resource Description Framework13 Database to RDF Query14 Inter-university Upper atmosphere Global Observation NETwork15 World Data System

A Semantic Transformation Methodology for the Secondary Use of Observational Healthcare Data in Postmarketing Safety Studies.

PubMed

Pacaci, Anil; Gonul, Suat; Sinaci, A Anil; Yuksel, Mustafa; Laleci Erturkmen, Gokce B

2018-01-01

Background: Utilization of the available observational healthcare datasets is key to complement and strengthen the postmarketing safety studies. Use of common data models (CDM) is the predominant approach in order to enable large scale systematic analyses on disparate data models and vocabularies. Current CDM transformation practices depend on proprietarily developed Extract-Transform-Load (ETL) procedures, which require knowledge both on the semantics and technical characteristics of the source datasets and target CDM. Purpose: In this study, our aim is to develop a modular but coordinated transformation approach in order to separate semantic and technical steps of transformation processes, which do not have a strict separation in traditional ETL approaches. Such an approach would discretize the operations to extract data from source electronic health record systems, alignment of the source, and target models on the semantic level and the operations to populate target common data repositories. Approach: In order to separate the activities that are required to transform heterogeneous data sources to a target CDM, we introduce a semantic transformation approach composed of three steps: (1) transformation of source datasets to Resource Description Framework (RDF) format, (2) application of semantic conversion rules to get the data as instances of ontological model of the target CDM, and (3) population of repositories, which comply with the specifications of the CDM, by processing the RDF instances from step 2. The proposed approach has been implemented on real healthcare settings where Observational Medical Outcomes Partnership (OMOP) CDM has been chosen as the common data model and a comprehensive comparative analysis between the native and transformed data has been conducted. Results: Health records of ~1 million patients have been successfully transformed to an OMOP CDM based database from the source database. Descriptive statistics obtained from the source and target databases present analogous and consistent results. Discussion and Conclusion: Our method goes beyond the traditional ETL approaches by being more declarative and rigorous. Declarative because the use of RDF based mapping rules makes each mapping more transparent and understandable to humans while retaining logic-based computability. Rigorous because the mappings would be based on computer readable semantics which are amenable to validation through logic-based inference methods.

An ontology-driven tool for structured data acquisition using Web forms.

PubMed

Gonçalves, Rafael S; Tu, Samson W; Nyulas, Csongor I; Tierney, Michael J; Musen, Mark A

2017-08-01

Structured data acquisition is a common task that is widely performed in biomedicine. However, current solutions for this task are far from providing a means to structure data in such a way that it can be automatically employed in decision making (e.g., in our example application domain of clinical functional assessment, for determining eligibility for disability benefits) based on conclusions derived from acquired data (e.g., assessment of impaired motor function). To use data in these settings, we need it structured in a way that can be exploited by automated reasoning systems, for instance, in the Web Ontology Language (OWL); the de facto ontology language for the Web. We tackle the problem of generating Web-based assessment forms from OWL ontologies, and aggregating input gathered through these forms as an ontology of "semantically-enriched" form data that can be queried using an RDF query language, such as SPARQL. We developed an ontology-based structured data acquisition system, which we present through its specific application to the clinical functional assessment domain. We found that data gathered through our system is highly amenable to automatic analysis using queries. We demonstrated how ontologies can be used to help structuring Web-based forms and to semantically enrich the data elements of the acquired structured data. The ontologies associated with the enriched data elements enable automated inferences and provide a rich vocabulary for performing queries.

Benchmarking Software Assurance Implementation

DTIC Science & Technology

2011-05-18

product The chicken#. (a.k.a. Process Focused Assessment ) – Management Systems ( ISO 9001, ISO 27001 , ISO 2000) – Capability Maturity Models (CMMI...Assurance PRM, RMM, Assurance for CMMI)) – Lifecycle Processes ( ISO /IEEE 15288, ISO /IEEE 12207) – COBIT, ITIL, MS SDL, OSAMM, BSIMM 5 The egg...a.k.a Product Focused Assessments) – SCAP - NIST-SCAP – ISO /OMG W3C – KDM, BPMN, RIF, XMI, RDF – OWASP Top 10 – SANS TOP 25 – Secure Code Check Lists

Group Centric Information Sharing Using Hierarchical Models

DTIC Science & Technology

2011-01-01

enable people to create data using RDF, build vocabularies using web ontology language (OWL), write rules and query data stores using SPARQL [8...a strict joined and the document was added with a strict add. In order to represent the fact that an action is allowed (or not), we have created a...greatly improve the system’s readiness to handle any number of access decision queries . a. The pair is tested against the gSIS Join and Add semantics

Performance of mechanical biological treatment of residual municipal waste in Poland

