A generalized strategy for building resident database interfaces

NASA Technical Reports Server (NTRS)

Moroh, Marsha; Wanderman, Ken

1990-01-01

A strategy for building resident interfaces to host heterogeneous distributed data base management systems is developed. The strategy is used to construct several interfaces. A set of guidelines is developed for users to construct their own interfaces.

Predictive distributions were developed for the extent of heterogeneity in meta-analyses of continuous outcome data.

PubMed

Rhodes, Kirsty M; Turner, Rebecca M; Higgins, Julian P T

2015-01-01

Estimation of between-study heterogeneity is problematic in small meta-analyses. Bayesian meta-analysis is beneficial because it allows incorporation of external evidence on heterogeneity. To facilitate this, we provide empirical evidence on the likely heterogeneity between studies in meta-analyses relating to specific research settings. Our analyses included 6,492 continuous-outcome meta-analyses within the Cochrane Database of Systematic Reviews. We investigated the influence of meta-analysis settings on heterogeneity by modeling study data from all meta-analyses on the standardized mean difference scale. Meta-analysis setting was described according to outcome type, intervention comparison type, and medical area. Predictive distributions for between-study variance expected in future meta-analyses were obtained, which can be used directly as informative priors. Among outcome types, heterogeneity was found to be lowest in meta-analyses of obstetric outcomes. Among intervention comparison types, heterogeneity was lowest in meta-analyses comparing two pharmacologic interventions. Predictive distributions are reported for different settings. In two example meta-analyses, incorporating external evidence led to a more precise heterogeneity estimate. Heterogeneity was influenced by meta-analysis characteristics. Informative priors for between-study variance were derived for each specific setting. Our analyses thus assist the incorporation of realistic prior information into meta-analyses including few studies. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Conceptual Model Formalization in a Semantic Interoperability Service Framework: Transforming Relational Database Schemas to OWL.

PubMed

Bravo, Carlos; Suarez, Carlos; González, Carolina; López, Diego; Blobel, Bernd

2014-01-01

Healthcare information is distributed through multiple heterogeneous and autonomous systems. Access to, and sharing of, distributed information sources are a challenging task. To contribute to meeting this challenge, this paper presents a formal, complete and semi-automatic transformation service from Relational Databases to Web Ontology Language. The proposed service makes use of an algorithm that allows to transform several data models of different domains by deploying mainly inheritance rules. The paper emphasizes the relevance of integrating the proposed approach into an ontology-based interoperability service to achieve semantic interoperability.

Integrating Distributed Homogeneous and Heterogeneous Databases: Prototypes. Volume 3.

DTIC Science & Technology

1987-12-01

Integrating Distributed3 Institute of Teholg Homogeneous and -Knowledge-Based eeokn usDtb e: Integrated Information Pooye Systems Engineering Pooye (KBIISE...Transportation Systems Center, December 1987 Broadway, NIA 02142 13. NUMBER OF PAGES IT ~ *n~1~ ArFre 218 Pages 14. kW rSi dTfrn front N Gr~in Office) IS...SECURITY CLASS. (of thie report) Transportation Systems Center, Unclassified Broadway, MA 02142 I5a. DECLASSIFICATION/ DOWNGRADING SCHEDULE 16. DISTRIBUTION

Distributed policy based access to networked heterogeneous ISR data sources

NASA Astrophysics Data System (ADS)

Bent, G.; Vyvyan, D.; Wood, David; Zerfos, Petros; Calo, Seraphin

2010-04-01

Within a coalition environment, ad hoc Communities of Interest (CoI's) come together, perhaps for only a short time, with different sensors, sensor platforms, data fusion elements, and networks to conduct a task (or set of tasks) with different coalition members taking different roles. In such a coalition, each organization will have its own inherent restrictions on how it will interact with the others. These are usually stated as a set of policies, including security and privacy policies. The capability that we want to enable for a coalition operation is to provide access to information from any coalition partner in conformance with the policies of all. One of the challenges in supporting such ad-hoc coalition operations is that of providing efficient access to distributed sources of data, where the applications requiring the data do not have knowledge of the location of the data within the network. To address this challenge the International Technology Alliance (ITA) program has been developing the concept of a Dynamic Distributed Federated Database (DDFD), also know as a Gaian Database. This type of database provides a means for accessing data across a network of distributed heterogeneous data sources where access to the information is controlled by a mixture of local and global policies. We describe how a network of disparate ISR elements can be expressed as a DDFD and how this approach enables sensor and other information sources to be discovered autonomously or semi-autonomously and/or combined, fused formally defined local and global policies.

Surviving the Glut: The Management of Event Streams in Cyberphysical Systems

NASA Astrophysics Data System (ADS)

Buchmann, Alejandro

Alejandro Buchmann is Professor in the Department of Computer Science, Technische Universität Darmstadt, where he heads the Databases and Distributed Systems Group. He received his MS (1977) and PhD (1980) from the University of Texas at Austin. He was an Assistant/Associate Professor at the Institute for Applied Mathematics and Systems IIMAS/UNAM in Mexico, doing research on databases for CAD, geographic information systems, and objectoriented databases. At Computer Corporation of America (later Xerox Advanced Information Systems) in Cambridge, Mass., he worked in the areas of active databases and real-time databases, and at GTE Laboratories, Waltham, in the areas of distributed object systems and the integration of heterogeneous legacy systems. 1991 he returned to academia and joined T.U. Darmstadt. His current research interests are at the intersection of middleware, databases, eventbased distributed systems, ubiquitous computing, and very large distributed systems (P2P, WSN). Much of the current research is concerned with guaranteeing quality of service and reliability properties in these systems, for example, scalability, performance, transactional behaviour, consistency, and end-to-end security. Many research projects imply collaboration with industry and cover a broad spectrum of application domains. Further information can be found at http://www.dvs.tu-darmstadt.de

Database interfaces on NASA's heterogeneous distributed database system

NASA Technical Reports Server (NTRS)

Huang, Shou-Hsuan Stephen

1987-01-01

The purpose of Distributed Access View Integrated Database (DAVID) interface module (Module 9: Resident Primitive Processing Package) is to provide data transfer between local DAVID systems and resident Data Base Management Systems (DBMSs). The result of current research is summarized. A detailed description of the interface module is provided. Several Pascal templates were constructed. The Resident Processor program was also developed. Even though it is designed for the Pascal templates, it can be modified for templates in other languages, such as C, without much difficulty. The Resident Processor itself can be written in any programming language. Since Module 5 routines are not ready yet, there is no way to test the interface module. However, simulation shows that the data base access programs produced by the Resident Processor do work according to the specifications.

Heterogenous database integration in a physician workstation.

PubMed

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

1991-01-01

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

Heterogenous database integration in a physician workstation.

PubMed Central

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

1991-01-01

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

Coordinating complex decision support activities across distributed applications

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1994-01-01

Knowledge-based technologies have been applied successfully to automate planning and scheduling in many problem domains. Automation of decision support can be increased further by integrating task-specific applications with supporting database systems, and by coordinating interactions between such tools to facilitate collaborative activities. Unfortunately, the technical obstacles that must be overcome to achieve this vision of transparent, cooperative problem-solving are daunting. Intelligent decision support tools are typically developed for standalone use, rely on incompatible, task-specific representational models and application programming interfaces (API's), and run on heterogeneous computing platforms. Getting such applications to interact freely calls for platform independent capabilities for distributed communication, as well as tools for mapping information across disparate representations. Symbiotics is developing a layered set of software tools (called NetWorks! for integrating and coordinating heterogeneous distributed applications. he top layer of tools consists of an extensible set of generic, programmable coordination services. Developers access these services via high-level API's to implement the desired interactions between distributed applications.

Clinical results of HIS, RIS, PACS integration using data integration CASE tools

NASA Astrophysics Data System (ADS)

Taira, Ricky K.; Chan, Hing-Ming; Breant, Claudine M.; Huang, Lu J.; Valentino, Daniel J.

1995-05-01

Current infrastructure research in PACS is dominated by the development of communication networks (local area networks, teleradiology, ATM networks, etc.), multimedia display workstations, and hierarchical image storage architectures. However, limited work has been performed on developing flexible, expansible, and intelligent information processing architectures for the vast decentralized image and text data repositories prevalent in healthcare environments. Patient information is often distributed among multiple data management systems. Current large-scale efforts to integrate medical information and knowledge sources have been costly with limited retrieval functionality. Software integration strategies to unify distributed data and knowledge sources is still lacking commercially. Systems heterogeneity (i.e., differences in hardware platforms, communication protocols, database management software, nomenclature, etc.) is at the heart of the problem and is unlikely to be standardized in the near future. In this paper, we demonstrate the use of newly available CASE (computer- aided software engineering) tools to rapidly integrate HIS, RIS, and PACS information systems. The advantages of these tools include fast development time (low-level code is generated from graphical specifications), and easy system maintenance (excellent documentation, easy to perform changes, and centralized code repository in an object-oriented database). The CASE tools are used to develop and manage the `middle-ware' in our client- mediator-serve architecture for systems integration. Our architecture is scalable and can accommodate heterogeneous database and communication protocols.

Competitive-Cooperative Automated Reasoning from Distributed and Multiple Source of Data

NASA Astrophysics Data System (ADS)

Fard, Amin Milani

Knowledge extraction from distributed database systems, have been investigated during past decade in order to analyze billions of information records. In this work a competitive deduction approach in a heterogeneous data grid environment is proposed using classic data mining and statistical methods. By applying a game theory concept in a multi-agent model, we tried to design a policy for hierarchical knowledge discovery and inference fusion. To show the system run, a sample multi-expert system has also been developed.

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

NASA Astrophysics Data System (ADS)

Thakore, Arun K.; Sauer, Frank

1994-05-01

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

Testing in Service-Oriented Environments

DTIC Science & Technology

2010-03-01

software releases (versions, service packs, vulnerability patches) for one com- mon ESB during the 13-month period from January 1, 2008 through...impact on quality of service : Unlike traditional software compo- nents, a single instance of a web service can be used by multiple consumers. Since the...distributed, with heterogeneous hardware and software (SOA infrastructure, services , operating systems, and databases). Because of cost and security, it

High statistical heterogeneity is more frequent in meta-analysis of continuous than binary outcomes.

PubMed

Alba, Ana C; Alexander, Paul E; Chang, Joanne; MacIsaac, John; DeFry, Samantha; Guyatt, Gordon H

2016-02-01

We compared the distribution of heterogeneity in meta-analyses of binary and continuous outcomes. We searched citations in MEDLINE and Cochrane databases for meta-analyses of randomized trials published in 2012 that reported a measure of heterogeneity of either binary or continuous outcomes. Two reviewers independently performed eligibility screening and data abstraction. We evaluated the distribution of I(2) in meta-analyses of binary and continuous outcomes and explored hypotheses explaining the difference in distributions. After full-text screening, we selected 671 meta-analyses evaluating 557 binary and 352 continuous outcomes. Heterogeneity as assessed by I(2) proved higher in continuous than in binary outcomes: the proportion of continuous and binary outcomes reporting an I(2) of 0% was 34% vs. 52%, respectively, and reporting an I(2) of 60-100% was 39% vs. 14%. In continuous but not binary outcomes, I(2) increased with larger number of studies included in a meta-analysis. Increased precision and sample size do not explain the larger I(2) found in meta-analyses of continuous outcomes with a larger number of studies. Meta-analyses evaluating continuous outcomes showed substantially higher I(2) than meta-analyses of binary outcomes. Results suggest differing standards for interpreting I(2) in continuous vs. binary outcomes may be appropriate. Copyright © 2016 Elsevier Inc. All rights reserved.

Distributed database kriging for adaptive sampling (D²KAS)

DOE PAGES

Roehm, Dominic; Pavel, Robert S.; Barros, Kipton; ...

2015-03-18

We present an adaptive sampling method supplemented by a distributed database and a prediction method for multiscale simulations using the Heterogeneous Multiscale Method. A finite-volume scheme integrates the macro-scale conservation laws for elastodynamics, which are closed by momentum and energy fluxes evaluated at the micro-scale. In the original approach, molecular dynamics (MD) simulations are launched for every macro-scale volume element. Our adaptive sampling scheme replaces a large fraction of costly micro-scale MD simulations with fast table lookup and prediction. The cloud database Redis provides the plain table lookup, and with locality aware hashing we gather input data for our predictionmore » scheme. For the latter we use kriging, which estimates an unknown value and its uncertainty (error) at a specific location in parameter space by using weighted averages of the neighboring points. We find that our adaptive scheme significantly improves simulation performance by a factor of 2.5 to 25, while retaining high accuracy for various choices of the algorithm parameters.« less

Design and implementation of a CORBA-based genome mapping system prototype.

PubMed

Hu, J; Mungall, C; Nicholson, D; Archibald, A L

1998-01-01

CORBA (Common Object Request Broker Architecture), as an open standard, is considered to be a good solution for the development and deployment of applications in distributed heterogeneous environments. This technology can be applied in the bioinformatics area to enhance utilization, management and interoperation between biological resources. This paper investigates issues in developing CORBA applications for genome mapping information systems in the Internet environment with emphasis on database connectivity and graphical user interfaces. The design and implementation of a CORBA prototype for an animal genome mapping database are described. The prototype demonstration is available via: http://www.ri.bbsrc.ac.uk/ark_corba/. jian.hu@bbsrc.ac.uk

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

PubMed Central

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

2003-01-01

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

Logical optimization for database uniformization

NASA Technical Reports Server (NTRS)

Grant, J.

1984-01-01

Data base uniformization refers to the building of a common user interface facility to support uniform access to any or all of a collection of distributed heterogeneous data bases. Such a system should enable a user, situated anywhere along a set of distributed data bases, to access all of the information in the data bases without having to learn the various data manipulation languages. Furthermore, such a system should leave intact the component data bases, and in particular, their already existing software. A survey of various aspects of the data bases uniformization problem and a proposed solution are presented.

Ontology based heterogeneous materials database integration and semantic query

NASA Astrophysics Data System (ADS)

Zhao, Shuai; Qian, Quan

2017-10-01

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

The Current Landscape of US Pediatric Anesthesiologists: Demographic Characteristics and Geographic Distribution.

PubMed

Muffly, Matthew K; Muffly, Tyler M; Weterings, Robbie; Singleton, Mark; Honkanen, Anita

2016-07-01

There is no comprehensive database of pediatric anesthesiologists, their demographic characteristics, or geographic location in the United States. We endeavored to create a comprehensive database of pediatric anesthesiologists by merging individuals identified as US pediatric anesthesiologists by the American Board of Anesthesiology, National Provider Identifier registry, Healthgrades.com database, and the Society for Pediatric Anesthesia membership list as of November 5, 2015. Professorial rank was accessed via the Association of American Medical Colleges and other online sources. Descriptive statistics characterized pediatric anesthesiologists' demographics. Pediatric anesthesiologists' locations at the city and state level were geocoded and mapped with the use of ArcGIS Desktop 10.1 mapping software (Redlands, CA). We identified 4048 pediatric anesthesiologists in the United States, which is approximately 8.8% of the physician anesthesiology workforce (n = 46,000). The median age of pediatric anesthesiologists was 49 years (interquartile range, 40-57 years), and the majority (56.4%) were men. Approximately two-thirds of identified pediatric anesthesiologists were subspecialty board certified in pediatric anesthesiology, and 33% of pediatric anesthesiologists had an identified academic affiliation. There is substantial heterogeneity in the geographic distribution of pediatric anesthesiologists by state and US Census Division with urban clustering. This description of pediatric anesthesiologists' demographic characteristics and geographic distribution fills an important gap in our understanding of pediatric anesthesia systems of care.

NASA Access Mechanism: Lessons learned document

NASA Technical Reports Server (NTRS)

Burdick, Lisa; Dunbar, Rick; Duncan, Denise; Generous, Curtis; Hunter, Judy; Lycas, John; Taber-Dudas, Ardeth

1994-01-01

The six-month beta test of the NASA Access Mechanism (NAM) prototype was completed on June 30, 1993. This report documents the lessons learned from the use of this Graphical User Interface to NASA databases such as the NASA STI Database, outside databases, Internet resources, and peers in the NASA R&D community. Design decisions, such as the use of XWindows software, a client-server distributed architecture, and use of the NASA Science Internet, are explained. Users' reactions to the interface and suggestions for design changes are reported, as are the changes made by the software developers based on new technology for information discovery and retrieval. The lessons learned section also reports reactions from the public, both at demonstrations and in response to articles in the trade press and journals. Recommendations are included for future versions, such as a World Wide Web (WWW) and Mosaic based interface to heterogeneous databases, and NAM-Lite, a version which allows customization to include utilities provided locally at NASA Centers.

Laplacian normalization and random walk on heterogeneous networks for disease-gene prioritization.

PubMed

Zhao, Zhi-Qin; Han, Guo-Sheng; Yu, Zu-Guo; Li, Jinyan

2015-08-01

Random walk on heterogeneous networks is a recently emerging approach to effective disease gene prioritization. Laplacian normalization is a technique capable of normalizing the weight of edges in a network. We use this technique to normalize the gene matrix and the phenotype matrix before the construction of the heterogeneous network, and also use this idea to define the transition matrices of the heterogeneous network. Our method has remarkably better performance than the existing methods for recovering known gene-phenotype relationships. The Shannon information entropy of the distribution of the transition probabilities in our networks is found to be smaller than the networks constructed by the existing methods, implying that a higher number of top-ranked genes can be verified as disease genes. In fact, the most probable gene-phenotype relationships ranked within top 3 or top 5 in our gene lists can be confirmed by the OMIM database for many cases. Our algorithms have shown remarkably superior performance over the state-of-the-art algorithms for recovering gene-phenotype relationships. All Matlab codes can be available upon email request. Copyright © 2015 Elsevier Ltd. All rights reserved.

A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data.

PubMed

Delussu, Giovanni; Lianas, Luca; Frexia, Francesca; Zanetti, Gianluigi

2016-01-01

This work presents a scalable data access layer, called PyEHR, designed to support the implementation of data management systems for secondary use of structured heterogeneous biomedical and clinical data. PyEHR adopts the openEHR's formalisms to guarantee the decoupling of data descriptions from implementation details and exploits structure indexing to accelerate searches. Data persistence is guaranteed by a driver layer with a common driver interface. Interfaces for two NoSQL Database Management Systems are already implemented: MongoDB and Elasticsearch. We evaluated the scalability of PyEHR experimentally through two types of tests, called "Constant Load" and "Constant Number of Records", with queries of increasing complexity on synthetic datasets of ten million records each, containing very complex openEHR archetype structures, distributed on up to ten computing nodes.

[Micro-simulation of firms' heterogeneity on pollution intensity and regional characteristics].

PubMed

Zhao, Nan; Liu, Yi; Chen, Ji-Ning

2009-11-01

In the same industrial sector, heterogeneity of pollution intensity exists among firms. There are some errors if using sector's average pollution intensity, which are calculated by limited number of firms in environmental statistic database to represent the sector's regional economic-environmental status. Based on the production function which includes environmental depletion as input, a micro-simulation model on firms' operational decision making is proposed. Then the heterogeneity of firms' pollution intensity can be mechanically described. Taking the mechanical manufacturing sector in Deyang city, 2005 as the case, the model's parameters were estimated. And the actual COD emission intensities of environmental statistic firms can be properly matched by the simulation. The model's results also show that the regional average COD emission intensity calculated by the environmental statistic firms (0.002 6 t per 10 000 yuan fixed asset, 0.001 5 t per 10 000 yuan production value) is lower than the regional average intensity calculated by all the firms in the region (0.003 0 t per 10 000 yuan fixed asset, 0.002 3 t per 10 000 yuan production value). The difference among average intensities in the six counties is significant as well. These regional characteristics of pollution intensity attribute to the sector's inner-structure (firms' scale distribution, technology distribution) and its spatial deviation.

A service-based framework for pharmacogenomics data integration

NASA Astrophysics Data System (ADS)

Wang, Kun; Bai, Xiaoying; Li, Jing; Ding, Cong

2010-08-01

Data are central to scientific research and practices. The advance of experiment methods and information retrieval technologies leads to explosive growth of scientific data and databases. However, due to the heterogeneous problems in data formats, structures and semantics, it is hard to integrate the diversified data that grow explosively and analyse them comprehensively. As more and more public databases are accessible through standard protocols like programmable interfaces and Web portals, Web-based data integration becomes a major trend to manage and synthesise data that are stored in distributed locations. Mashup, a Web 2.0 technique, presents a new way to compose content and software from multiple resources. The paper proposes a layered framework for integrating pharmacogenomics data in a service-oriented approach using the mashup technology. The framework separates the integration concerns from three perspectives including data, process and Web-based user interface. Each layer encapsulates the heterogeneous issues of one aspect. To facilitate the mapping and convergence of data, the ontology mechanism is introduced to provide consistent conceptual models across different databases and experiment platforms. To support user-interactive and iterative service orchestration, a context model is defined to capture information of users, tasks and services, which can be used for service selection and recommendation during a dynamic service composition process. A prototype system is implemented and cases studies are presented to illustrate the promising capabilities of the proposed approach.

Managing Heterogeneous Information Systems through Discovery and Retrieval of Generic Concepts.

ERIC Educational Resources Information Center

Srinivasan, Uma; Ngu, Anne H. H.; Gedeon, Tom

2000-01-01

Introduces a conceptual integration approach to heterogeneous databases or information systems that exploits the similarity in metalevel information and performs metadata mining on database objects to discover a set of concepts that serve as a domain abstraction and provide a conceptual layer above existing legacy systems. Presents results of…

Methods to elicit probability distributions from experts: a systematic review of reported practice in health technology assessment.

PubMed

Grigore, Bogdan; Peters, Jaime; Hyde, Christopher; Stein, Ken

2013-11-01

Elicitation is a technique that can be used to obtain probability distribution from experts about unknown quantities. We conducted a methodology review of reports where probability distributions had been elicited from experts to be used in model-based health technology assessments. Databases including MEDLINE, EMBASE and the CRD database were searched from inception to April 2013. Reference lists were checked and citation mapping was also used. Studies describing their approach to the elicitation of probability distributions were included. Data was abstracted on pre-defined aspects of the elicitation technique. Reports were critically appraised on their consideration of the validity, reliability and feasibility of the elicitation exercise. Fourteen articles were included. Across these studies, the most marked features were heterogeneity in elicitation approach and failure to report key aspects of the elicitation method. The most frequently used approaches to elicitation were the histogram technique and the bisection method. Only three papers explicitly considered the validity, reliability and feasibility of the elicitation exercises. Judged by the studies identified in the review, reports of expert elicitation are insufficient in detail and this impacts on the perceived usability of expert-elicited probability distributions. In this context, the wider credibility of elicitation will only be improved by better reporting and greater standardisation of approach. Until then, the advantage of eliciting probability distributions from experts may be lost.

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

Not Available

This report contains papers on the following topics: NREN Security Issues: Policies and Technologies; Layer Wars: Protect the Internet with Network Layer Security; Electronic Commission Management; Workflow 2000 - Electronic Document Authorization in Practice; Security Issues of a UNIX PEM Implementation; Implementing Privacy Enhanced Mail on VMS; Distributed Public Key Certificate Management; Protecting the Integrity of Privacy-enhanced Electronic Mail; Practical Authorization in Large Heterogeneous Distributed Systems; Security Issues in the Truffles File System; Issues surrounding the use of Cryptographic Algorithms and Smart Card Applications; Smart Card Augmentation of Kerberos; and An Overview of the Advanced Smart Card Access Control System.more » Selected papers were processed separately for inclusion in the Energy Science and Technology Database.« less

FRED, a Front End for Databases.

ERIC Educational Resources Information Center

Crystal, Maurice I.; Jakobson, Gabriel E.

1982-01-01

FRED (a Front End for Databases) was conceived to alleviate data access difficulties posed by the heterogeneous nature of online databases. A hardware/software layer interposed between users and databases, it consists of three subsystems: user-interface, database-interface, and knowledge base. Architectural alternatives for this database machine…

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

Earthquake scaling laws for rupture geometry and slip heterogeneity

NASA Astrophysics Data System (ADS)

Thingbaijam, Kiran K. S.; Mai, P. Martin; Goda, Katsuichiro

2016-04-01

We analyze an extensive compilation of finite-fault rupture models to investigate earthquake scaling of source geometry and slip heterogeneity to derive new relationships for seismic and tsunami hazard assessment. Our dataset comprises 158 earthquakes with a total of 316 rupture models selected from the SRCMOD database (http://equake-rc.info/srcmod). We find that fault-length does not saturate with earthquake magnitude, while fault-width reveals inhibited growth due to the finite seismogenic thickness. For strike-slip earthquakes, fault-length grows more rapidly with increasing magnitude compared to events of other faulting types. Interestingly, our derived relationship falls between the L-model and W-model end-members. In contrast, both reverse and normal dip-slip events are more consistent with self-similar scaling of fault-length. However, fault-width scaling relationships for large strike-slip and normal dip-slip events, occurring on steeply dipping faults (δ~90° for strike-slip faults, and δ~60° for normal faults), deviate from self-similarity. Although reverse dip-slip events in general show self-similar scaling, the restricted growth of down-dip fault extent (with upper limit of ~200 km) can be seen for mega-thrust subduction events (M~9.0). Despite this fact, for a given earthquake magnitude, subduction reverse dip-slip events occupy relatively larger rupture area, compared to shallow crustal events. In addition, we characterize slip heterogeneity in terms of its probability distribution and spatial correlation structure to develop a complete stochastic random-field characterization of earthquake slip. We find that truncated exponential law best describes the probability distribution of slip, with observable scale parameters determined by the average and maximum slip. Applying Box-Cox transformation to slip distributions (to create quasi-normal distributed data) supports cube-root transformation, which also implies distinctive non-Gaussian slip distributions. To further characterize the spatial correlations of slip heterogeneity, we analyze the power spectral decay of slip applying the 2-D von Karman auto-correlation function (parameterized by the Hurst exponent, H, and correlation lengths along strike and down-slip). The Hurst exponent is scale invariant, H = 0.83 (± 0.12), while the correlation lengths scale with source dimensions (seismic moment), thus implying characteristic physical scales of earthquake ruptures. Our self-consistent scaling relationships allow constraining the generation of slip-heterogeneity scenarios for physics-based ground-motion and tsunami simulations.

Data Aggregation System: A system for information retrieval on demand over relational and non-relational distributed data sources

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

Ball, G.; Kuznetsov, V.; Evans, D.

We present the Data Aggregation System, a system for information retrieval and aggregation from heterogenous sources of relational and non-relational data for the Compact Muon Solenoid experiment on the CERN Large Hadron Collider. The experiment currently has a number of organically-developed data sources, including front-ends to a number of different relational databases and non-database data services which do not share common data structures or APIs (Application Programming Interfaces), and cannot at this stage be readily converged. DAS provides a single interface for querying all these services, a caching layer to speed up access to expensive underlying calls and the abilitymore » to merge records from different data services pertaining to a single primary key.« less

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

PubMed

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

1996-03-01

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

Distributed spatial information integration based on web service

NASA Astrophysics Data System (ADS)

Tong, Hengjian; Zhang, Yun; Shao, Zhenfeng

2008-10-01

Spatial information systems and spatial information in different geographic locations usually belong to different organizations. They are distributed and often heterogeneous and independent from each other. This leads to the fact that many isolated spatial information islands are formed, reducing the efficiency of information utilization. In order to address this issue, we present a method for effective spatial information integration based on web service. The method applies asynchronous invocation of web service and dynamic invocation of web service to implement distributed, parallel execution of web map services. All isolated information islands are connected by the dispatcher of web service and its registration database to form a uniform collaborative system. According to the web service registration database, the dispatcher of web services can dynamically invoke each web map service through an asynchronous delegating mechanism. All of the web map services can be executed at the same time. When each web map service is done, an image will be returned to the dispatcher. After all of the web services are done, all images are transparently overlaid together in the dispatcher. Thus, users can browse and analyze the integrated spatial information. Experiments demonstrate that the utilization rate of spatial information resources is significantly raised thought the proposed method of distributed spatial information integration.

Distributed spatial information integration based on web service

NASA Astrophysics Data System (ADS)

Tong, Hengjian; Zhang, Yun; Shao, Zhenfeng

2009-10-01

Spatial information systems and spatial information in different geographic locations usually belong to different organizations. They are distributed and often heterogeneous and independent from each other. This leads to the fact that many isolated spatial information islands are formed, reducing the efficiency of information utilization. In order to address this issue, we present a method for effective spatial information integration based on web service. The method applies asynchronous invocation of web service and dynamic invocation of web service to implement distributed, parallel execution of web map services. All isolated information islands are connected by the dispatcher of web service and its registration database to form a uniform collaborative system. According to the web service registration database, the dispatcher of web services can dynamically invoke each web map service through an asynchronous delegating mechanism. All of the web map services can be executed at the same time. When each web map service is done, an image will be returned to the dispatcher. After all of the web services are done, all images are transparently overlaid together in the dispatcher. Thus, users can browse and analyze the integrated spatial information. Experiments demonstrate that the utilization rate of spatial information resources is significantly raised thought the proposed method of distributed spatial information integration.

A Latency-Tolerant Partitioner for Distributed Computing on the Information Power Grid

NASA Technical Reports Server (NTRS)

Das, Sajal K.; Harvey, Daniel J.; Biwas, Rupak; Kwak, Dochan (Technical Monitor)

2001-01-01

NASA's Information Power Grid (IPG) is an infrastructure designed to harness the power of graphically distributed computers, databases, and human expertise, in order to solve large-scale realistic computational problems. This type of a meta-computing environment is necessary to present a unified virtual machine to application developers that hides the intricacies of a highly heterogeneous environment and yet maintains adequate security. In this paper, we present a novel partitioning scheme. called MinEX, that dynamically balances processor workloads while minimizing data movement and runtime communication, for applications that are executed in a parallel distributed fashion on the IPG. We also analyze the conditions that are required for the IPG to be an effective tool for such distributed computations. Our results show that MinEX is a viable load balancer provided the nodes of the IPG are connected by a high-speed asynchronous interconnection network.

A Scalable Data Access Layer to Manage Structured Heterogeneous Biomedical Data

PubMed Central

Lianas, Luca; Frexia, Francesca; Zanetti, Gianluigi

2016-01-01

This work presents a scalable data access layer, called PyEHR, designed to support the implementation of data management systems for secondary use of structured heterogeneous biomedical and clinical data. PyEHR adopts the openEHR’s formalisms to guarantee the decoupling of data descriptions from implementation details and exploits structure indexing to accelerate searches. Data persistence is guaranteed by a driver layer with a common driver interface. Interfaces for two NoSQL Database Management Systems are already implemented: MongoDB and Elasticsearch. We evaluated the scalability of PyEHR experimentally through two types of tests, called “Constant Load” and “Constant Number of Records”, with queries of increasing complexity on synthetic datasets of ten million records each, containing very complex openEHR archetype structures, distributed on up to ten computing nodes. PMID:27936191

An XML-based Generic Tool for Information Retrieval in Solar Databases

NASA Astrophysics Data System (ADS)

Scholl, Isabelle F.; Legay, Eric; Linsolas, Romain

This paper presents the current architecture of the `Solar Web Project' now in its development phase. This tool will provide scientists interested in solar data with a single web-based interface for browsing distributed and heterogeneous catalogs of solar observations. The main goal is to have a generic application that can be easily extended to new sets of data or to new missions with a low level of maintenance. It is developed with Java and XML is used as a powerful configuration language. The server, independent of any database scheme, can communicate with a client (the user interface) and several local or remote archive access systems (such as existing web pages, ftp sites or SQL databases). Archive access systems are externally described in XML files. The user interface is also dynamically generated from an XML file containing the window building rules and a simplified database description. This project is developed at MEDOC (Multi-Experiment Data and Operations Centre), located at the Institut d'Astrophysique Spatiale (Orsay, France). Successful tests have been conducted with other solar archive access systems.

COSPO/CENDI Industry Day Conference

NASA Technical Reports Server (NTRS)

1995-01-01

The conference's objective was to provide a forum where government information managers and industry information technology experts could have an open exchange and discuss their respective needs and compare them to the available, or soon to be available, solutions. Technical summaries and points of contact are provided for the following sessions: secure products, protocols, and encryption; information providers; electronic document management and publishing; information indexing, discovery, and retrieval (IIDR); automated language translators; IIDR - natural language capabilities; IIDR - advanced technologies; IIDR - distributed heterogeneous and large database support; and communications - speed, bandwidth, and wireless.

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

PubMed Central

Chowdhury, Saikat; Sarkar, Ram Rup

2015-01-01

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

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

PubMed Central

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

2006-01-01

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

A probabilistic approach to information retrieval in heterogeneous databases

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

Chatterjee, A.; Segev, A.

During the post decade, organizations have increased their scope and operations beyond their traditional geographic boundaries. At the same time, they have adopted heterogeneous and incompatible information systems independent of each other without a careful consideration that one day they may need to be integrated. As a result of this diversity, many important business applications today require access to data stored in multiple autonomous databases. This paper examines a problem of inter-database information retrieval in a heterogeneous environment, where conventional techniques are no longer efficient. To solve the problem, broader definitions for join, union, intersection and selection operators are proposed.more » Also, a probabilistic method to specify the selectivity of these operators is discussed. An algorithm to compute these probabilities is provided in pseudocode.« less

Global distribution of minerals in arid soils as lower boundary condition in dust models

NASA Astrophysics Data System (ADS)

Nickovic, Slobodan

2010-05-01

Mineral dust eroded from arid soils affects the radiation budget of the Earth system, modifies ocean bioproductivity and influences human health. Dust aerosol is a complex mixture of minerals. Dust mineral composition has several potentially important impacts to environment and society. Iron and phosphorus embedded in mineral aerosol are essential for the primary marine productivity when dust deposits over the open ocean. Dust also acts as efficient agent for heterogeneous ice nucleation and this process is dependent on mineralogical structure of dust. Recent findings in medical geology indicate possible role of minerals to human health. In this study, a new 1-km global database was developed for several minerals (Illite, Kaolinite, Smectite, Calcite, Quartz, Feldspar, Hematite and Gypsum) embedded in clay and silt populations of arid soils. For the database generation, high-resolution data sets on soil textures, soil types and land cover was used. Tin addition to the selected minerals, phosphorus was also added whose geographical distribution was specified from compiled literature and data on soil types. The developed global database was used to specify sources of mineral fractions in the DREAM dust model and to simulate atmospheric paths of minerals and their potential impacts on marine biochemistry and tropospheric ice nucleation.