NASA Astrophysics Data System (ADS)

den Boer, Emilia; Jędrczak, Andrzej

2017-11-01

The number and capacity of mechanical-biological treatment (MBT) plants in Europe increased significantly in the past two decades as a response to the legal obligation to limit the landfilling of biodegradable waste in landfills and to increase recycling and energy recovery from waste. The aim of these plants is to prepare residual municipal waste for recovery and disposal operations, including especially separation and stabilization of the easily biodegradable fraction (the biofraction). The final products of MBP technology are recyclables, stabilate, high calorific fraction which is used for the production of refuse derived fuel (RDF) and the remaining residual fraction. The shares of the output fractions, especially of the recyclables and RDF determine the overall efficiency of MBT technology in diverting waste from landfills. In this paper results of an assessment of one exemplary MBT plant are provided. The analysis was performed within a comparative study in which 20 selected MBT plants in Poland were subject to a detailed analysis, focusing, both at the design parameters as well as operational ones. The selected plant showed relatively higher overall materials recovery efficiency. With the view to circular economy targets, increased automation of the mechanical waste treatment will be required to support achieving high level diversion from landfills. The study reviled that stabilisation of biofraction should be improved by a better control of process conditions, especially moisture content.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

PubMed

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-04

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Refuse Derived Fuel (RDF) production and gasification in a pilot plant integrated with an Otto cycle ICE through Aspen plus™ modelling: Thermodynamic and economic viability.

PubMed

Násner, Albany Milena Lozano; Lora, Electo Eduardo Silva; Palacio, José Carlos Escobar; Rocha, Mateus Henrique; Restrepo, Julian Camilo; Venturini, Osvaldo José; Ratner, Albert

2017-11-01

This work deals with the development of a Refuse Derived Fuel (RDF) gasification pilot plant using air as a gasification agent. A downdraft fixed bed reactor is integrated with an Otto cycle Internal Combustion Engine (ICE). Modelling was carried out using the Aspen Plus™ software to predict the ideal operational conditions for maximum efficiency. Thermodynamics package used in the simulation comprised the Non-Random Two-Liquid (NRTL) model and the Hayden-O'Connell (HOC) equation of state. As expected, the results indicated that the Equivalence Ratio (ER) has a direct influence over the gasification temperature and the composition of the Raw Produced Gas (RPG), and effects of ER over the Lower Heating Value (LHV) and Cold Gasification Efficiency (CGE) of the RPG are also discussed. A maximum CGE efficiency of 57-60% was reached for ER values between 0.25 and 0.3, also an average reactor temperature values in the range of 680-700°C, with a peak LHV of 5.8MJ/Nm 3 . RPG was burned in an ICE, reaching an electrical power of 50kW el . The economic assessment of the pilot plant implementation was also performed, showing the project is feasible, with power above 120kW el with an initial investment of approximately US$ 300,000. Copyright © 2017 Elsevier Ltd. All rights reserved.

Creating Actionable Data from an Optical Depth Measurement Network using RDF

NASA Astrophysics Data System (ADS)

Freemantle, J. R.; O'Neill, N. T.; Lumb, L. I.; Abboud, I.; McArthur, B.

2010-12-01

The AEROCAN sunphotometery network has, for more than a decade, generated optical indicators of aerosol concentration and size on a regional and national scale. We believe this optical information can be rendered more “actionable” to the health care community by developing a technical and interpretative information-sharing geospatial strategy with that community. By actionable data we mean information that is presented in manner that can be understood and then used in the decision making process. The decision may be that of a technical professional, a policy maker or a machine. The information leading up to a decision may come from many sources; this means it is particularly important that data are well defined across knowledge fields, in our case atmospheric science and respiratory health science. As part of the AEROCAN operational quality assurance (QA) methodology we have written automatic procedures to make some of the AEROCAN data more accessible or “actionable”. Tim Berners-Lee has advocated making datasets, “Linked Data”, available on the web with a proper structural description (metadata). We have been using RDF (Resource Description Framework) to enhance the utility of our sunphotometer data; the resulting self-describing representation is structured so that it is machine readable. This allows semantically based queries (e.g., via SPARQL) on our dataset that in the past were only viewable as passive Web tables of data.

Standard Biological Parts Knowledgebase

PubMed Central

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M.; Gennari, John H.

2011-01-01

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible. PMID:21390321

Linked Metadata - lightweight semantics for data integration (Invited)

NASA Astrophysics Data System (ADS)

Hendler, J. A.