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

PubMed

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

2017-03-01

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

Use of Graph Database for the Integration of Heterogeneous Biological Data

PubMed Central

Yoon, Byoung-Ha; Kim, Seon-Kyu

2017-01-01

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

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

PubMed

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

2014-01-01

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

LHCb Conditions database operation assistance systems

NASA Astrophysics Data System (ADS)

Clemencic, M.; Shapoval, I.; Cattaneo, M.; Degaudenzi, H.; Santinelli, R.

2012-12-01

The Conditions Database (CondDB) of the LHCb experiment provides versioned, time dependent geometry and conditions data for all LHCb data processing applications (simulation, high level trigger (HLT), reconstruction, analysis) in a heterogeneous computing environment ranging from user laptops to the HLT farm and the Grid. These different use cases impose front-end support for multiple database technologies (Oracle and SQLite are used). Sophisticated distribution tools are required to ensure timely and robust delivery of updates to all environments. The content of the database has to be managed to ensure that updates are internally consistent and externally compatible with multiple versions of the physics application software. In this paper we describe three systems that we have developed to address these issues. The first system is a CondDB state tracking extension to the Oracle 3D Streams replication technology, to trap cases when the CondDB replication was corrupted. Second, an automated distribution system for the SQLite-based CondDB, providing also smart backup and checkout mechanisms for the CondDB managers and LHCb users respectively. And, finally, a system to verify and monitor the internal (CondDB self-consistency) and external (LHCb physics software vs. CondDB) compatibility. The former two systems are used in production in the LHCb experiment and have achieved the desired goal of higher flexibility and robustness for the management and operation of the CondDB. The latter one has been fully designed and is passing currently to the implementation stage.

KA-SB: from data integration to large scale reasoning

PubMed Central

Roldán-García, María del Mar; Navas-Delgado, Ismael; Kerzazi, Amine; Chniber, Othmane; Molina-Castro, Joaquín; Aldana-Montes, José F

2009-01-01

Background The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data. Methods KA-SB is a querying and analysis system for final users based on combining a data integration solution with a reasoner. Thus, the tool has been created with a process divided into two steps: 1) KOMF, the Khaos Ontology-based Mediator Framework, is used to retrieve information from heterogeneous and distributed databases; 2) the integrated information is crystallized in a (persistent and high performance) reasoner (DBOWL). This information could be further analyzed later (by means of querying and reasoning). Results In this paper we present a novel system that combines the use of a mediation system with the reasoning capabilities of a large scale reasoner to provide a way of finding new knowledge and of analyzing the integrated information from different databases, which is retrieved as a set of ontology instances. This tool uses a graphical query interface to build user queries easily, which shows a graphical representation of the ontology and allows users o build queries by clicking on the ontology concepts. Conclusion These kinds of systems (based on KOMF) will provide users with very large amounts of information (interpreted as ontology instances once retrieved), which cannot be managed using traditional main memory-based reasoners. We propose a process for creating persistent and scalable knowledgebases from sets of OWL instances obtained by integrating heterogeneous data sources with KOMF. This process has been applied to develop a demo tool , which uses the BioPax Level 3 ontology as the integration schema, and integrates UNIPROT, KEGG, CHEBI, BRENDA and SABIORK databases. PMID:19796402

Expectation-maximization algorithms for learning a finite mixture of univariate survival time distributions from partially specified class values

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

Lee, Youngrok

2013-05-15

Heterogeneity exists on a data set when samples from di erent classes are merged into the data set. Finite mixture models can be used to represent a survival time distribution on heterogeneous patient group by the proportions of each class and by the survival time distribution within each class as well. The heterogeneous data set cannot be explicitly decomposed to homogeneous subgroups unless all the samples are precisely labeled by their origin classes; such impossibility of decomposition is a barrier to overcome for estimating nite mixture models. The expectation-maximization (EM) algorithm has been used to obtain maximum likelihood estimates ofmore » nite mixture models by soft-decomposition of heterogeneous samples without labels for a subset or the entire set of data. In medical surveillance databases we can find partially labeled data, that is, while not completely unlabeled there is only imprecise information about class values. In this study we propose new EM algorithms that take advantages of using such partial labels, and thus incorporate more information than traditional EM algorithms. We particularly propose four variants of the EM algorithm named EM-OCML, EM-PCML, EM-HCML and EM-CPCML, each of which assumes a specific mechanism of missing class values. We conducted a simulation study on exponential survival trees with five classes and showed that the advantages of incorporating substantial amount of partially labeled data can be highly signi cant. We also showed model selection based on AIC values fairly works to select the best proposed algorithm on each specific data set. A case study on a real-world data set of gastric cancer provided by Surveillance, Epidemiology and End Results (SEER) program showed a superiority of EM-CPCML to not only the other proposed EM algorithms but also conventional supervised, unsupervised and semi-supervised learning algorithms.« less

Using an object-based grid system to evaluate a newly developed EP approach to formulate SVMs as applied to the classification of organophosphate nerve agents

NASA Astrophysics Data System (ADS)

Land, Walker H., Jr.; Lewis, Michael; Sadik, Omowunmi; Wong, Lut; Wanekaya, Adam; Gonzalez, Richard J.; Balan, Arun

2004-04-01

This paper extends the classification approaches described in reference [1] in the following way: (1.) developing and evaluating a new method for evolving organophosphate nerve agent Support Vector Machine (SVM) classifiers using Evolutionary Programming, (2.) conducting research experiments using a larger database of organophosphate nerve agents, and (3.) upgrading the architecture to an object-based grid system for evaluating the classification of EP derived SVMs. Due to the increased threats of chemical and biological weapons of mass destruction (WMD) by international terrorist organizations, a significant effort is underway to develop tools that can be used to detect and effectively combat biochemical warfare. This paper reports the integration of multi-array sensors with Support Vector Machines (SVMs) for the detection of organophosphates nerve agents using a grid computing system called Legion. Grid computing is the use of large collections of heterogeneous, distributed resources (including machines, databases, devices, and users) to support large-scale computations and wide-area data access. Finally, preliminary results using EP derived support vector machines designed to operate on distributed systems have provided accurate classification results. In addition, distributed training time architectures are 50 times faster when compared to standard iterative training time methods.

Regional trends and controlling factors of fatal landslides in Latin America and the Caribbean

NASA Astrophysics Data System (ADS)

Sepúlveda, S. A.; Petley, D. N.

2015-04-01

A database of landslides that caused loss of life in Latin America and the Caribbean in the period from 2004 and 2013 inclusive has been compiled using established techniques. This database indicates that in the ten year period a total of 11 631 people lost their lives across the region in 611 landslides. The geographical distribution of the landslides is very heterogeneous, with areas of high incidence in parts of the Caribbean (most notably Haiti), Central America, Colombia, and SE. Brazil. The number of landslides varies considerably between years; the El Niño/La Niña cycle emerges as a major factor controlling this variation, although the study period did not capture a large event. Analysis suggests that on a continental scale the mapped factors that best explain the observed distribution are topography, annual precipitation and population density. On a national basis we have compared the occurrence of fatality-inducing landslide occurrence with the production of research articles with a local author, which shows that there is a landslide research deficit in Latin America and the Caribbean. Understanding better the mechanisms, distributions causes and triggers of landslides in Latin America and the Caribbean must be an essential first step towards managing the hazard.

Individual vision and peak distribution in collective actions

NASA Astrophysics Data System (ADS)

Lu, Peng

2017-06-01

People make decisions on whether they should participate as participants or not as free riders in collective actions with heterogeneous visions. Besides of the utility heterogeneity and cost heterogeneity, this work includes and investigates the effect of vision heterogeneity by constructing a decision model, i.e. the revised peak model of participants. In this model, potential participants make decisions under the joint influence of utility, cost, and vision heterogeneities. The outcomes of simulations indicate that vision heterogeneity reduces the values of peaks, and the relative variance of peaks is stable. Under normal distributions of vision heterogeneity and other factors, the peaks of participants are normally distributed as well. Therefore, it is necessary to predict distribution traits of peaks based on distribution traits of related factors such as vision heterogeneity and so on. We predict the distribution of peaks with parameters of both mean and standard deviation, which provides the confident intervals and robust predictions of peaks. Besides, we validate the peak model of via the Yuyuan Incident, a real case in China (2014), and the model works well in explaining the dynamics and predicting the peak of real case.

National Emphysema Treatment Trial redux: accentuating the positive.

PubMed

Sanchez, Pablo Gerardo; Kucharczuk, John Charles; Su, Stacey; Kaiser, Larry Robert; Cooper, Joel David

2010-09-01

Under the Freedom of Information Act, we obtained the follow-up data of the National Emphysema Treatment Trial (NETT) to determine the long-term outcome for "a heterogeneous distribution of emphysema with upper lobe predominance," postulated by the NETT hypothesis to be optimal candidates for lung volume reduction surgery. Using the NETT database, we identified patients with heterogeneous distribution of emphysema with upper lobe predominance and analyzed for the first time follow-up data for those receiving lung volume reduction surgery and those receiving medical management. Furthermore, we compared the results of the NETT reduction surgery group with a previously reported consecutive case series of 250 patients undergoing bilateral lung volume reduction surgery using similar selection criteria. Of the 1218 patients enrolled, 511 (42%) conformed to the NETT hypothesis selection criteria and received the randomly assigned surgical or medical treatment (surgical = 261; medical = 250). Lung volume reduction surgery resulted in a 5-year survival benefit (70% vs 60%; P = .02). Results at 3 years compared with baseline data favored surgical reduction in terms of residual volume reduction (25% vs 2%; P < .001), University of California San Diego dyspnea score (16 vs 0 points; P < .001), and improved St George Respiratory Questionnaire quality of life score (12 points vs 0 points; P < .001). For the 513 patients with a homogeneous pattern of emphysema randomized to surgical or medical treatment, lung volume reduction surgery produced no survival advantage and very limited functional benefit. Patients most likely to benefit from lung volume reduction surgery have heterogeneously distributed emphysema involving the upper lung zones predominantly. Such patients in the NETT trial had results nearly identical to those previously reported in a nonrandomized series of similar patients undergoing lung volume reduction surgery. 2010 The American Association for Thoracic Surgery. Published by Mosby, Inc. All rights reserved.

Design of a graphical user interface for an intelligent multimedia information system for radiology research

NASA Astrophysics Data System (ADS)

Taira, Ricky K.; Wong, Clement; Johnson, David; Bhushan, Vikas; Rivera, Monica; Huang, Lu J.; Aberle, Denise R.; Cardenas, Alfonso F.; Chu, Wesley W.

1995-05-01

With the increase in the volume and distribution of images and text available in PACS and medical electronic health-care environments it becomes increasingly important to maintain indexes that summarize the content of these multi-media documents. Such indices are necessary to quickly locate relevant patient cases for research, patient management, and teaching. The goal of this project is to develop an intelligent document retrieval system that allows researchers to request for patient cases based on document content. Thus we wish to retrieve patient cases from electronic information archives that could include a combined specification of patient demographics, low level radiologic findings (size, shape, number), intermediate-level radiologic findings (e.g., atelectasis, infiltrates, etc.) and/or high-level pathology constraints (e.g., well-differentiated small cell carcinoma). The cases could be distributed among multiple heterogeneous databases such as PACS, RIS, and HIS. Content- based retrieval systems go beyond the capabilities of simple key-word or string-based retrieval matching systems. These systems require a knowledge base to comprehend the generality/specificity of a concept (thus knowing the subclasses or related concepts to a given concept) and knowledge of the various string representations for each concept (i.e., synonyms, lexical variants, etc.). We have previously reported on a data integration mediation layer that allows transparent access to multiple heterogeneous distributed medical databases (HIS, RIS, and PACS). The data access layer of our architecture currently has limited query processing capabilities. Given a patient hospital identification number, the access mediation layer collects all documents in RIS and HIS and returns this information to a specified workstation location. In this paper we report on our efforts to extend the query processing capabilities of the system by creation of custom query interfaces, an intelligent query processing engine, and a document-content index that can be generated automatically (i.e., no manual authoring or changes to the normal clinical protocols).

Distributed parameterization of complex terrain

NASA Astrophysics Data System (ADS)

Band, Lawrence E.

1991-03-01

This paper addresses the incorporation of high resolution topography, soils and vegetation information into the simulation of land surface processes in atmospheric circulation models (ACM). Recent work has concentrated on detailed representation of one-dimensional exchange processes, implicitly assuming surface homogeneity over the atmospheric grid cell. Two approaches that could be taken to incorporate heterogeneity are the integration of a surface model over distributed, discrete portions of the landscape, or over a distribution function of the model parameters. However, the computational burden and parameter intensive nature of current land surface models in ACM limits the number of independent model runs and parameterizations that are feasible to accomplish for operational purposes. Therefore, simplications in the representation of the vertical exchange processes may be necessary to incorporate the effects of landscape variability and horizontal divergence of energy and water. The strategy is then to trade off the detail and rigor of point exchange calculations for the ability to repeat those calculations over extensive, complex terrain. It is clear the parameterization process for this approach must be automated such that large spatial databases collected from remotely sensed images, digital terrain models and digital maps can be efficiently summarized and transformed into the appropriate parameter sets. Ideally, the landscape should be partitioned into surface units that maximize between unit variance while minimizing within unit variance, although it is recognized that some level of surface heterogeneity will be retained at all scales. Therefore, the geographic data processing necessary to automate the distributed parameterization should be able to estimate or predict parameter distributional information within each surface unit.

Case retrieval in medical databases by fusing heterogeneous information.

PubMed

Quellec, Gwénolé; Lamard, Mathieu; Cazuguel, Guy; Roux, Christian; Cochener, Béatrice

2011-01-01

A novel content-based heterogeneous information retrieval framework, particularly well suited to browse medical databases and support new generation computer aided diagnosis (CADx) systems, is presented in this paper. It was designed to retrieve possibly incomplete documents, consisting of several images and semantic information, from a database; more complex data types such as videos can also be included in the framework. The proposed retrieval method relies on image processing, in order to characterize each individual image in a document by their digital content, and information fusion. Once the available images in a query document are characterized, a degree of match, between the query document and each reference document stored in the database, is defined for each attribute (an image feature or a metadata). A Bayesian network is used to recover missing information if need be. Finally, two novel information fusion methods are proposed to combine these degrees of match, in order to rank the reference documents by decreasing relevance for the query. In the first method, the degrees of match are fused by the Bayesian network itself. In the second method, they are fused by the Dezert-Smarandache theory: the second approach lets us model our confidence in each source of information (i.e., each attribute) and take it into account in the fusion process for a better retrieval performance. The proposed methods were applied to two heterogeneous medical databases, a diabetic retinopathy database and a mammography screening database, for computer aided diagnosis. Precisions at five of 0.809 ± 0.158 and 0.821 ± 0.177, respectively, were obtained for these two databases, which is very promising.

Engineering the object-relation database model in O-Raid

NASA Technical Reports Server (NTRS)

Dewan, Prasun; Vikram, Ashish; Bhargava, Bharat

1989-01-01

Raid is a distributed database system based on the relational model. O-raid is an extension of the Raid system and will support complex data objects. The design of O-Raid is evolutionary and retains all features of relational data base systems and those of a general purpose object-oriented programming language. O-Raid has several novel properties. Objects, classes, and inheritance are supported together with a predicate-base relational query language. O-Raid objects are compatible with C++ objects and may be read and manipulated by a C++ program without any 'impedance mismatch'. Relations and columns within relations may themselves be treated as objects with associated variables and methods. Relations may contain heterogeneous objects, that is, objects of more than one class in a certain column, which can individually evolve by being reclassified. Special facilities are provided to reduce the data search in a relation containing complex objects.

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.

Pore Pressure and Stress Distributions Around a Hydraulic Fracture in Heterogeneous Rock

NASA Astrophysics Data System (ADS)

Gao, Qian; Ghassemi, Ahmad

2017-12-01

One of the most significant characteristics of unconventional petroleum bearing formations is their heterogeneity, which affects the stress distribution, hydraulic fracture propagation and also fluid flow. This study focuses on the stress and pore pressure redistributions during hydraulic stimulation in a heterogeneous poroelastic rock. Lognormal random distributions of Young's modulus and permeability are generated to simulate the heterogeneous distributions of material properties. A 3D fully coupled poroelastic model based on the finite element method is presented utilizing a displacement-pressure formulation. In order to verify the model, numerical results are compared with analytical solutions showing excellent agreements. The effects of heterogeneities on stress and pore pressure distributions around a penny-shaped fracture in poroelastic rock are then analyzed. Results indicate that the stress and pore pressure distributions are more complex in a heterogeneous reservoir than in a homogeneous one. The spatial extent of stress reorientation during hydraulic stimulations is a function of time and is continuously changing due to the diffusion of pore pressure in the heterogeneous system. In contrast to the stress distributions in homogeneous media, irregular distributions of stresses and pore pressure are observed. Due to the change of material properties, shear stresses and nonuniform deformations are generated. The induced shear stresses in heterogeneous rock cause the initial horizontal principal stresses to rotate out of horizontal planes.

Heterogeneity in Health Care Computing Environments

PubMed Central

Sengupta, Soumitra

1989-01-01

This paper discusses issues of heterogeneity in computer systems, networks, databases, and presentation techniques, and the problems it creates in developing integrated medical information systems. The need for institutional, comprehensive goals are emphasized. Using the Columbia-Presbyterian Medical Center's computing environment as the case study, various steps to solve the heterogeneity problem are presented.

Heterogeneous Face Attribute Estimation: A Deep Multi-Task Learning Approach.

PubMed

Han, Hu; K Jain, Anil; Shan, Shiguang; Chen, Xilin

2017-08-10

Face attribute estimation has many potential applications in video surveillance, face retrieval, and social media. While a number of methods have been proposed for face attribute estimation, most of them did not explicitly consider the attribute correlation and heterogeneity (e.g., ordinal vs. nominal and holistic vs. local) during feature representation learning. In this paper, we present a Deep Multi-Task Learning (DMTL) approach to jointly estimate multiple heterogeneous attributes from a single face image. In DMTL, we tackle attribute correlation and heterogeneity with convolutional neural networks (CNNs) consisting of shared feature learning for all the attributes, and category-specific feature learning for heterogeneous attributes. We also introduce an unconstrained face database (LFW+), an extension of public-domain LFW, with heterogeneous demographic attributes (age, gender, and race) obtained via crowdsourcing. Experimental results on benchmarks with multiple face attributes (MORPH II, LFW+, CelebA, LFWA, and FotW) show that the proposed approach has superior performance compared to state of the art. Finally, evaluations on a public-domain face database (LAP) with a single attribute show that the proposed approach has excellent generalization ability.

A New Approach To Secure Federated Information Bases Using Agent Technology.

ERIC Educational Resources Information Center

Weippi, Edgar; Klug, Ludwig; Essmayr, Wolfgang

2003-01-01

Discusses database agents which can be used to establish federated information bases by integrating heterogeneous databases. Highlights include characteristics of federated information bases, including incompatible database management systems, schemata, and frequently changing context; software agent technology; Java agents; system architecture;…

Design of a decentralized reusable research database architecture to support data acquisition in large research projects.

PubMed

Iavindrasana, Jimison; Depeursinge, Adrien; Ruch, Patrick; Spahni, Stéphane; Geissbuhler, Antoine; Müller, Henning

2007-01-01

The diagnostic and therapeutic processes, as well as the development of new treatments, are hindered by the fragmentation of information which underlies them. In a multi-institutional research study database, the clinical information system (CIS) contains the primary data input. An important part of the money of large scale clinical studies is often paid for data creation and maintenance. The objective of this work is to design a decentralized, scalable, reusable database architecture with lower maintenance costs for managing and integrating distributed heterogeneous data required as basis for a large-scale research project. Technical and legal aspects are taken into account based on various use case scenarios. The architecture contains 4 layers: data storage and access are decentralized at their production source, a connector as a proxy between the CIS and the external world, an information mediator as a data access point and the client side. The proposed design will be implemented inside six clinical centers participating in the @neurIST project as part of a larger system on data integration and reuse for aneurism treatment.

SIMS: addressing the problem of heterogeneity in databases

NASA Astrophysics Data System (ADS)

Arens, Yigal

1997-02-01

The heterogeneity of remotely accessible databases -- with respect to contents, query language, semantics, organization, etc. -- presents serious obstacles to convenient querying. The SIMS (single interface to multiple sources) system addresses this global integration problem. It does so by defining a single language for describing the domain about which information is stored in the databases and using this language as the query language. Each database to which SIMS is to provide access is modeled using this language. The model describes a database's contents, organization, and other relevant features. SIMS uses these models, together with a planning system drawing on techniques from artificial intelligence, to decompose a given user's high-level query into a series of queries against the databases and other data manipulation steps. The retrieval plan is constructed so as to minimize data movement over the network and maximize parallelism to increase execution speed. SIMS can recover from network failures during plan execution by obtaining data from alternate sources, when possible. SIMS has been demonstrated in the domains of medical informatics and logistics, using real databases.

Java-based browsing, visualization and processing of heterogeneous medical data from remote repositories.

PubMed

Masseroli, M; Bonacina, S; Pinciroli, F

2004-01-01

The actual development of distributed information technologies and Java programming enables employing them also in the medical arena to support the retrieval, integration and evaluation of heterogeneous data and multimodal images in a web browser environment. With this aim, we used them to implement a client-server architecture based on software agents. The client side is a Java applet running in a web browser and providing a friendly medical user interface to browse and visualize different patient and medical test data, integrating them properly. The server side manages secure connections and queries to heterogeneous remote databases and file systems containing patient personal and clinical data. Based on the Java Advanced Imaging API, processing and analysis tools were developed to support the evaluation of remotely retrieved bioimages through the quantification of their features in different regions of interest. The Java platform-independence allows the centralized management of the implemented prototype and its deployment to each site where an intranet or internet connection is available. Giving healthcare providers effective support for comprehensively browsing, visualizing and evaluating medical images and records located in different remote repositories, the developed prototype can represent an important aid in providing more efficient diagnoses and medical treatments.

Heterogeneous game resource distributions promote cooperation in spatial prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Cui, Guang-Hai; Wang, Zhen; Yang, Yan-Cun; Tian, Sheng-Wen; Yue, Jun

2018-01-01

In social networks, individual abilities to establish interactions are always heterogeneous and independent of the number of topological neighbors. We here study the influence of heterogeneous distributions of abilities on the evolution of individual cooperation in the spatial prisoner's dilemma game. First, we introduced a prisoner's dilemma game, taking into account individual heterogeneous abilities to establish games, which are determined by the owned game resources. Second, we studied three types of game resource distributions that follow the power-law property. Simulation results show that the heterogeneous distribution of individual game resources can promote cooperation effectively, and the heterogeneous level of resource distributions has a positive influence on the maintenance of cooperation. Extensive analysis shows that cooperators with large resource capacities can foster cooperator clusters around themselves. Furthermore, when the temptation to defect is high, cooperator clusters in which the central pure cooperators have larger game resource capacities are more stable than other cooperator clusters.

CT Identification and Fractal Characterization of 3-D Propagation and Distribution of Hydrofracturing Cracks in Low-Permeability Heterogeneous Rocks

NASA Astrophysics Data System (ADS)

Liu, Peng; Ju, Yang; Gao, Feng; Ranjith, Pathegama G.; Zhang, Qianbing

2018-03-01

Understanding and characterization of the three-dimensional (3-D) propagation and distribution of hydrofracturing cracks in heterogeneous rock are key for enhancing the stimulation of low-permeability petroleum reservoirs. In this study, we investigated the propagation and distribution characteristics of hydrofracturing cracks, by conducting true triaxial hydrofracturing tests and computed tomography on artificial heterogeneous rock specimens. Silica sand, Portland cement, and aedelforsite were mixed to create artificial heterogeneous rock specimens using the data of mineral compositions, coarse gravel distribution, and mechanical properties that were measured from the natural heterogeneous glutenite cores. To probe the effects of material heterogeneity on hydrofracturing cracks, the artificial homogenous specimens were created using the identical matrix compositions of the heterogeneous rock specimens and then fractured for comparison. The effects of horizontal geostress ratio on the 3-D growth and distribution of cracks during hydrofracturing were examined. A fractal-based method was proposed to characterize the complexity of fractures and the efficiency of hydrofracturing stimulation of heterogeneous media. The material heterogeneity and horizontal geostress ratio were found to significantly influence the 3-D morphology, growth, and distribution of hydrofracturing cracks. A horizontal geostress ratio of 1.7 appears to be the upper limit for the occurrence of multiple cracks, and higher ratios cause a single crack perpendicular to the minimum horizontal geostress component. The fracturing efficiency is associated with not only the fractured volume but also the complexity of the crack network.

Nationwide survey on the organ-specific prevalence and its interaction with sarcoidosis in Japan.

PubMed

Hattori, Takeshi; Konno, Satoshi; Shijubo, Noriharu; Yamaguchi, Tetsuo; Sugiyama, Yukihiko; Honma, Sakae; Inase, Naohiko; Ito, Yoichi M; Nishimura, Masaharu

2018-06-21

Previous studies attempted to characterize the subjects with sarcoidosis according to differences in sex, age, and the presence of specific organ involvement. However, significant interactions among these factors precluded a clear conclusion based on simple comparison. This study aimed to clarify the age- and sex-stratified prevalence of specific organ involvement and the heterogenous nature of sarcoidosis. Using the data of 9,965 patients who were newly registered into a database at the Ministry of Health, Labour and Welfare, Japan between 2002 and 2011, we evaluated the age- and sex-specific prevalence of the eye, lung, and skin involvement of sarcoidosis. We also attempted corresponding analysis considering multiple factors. As compared with several decades ago, the monophasic age distribution in men became biphasic, and the biphasic distribution in women, monophasic. The prevalence of pulmonary and cutaneous lesions was significantly associated with age, whereas the prevalence of ocular involvement showed a biphasic pattern. The prevalence of bilateral hilar lymphadenopathy was significantly higher, whereas the prevalence of diffuse lung shadow was significantly lower, in subjects with ocular involvement than those without ocular involvement. Corresponding analysis visually clarified the complex interactions among factors. Our results contribute to a better understanding of the heterogeneous features of sarcoidosis.

Heterogeneous Ensemble Combination Search Using Genetic Algorithm for Class Imbalanced Data Classification.

PubMed

Haque, Mohammad Nazmul; Noman, Nasimul; Berretta, Regina; Moscato, Pablo

2016-01-01

Classification of datasets with imbalanced sample distributions has always been a challenge. In general, a popular approach for enhancing classification performance is the construction of an ensemble of classifiers. However, the performance of an ensemble is dependent on the choice of constituent base classifiers. Therefore, we propose a genetic algorithm-based search method for finding the optimum combination from a pool of base classifiers to form a heterogeneous ensemble. The algorithm, called GA-EoC, utilises 10 fold-cross validation on training data for evaluating the quality of each candidate ensembles. In order to combine the base classifiers decision into ensemble's output, we used the simple and widely used majority voting approach. The proposed algorithm, along with the random sub-sampling approach to balance the class distribution, has been used for classifying class-imbalanced datasets. Additionally, if a feature set was not available, we used the (α, β) - k Feature Set method to select a better subset of features for classification. We have tested GA-EoC with three benchmarking datasets from the UCI-Machine Learning repository, one Alzheimer's disease dataset and a subset of the PubFig database of Columbia University. In general, the performance of the proposed method on the chosen datasets is robust and better than that of the constituent base classifiers and many other well-known ensembles. Based on our empirical study we claim that a genetic algorithm is a superior and reliable approach to heterogeneous ensemble construction and we expect that the proposed GA-EoC would perform consistently in other cases.

Heterogeneous Ensemble Combination Search Using Genetic Algorithm for Class Imbalanced Data Classification

PubMed Central

Haque, Mohammad Nazmul; Noman, Nasimul; Berretta, Regina; Moscato, Pablo

2016-01-01

Classification of datasets with imbalanced sample distributions has always been a challenge. In general, a popular approach for enhancing classification performance is the construction of an ensemble of classifiers. However, the performance of an ensemble is dependent on the choice of constituent base classifiers. Therefore, we propose a genetic algorithm-based search method for finding the optimum combination from a pool of base classifiers to form a heterogeneous ensemble. The algorithm, called GA-EoC, utilises 10 fold-cross validation on training data for evaluating the quality of each candidate ensembles. In order to combine the base classifiers decision into ensemble’s output, we used the simple and widely used majority voting approach. The proposed algorithm, along with the random sub-sampling approach to balance the class distribution, has been used for classifying class-imbalanced datasets. Additionally, if a feature set was not available, we used the (α, β) − k Feature Set method to select a better subset of features for classification. We have tested GA-EoC with three benchmarking datasets from the UCI-Machine Learning repository, one Alzheimer’s disease dataset and a subset of the PubFig database of Columbia University. In general, the performance of the proposed method on the chosen datasets is robust and better than that of the constituent base classifiers and many other well-known ensembles. Based on our empirical study we claim that a genetic algorithm is a superior and reliable approach to heterogeneous ensemble construction and we expect that the proposed GA-EoC would perform consistently in other cases. PMID:26764911

Comparing methods for estimation of heterogeneous treatment effects using observational data from health care databases.

PubMed

Wendling, T; Jung, K; Callahan, A; Schuler, A; Shah, N H; Gallego, B

2018-06-03

There is growing interest in using routinely collected data from health care databases to study the safety and effectiveness of therapies in "real-world" conditions, as it can provide complementary evidence to that of randomized controlled trials. Causal inference from health care databases is challenging because the data are typically noisy, high dimensional, and most importantly, observational. It requires methods that can estimate heterogeneous treatment effects while controlling for confounding in high dimensions. Bayesian additive regression trees, causal forests, causal boosting, and causal multivariate adaptive regression splines are off-the-shelf methods that have shown good performance for estimation of heterogeneous treatment effects in observational studies of continuous outcomes. However, it is not clear how these methods would perform in health care database studies where outcomes are often binary and rare and data structures are complex. In this study, we evaluate these methods in simulation studies that recapitulate key characteristics of comparative effectiveness studies. We focus on the conditional average effect of a binary treatment on a binary outcome using the conditional risk difference as an estimand. To emulate health care database studies, we propose a simulation design where real covariate and treatment assignment data are used and only outcomes are simulated based on nonparametric models of the real outcomes. We apply this design to 4 published observational studies that used records from 2 major health care databases in the United States. Our results suggest that Bayesian additive regression trees and causal boosting consistently provide low bias in conditional risk difference estimates in the context of health care database studies. Copyright © 2018 John Wiley & Sons, Ltd.

Combining evidence from multiple electronic health care databases: performances of one-stage and two-stage meta-analysis in matched case-control studies.

PubMed

La Gamba, Fabiola; Corrao, Giovanni; Romio, Silvana; Sturkenboom, Miriam; Trifirò, Gianluca; Schink, Tania; de Ridder, Maria

2017-10-01

Clustering of patients in databases is usually ignored in one-stage meta-analysis of multi-database studies using matched case-control data. The aim of this study was to compare bias and efficiency of such a one-stage meta-analysis with a two-stage meta-analysis. First, we compared the approaches by generating matched case-control data under 5 simulated scenarios, built by varying: (1) the exposure-outcome association; (2) its variability among databases; (3) the confounding strength of one covariate on this association; (4) its variability; and (5) the (heterogeneous) confounding strength of two covariates. Second, we made the same comparison using empirical data from the ARITMO project, a multiple database study investigating the risk of ventricular arrhythmia following the use of medications with arrhythmogenic potential. In our study, we specifically investigated the effect of current use of promethazine. Bias increased for one-stage meta-analysis with increasing (1) between-database variance of exposure effect and (2) heterogeneous confounding generated by two covariates. The efficiency of one-stage meta-analysis was slightly lower than that of two-stage meta-analysis for the majority of investigated scenarios. Based on ARITMO data, there were no evident differences between one-stage (OR = 1.50, CI = [1.08; 2.08]) and two-stage (OR = 1.55, CI = [1.12; 2.16]) approaches. When the effect of interest is heterogeneous, a one-stage meta-analysis ignoring clustering gives biased estimates. Two-stage meta-analysis generates estimates at least as accurate and precise as one-stage meta-analysis. However, in a study using small databases and rare exposures and/or outcomes, a correct one-stage meta-analysis becomes essential. Copyright © 2017 John Wiley & Sons, Ltd.

Common Database Interface for Heterogeneous Software Engineering Tools.

DTIC Science & Technology

1987-12-01

SUB-GROUP Database Management Systems ;Programming(Comuters); 1e 05 Computer Files;Information Transfer;Interfaces; 19. ABSTRACT (Continue on reverse...Air Force Institute of Technology Air University In Partial Fulfillment of the Requirements for the Degree of Master of Science in Information Systems ...Literature ..... 8 System 690 Configuration ......... 8 Database Functionis ............ 14 Software Engineering Environments ... 14 Data Manager

CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies.

PubMed

Paananen, Jussi; Storvik, Markus; Wong, Garry

2006-09-22

Current genomic research methods provide researchers with enormous amounts of data. Combining data from different high-throughput research technologies commonly available in biological databases can lead to novel findings and increase research efficiency. However, combining data from different heterogeneous sources is often a very arduous task. These sources can be different microarray technology platforms, genomic databases, or experiments performed on various species. Our aim was to develop a software program that could facilitate the combining of data from heterogeneous sources, and thus allow researchers to perform genomic cross-platform/cross-species studies and to use existing experimental data for compendium studies. We have developed a web-based software resource, called CROPPER that uses the latest genomic information concerning different data identifiers and orthologous genes from the Ensembl database. CROPPER can be used to combine genomic data from different heterogeneous sources, allowing researchers to perform cross-platform/cross-species compendium studies without the need for complex computational tools or the requirement of setting up one's own in-house database. We also present an example of a simple cross-platform/cross-species compendium study based on publicly available Parkinson's disease data derived from different sources. CROPPER is a user-friendly and freely available web-based software resource that can be successfully used for cross-species/cross-platform compendium studies.

Complexity of the international agro-food trade network and its impact on food safety.