2013-12-01

The "Linked Open Data" cloud (http://linkeddata.org) is currently used to show how the linking of datasets, supported by SPARQL endpoints, is creating a growing set of linked data assets. This linked data space has been growing rapidly, and the last version collected is estimated to have had over 35 billion 'triples.' As impressive as this may sound, there is an inherent flaw in the way the linked data story is conceived. The idea is that all of the data is represented in a linked format (generally RDF) and applications will essentially query this cloud and provide mashup capabilities between the various kinds of data that are found. The view of linking in the cloud is fairly simple -links are provided by either shared URIs or by URIs that are asserted to be owl:sameAs. This view of the linking, which primarily focuses on shared objects and subjects in RDF's subject-predicate-object representation, misses a critical aspect of Semantic Web technology. Given triples such as * A:person1 foaf:knows A:person2 * B:person3 foaf:knows B:person4 * C:person5 foaf:name 'John Doe' this view would not consider them linked (barring other assertions) even though they share a common vocabulary. In fact, we get significant clues that there are commonalities in these data items from the shared namespaces and predicates, even if the traditional 'graph' view of RDF doesn't appear to join on these. Thus, it is the linking of the data descriptions, whether as metadata or other vocabularies, that provides the linking in these cases. This observation is crucial to scientific data integration where the size of the datasets, or even the individual relationships within them, can be quite large. (Note that this is not restricted to scientific data - search engines, social networks, and massive multiuser games also create huge amounts of data.) To convert all the triples into RDF and provide individual links is often unnecessary, and is both time and space intensive. Those looking to do on the fly integration may prefer to do more traditional data queries and then convert and link the 'views' returned at retrieval time, providing another means of using the linked data infrastructure without having to convert whole datasets to triples to provide linking. Web companies have been taking advantage of 'lightweight' semantic metadata for search quality and optimization (cf. schema.org), linking networks within and without web sites (cf. Facebook's Open Graph Protocol), and in doing various kinds of advertisement and user modeling across datasets. Scientific metadata, on the other hand, has traditionally been geared at being largescale and highly descriptive, and scientific ontologies have been aimed at high expressivity, essentially providing complex reasoning services rather than the less expressive vocabularies needed for data discovery and simple mappings that can allow humans (or more complex systems) when full scale integration is needed. Although this work is just the beginning for providing integration, as the community creates more and more datasets, discovery of these data resources on the Web becomes a crucial starting place. Simple descriptors, that can be combined with textual fields and/or common community vocabularies, can be a great starting place on bringing scientific data into the Web of Data that is growing in other communities. References: [1] Pouchard, Line C., et al. "A Linked Science investigation: enhancing climate change data discovery with semantic technologies." Earth science informatics 6.3 (2013): 175-185.

Simulation Modeling and Analysis of Device-Aware Network Architectures

DTIC Science & Technology

2004-12-01

However, a potential issue lies in the location of the intermediate proxy with respect to the content servers; if the proxy is far away from the...to 11 guide the adaptation of content presented to that device [CC/PP, 2004]. The strength of CC/PP lies in its flexibility. CC/PP is based on RDF...from: http://ieeexplore.ieee.org/iel4/98/15881/00736473.pdf. Accessed October 2004. [Hu and Bagga, 2004] Jianying Hu and Amit Bagga, “Categorizing

RelFinder: Revealing Relationships in RDF Knowledge Bases

NASA Astrophysics Data System (ADS)

Heim, Philipp; Hellmann, Sebastian; Lehmann, Jens; Lohmann, Steffen; Stegemann, Timo

The Semantic Web has recently seen a rise of large knowledge bases (such as DBpedia) that are freely accessible via SPARQL endpoints. The structured representation of the contained information opens up new possibilities in the way it can be accessed and queried. In this paper, we present an approach that extracts a graph covering relationships between two objects of interest. We show an interactive visualization of this graph that supports the systematic analysis of the found relationships by providing highlighting, previewing, and filtering features.

Chemical markup, XML, and the World Wide Web. 5. Applications of chemical metadata in RSS aggregators.

PubMed

Murray-Rust, Peter; Rzepa, Henry S; Williamson, Mark J; Willighagen, Egon L

2004-01-01

Examples of the use of the RSS 1.0 (RDF Site Summary) specification together with CML (Chemical Markup Language) to create a metadata based alerting service termed CMLRSS for molecular content are presented. CMLRSS can be viewed either using generic software or with modular opensource chemical viewers and editors enhanced with CMLRSS modules. We discuss the more automated use of CMLRSS as a component of a World Wide Molecular Matrix of semantically rich chemical information.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface.

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2011-05-16

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface

PubMed Central

2011-01-01

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations. The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems. PMID:21575202

Characterization of Viscoelastic Materials Through an Active Mixer by Direct-Ink Writing

NASA Astrophysics Data System (ADS)

Drake, Eric

The goal of this thesis is two-fold: First, to determine mixing effectiveness of an active mixer attachment to a three-dimensional (3D) printer by characterizing actively-mixed, three-dimensionally printed silicone elastomers. Second, to understand mechanical properties of a printed lattice structure with varying geometry and composition. Ober et al defines mixing effectiveness as a measureable quantity characterized by two key variables: (i) a dimensionless impeller parameter (O ) that depends on mixer geometry as well as Peclet number (Pe) and (ii) a coefficient of variation (COV) that describes the mixer effectiveness based upon image intensity. The first objective utilizes tungsten tracer particles distributed throughout a batch of Dow Corning SE1700 (two parts silicone) - ink "A". Ink "B" is made from pure SE1700. Using the in-site active mixer, both ink "A" and "B" coalesce to form a hybrid ink just before extrusion. Two samples of varying mixer speeds and composition ratios are printed and analyzed by microcomputed tomography (MicroCT). A continuous stirred tank reactor (CSTR) model is applied to better understand mixing behavior. Results are then compared with computer models to verify the hypothesis. Data suggests good mixing for the sample with higher impeller speed. A Radial Distrubtion Function (RDF) macro is used to provide further qualitative analysis of mixing efficiency. The second objective of this thesis utilized three-dimensionally printed samples of varying geometry and composition to ascertain mechanical properties. Samples were printed using SE1700 provided by Lawrence Livermore National Laboratory with a face-centered tetragonal (FCT) structure. Hardness testing is conducted using a Shore OO durometer guided by a computer-controlled, three-axis translation stage to provide precise movements. Data is collected across an 'x-y' plane of the specimen. To explain the data, a simply supported beam model is applied to a single unit cell which yields basic structural behavior per cell. Characterizing the sample as a whole requires a more rigorous approach and non-trivial complexities due to varying geometries and compositions exist. The data demonstrates a uniform change in hardness as a function of position. Additionally, the data indicates periodicities in the lattice structure.