PubMed

Ercsey-Ravasz, Mária; Toroczkai, Zoltán; Lakner, Zoltán; Baranyi, József

2012-01-01

With the world's population now in excess of 7 billion, it is vital to ensure the chemical and microbiological safety of our food, while maintaining the sustainability of its production, distribution and trade. Using UN databases, here we show that the international agro-food trade network (IFTN), with nodes and edges representing countries and import-export fluxes, respectively, has evolved into a highly heterogeneous, complex supply-chain network. Seven countries form the core of the IFTN, with high values of betweenness centrality and each trading with over 77% of all the countries in the world. Graph theoretical analysis and a dynamic food flux model show that the IFTN provides a vehicle suitable for the fast distribution of potential contaminants but unsuitable for tracing their origin. In particular, we show that high values of node betweenness and vulnerability correlate well with recorded large food poisoning outbreaks.

Arcade: A Web-Java Based Framework for Distributed Computing

NASA Technical Reports Server (NTRS)

Chen, Zhikai; Maly, Kurt; Mehrotra, Piyush; Zubair, Mohammad; Bushnell, Dennis M. (Technical Monitor)

2000-01-01

Distributed heterogeneous environments are being increasingly used to execute a variety of large size simulations and computational problems. We are developing Arcade, a web-based environment to design, execute, monitor, and control distributed applications. These targeted applications consist of independent heterogeneous modules which can be executed on a distributed heterogeneous environment. In this paper we describe the overall design of the system and discuss the prototype implementation of the core functionalities required to support such a framework.

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

PubMed

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

2014-01-01

Inherited retinal degeneration (IRD), a leading cause of human blindness worldwide, is exceptionally heterogeneous with clinical heterogeneity and genetic variety. During the past decades, tremendous efforts have been made to explore the complex heterogeneity, and massive mutations have been identified in different genes underlying IRD with the significant advancement of sequencing technology. In this study, we developed a comprehensive database, 'RetinoGenetics', which contains informative knowledge about all known IRD-related genes and mutations for IRD. 'RetinoGenetics' currently contains 4270 mutations in 186 genes, with detailed information associated with 164 phenotypes from 934 publications and various types of functional annotations. Then extensive annotations were performed to each gene using various resources, including Gene Ontology, KEGG pathways, protein-protein interaction, mutational annotations and gene-disease network. Furthermore, by using the search functions, convenient browsing ways and intuitive graphical displays, 'RetinoGenetics' could serve as a valuable resource for unveiling the genetic basis of IRD. Taken together, 'RetinoGenetics' is an integrative, informative and updatable resource for IRD-related genetic predispositions. Database URL: http://www.retinogenetics.org/. © The Author(s) 2014. Published by Oxford University Press.

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

Roehm, Dominic; Pavel, Robert S.; Barros, Kipton

We present an adaptive sampling method supplemented by a distributed database and a prediction method for multiscale simulations using the Heterogeneous Multiscale Method. A finite-volume scheme integrates the macro-scale conservation laws for elastodynamics, which are closed by momentum and energy fluxes evaluated at the micro-scale. In the original approach, molecular dynamics (MD) simulations are launched for every macro-scale volume element. Our adaptive sampling scheme replaces a large fraction of costly micro-scale MD simulations with fast table lookup and prediction. The cloud database Redis provides the plain table lookup, and with locality aware hashing we gather input data for our predictionmore » scheme. For the latter we use kriging, which estimates an unknown value and its uncertainty (error) at a specific location in parameter space by using weighted averages of the neighboring points. We find that our adaptive scheme significantly improves simulation performance by a factor of 2.5 to 25, while retaining high accuracy for various choices of the algorithm parameters.« less

Gene Signal Distribution and HER2 Amplification in Gastroesophageal Cancer.

PubMed

Jørgensen, Jan Trøst; Nielsen, Karsten Bork; Kjærsgaard, Gitte; Jepsen, Anna; Mollerup, Jens

2017-01-01

Background : HER2 serves as an important therapeutic target in gastroesophageal cancer. Differences in HER2 gene signal distribution patterns can be observed at the tissue level, but how it influences the HER2 amplification status has not been studied so far. Here, we investigated the link between HER2 amplification and the different types of gene signal distribution. Methods : Tumor samples from 140 patients with gastroesophageal adenocarcinoma where analyzed using the HER2 IQFISH pharmDx™ assay. Specimens covered non-amplified and amplified cases with a preselected high proportion of HER2 amplified cases. Based on the HER2 /CEN-17 ratio, specimens were categorized into amplified or non-amplified. The signal distribution patterns were divided into homogeneous, heterogeneous focal or heterogeneous mosaic. The study was conducted based on anonymized specimens with limited access to clinicopathological data. Results: Among the 140 analyzed specimens 83 had a heterogeneous HER2 signal distribution, with 62 being focal and 21 of the mosaic type. The remaining 57 specimens had a homogeneous signal distribution. HER2 amplification was observed in 63 of the 140 specimens, and nearly all (93.7%) were found among specimens with a heterogeneous focal signal distribution (p<0.0001). The mean HER2 /CEN-17 ratio for the focal heterogeneous group was 8.75 (CI95%: 6.87 - 10.63), compared to 1.53 (CI95%: 1.45 - 1.61) and 1.70 (CI95%: 1.22 - 2.18) for the heterogeneous mosaic and homogeneous groups, respectively, (p<0.0001). Conclusions: A clear relationship between HER2 amplification and the focal heterogeneous signal distribution was demonstrated in tumor specimens from patients with gastroesophageal cancer. Furthermore, we raise the hypothesis that the signal distribution patterns observed with FISH might be related to different subpopulations of HER2 positive tumor cells.

Evaluating the Impact of Database Heterogeneity on Observational Study Results

PubMed Central

Madigan, David; Ryan, Patrick B.; Schuemie, Martijn; Stang, Paul E.; Overhage, J. Marc; Hartzema, Abraham G.; Suchard, Marc A.; DuMouchel, William; Berlin, Jesse A.

2013-01-01

Clinical studies that use observational databases to evaluate the effects of medical products have become commonplace. Such studies begin by selecting a particular database, a decision that published papers invariably report but do not discuss. Studies of the same issue in different databases, however, can and do generate different results, sometimes with strikingly different clinical implications. In this paper, we systematically study heterogeneity among databases, holding other study methods constant, by exploring relative risk estimates for 53 drug-outcome pairs and 2 widely used study designs (cohort studies and self-controlled case series) across 10 observational databases. When holding the study design constant, our analysis shows that estimated relative risks range from a statistically significant decreased risk to a statistically significant increased risk in 11 of 53 (21%) of drug-outcome pairs that use a cohort design and 19 of 53 (36%) of drug-outcome pairs that use a self-controlled case series design. This exceeds the proportion of pairs that were consistent across databases in both direction and statistical significance, which was 9 of 53 (17%) for cohort studies and 5 of 53 (9%) for self-controlled case series. Our findings show that clinical studies that use observational databases can be sensitive to the choice of database. More attention is needed to consider how the choice of data source may be affecting results. PMID:23648805

A Metric and Workflow for Quality Control in the Analysis of Heterogeneity in Phenotypic Profiles and Screens

PubMed Central

Gough, Albert; Shun, Tongying; Taylor, D. Lansing; Schurdak, Mark

2016-01-01

Heterogeneity is well recognized as a common property of cellular systems that impacts biomedical research and the development of therapeutics and diagnostics. Several studies have shown that analysis of heterogeneity: gives insight into mechanisms of action of perturbagens; can be used to predict optimal combination therapies; and to quantify heterogeneity in tumors where heterogeneity is believed to be associated with adaptation and resistance. Cytometry methods including high content screening (HCS), high throughput microscopy, flow cytometry, mass spec imaging and digital pathology capture cell level data for populations of cells. However it is often assumed that the population response is normally distributed and therefore that the average adequately describes the results. A deeper understanding of the results of the measurements and more effective comparison of perturbagen effects requires analysis that takes into account the distribution of the measurements, i.e. the heterogeneity. However, the reproducibility of heterogeneous data collected on different days, and in different plates/slides has not previously been evaluated. Here we show that conventional assay quality metrics alone are not adequate for quality control of the heterogeneity in the data. To address this need, we demonstrate the use of the Kolmogorov-Smirnov statistic as a metric for monitoring the reproducibility of heterogeneity in an SAR screen, describe a workflow for quality control in heterogeneity analysis. One major challenge in high throughput biology is the evaluation and interpretation of heterogeneity in thousands of samples, such as compounds in a cell-based screen. In this study we also demonstrate that three heterogeneity indices previously reported, capture the shapes of the distributions and provide a means to filter and browse big data sets of cellular distributions in order to compare and identify distributions of interest. These metrics and methods are presented as a workflow for analysis of heterogeneity in large scale biology projects. PMID:26476369

Long-range Ising model for credit portfolios with heterogeneous credit exposures

NASA Astrophysics Data System (ADS)

Kato, Kensuke

2016-11-01

We propose the finite-size long-range Ising model as a model for heterogeneous credit portfolios held by a financial institution in the view of econophysics. The model expresses the heterogeneity of the default probability and the default correlation by dividing a credit portfolio into multiple sectors characterized by credit rating and industry. The model also expresses the heterogeneity of the credit exposure, which is difficult to evaluate analytically, by applying the replica exchange Monte Carlo method to numerically calculate the loss distribution. To analyze the characteristics of the loss distribution for credit portfolios with heterogeneous credit exposures, we apply this model to various credit portfolios and evaluate credit risk. As a result, we show that the tail of the loss distribution calculated by this model has characteristics that are different from the tail of the loss distribution of the standard models used in credit risk modeling. We also show that there is a possibility of different evaluations of credit risk according to the pattern of heterogeneity.

Modeling Transport of Cesium in Grimsel Granodiorite With Micrometer Scale Heterogeneities and Dynamic Update of Kd

NASA Astrophysics Data System (ADS)

Voutilainen, Mikko; Kekäläinen, Pekka; Siitari-Kauppi, Marja; Sardini, Paul; Muuri, Eveliina; Timonen, Jussi; Martin, Andrew

2017-11-01

Transport and retardation of cesium in Grimsel granodiorite taking into account heterogeneity of mineral and pore structure was studied using rock samples overcored from an in situ diffusion test at the Grimsel Test Site. The field test was part of the Long-Term Diffusion (LTD) project designed to characterize retardation properties (diffusion and distribution coefficients) under in situ conditions. Results of the LTD experiment for cesium showed that in-diffusion profiles and spatial concentration distributions were strongly influenced by the heterogeneous pore structure and mineral distribution. In order to study the effect of heterogeneity on the in-diffusion profile and spatial concentration distribution, a Time Domain Random Walk (TDRW) method was applied along with a feature for modeling chemical sorption in geological materials. A heterogeneous mineral structure of Grimsel granodiorite was constructed using X-ray microcomputed tomography (X-μCT) and the map was linked to previous results for mineral specific porosities and distribution coefficients (Kd) that were determined using C-14-PMMA autoradiography and batch sorption experiments, respectively. After this the heterogeneous structure contains information on local porosity and Kd in 3-D. It was found that the heterogeneity of the mineral structure on the micrometer scale affects significantly the diffusion and sorption of cesium in Grimsel granodiorite at the centimeter scale. Furthermore, the modeled in-diffusion profiles and spatial concentration distributions show similar shape and pattern to those from the LTD experiment. It was concluded that the use of detailed structure characterization and quantitative data on heterogeneity can significantly improve the interpretation and evaluation of transport experiments.

Regional gas transport in the heterogeneous lung during oscillatory ventilation

PubMed Central

Herrmann, Jacob; Tawhai, Merryn H.

2016-01-01

Regional ventilation in the injured lung is heterogeneous and frequency dependent, making it difficult to predict how an oscillatory flow waveform at a specified frequency will be distributed throughout the periphery. To predict the impact of mechanical heterogeneity on regional ventilation distribution and gas transport, we developed a computational model of distributed gas flow and CO2 elimination during oscillatory ventilation from 0.1 to 30 Hz. The model consists of a three-dimensional airway network of a canine lung, with heterogeneous parenchymal tissues to mimic effects of gravity and injury. Model CO2 elimination during single frequency oscillation was validated against previously published experimental data (Venegas JG, Hales CA, Strieder DJ, J Appl Physiol 60: 1025–1030, 1986). Simulations of gas transport demonstrated a critical transition in flow distribution at the resonant frequency, where the reactive components of mechanical impedance due to airway inertia and parenchymal elastance were equal. For frequencies above resonance, the distribution of ventilation became spatially clustered and frequency dependent. These results highlight the importance of oscillatory frequency in managing the regional distribution of ventilation and gas exchange in the heterogeneous lung. PMID:27763872

Distributed Earth observation data integration and on-demand services based on a collaborative framework of geospatial data service gateway

NASA Astrophysics Data System (ADS)

Xie, Jibo; Li, Guoqing

2015-04-01

Earth observation (EO) data obtained by air-borne or space-borne sensors has the characteristics of heterogeneity and geographical distribution of storage. These data sources belong to different organizations or agencies whose data management and storage methods are quite different and geographically distributed. Different data sources provide different data publish platforms or portals. With more Remote sensing sensors used for Earth Observation (EO) missions, different space agencies have distributed archived massive EO data. The distribution of EO data archives and system heterogeneity makes it difficult to efficiently use geospatial data for many EO applications, such as hazard mitigation. To solve the interoperable problems of different EO data systems, an advanced architecture of distributed geospatial data infrastructure is introduced to solve the complexity of distributed and heterogeneous EO data integration and on-demand processing in this paper. The concept and architecture of geospatial data service gateway (GDSG) is proposed to build connection with heterogeneous EO data sources by which EO data can be retrieved and accessed with unified interfaces. The GDSG consists of a set of tools and service to encapsulate heterogeneous geospatial data sources into homogenous service modules. The GDSG modules includes EO metadata harvesters and translators, adaptors to different type of data system, unified data query and access interfaces, EO data cache management, and gateway GUI, etc. The GDSG framework is used to implement interoperability and synchronization between distributed EO data sources with heterogeneous architecture. An on-demand distributed EO data platform is developed to validate the GDSG architecture and implementation techniques. Several distributed EO data achieves are used for test. Flood and earthquake serves as two scenarios for the use cases of distributed EO data integration and interoperability.

BioWarehouse: a bioinformatics database warehouse toolkit

PubMed Central

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

2006-01-01

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

BioWarehouse: a bioinformatics database warehouse toolkit.

PubMed

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

2006-03-23

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

Anomalous dispersion in correlated porous media: a coupled continuous time random walk approach

NASA Astrophysics Data System (ADS)

Comolli, Alessandro; Dentz, Marco

2017-09-01

We study the causes of anomalous dispersion in Darcy-scale porous media characterized by spatially heterogeneous hydraulic properties. Spatial variability in hydraulic conductivity leads to spatial variability in the flow properties through Darcy's law and thus impacts on solute and particle transport. We consider purely advective transport in heterogeneity scenarios characterized by broad distributions of heterogeneity length scales and point values. Particle transport is characterized in terms of the stochastic properties of equidistantly sampled Lagrangian velocities, which are determined by the flow and conductivity statistics. The persistence length scales of flow and transport velocities are imprinted in the spatial disorder and reflect the distribution of heterogeneity length scales. Particle transitions over the velocity length scales are kinematically coupled with the transition time through velocity. We show that the average particle motion follows a coupled continuous time random walk (CTRW), which is fully parameterized by the distribution of flow velocities and the medium geometry in terms of the heterogeneity length scales. The coupled CTRW provides a systematic framework for the investigation of the origins of anomalous dispersion in terms of heterogeneity correlation and the distribution of conductivity point values. We derive analytical expressions for the asymptotic scaling of the moments of the spatial particle distribution and first arrival time distribution (FATD), and perform numerical particle tracking simulations of the coupled CTRW to capture the full average transport behavior. Broad distributions of heterogeneity point values and lengths scales may lead to very similar dispersion behaviors in terms of the spatial variance. Their mechanisms, however are very different, which manifests in the distributions of particle positions and arrival times, which plays a central role for the prediction of the fate of dissolved substances in heterogeneous natural and engineered porous materials. Contribution to the Topical Issue "Continuous Time Random Walk Still Trendy: Fifty-year History, Current State and Outlook", edited by Ryszard Kutner and Jaume Masoliver.

Universal Index System

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos; Wallace, Sarah

1993-01-01

The Universal Index System (UIS) is an index management system that uses a uniform interface to solve the heterogeneity problem among database management systems. UIS provides an easy-to-use common interface to access all underlying data, but also allows different underlying database management systems, storage representations, and access methods.

Effects of the duration and inorganic nitrogen composition of a nutrient-rich patch on soil exploration by the roots of Lolium perenne in a heterogeneous environment.

PubMed

Nakamura, Ryoji; Kachi, N; Suzuki, J-I

2010-05-01

We investigated the growth of and soil exploration by Lolium perenne under a heterogeneous environment before its roots reached a nutrient-rich patch. Temporal changes in the distribution of inorganic nitrogen, i.e., NO(3)(-)-N and NH(4)(+)-N, in the heterogeneous environment during the experimental period were also examined. The results showed that roots randomly explored soil, irrespective of the patchy distribution of inorganic nitrogen and differences in the chemical composition of inorganic nitrogen distribution between heterogeneous and homogeneous environments. We have also elucidated the potential effects of patch duration and inorganic nitrogen distribution on soil exploration by roots and thus on plant growth.

Organization of Heterogeneous Scientific Data Using the EAV/CR Representation

PubMed Central

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

1999-01-01

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

Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates: BIOFILM DISTRIBUTION AND RATE SCALING

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

Yan, Zhifeng; Liu, Chongxuan; Liu, Yuanyuan

Biofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models, and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X-ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical propertiesmore » was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.« less

Hierarchical Distributed-Lag Models: Exploring Varying Geographic Scale and Magnitude in Associations Between the Built Environment and Health

PubMed Central

Baek, Jonggyu; Sanchez-Vaznaugh, Emma V.; Sánchez, Brisa N.

2016-01-01

It is well known that associations between features of the built environment and health depend on the geographic scale used to construct environmental attributes. In the built environment literature, it has long been argued that geographic scales may vary across study locations. However, this hypothesized variation has not been systematically examined due to a lack of available statistical methods. We propose a hierarchical distributed-lag model (HDLM) for estimating the underlying overall shape of food environment–health associations as a function of distance from locations of interest. This method enables indirect assessment of relevant geographic scales and captures area-level heterogeneity in the magnitudes of associations, along with relevant distances within areas. The proposed model was used to systematically examine area-level variation in the association between availability of convenience stores around schools and children's weights. For this case study, body mass index (weight kg)/height (m)2) z scores (BMIz) for 7th grade children collected via California's 2001–2009 FitnessGram testing program were linked to a commercial database that contained locations of food outlets statewide. Findings suggested that convenience store availability may influence BMIz only in some places and at varying distances from schools. Future research should examine localized environmental or policy differences that may explain the heterogeneity in convenience store–BMIz associations. PMID:26888753

Heterogeneous slip distribution on faults responsible for large earthquakes: characterization and implications for tsunami modelling

NASA Astrophysics Data System (ADS)

Baglione, Enrico; Armigliato, Alberto; Pagnoni, Gianluca; Tinti, Stefano

2017-04-01

The fact that ruptures on the generating faults of large earthquakes are strongly heterogeneous has been demonstrated over the last few decades by a large number of studies. The effort to retrieve reliable finite-fault models (FFMs) for large earthquakes occurred worldwide, mainly by means of the inversion of different kinds of geophysical data, has been accompanied in the last years by the systematic collection and format homogenisation of the published/proposed FFMs for different earthquakes into specifically conceived databases, such as SRCMOD. The main aim of this study is to explore characteristic patterns of the slip distribution of large earthquakes, by using a subset of the FFMs contained in SRCMOD, covering events with moment magnitude equal or larger than 6 and occurred worldwide over the last 25 years. We focus on those FFMs that exhibit a single and clear region of high slip (i.e. a single asperity), which is found to represent the majority of the events. For these FFMs, it sounds reasonable to best-fit the slip model by means of a 2D Gaussian distributions. Two different methods are used (least-square and highest-similarity) and correspondingly two "best-fit" indexes are introduced. As a result, two distinct 2D Gaussian distributions for each FFM are obtained. To quantify how well these distributions are able to mimic the original slip heterogeneity, we calculate and compare the vertical displacements at the Earth surface in the near field induced by the original FFM slip, by an equivalent uniform-slip model, by a depth-dependent slip model, and by the two "best" Gaussian slip models. The coseismic vertical surface displacement is used as the metric for comparison. Results show that, on average, the best results are the ones obtained with 2D Gaussian distributions based on similarity index fitting. Finally, we restrict our attention to those single-asperity FFMs associated to earthquakes which generated tsunamis. We choose few events for which tsunami data (water level time series and/or run-up measurements) are available. Using the results mentioned above, for each chosen event the coseismic vertical displacement fields computed for different slip distributions are used as initial conditions for numerical tsunami simulations, performed by means of the shallow-water code UBO-TSUFD. The comparison of the numerical results for different initial conditions to the experimental data is presented and discussed. This study was funded in the frame of the EU Project called ASTARTE - "Assessment, STrategy And Risk Reduction for Tsunamis in Europe", Grant 603839, 7th FP (ENV.2013.6.4-3).

A normalization method for combination of laboratory test results from different electronic healthcare databases in a distributed research network.

PubMed

Yoon, Dukyong; Schuemie, Martijn J; Kim, Ju Han; Kim, Dong Ki; Park, Man Young; Ahn, Eun Kyoung; Jung, Eun-Young; Park, Dong Kyun; Cho, Soo Yeon; Shin, Dahye; Hwang, Yeonsoo; Park, Rae Woong

2016-03-01

Distributed research networks (DRNs) afford statistical power by integrating observational data from multiple partners for retrospective studies. However, laboratory test results across care sites are derived using different assays from varying patient populations, making it difficult to simply combine data for analysis. Additionally, existing normalization methods are not suitable for retrospective studies. We normalized laboratory results from different data sources by adjusting for heterogeneous clinico-epidemiologic characteristics of the data and called this the subgroup-adjusted normalization (SAN) method. Subgroup-adjusted normalization renders the means and standard deviations of distributions identical under population structure-adjusted conditions. To evaluate its performance, we compared SAN with existing methods for simulated and real datasets consisting of blood urea nitrogen, serum creatinine, hematocrit, hemoglobin, serum potassium, and total bilirubin. Various clinico-epidemiologic characteristics can be applied together in SAN. For simplicity of comparison, age and gender were used to adjust population heterogeneity in this study. In simulations, SAN had the lowest standardized difference in means (SDM) and Kolmogorov-Smirnov values for all tests (p < 0.05). In a real dataset, SAN had the lowest SDM and Kolmogorov-Smirnov values for blood urea nitrogen, hematocrit, hemoglobin, and serum potassium, and the lowest SDM for serum creatinine (p < 0.05). Subgroup-adjusted normalization performed better than normalization using other methods. The SAN method is applicable in a DRN environment and should facilitate analysis of data integrated across DRN partners for retrospective observational studies. Copyright © 2015 John Wiley & Sons, Ltd.

Recovery and validation of historical sediment quality data from coastal and estuarine areas: An integrated approach

USGS Publications Warehouse

Manheim, F.T.; Buchholtz ten Brink, Marilyn R.; Mecray, E.L.

1998-01-01

A comprehensive database of sediment chemistry and environmental parameters has been compiled for Boston Harbor and Massachusetts Bay. This work illustrates methodologies for rescuing and validating sediment data from heterogeneous historical sources. It greatly expands spatial and temporal data coverage of estuarine and coastal sediments. The database contains about 3500 samples containing inorganic chemical, organic, texture and other environmental data dating from 1955 to 1994. Cooperation with local and federal agencies as well as universities was essential in locating and screening documents for the database. More than 80% of references utilized came from sources with limited distribution (gray literature). Task sharing was facilitated by a comprehensive and clearly defined data dictionary for sediments. It also served as a data entry template and flat file format for data processing and as a basis for interpretation and graphical illustration. Standard QA/QC protocols are usually inapplicable to historical sediment data. In this work outliers and data quality problems were identified by batch screening techniques that also provide visualizations of data relationships and geochemical affinities. No data were excluded, but qualifying comments warn users of problem data. For Boston Harbor, the proportion of irreparable or seriously questioned data was remarkably small (<5%), although concentration values for metals and organic contaminants spanned 3 orders of magnitude for many elements or compounds. Data from the historical database provide alternatives to dated cores for measuring changes in surficial sediment contamination level with time. The data indicate that spatial inhomogeneity in harbor environments can be large with respect to sediment-hosted contaminants. Boston Inner Harbor surficial sediments showed decreases in concentrations of Cu, Hg, and Zn of 40 to 60% over a 17-year period.A comprehensive database of sediment chemistry and environmental parameters has been compiled for Boston Harbor and Massachusetts Bay. This work illustrates methodologies for rescuing and validating sediment data from heterogeneous historical sources. It greatly expands spatial and temporal data coverage of estuarine and coastal sediments. The database contains about 3500 samples containing inorganic chemical, organic, texture and other environmental data dating from 1995 to 1994. Cooperation with local and federal agencies as well as universities was essential in locating and screening documents for the database. More than 80% of references utilized came from sources with limited distribution (gray Task sharing was facilitated by a comprehensive and clearly defined data dictionary for sediments. It also served as a data entry template and flat file format for data processing and as a basis for interpretation and graphical illustration. Standard QA/QC protocols are usually inapplicable to historical sediment data. In this work outliers and data quality problems were identified by batch screening techniques that also provide visualizations of data relationships and geochemical affinities. No data were excluded, but qualifying comments warn users of problem data. For Boston Harbor, the proportion of irreparable or seriously questioned data was remarkably small (<5%), although concentration values for metals and organic contaminants spanned 3 orders of magnitude for many elements or compounds. Data from the historical database provide alternatives to dated cores for measuring changes in surficial sediment contamination level with time. The data indicate that spatial inhomogeneity in harbor environments can be large with respect to sediment-hosted contaminants. Boston Inner Harbor surficial sediments showed decreases in concentrations Cu, Hg, and Zn of 40 to 60% over a 17-year period.

Regional gas transport in the heterogeneous lung during oscillatory ventilation.

PubMed

Herrmann, Jacob; Tawhai, Merryn H; Kaczka, David W

2016-12-01

Regional ventilation in the injured lung is heterogeneous and frequency dependent, making it difficult to predict how an oscillatory flow waveform at a specified frequency will be distributed throughout the periphery. To predict the impact of mechanical heterogeneity on regional ventilation distribution and gas transport, we developed a computational model of distributed gas flow and CO 2 elimination during oscillatory ventilation from 0.1 to 30 Hz. The model consists of a three-dimensional airway network of a canine lung, with heterogeneous parenchymal tissues to mimic effects of gravity and injury. Model CO 2 elimination during single frequency oscillation was validated against previously published experimental data (Venegas JG, Hales CA, Strieder DJ, J Appl Physiol 60: 1025-1030, 1986). Simulations of gas transport demonstrated a critical transition in flow distribution at the resonant frequency, where the reactive components of mechanical impedance due to airway inertia and parenchymal elastance were equal. For frequencies above resonance, the distribution of ventilation became spatially clustered and frequency dependent. These results highlight the importance of oscillatory frequency in managing the regional distribution of ventilation and gas exchange in the heterogeneous lung. Copyright © 2016 the American Physiological Society.

Multiscale Investigation on Biofilm Distribution and Its Impact on Macroscopic Biogeochemical Reaction Rates

NASA Astrophysics Data System (ADS)

Yan, Zhifeng; Liu, Chongxuan; Liu, Yuanyuan; Bailey, Vanessa L.

2017-11-01

Biofilms are critical locations for biogeochemical reactions in the subsurface environment. The occurrence and distribution of biofilms at microscale as well as their impacts on macroscopic biogeochemical reaction rates are still poorly understood. This paper investigated the formation and distributions of biofilms in heterogeneous sediments using multiscale models and evaluated the effects of biofilm heterogeneity on local and macroscopic biogeochemical reaction rates. Sediment pore structures derived from X-ray computed tomography were used to simulate the microscale flow dynamics and biofilm distribution in the sediment column. The response of biofilm formation and distribution to the variations in hydraulic and chemical properties was first examined. One representative biofilm distribution was then utilized to evaluate its effects on macroscopic reaction rates using nitrate reduction as an example. The results revealed that microorganisms primarily grew on the surfaces of grains and aggregates near preferential flow paths where both electron donor and acceptor were readily accessible, leading to the heterogeneous distribution of biofilms in the sediments. The heterogeneous biofilm distribution decreased the macroscopic rate of biogeochemical reactions as compared with those in homogeneous cases. Operationally considering the heterogeneous biofilm distribution in macroscopic reactive transport models such as using dual porosity domain concept can significantly improve the prediction of biogeochemical reaction rates. Overall, this study provided important insights into the biofilm formation and distribution in soils and sediments as well as their impacts on the macroscopic manifestation of reaction rates.

A distributed scheduling algorithm for heterogeneous real-time systems

NASA Technical Reports Server (NTRS)

Zeineldine, Osman; El-Toweissy, Mohamed; Mukkamala, Ravi

1991-01-01

Much of the previous work on load balancing and scheduling in distributed environments was concerned with homogeneous systems and homogeneous loads. Several of the results indicated that random policies are as effective as other more complex load allocation policies. The effects of heterogeneity on scheduling algorithms for hard real time systems is examined. A distributed scheduler specifically to handle heterogeneities in both nodes and node traffic is proposed. The performance of the algorithm is measured in terms of the percentage of jobs discarded. While a random task allocation is very sensitive to heterogeneities, the algorithm is shown to be robust to such non-uniformities in system components and load.

Measuring the effects of heterogeneity on distributed systems

NASA Technical Reports Server (NTRS)

El-Toweissy, Mohamed; Zeineldine, Osman; Mukkamala, Ravi

1991-01-01

Distributed computer systems in daily use are becoming more and more heterogeneous. Currently, much of the design and analysis studies of such systems assume homogeneity. This assumption of homogeneity has been mainly driven by the resulting simplicity in modeling and analysis. A simulation study is presented which investigated the effects of heterogeneity on scheduling algorithms for hard real time distributed systems. In contrast to previous results which indicate that random scheduling may be as good as a more complex scheduler, this algorithm is shown to be consistently better than a random scheduler. This conclusion is more prevalent at high workloads as well as at high levels of heterogeneity.

Brief Report: The Negev Hospital-University-Based (HUB) Autism Database

ERIC Educational Resources Information Center

Meiri, Gal; Dinstein, Ilan; Michaelowski, Analya; Flusser, Hagit; Ilan, Michal; Faroy, Michal; Bar-Sinai, Asif; Manelis, Liora; Stolowicz, Dana; Yosef, Lili Lea; Davidovitch, Nadav; Golan, Hava; Arbelle, Shosh; Menashe, Idan

2017-01-01

Elucidating the heterogeneous etiologies of autism will require investment in comprehensive longitudinal data acquisition from large community based cohorts. With this in mind, we have established a hospital-university-based (HUB) database of autism which incorporates prospective and retrospective data from a large and ethnically diverse…

Variable synaptic strengths controls the firing rate distribution in feedforward neural networks.

PubMed

Ly, Cheng; Marsat, Gary

2018-02-01

Heterogeneity of firing rate statistics is known to have severe consequences on neural coding. Recent experimental recordings in weakly electric fish indicate that the distribution-width of superficial pyramidal cell firing rates (trial- and time-averaged) in the electrosensory lateral line lobe (ELL) depends on the stimulus, and also that network inputs can mediate changes in the firing rate distribution across the population. We previously developed theoretical methods to understand how two attributes (synaptic and intrinsic heterogeneity) interact and alter the firing rate distribution in a population of integrate-and-fire neurons with random recurrent coupling. Inspired by our experimental data, we extend these theoretical results to a delayed feedforward spiking network that qualitatively capture the changes of firing rate heterogeneity observed in in-vivo recordings. We demonstrate how heterogeneous neural attributes alter firing rate heterogeneity, accounting for the effect with various sensory stimuli. The model predicts how the strength of the effective network connectivity is related to intrinsic heterogeneity in such delayed feedforward networks: the strength of the feedforward input is positively correlated with excitability (threshold value for spiking) when firing rate heterogeneity is low and is negatively correlated with excitability with high firing rate heterogeneity. We also show how our theory can be used to predict effective neural architecture. We demonstrate that neural attributes do not interact in a simple manner but rather in a complex stimulus-dependent fashion to control neural heterogeneity and discuss how it can ultimately shape population codes.

Estimation of blood flow heterogeneity in human skeletal muscle using intravascular tracer data: importance for modeling transcapillary exchange.

PubMed

Vicini, P; Bonadonna, R C; Lehtovirta, M; Groop, L C; Cobelli, C

1998-01-01

Distributed models of blood-tissue exchange are widely used to measure kinetic events of various solutes from multiple tracer dilution experiments. Their use requires, however, a careful description of blood flow heterogeneity along the capillary bed. Since they have mostly been applied in animal studies, direct measurement of the heterogeneity distribution was possible, e.g., with the invasive microsphere method. Here we apply distributed modeling to a dual tracer experiment in humans, performed using an intravascular (indocyanine green dye, subject to distribution along the vascular tree and confined to the capillary bed) and an extracellular ([3H]-D-mannitol, tracing passive transcapillary transfer across the capillary membrane in the interstitial fluid) tracer. The goal is to measure relevant parameters of transcapillary exchange in human skeletal muscle. We show that assuming an accurate description of blood flow heterogeneity is crucial for modeling, and in particular that assuming for skeletal muscle the well-studied cardiac muscle blood flow heterogeneity is inappropriate. The same reason prevents the use of the common method of estimating the input function of the distributed model via deconvolution, which assumes a known blood flow heterogeneity, either defined from literature or measured, when possible. We present a novel approach for the estimation of blood flow heterogeneity in each individual from the intravascular tracer data. When this newly estimated blood flow heterogeneity is used, a more satisfactory model fit is obtained and it is possible to reliably measure parameters of capillary membrane permeability-surface product and interstitial fluid volume describing transcapillary transfer in vivo.

A broadband multimedia TeleLearning system

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

Wang, Ruiping; Karmouch, A.