A new approach for design and investigation of junction-less tunnel FET using electrically doped mechanism

NASA Astrophysics Data System (ADS)

Nigam, Kaushal; Kondekar, Pravin; Sharma, Dheeraj; Raad, Bhagwan Ram

2016-10-01

For the first time, a distinctive approach based on electrically doped concept is used for the formation of novel double gate tunnel field effect transistor (TFET). For this, the initially heavily doped n+ substrate is converted into n+-i-n+-i (Drain-Channel-Source) by the selection of appropriate work functions of control gate (CG) and polarity gate (PG) as 4.7 eV. Further, the formation of p+ region for source is performed by applying -1.2 V at PG. Hence, the structure behave like a n+-i-n+-p+ gated TFET, whereas, the control gate is used to modulate the effective tunneling barrier width. The physical realization of delta doped n+ layer near to source region is a challenging task for improving the device performance in terms of ON current and subthreshold slope. So, the proposed work will provide a better platform for fabrication of n+-i-n+-p+ TFET with low cost and suppressed random dopant fluctuation (RDF) effects. ATLAS TCAD device simulator is used to carry out the simulation work.

Vigi4Med Scraper: A Framework for Web Forum Structured Data Extraction and Semantic Representation

PubMed Central

Audeh, Bissan; Beigbeder, Michel; Zimmermann, Antoine; Jaillon, Philippe; Bousquet, Cédric

2017-01-01

The extraction of information from social media is an essential yet complicated step for data analysis in multiple domains. In this paper, we present Vigi4Med Scraper, a generic open source framework for extracting structured data from web forums. Our framework is highly configurable; using a configuration file, the user can freely choose the data to extract from any web forum. The extracted data are anonymized and represented in a semantic structure using Resource Description Framework (RDF) graphs. This representation enables efficient manipulation by data analysis algorithms and allows the collected data to be directly linked to any existing semantic resource. To avoid server overload, an integrated proxy with caching functionality imposes a minimal delay between sequential requests. Vigi4Med Scraper represents the first step of Vigi4Med, a project to detect adverse drug reactions (ADRs) from social networks founded by the French drug safety agency Agence Nationale de Sécurité du Médicament (ANSM). Vigi4Med Scraper has successfully extracted greater than 200 gigabytes of data from the web forums of over 20 different websites. PMID:28122056

Building biomedical web communities using a semantically aware content management system.

PubMed

Das, Sudeshna; Girard, Lisa; Green, Tom; Weitzman, Louis; Lewis-Bowen, Alister; Clark, Tim

2009-03-01

Web-based biomedical communities are becoming an increasingly popular vehicle for sharing information amongst researchers and are fast gaining an online presence. However, information organization and exchange in such communities is usually unstructured, rendering interoperability between communities difficult. Furthermore, specialized software to create such communities at low cost-targeted at the specific common information requirements of biomedical researchers-has been largely lacking. At the same time, a growing number of biological knowledge bases and biomedical resources are being structured for the Semantic Web. Several groups are creating reference ontologies for the biomedical domain, actively publishing controlled vocabularies and making data available in Resource Description Framework (RDF) language. We have developed the Science Collaboration Framework (SCF) as a reusable platform for advanced structured online collaboration in biomedical research that leverages these ontologies and RDF resources. SCF supports structured 'Web 2.0' style community discourse amongst researchers, makes heterogeneous data resources available to the collaborating scientist, captures the semantics of the relationship among the resources and structures discourse around the resources. The first instance of the SCF framework is being used to create an open-access online community for stem cell research-StemBook (http://www.stembook.org). We believe that such a framework is required to achieve optimal productivity and leveraging of resources in interdisciplinary scientific research. We expect it to be particularly beneficial in highly interdisciplinary areas, such as neurodegenerative disease and neurorepair research, as well as having broad utility across the natural sciences.

Knowledge-Centric Management of Business Rules in a Pharmacy

NASA Astrophysics Data System (ADS)

Puustjärvi, Juha; Puustjärvi, Leena

A business rule defines or constraints some aspect of the business. In healthcare sector many of the business rules are dictated by law or medical regulations, which are constantly changing. This is a challenge for the healthcare organizations. Although there is available several commercial business rule management systems the problem from pharmacies point of view is that these systems are overly geared towards the automation and manipulation of business rules, while the main need in pharmacies lies in easy retrieving of business rules within daily routines. Another problem is that business rule management systems are isolated in the sense that they have their own data stores that cannot be accessed by other information systems used in pharmacies. As a result, a pharmacist is burdened by accessing many systems inside a user task. In order to avoid this problem we have modeled business rules as well as their relationships to other relevant information by OWL (Web Ontology Language) such that the ontology is shared among the pharmacy's applications. In this way we can avoid the problems of isolated applications and replicated data. The ontology also encourages pharmacies business agility, i.e., the ability to react more rapidly to the changes required by the new business rules. The deployment of the ontology requires that stored business rules are annotated by appropriate metadata descriptions, which are presented by RDF/XML serialization format. However, neither the designer nor the pharmacists are burdened by RDF/XML format as there are sophisticated graphical editors that can be used.

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

Zhang, Guo Qiang; Luo, Lingyun; Ogbuji, Chime

The interaction of multiple types of relationships among anatomical classes in the Foundational Model of Anatomy (FMA) can provide inferred information valuable for quality assurance. This paper introduces a method called Motif Checking (MOCH) to study the effects of such multi-relation type interactions. MOCH represents patterns of multitype interaction as small labeled sub-graph motifs, whose nodes represent class variables, and labeled edges represent relational types. By representing FMA as an RDF graph and motifs as SPARQL queries, fragments of FMA are automatically obtained as auditing candidates. Leveraging the scalability and reconfigurability of Semantic Web Technology (OWL, RDF and SPARQL) andmore » Virtuoso, we performed exhaustive analyses of three 2-node motifs, resulting in 638 matching FMA configurations; twelve 3-node motifs, resulting in 202,960 configurations. Using the Principal Ideal Explorer (PIE) methodology as an extension of MOCH, we were able to identify 755 root nodes with 4,100 respective descendants with opposing antonyms in their class names for arbitrary-length motifs. With possible disjointness implied by antonyms, we performed manual inspection of a subset of the resulting FMA fragments and tracked down a source of abnormal inferred conclusions (captured by the motifs), coming from a gender-neutral class being modeled as a part of gender-specific class, such as “Urinary system” is a part of “Female human body.” Our results demonstrate that MOCH and PIE provide a unique source of valuable information for quality assurance. Since our approach is general, it is applicable to any ontological system with an OWL representation.« less

Kinetics of intercalation of fluorescent probes in magnesium–aluminium layered double hydroxide within a multiscale reaction–diffusion framework

PubMed Central

Saliba, Daniel

2016-01-01

We report the synthesis of magnesium–aluminium layered double hydroxide (LDH) using a reaction–diffusion framework (RDF) that exploits the multiscale coupling of molecular diffusion with chemical reactions, nucleation and growth of crystals. In an RDF, the hydroxide anions are allowed to diffuse into an organic gel matrix containing the salt mixture needed for the precipitation of the LDH. The chemical structure and composition of the synthesized magnesium–aluminium LDHs are determined using powder X-ray diffraction (PXRD), thermo-gravimetric analysis, differential scanning calorimetry, solid-state nuclear magnetic resonance (SSNMR), Fourier transform infrared and energy dispersive X-ray spectroscopy. This novel technique also allows the investigation of the mechanism of intercalation of some fluorescent probes, such as the neutral three-dimensional rhodamine B (RhB) and the negatively charged two-dimensional 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS), using in situ steady-state fluorescence spectroscopy. The incorporation of these organic dyes inside the interlayer region of the LDH is confirmed via fluorescence microscopy, solid-state lifetime, SSNMR and PXRD. The activation energies of intercalation of the corresponding molecules (RhB and HPTS) are computed and exhibit dependence on the geometry of the involved probe (two or three dimensions), the charge of the fluorescent molecule (anionic, cationic or neutral) and the cationic ratio of the corresponding LDH. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’. PMID:27698034

Kinetics of intercalation of fluorescent probes in magnesium-aluminium layered double hydroxide within a multiscale reaction-diffusion framework

NASA Astrophysics Data System (ADS)

Saliba, Daniel; Al-Ghoul, Mazen

2016-11-01

We report the synthesis of magnesium-aluminium layered double hydroxide (LDH) using a reaction-diffusion framework (RDF) that exploits the multiscale coupling of molecular diffusion with chemical reactions, nucleation and growth of crystals. In an RDF, the hydroxide anions are allowed to diffuse into an organic gel matrix containing the salt mixture needed for the precipitation of the LDH. The chemical structure and composition of the synthesized magnesium-aluminium LDHs are determined using powder X-ray diffraction (PXRD), thermo-gravimetric analysis, differential scanning calorimetry, solid-state nuclear magnetic resonance (SSNMR), Fourier transform infrared and energy dispersive X-ray spectroscopy. This novel technique also allows the investigation of the mechanism of intercalation of some fluorescent probes, such as the neutral three-dimensional rhodamine B (RhB) and the negatively charged two-dimensional 8-hydroxypyrene-1,3,6-trisulfonic acid (HPTS), using in situ steady-state fluorescence spectroscopy. The incorporation of these organic dyes inside the interlayer region of the LDH is confirmed via fluorescence microscopy, solid-state lifetime, SSNMR and PXRD. The activation energies of intercalation of the corresponding molecules (RhB and HPTS) are computed and exhibit dependence on the geometry of the involved probe (two or three dimensions), the charge of the fluorescent molecule (anionic, cationic or neutral) and the cationic ratio of the corresponding LDH. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Alternative strategies for energy recovery from municipal solid waste Part B: Emission and cost estimates.