1996-12-31

In this paper we discuss a broadband multimedia TeleLearning system under development in the Multimedia Information Research Laboratory at the University of Ottawa. The system aims at providing a seamless environment for TeleLearning using the latest telecommunication and multimedia information processing technology. It basically consists of a media production center, a courseware author site, a courseware database, a courseware user site, and an on-line facilitator site. All these components are distributed over an ATM network and work together to offer a multimedia interactive courseware service. An MHEG-based model is exploited in designing the system architecture to achieve the real-time, interactive,more » and reusable information interchange through heterogeneous platforms. The system architecture, courseware processing strategies, courseware document models are presented.« less

Proceedings of the Seventh International Symposium on Methodologies for Intelligent Systems (Poster Session)

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

Harber, K.S.

1993-05-01

This report contains the following papers: Implications in vivid logic; a self-learning bayesian expert system; a natural language generation system for a heterogeneous distributed database system; competence-switching'' managed by intelligent systems; strategy acquisition by an artificial neural network: Experiments in learning to play a stochastic game; viewpoints and selective inheritance in object-oriented modeling; multivariate discretization of continuous attributes for machine learning; utilization of the case-based reasoning method to resolve dynamic problems; formalization of an ontology of ceramic science in CLASSIC; linguistic tools for intelligent systems; an application of rough sets in knowledge synthesis; and a relational model for imprecise queries.more » These papers have been indexed separately.« less

Proceedings of the Seventh International Symposium on Methodologies for Intelligent Systems (Poster Session)

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

Harber, K.S.

1993-05-01

This report contains the following papers: Implications in vivid logic; a self-learning Bayesian Expert System; a natural language generation system for a heterogeneous distributed database system; ``competence-switching`` managed by intelligent systems; strategy acquisition by an artificial neural network: Experiments in learning to play a stochastic game; viewpoints and selective inheritance in object-oriented modeling; multivariate discretization of continuous attributes for machine learning; utilization of the case-based reasoning method to resolve dynamic problems; formalization of an ontology of ceramic science in CLASSIC; linguistic tools for intelligent systems; an application of rough sets in knowledge synthesis; and a relational model for imprecise queries.more » These papers have been indexed separately.« less

Uranium distribution and 'excessive' U-He ages in iron meteoritic troilite

NASA Technical Reports Server (NTRS)

Fisher, D. E.

1985-01-01

Fission tracking techniques were used to measure the uranium distribution in meteoritic troilite and graphite. The obtained fission tracking data showed a heterogeneous distribution of tracks with a significant portion of track density present in the form of uranium clusters at least 10 microns in size. The matrix containing the clusters was also heterogeneous in composition with U concentrations of about 0.2-4.7 ppb. U/He ages could not be estimated on the basis of the heterogeneous U distributions, so previously reported estimates of U/He ages in the presolar range are probably invalid.

Effects of species biological traits and environmental heterogeneity on simulated tree species distribution shifts under climate change.

PubMed

Wang, Wen J; He, Hong S; Thompson, Frank R; Spetich, Martin A; Fraser, Jacob S

2018-09-01

Demographic processes (fecundity, dispersal, colonization, growth, and mortality) and their interactions with environmental changes are not well represented in current climate-distribution models (e.g., niche and biophysical process models) and constitute a large uncertainty in projections of future tree species distribution shifts. We investigate how species biological traits and environmental heterogeneity affect species distribution shifts. We used a species-specific, spatially explicit forest dynamic model LANDIS PRO, which incorporates site-scale tree species demography and competition, landscape-scale dispersal and disturbances, and regional-scale abiotic controls, to simulate the distribution shifts of four representative tree species with distinct biological traits in the central hardwood forest region of United States. Our results suggested that biological traits (e.g., dispersal capacity, maturation age) were important for determining tree species distribution shifts. Environmental heterogeneity, on average, reduced shift rates by 8% compared to perfect environmental conditions. The average distribution shift rates ranged from 24 to 200myear -1 under climate change scenarios, implying that many tree species may not able to keep up with climate change because of limited dispersal capacity, long generation time, and environmental heterogeneity. We suggest that climate-distribution models should include species demographic processes (e.g., fecundity, dispersal, colonization), biological traits (e.g., dispersal capacity, maturation age), and environmental heterogeneity (e.g., habitat fragmentation) to improve future predictions of species distribution shifts in response to changing climates. Copyright © 2018 Elsevier B.V. All rights reserved.

Integration of environmental simulation models with satellite remote sensing and geographic information systems technologies: case studies

USGS Publications Warehouse

Steyaert, Louis T.; Loveland, Thomas R.; Brown, Jesslyn F.; Reed, Bradley C.

1993-01-01

Environmental modelers are testing and evaluating a prototype land cover characteristics database for the conterminous United States developed by the EROS Data Center of the U.S. Geological Survey and the University of Nebraska Center for Advanced Land Management Information Technologies. This database was developed from multi temporal, 1-kilometer advanced very high resolution radiometer (AVHRR) data for 1990 and various ancillary data sets such as elevation, ecological regions, and selected climatic normals. Several case studies using this database were analyzed to illustrate the integration of satellite remote sensing and geographic information systems technologies with land-atmosphere interactions models at a variety of spatial and temporal scales. The case studies are representative of contemporary environmental simulation modeling at local to regional levels in global change research, land and water resource management, and environmental simulation modeling at local to regional levels in global change research, land and water resource management and environmental risk assessment. The case studies feature land surface parameterizations for atmospheric mesoscale and global climate models; biogenic-hydrocarbons emissions models; distributed parameter watershed and other hydrological models; and various ecological models such as ecosystem, dynamics, biogeochemical cycles, ecotone variability, and equilibrium vegetation models. The case studies demonstrate the important of multi temporal AVHRR data to develop to develop and maintain a flexible, near-realtime land cover characteristics database. Moreover, such a flexible database is needed to derive various vegetation classification schemes, to aggregate data for nested models, to develop remote sensing algorithms, and to provide data on dynamic landscape characteristics. The case studies illustrate how such a database supports research on spatial heterogeneity, land use, sensitivity analysis, and scaling issues involving regional extrapolations and parameterizations of dynamic land processes within simulation models.

Spatial variation of volcanic rock geochemistry in the Virunga Volcanic Province: Statistical analysis of an integrated database

NASA Astrophysics Data System (ADS)

Barette, Florian; Poppe, Sam; Smets, Benoît; Benbakkar, Mhammed; Kervyn, Matthieu

2017-10-01

We present an integrated, spatially-explicit database of existing geochemical major-element analyses available from (post-) colonial scientific reports, PhD Theses and international publications for the Virunga Volcanic Province, located in the western branch of the East African Rift System. This volcanic province is characterised by alkaline volcanism, including silica-undersaturated, alkaline and potassic lavas. The database contains a total of 908 geochemical analyses of eruptive rocks for the entire volcanic province with a localisation for most samples. A preliminary analysis of the overall consistency of the database, using statistical techniques on sets of geochemical analyses with contrasted analytical methods or dates, demonstrates that the database is consistent. We applied a principal component analysis and cluster analysis on whole-rock major element compositions included in the database to study the spatial variation of the chemical composition of eruptive products in the Virunga Volcanic Province. These statistical analyses identify spatially distributed clusters of eruptive products. The known geochemical contrasts are highlighted by the spatial analysis, such as the unique geochemical signature of Nyiragongo lavas compared to other Virunga lavas, the geochemical heterogeneity of the Bulengo area, and the trachyte flows of Karisimbi volcano. Most importantly, we identified separate clusters of eruptive products which originate from primitive magmatic sources. These lavas of primitive composition are preferentially located along NE-SW inherited rift structures, often at distance from the central Virunga volcanoes. Our results illustrate the relevance of a spatial analysis on integrated geochemical data for a volcanic province, as a complement to classical petrological investigations. This approach indeed helps to characterise geochemical variations within a complex of magmatic systems and to identify specific petrologic and geochemical investigations that should be tackled within a study area.

Population and forensic genetic analyses of mitochondrial DNA control region variation from six major provinces in the Korean population.

PubMed

Hong, Seung Beom; Kim, Ki Cheol; Kim, Wook

2015-07-01

We generated complete mitochondrial DNA (mtDNA) control region sequences from 704 unrelated individuals residing in six major provinces in Korea. In addition to our earlier survey of the distribution of mtDNA haplogroup variation, a total of 560 different haplotypes characterized by 271 polymorphic sites were identified, of which 473 haplotypes were unique. The gene diversity and random match probability were 0.9989 and 0.0025, respectively. According to the pairwise comparison of the 704 control region sequences, the mean number of pairwise differences between individuals was 13.47±6.06. Based on the result of mtDNA control region sequences, pairwise FST genetic distances revealed genetic homogeneity of the Korean provinces on a peninsular level, except in samples from Jeju Island. This result indicates there may be a need to formulate a local mtDNA database for Jeju Island, to avoid bias in forensic parameter estimates caused by genetic heterogeneity of the population. Thus, the present data may help not only in personal identification but also in determining maternal lineages to provide an expanded and reliable Korean mtDNA database. These data will be available on the EMPOP database via accession number EMP00661. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Building a generalized distributed system model

NASA Technical Reports Server (NTRS)

Mukkamala, Ravi

1991-01-01

A number of topics related to building a generalized distributed system model are discussed. The effects of distributed database modeling on evaluation of transaction rollbacks, the measurement of effects of distributed database models on transaction availability measures, and a performance analysis of static locking in replicated distributed database systems are covered.

Availability and temporal heterogeneity of water supply affect the vertical distribution and mortality of a belowground herbivore and consequently plant growth.

PubMed

Tsunoda, Tomonori; Kachi, Naoki; Suzuki, Jun-Ichirou

2014-01-01

We examined how the volume and temporal heterogeneity of water supply changed the vertical distribution and mortality of a belowground herbivore, and consequently affected plant biomass. Plantago lanceolata (Plantaginaceae) seedlings were grown at one per pot under different combinations of water volume (large or small volume) and heterogeneity (homogeneous water conditions, watered every day; heterogeneous conditions, watered every 4 days) in the presence or absence of a larva of the belowground herbivorous insect, Anomala cuprea (Coleoptera: Scarabaeidae). The larva was confined in different vertical distributions to top feeding zone (top treatment), middle feeding zone (middle treatment), or bottom feeding zone (bottom treatment); alternatively no larva was introduced (control treatment) or larval movement was not confined (free treatment). Three-way interaction between water volume, heterogeneity, and the herbivore significantly affected plant biomass. With a large water volume, plant biomass was lower in free treatment than in control treatment regardless of heterogeneity. Plant biomass in free treatment was as low as in top treatment. With a small water volume and in free treatment, plant biomass was low (similar to that under top treatment) under homogeneous water conditions but high under heterogeneous ones (similar to that under middle or bottom treatment). Therefore, there was little effect of belowground herbivory on plant growth under heterogeneous water conditions. In other watering regimes, herbivores would be distributed in the shallow soil and reduced root biomass. Herbivore mortality was high with homogeneous application of a large volume or heterogeneous application of a small water volume. Under the large water volume, plant biomass was high in pots in which the herbivore had died. Thus, the combinations of water volume and heterogeneity affected plant growth via the change of a belowground herbivore.

Distributional assumptions in food and feed commodities- development of fit-for-purpose sampling protocols.

PubMed

Paoletti, Claudia; Esbensen, Kim H

2015-01-01

Material heterogeneity influences the effectiveness of sampling procedures. Most sampling guidelines used for assessment of food and/or feed commodities are based on classical statistical distribution requirements, the normal, binomial, and Poisson distributions-and almost universally rely on the assumption of randomness. However, this is unrealistic. The scientific food and feed community recognizes a strong preponderance of non random distribution within commodity lots, which should be a more realistic prerequisite for definition of effective sampling protocols. Nevertheless, these heterogeneity issues are overlooked as the prime focus is often placed only on financial, time, equipment, and personnel constraints instead of mandating acquisition of documented representative samples under realistic heterogeneity conditions. This study shows how the principles promulgated in the Theory of Sampling (TOS) and practically tested over 60 years provide an effective framework for dealing with the complete set of adverse aspects of both compositional and distributional heterogeneity (material sampling errors), as well as with the errors incurred by the sampling process itself. The results of an empirical European Union study on genetically modified soybean heterogeneity, Kernel Lot Distribution Assessment are summarized, as they have a strong bearing on the issue of proper sampling protocol development. TOS principles apply universally in the food and feed realm and must therefore be considered the only basis for development of valid sampling protocols free from distributional constraints.

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

PubMed

Legehar, Ashenafi; Xhaard, Henri; Ghemtio, Leo

2016-01-01

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

Trauma facilities in Denmark - a nationwide cross-sectional benchmark study of facilities and trauma care organisation.

PubMed

Weile, Jesper; Nielsen, Klaus; Primdahl, Stine C; Frederiksen, Christian A; Laursen, Christian B; Sloth, Erik; Mølgaard, Ole; Knudsen, Lars; Kirkegaard, Hans

2018-03-27

Trauma is a leading cause of death among adults aged < 44 years, and optimal care is a challenge. Evidence supports the centralization of trauma facilities and the use multidisciplinary trauma teams. Because knowledge is sparse on the existing distribution of trauma facilities and the organisation of trauma care in Denmark, the aim of this study was to identify all Danish facilities that care for traumatized patients and to investigate the diversity in organization of trauma management. We conducted a systematic observational cross-sectional study. First, all hospitals in Denmark were identified via online services and clarifying phone calls to each facility. Second, all trauma care manuals on all facilities that receive traumatized patients were gathered. Third, anesthesiologists and orthopedic surgeons on call at all trauma facilities were contacted via telephone for structured interviews. A total of 22 facilities in Denmark were found to receive traumatized patients. All facilities used a trauma care manual and all had a multidisciplinary trauma team. The study found three different trauma team activation criteria and nine different compositions of teams who participate in trauma care. Training was heterogeneous and, beyond the major trauma centers, databases were only maintained in a few facilities. The study established an inventory of the existing Danish facilities that receive traumatized patients. The trauma team activation criteria and the trauma teams were heterogeneous in both size and composition. A national database for traumatized patients, research on nationwide trauma team activation criteria, and team composition guidelines are all called for.

Airborne Spectral BRDF of Various Surface Types (Ocean, Vegetation, Snow, Desert, Wetlands, Cloud Decks, Smoke Layers) for Remote Sensing Applications

NASA Technical Reports Server (NTRS)

Gatebe, Charles K.; King, Michael D.

2016-01-01

In this paper we describe measurements of the bidirectional reflectance-distribution function (BRDF) acquired over a 30-year period (1984-2014) by the National Aeronautics and Space Administration's (NASA's) Cloud Absorption Radiometer (CAR). Our BRDF database encompasses various natural surfaces that are representative of many land cover or ecosystem types found throughout the world. CAR's unique measurement geometry allows a comparison of measurements acquired from different satellite instruments with various geometrical configurations, none of which are capable of obtaining such a complete and nearly instantaneous BRDF. This database is therefore of great value in validating many satellite sensors and assessing corrections of reflectances for angular effects. These data can also be used to evaluate the ability of analytical models to reproduce the observed directional signatures, to develop BRDF models that are suitable for sub-kilometer-scale satellite observations over both homogeneous and heterogeneous landscape types, and to test future spaceborne sensors. All of these BRDF data are publicly available and accessible in hierarchical data format (http:car.gsfc.nasa.gov/).

Stochastical analysis of surfactant-enhanced remediation of denser-than-water nonaqueous phase liquid (DNAPL)-contaminated soils.

PubMed

Zhang, Renduo; Wood, A Lynn; Enfield, Carl G; Jeong, Seung-Woo

2003-01-01

Stochastical analysis was performed to assess the effect of soil spatial variability and heterogeneity on the recovery of denser-than-water nonaqueous phase liquids (DNAPL) during the process of surfactant-enhanced remediation. UTCHEM, a three-dimensional, multicomponent, multiphase, compositional model, was used to simulate water flow and chemical transport processes in heterogeneous soils. Soil spatial variability and heterogeneity were accounted for by considering the soil permeability as a spatial random variable and a geostatistical method was used to generate random distributions of the permeability. The randomly generated permeability fields were incorporated into UTCHEM to simulate DNAPL transport in heterogeneous media and stochastical analysis was conducted based on the simulated results. From the analysis, an exponential relationship between average DNAPL recovery and soil heterogeneity (defined as the standard deviation of log of permeability) was established with a coefficient of determination (r2) of 0.991, which indicated that DNAPL recovery decreased exponentially with increasing soil heterogeneity. Temporal and spatial distributions of relative saturations in the water phase, DNAPL, and microemulsion in heterogeneous soils were compared with those in homogeneous soils and related to soil heterogeneity. Cleanup time and uncertainty to determine DNAPL distributions in heterogeneous soils were also quantified. The study would provide useful information to design strategies for the characterization and remediation of nonaqueous phase liquid-contaminated soils with spatial variability and heterogeneity.

What Information Does Your EHR Contain? Automatic Generation of a Clinical Metadata Warehouse (CMDW) to Support Identification and Data Access Within Distributed Clinical Research Networks.