PubMed

Consonni, S; Giugliano, M; Grosso, M

2005-01-01

This two-part paper assesses four strategies for energy recovery from Municipal Solid Waste (MSW) by dedicated Waste-To-Energy (WTE) plants. In strategy 1, the residue of Material Recovery (MR) is fed directly to a grate combustor, while in strategy 2 the grate combustor comes downstream of light mechanical treatment. In strategies 3 and 4, the MR residue is converted into Refuse Derived Fuel (RDF), in a fluidized cumbuster bed. The results of Part A, devoted to mass and energy balances, clearly show that pre-treating the MR residue in order to increase the heating value of the feedstock fed to the WTE plant has marginal effects on the energy efficiency of the WTE plant. When considering the efficiency of the whole strategy of waste management, the energy balances show that the more thorough the pre-treatment, the smaller the amount of energy recovered per unit of MR residue. Starting from the heat/mass balances illustrated in Part A, Part B examines the environmental impacts and economics of the various strategies by means of a Life Cycle Assessment (LCA). Results show that treating the MR residues ahead of the WTE plant does not provide environmental or economic benefits. RDF production worsens almost all impact indicators because it reduces net electricity production and thus the displacement of power plant emissions; it also increases costs, because the benefits of improving the quality of the material fed to the WTE plant do not compensate the cost of such improvement.

Semantic Approaches Applied to Scientific Ocean Drilling Data

NASA Astrophysics Data System (ADS)

Fils, D.; Jenkins, C. J.; Arko, R. A.

2012-12-01

The application of Linked Open Data methods to 40 years of data from scientific ocean drilling is providing users with several new methods for rich-content data search and discovery. Data from the Deep Sea Drilling Project (DSDP), Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) have been translated and placed in RDF triple stores to provide access via SPARQL, linked open data patterns, and by embedded structured data through schema.org / RDFa. Existing search services have been re-encoded in this environment which allows the new and established architectures to be contrasted. Vocabularies including computed semantic relations between concepts, allow separate but related data sets to be connected on their concepts and resources even when they are expressed somewhat differently. Scientific ocean drilling produces a wide range of data types and data sets: borehole logging file-based data, images, measurements, visual observations and the physical sample data. The steps involved in connecting these data to concepts using vocabularies will be presented, including the connection of data sets through Vocabulary of Interlinked Datasets (VoID) and open entity collections such as Freebase and dbPedia. Demonstrated examples will include: (i) using RDF Schema for inferencing and in federated searches across NGDC and IODP data, (ii) using structured data in the data.oceandrilling.org web site, (iii) association through semantic methods of age models and depth recorded data to facilitate age based searches for data recorded by depth only.

Noncontrast MRA of pedal arteries in type II diabetes: effect of disease load on vessel visibility.

PubMed

Zhang, Lijuan; Liu, Xin; Fan, Zhaoyang; Zhang, Na; Chung, Yiu-Cho; Liao, Weiqi; Zheng, Hairong; Li, Debiao

2015-04-01

Noncontrast magnetic resonance angiography (NC-MRA) of pedal artery remains challenging because of the global and regional disease load, tissue integrity, and altered microcirculation. This study aims to investigate the feasibility of the NC-MRA of pedal arteries with flow-sensitive dephasing-prepared steady-state free precession (FSD-SSFP) and to explore the effect of disease load of type II diabetes on the vessel depiction. FSD-SSFP was performed on a 1.5-T magnetic resonance system before the contrast-enhanced MRA (CE-MRA) as a reference standard in 39 consecutive diabetic subjects (29 men and 16 women, aged 57.9 ± 11.4 years). Two experienced radiologists evaluated the overall artery visibility (VA) and the contamination from soft tissue (SC) and veins (VC) with a four-point scale. Chronic complications and measures including random blood glucose (RBG), lipid panel, body mass index, risk of diabetic foot ulcers (RDF), and glycated hemoglobin (HbA1c) by the imaging were recorded as disease load indicators. Spearman rank correlation and ordinal regression were performed to investigate the effect of disease load on the depiction of pedal arteries. The measurement of RBG and RDF were significantly correlated with the VC in CE-MRA and with the overall visibility of pedal arteries in NC-MRA (P < .025 and P < .001, respectively). Blood pressure was the only parameter that was significantly associated with SC in NC-MRA with FSD-SSFP (P < .025). For CE-MRA the effect of RDF on the overall VA manifested a significant linear trend (P < .001), and the level of RBG was substantially associated with the VC (P < .025) without significantly impacting VA and SC. Hypertension only correlated with SC in NC-MRA. VA was found independent of the presence of diabetic nephropathy, coronary artery disease, abnormal lipid panel, HbA1c (75.0%), or optimized m1 value that ranged from 70 to 160 mT⋅ms(2)/m (mean, 125 ± 18 mT⋅ms(2)/m) in this study. FSD-SSFP proved to be a useful modality of NC-MRA for pedal artery imaging in diabetic patients. The vessel depiction is subject to the local and systemic disease load of type II diabetes. Technical optimization of the flow-sensitive dephasing gradient moment and properly choosing candidate would help augment the potential of this technique in patient care of peripheral artery disease. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

Semantic Document Library: A Virtual Research Environment for Documents, Data and Workflows Sharing

NASA Astrophysics Data System (ADS)

Kotwani, K.; Liu, Y.; Myers, J.; Futrelle, J.

2008-12-01

The Semantic Document Library (SDL) was driven by use cases from the environmental observatory communities and is designed to provide conventional document repository features of uploading, downloading, editing and versioning of documents as well as value adding features of tagging, querying, sharing, annotating, ranking, provenance, social networking and geo-spatial mapping services. It allows users to organize a catalogue of watershed observation data, model output, workflows, as well publications and documents related to the same watershed study through the tagging capability. Users can tag all relevant materials using the same watershed name and find all of them easily later using this tag. The underpinning semantic content repository can store materials from other cyberenvironments such as workflow or simulation tools and SDL provides an effective interface to query and organize materials from various sources. Advanced features of the SDL allow users to visualize the provenance of the materials such as the source and how the output data is derived. Other novel features include visualizing all geo-referenced materials on a geospatial map. SDL as a component of a cyberenvironment portal (the NCSA Cybercollaboratory) has goal of efficient management of information and relationships between published artifacts (Validated models, vetted data, workflows, annotations, best practices, reviews and papers) produced from raw research artifacts (data, notes, plans etc.) through agents (people, sensors etc.). Tremendous scientific potential of artifacts is achieved through mechanisms of sharing, reuse and collaboration - empowering scientists to spread their knowledge and protocols and to benefit from the knowledge of others. SDL successfully implements web 2.0 technologies and design patterns along with semantic content management approach that enables use of multiple ontologies and dynamic evolution (e.g. folksonomies) of terminology. Scientific documents involved with many interconnected entities (artifacts or agents) are represented as RDF triples using semantic content repository middleware Tupelo in one or many data/metadata RDF stores. Queries to the RDF enables discovery of relations among data, process and people, digging out valuable aspects, making recommendations to users, such as what tools are typically used to answer certain kinds of questions or with certain types of dataset. This innovative concept brings out coherent information about entities from four different perspectives of the social context (Who-human relations and interactions), the casual context (Why - provenance and history), the geo-spatial context (Where - location or spatially referenced information) and the conceptual context (What - domain specific relations, ontologies etc.).

Destruction behavior of hexabromocyclododecanes during incineration of solid waste containing expanded and extruded polystyrene insulation foams.

PubMed

Takigami, Hidetaka; Watanabe, Mafumi; Kajiwara, Natsuko

2014-12-01

Hexabromocyclododecanes (HBCDs) have been used for flame retardation mainly in expanded polystyrene (EPS) and extruded polystyrene (XPS) insulation foams. Controlled incineration experiments with solid wastes containing each of EPS and XPS were conducted using a pilot-scale incinerator to investigate the destruction behavior of HBCDs and their influence on the formation of polybrominated dibenzo-p-dioxins and dibenzofurans (PBDD/DFs). EPS and XPS materials were respectively blended with refuse derived fuel (RDF) as input wastes for incineration. Concentrations of HBCDs contained in the EPS- and XPS-added RDFs, were 140 and 1100 mg kg(-1), respectively. In which γ-HBCD was dominant (68% of the total HBCD content) in EPS-added RDF and α-HBCD accounted for 73% of the total HBCDs in XPS-added RDF. During the incineration experiments with EPS and XPS, primary and secondary combustion zones were maintained at temperatures of 840 °C and 900 °C. The residence times of waste in the primary combustion zone and flue gas in the secondary combustion zone was 30 min and three seconds, respectively. HBCDs were steadily degraded in the combustion chambers and α-, β-, and γ-HBCD behaved similarly. Concentration levels of the total HBCDs in the bag filter exit gas for the two experiments with EPS and XPS were 0.7 and 0.6ngmN(-3), respectively. HBCDs were also not detected (<0.2 ng g(-1)) in the bottom and fly ash samples. From the obtained results, it was calculated that HBCDs were sufficiently destroyed in the whole incineration process with destruction efficiencies of more than 99.9999 for both of EPS and XPS cases. For PBDD/DFs, the levels detected in the bottom and fly ash samples were very low (0.028 ng g(-1) at maximum). In the case of XPS-added experiment, 2,3,7,8-TeBDD and 2,3,7,8-TeBDF were determined in the flue gas at levels (0.05-0.07 ng mN(-3)) slightly over the detection limits in the environmental emission gas samples, suggesting HBCDs in XPS are possibly a precursor of detected PBDD/DFs. Operational care should be taken when the ratio of HBCD-containing polystyrene is increased in the input wastes just to make sure of formation prevention and emission control of PBDD/DFs. The concentrations and congener patterns of PCDD/DFs and dl-PCBs in the samples during the three experiments were not affected by an addition of HBCDs. Copyright © 2014 Elsevier Ltd. All rights reserved.

A semantically rich and standardised approach enhancing discovery of sensor data and metadata

NASA Astrophysics Data System (ADS)

Kokkinaki, Alexandra; Buck, Justin; Darroch, Louise

2016-04-01

The marine environment plays an essential role in the earth's climate. To enhance the ability to monitor the health of this important system, innovative sensors are being produced and combined with state of the art sensor technology. As the number of sensors deployed is continually increasing,, it is a challenge for data users to find the data that meet their specific needs. Furthermore, users need to integrate diverse ocean datasets originating from the same or even different systems. Standards provide a solution to the above mentioned challenges. The Open Geospatial Consortium (OGC) has created Sensor Web Enablement (SWE) standards that enable different sensor networks to establish syntactic interoperability. When combined with widely accepted controlled vocabularies, they become semantically rich and semantic interoperability is achievable. In addition, Linked Data is the recommended best practice for exposing, sharing and connecting information on the Semantic Web using Uniform Resource Identifiers (URIs), Resource Description Framework (RDF) and RDF Query Language (SPARQL). As part of the EU-funded SenseOCEAN project, the British Oceanographic Data Centre (BODC) is working on the standardisation of sensor metadata enabling 'plug and play' sensor integration. Our approach combines standards, controlled vocabularies and persistent URIs to publish sensor descriptions, their data and associated metadata as 5 star Linked Data and OGC SWE (SensorML, Observations & Measurements) standard. Thus sensors become readily discoverable, accessible and useable via the web. Content and context based searching is also enabled since sensors descriptions are understood by machines. Additionally, sensor data can be combined with other sensor or Linked Data datasets to form knowledge. This presentation will describe the work done in BODC to achieve syntactic and semantic interoperability in the sensor domain. It will illustrate the reuse and extension of the Semantic Sensor Network (SSN) ontology to Linked Sensor Ontology (LSO) and the steps taken to combine OGC SWE with the Linked Data approach through alignment and embodiment of other ontologies. It will then explain how data and models were annotated with controlled vocabularies to establish unambiguous semantics and interconnect them with data from different sources. Finally, it will introduce the RDF triple store where the sensor descriptions and metadata are stored and can be queried through the standard query language SPARQL. Providing different flavours of machine readable interpretations of sensors, sensor data and metadata enhances discoverability but most importantly allows seamless aggregation of information from different networks that will finally produce knowledge.

Estimation of marginal costs at existing waste treatment facilities.

PubMed

Martinez-Sanchez, Veronica; Hulgaard, Tore; Hindsgaul, Claus; Riber, Christian; Kamuk, Bettina; Astrup, Thomas F

2016-04-01

This investigation aims at providing an improved basis for assessing economic consequences of alternative Solid Waste Management (SWM) strategies for existing waste facilities. A bottom-up methodology was developed to determine marginal costs in existing facilities due to changes in the SWM system, based on the determination of average costs in such waste facilities as function of key facility and waste compositional parameters. The applicability of the method was demonstrated through a case study including two existing Waste-to-Energy (WtE) facilities, one with co-generation of heat and power (CHP) and another with only power generation (Power), affected by diversion strategies of five waste fractions (fibres, plastic, metals, organics and glass), named "target fractions". The study assumed three possible responses to waste diversion in the WtE facilities: (i) biomass was added to maintain a constant thermal load, (ii) Refused-Derived-Fuel (RDF) was included to maintain a constant thermal load, or (iii) no reaction occurred resulting in a reduced waste throughput without full utilization of the facility capacity. Results demonstrated that marginal costs of diversion from WtE were up to eleven times larger than average costs and dependent on the response in the WtE plant. Marginal cost of diversion were between 39 and 287 € Mg(-1) target fraction when biomass was added in a CHP (from 34 to 303 € Mg(-1) target fraction in the only Power case), between -2 and 300 € Mg(-1) target fraction when RDF was added in a CHP (from -2 to 294 € Mg(-1) target fraction in the only Power case) and between 40 and 303 € Mg(-1) target fraction when no reaction happened in a CHP (from 35 to 296 € Mg(-1) target fraction in the only Power case). Although average costs at WtE facilities were highly influenced by energy selling prices, marginal costs were not (provided a response was initiated at the WtE to keep constant the utilized thermal capacity). Failing to systematically address and include costs in existing waste facilities in decision-making may unintendedly lead to higher overall costs at societal level. To avoid misleading conclusions, economic assessment of alternative SWM solutions should not only consider potential costs associated with alternative treatment but also include marginal costs associated with existing facilities. Copyright © 2016 Elsevier Ltd. All rights reserved.

A data fusion approach to indications and warnings of terrorist attacks

NASA Astrophysics Data System (ADS)

McDaniel, David; Schaefer, Gregory

2014-05-01

Indications and Warning (I&W) of terrorist attacks, particularly IED attacks, require detection of networks of agents and patterns of behavior. Social Network Analysis tries to detect a network; activity analysis tries to detect anomalous activities. This work builds on both to detect elements of an activity model of terrorist attack activity - the agents, resources, networks, and behaviors. The activity model is expressed as RDF triples statements where the tuple positions are elements or subsets of a formal ontology for activity models. The advantage of a model is that elements are interdependent and evidence for or against one will influence others so that there is a multiplier effect. The advantage of the formality is that detection could occur hierarchically, that is, at different levels of abstraction. The model matching is expressed as a likelihood ratio between input text and the model triples. The likelihood ratio is designed to be analogous to track correlation likelihood ratios common in JDL fusion level 1. This required development of a semantic distance metric for positive and null hypotheses as well as for complex objects. The metric uses the Web 1Terabype database of one to five gram frequencies for priors. This size requires the use of big data technologies so a Hadoop cluster is used in conjunction with OpenNLP natural language and Mahout clustering software. Distributed data fusion Map Reduce jobs distribute parts of the data fusion problem to the Hadoop nodes. For the purposes of this initial testing, open source models and text inputs of similar complexity to terrorist events were used as surrogates for the intended counter-terrorist application.