PubMed

Bruland, Philipp; Doods, Justin; Storck, Michael; Dugas, Martin

2017-01-01

Data dictionaries provide structural meta-information about data definitions in health information technology (HIT) systems. In this regard, reusing healthcare data for secondary purposes offers several advantages (e.g. reduce documentation times or increased data quality). Prerequisites for data reuse are its quality, availability and identical meaning of data. In diverse projects, research data warehouses serve as core components between heterogeneous clinical databases and various research applications. Given the complexity (high number of data elements) and dynamics (regular updates) of electronic health record (EHR) data structures, we propose a clinical metadata warehouse (CMDW) based on a metadata registry standard. Metadata of two large hospitals were automatically inserted into two CMDWs containing 16,230 forms and 310,519 data elements. Automatic updates of metadata are possible as well as semantic annotations. A CMDW allows metadata discovery, data quality assessment and similarity analyses. Common data models for distributed research networks can be established based on similarity analyses.

The relationship between RASSF1A promoter methylation and thyroid carcinoma: A meta-analysis of 14 articles and a bioinformatics of 2 databases (PRISMA).

PubMed

Niu, Heng; Yang, Jingyu; Yang, Kunxian; Huang, Yingze

2017-11-01

DNA promoter methylation can suppresses gene expression and shows an important role in the biological functions of Ras association domain family 1A (RASSF1A). Many studies have performed to elucidate the role of RASSF1A promoter methylation in thyroid carcinoma, while the results were conflicting and heterogeneous. Here, we analyzed the data of databases to determine the relationship between RASSF1A promoter methylation and thyroid carcinoma. We used the data from 14 cancer-normal studies and Gene Expression Omnibus (GEO) database to analyze RASSF1A promoter methylation in thyroid carcinoma susceptibility. The data from the Cancer Genome Atlas project (TCGA) database was used to analyze the relationship between RASSF1A promoter methylation and thyroid carcinoma susceptibility, clinical characteristics, prognosis. Odds ratios were estimated for thyroid carcinoma susceptibility and hazard ratios were estimated for thyroid carcinoma prognosis. The heterogeneity between studies of meta-analysis was explored using H, I values, and meta-regression. We adopted quality criteria to classify the studies of meta-analysis. Subgroup analyses were done for thyroid carcinoma susceptibility according to ethnicity, methods, and primers. Result of meta-analysis indicated that RASSF1A promoter methylation is associated with higher susceptibility to thyroid carcinoma with small heterogeneity. Similarly, the result from GEO database also showed that a significant association between RASSF1A gene promoter methylation and thyroid carcinoma susceptibility. For the results of TCGA database, we found that RASSF1A promoter methylation is associated with susceptibility and poor disease-free survival (DFS) of thyroid carcinoma. In addition, we also found a close association between RASSF1A promoter methylation and patient tumor stage and age, but not in patients of different genders. The methylation status of RASSF1A promoter is strongly associated with thyroid carcinoma susceptibility and DFS. The RASSF1A promoter methylation test can be applied in the clinical diagnosis of thyroid carcinoma.

Heterogeneity of D-Serine Distribution in the Human Central Nervous System

PubMed Central

Suzuki, Masataka; Imanishi, Nobuaki; Mita, Masashi; Hamase, Kenji; Aiso, Sadakazu; Sasabe, Jumpei

2017-01-01

D-serine is an endogenous ligand for N-methyl-D-aspartate glutamate receptors. Accumulating evidence including genetic associations of D-serine metabolism with neurological or psychiatric diseases suggest that D-serine is crucial in human neurophysiology. However, distribution and regulation of D-serine in humans are not well understood. Here, we found that D-serine is heterogeneously distributed in the human central nervous system (CNS). The cerebrum contains the highest level of D-serine among the areas in the CNS. There is heterogeneity in its distribution in the cerebrum and even within the cerebral neocortex. The neocortical heterogeneity is associated with Brodmann or functional areas but is unrelated to basic patterns of cortical layer structure or regional expressional variation of metabolic enzymes for D-serine. Such D-serine distribution may reflect functional diversity of glutamatergic neurons in the human CNS, which may serve as a basis for clinical and pharmacological studies on D-serine modulation. PMID:28604057

Interdisciplinary Collaboration amongst Colleagues and between Initiatives with the Magnetics Information Consortium (MagIC) Database

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A. A. P.; Jarboe, N.; Tauxe, L.; Constable, C.; Jonestrask, L.; Shaar, R.

2014-12-01

Earth science grand challenges often require interdisciplinary and geographically distributed scientific collaboration to make significant progress. However, this organic collaboration between researchers, educators, and students only flourishes with the reduction or elimination of technological barriers. The Magnetics Information Consortium (http://earthref.org/MagIC/) is a grass-roots cyberinfrastructure effort envisioned by the geo-, paleo-, and rock magnetic scientific community to archive their wealth of peer-reviewed raw data and interpretations from studies on natural and synthetic samples. MagIC is dedicated to facilitating scientific progress towards several highly multidisciplinary grand challenges and the MagIC Database team is currently beta testing a new MagIC Search Interface and API designed to be flexible enough for the incorporation of large heterogeneous datasets and for horizontal scalability to tens of millions of records and hundreds of requests per second. In an effort to reduce the barriers to effective collaboration, the search interface includes a simplified data model and upload procedure, support for online editing of datasets amongst team members, commenting by reviewers and colleagues, and automated contribution workflows and data retrieval through the API. This web application has been designed to generalize to other databases in MagIC's umbrella website (EarthRef.org) so the Geochemical Earth Reference Model (http://earthref.org/GERM/) portal, Seamount Biogeosciences Network (http://earthref.org/SBN/), EarthRef Digital Archive (http://earthref.org/ERDA/) and EarthRef Reference Database (http://earthref.org/ERR/) will benefit from its development.

LAILAPS: the plant science search engine.

PubMed

Esch, Maria; Chen, Jinbo; Colmsee, Christian; Klapperstück, Matthias; Grafahrend-Belau, Eva; Scholz, Uwe; Lange, Matthias

2015-01-01

With the number of sequenced plant genomes growing, the number of predicted genes and functional annotations is also increasing. The association between genes and phenotypic traits is currently of great interest. Unfortunately, the information available today is widely scattered over a number of different databases. Information retrieval (IR) has become an all-encompassing bioinformatics methodology for extracting knowledge from complex, heterogeneous and distributed databases, and therefore can be a useful tool for obtaining a comprehensive view of plant genomics, from genes to traits. Here we describe LAILAPS (http://lailaps.ipk-gatersleben.de), an IR system designed to link plant genomic data in the context of phenotypic attributes for a detailed forward genetic research. LAILAPS comprises around 65 million indexed documents, encompassing >13 major life science databases with around 80 million links to plant genomic resources. The LAILAPS search engine allows fuzzy querying for candidate genes linked to specific traits over a loosely integrated system of indexed and interlinked genome databases. Query assistance and an evidence-based annotation system enable time-efficient and comprehensive information retrieval. An artificial neural network incorporating user feedback and behavior tracking allows relevance sorting of results. We fully describe LAILAPS's functionality and capabilities by comparing this system's performance with other widely used systems and by reporting both a validation in maize and a knowledge discovery use-case focusing on candidate genes in barley. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

An approach for heterogeneous and loosely coupled geospatial data distributed computing

NASA Astrophysics Data System (ADS)

Chen, Bin; Huang, Fengru; Fang, Yu; Huang, Zhou; Lin, Hui

2010-07-01

Most GIS (Geographic Information System) applications tend to have heterogeneous and autonomous geospatial information resources, and the availability of these local resources is unpredictable and dynamic under a distributed computing environment. In order to make use of these local resources together to solve larger geospatial information processing problems that are related to an overall situation, in this paper, with the support of peer-to-peer computing technologies, we propose a geospatial data distributed computing mechanism that involves loosely coupled geospatial resource directories and a term named as Equivalent Distributed Program of global geospatial queries to solve geospatial distributed computing problems under heterogeneous GIS environments. First, a geospatial query process schema for distributed computing as well as a method for equivalent transformation from a global geospatial query to distributed local queries at SQL (Structured Query Language) level to solve the coordinating problem among heterogeneous resources are presented. Second, peer-to-peer technologies are used to maintain a loosely coupled network environment that consists of autonomous geospatial information resources, thus to achieve decentralized and consistent synchronization among global geospatial resource directories, and to carry out distributed transaction management of local queries. Finally, based on the developed prototype system, example applications of simple and complex geospatial data distributed queries are presented to illustrate the procedure of global geospatial information processing.

Computer Science Research in Europe.

DTIC Science & Technology

1984-08-29

most attention, multi- database and its structure, and (3) the dependencies between databases Distributed Systems and multi- databases . Having...completed a multi- database Newcastle University, UK system for distributed data management, At the University of Newcastle the INRIA is now working on a real...communications re- INRIA quirements of distributed database A project called SIRIUS was estab- systems, protocols for checking the lished in 1977 at the

BIOZON: a system for unification, management and analysis of heterogeneous biological data.

PubMed

Birkland, Aaron; Yona, Golan

2006-02-15

Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. Here we present a system (Biozon) that addresses these problems, and offers biologists a new knowledge resource to navigate through and explore. Biozon unifies multiple biological databases consisting of a variety of data types (such as DNA sequences, proteins, interactions and cellular pathways). It is fundamentally different from previous efforts as it uses a single extensive and tightly connected graph schema wrapped with hierarchical ontology of documents and relations. Beyond warehousing existing data, Biozon computes and stores novel derived data, such as similarity relationships and functional predictions. The integration of similarity data allows propagation of knowledge through inference and fuzzy searches. Sophisticated methods of query that span multiple data types were implemented and first-of-a-kind biological ranking systems were explored and integrated. The Biozon system is an extensive knowledge resource of heterogeneous biological data. Currently, it holds more than 100 million biological documents and 6.5 billion relations between them. The database is accessible through an advanced web interface that supports complex queries, "fuzzy" searches, data materialization and more, online at http://biozon.org.

Effects of Fiber Type and Size on the Heterogeneity of Oxygen Distribution in Exercising Skeletal Muscle

PubMed Central

Liu, Gang; Mac Gabhann, Feilim; Popel, Aleksander S.

2012-01-01

The process of oxygen delivery from capillary to muscle fiber is essential for a tissue with variable oxygen demand, such as skeletal muscle. Oxygen distribution in exercising skeletal muscle is regulated by convective oxygen transport in the blood vessels, oxygen diffusion and consumption in the tissue. Spatial heterogeneities in oxygen supply, such as microvascular architecture and hemodynamic variables, had been observed experimentally and their marked effects on oxygen exchange had been confirmed using mathematical models. In this study, we investigate the effects of heterogeneities in oxygen demand on tissue oxygenation distribution using a multiscale oxygen transport model. Muscles are composed of different ratios of the various fiber types. Each fiber type has characteristic values of several parameters, including fiber size, oxygen consumption, myoglobin concentration, and oxygen diffusivity. Using experimentally measured parameters for different fiber types and applying them to the rat extensor digitorum longus muscle, we evaluated the effects of heterogeneous fiber size and fiber type properties on the oxygen distribution profile. Our simulation results suggest a marked increase in spatial heterogeneity of oxygen due to fiber size distribution in a mixed muscle. Our simulations also suggest that the combined effects of fiber type properties, except size, do not contribute significantly to the tissue oxygen spatial heterogeneity. However, the incorporation of the difference in oxygen consumption rates of different fiber types alone causes higher oxygen heterogeneity compared to control cases with uniform fiber properties. In contrast, incorporating variation in other fiber type-specific properties, such as myoglobin concentration, causes little change in spatial tissue oxygenation profiles. PMID:23028531

Monte Carlo Estimation of Absorbed Dose Distributions Obtained from Heterogeneous 106Ru Eye Plaques.

PubMed

Zaragoza, Francisco J; Eichmann, Marion; Flühs, Dirk; Sauerwein, Wolfgang; Brualla, Lorenzo

2017-09-01

The distribution of the emitter substance in 106 Ru eye plaques is usually assumed to be homogeneous for treatment planning purposes. However, this distribution is never homogeneous, and it widely differs from plaque to plaque due to manufacturing factors. By Monte Carlo simulation of radiation transport, we study the absorbed dose distribution obtained from the specific CCA1364 and CCB1256 106 Ru plaques, whose actual emitter distributions were measured. The idealized, homogeneous CCA and CCB plaques are also simulated. The largest discrepancy in depth dose distribution observed between the heterogeneous and the homogeneous plaques was 7.9 and 23.7% for the CCA and CCB plaques, respectively. In terms of isodose lines, the line referring to 100% of the reference dose penetrates 0.2 and 1.8 mm deeper in the case of heterogeneous CCA and CCB plaques, respectively, with respect to the homogeneous counterpart. The observed differences in absorbed dose distributions obtained from heterogeneous and homogeneous plaques are clinically irrelevant if the plaques are used with a lateral safety margin of at least 2 mm. However, these differences may be relevant if the plaques are used in eccentric positioning.

Chemical and seismological constraints on mantle heterogeneity.

PubMed

Helffrich, George

2002-11-15

Recent seismological studies that use scattered waves to detect heterogeneities in the mantle reveal the presence of a small, distributed elastic heterogeneity in the lower mantle which does not appear to be thermal in nature. The characteristic size of these heterogeneities appears to be ca. 8 km, suggesting that they represent subducted recycled oceanic crust. With this stimulus, old ideas that the mantle is heterogeneous in structure, rather than stratified, are reinterpreted and a simple, end-member model for the heterogeneity structure is proposed. The volumetrically largest components in the model are recycled oceanic crust, which contains the heat-producing elements, and mantle depleted of these and other incompatible trace elements. About 10% of the mantle's mass is made up of recycled oceanic crust, which is associated with the observed small-scale seismic heterogeneity. The way this heterogeneity is distributed is in convectively stretched and thinned bodies ranging downwards in size from 8 km. With the present techniques to detect small bodies through scattering, only ca. 55% of the mantle's small-scale heterogeneities are detectable seismically.

Distribution Grid Integration Unit Cost Database | Solar Research | NREL

Science.gov Websites

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

A semantic data dictionary method for database schema integration in CIESIN

NASA Astrophysics Data System (ADS)

Hinds, N.; Huang, Y.; Ravishankar, C.

1993-08-01

CIESIN (Consortium for International Earth Science Information Network) is funded by NASA to investigate the technology necessary to integrate and facilitate the interdisciplinary use of Global Change information. A clear of this mission includes providing a link between the various global change data sets, in particular the physical sciences and the human (social) sciences. The typical scientist using the CIESIN system will want to know how phenomena in an outside field affects his/her work. For example, a medical researcher might ask: how does air-quality effect emphysema? This and many similar questions will require sophisticated semantic data integration. The researcher who raised the question may be familiar with medical data sets containing emphysema occurrences. But this same investigator may know little, if anything, about the existance or location of air-quality data. It is easy to envision a system which would allow that investigator to locate and perform a ``join'' on two data sets, one containing emphysema cases and the other containing air-quality levels. No such system exists today. One major obstacle to providing such a system will be overcoming the heterogeneity which falls into two broad categories. ``Database system'' heterogeneity involves differences in data models and packages. ``Data semantic'' heterogeneity involves differences in terminology between disciplines which translates into data semantic issues, and varying levels of data refinement, from raw to summary. Our work investigates a global data dictionary mechanism to facilitate a merged data service. Specially, we propose using a semantic tree during schema definition to aid in locating and integrating heterogeneous databases.

Constructing compact and effective graphs for recommender systems via node and edge aggregations

DOE PAGES

Lee, Sangkeun; Kahng, Minsuk; Lee, Sang-goo

2014-12-10

Exploiting graphs for recommender systems has great potential to flexibly incorporate heterogeneous information for producing better recommendation results. As our baseline approach, we first introduce a naive graph-based recommendation method, which operates with a heterogeneous log-metadata graph constructed from user log and content metadata databases. Although the na ve graph-based recommendation method is simple, it allows us to take advantages of heterogeneous information and shows promising flexibility and recommendation accuracy. However, it often leads to extensive processing time due to the sheer size of the graphs constructed from entire user log and content metadata databases. In this paper, we proposemore » node and edge aggregation approaches to constructing compact and e ective graphs called Factor-Item bipartite graphs by aggregating nodes and edges of a log-metadata graph. Furthermore, experimental results using real world datasets indicate that our approach can significantly reduce the size of graphs exploited for recommender systems without sacrificing the recommendation quality.« less

Semantic mediation in the national geologic map database (US)

USGS Publications Warehouse

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

2008-01-01

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

Development of a One-Stop Data Search and Discovery Engine using Ontologies for Semantic Mappings (HydroSeek)

NASA Astrophysics Data System (ADS)

Piasecki, M.; Beran, B.

2007-12-01

Search engines have changed the way we see the Internet. The ability to find the information by just typing in keywords was a big contribution to the overall web experience. While the conventional search engine methodology worked well for textual documents, locating scientific data remains a problem since they are stored in databases not readily accessible by search engine bots. Considering different temporal, spatial and thematic coverage of different databases, especially for interdisciplinary research it is typically necessary to work with multiple data sources. These sources can be federal agencies which generally offer national coverage or regional sources which cover a smaller area with higher detail. However for a given geographic area of interest there often exists more than one database with relevant data. Thus being able to query multiple databases simultaneously is a desirable feature that would be tremendously useful for scientists. Development of such a search engine requires dealing with various heterogeneity issues. In scientific databases, systems often impose controlled vocabularies which ensure that they are generally homogeneous within themselves but are semantically heterogeneous when moving between different databases. This defines the boundaries of possible semantic related problems making it easier to solve than with the conventional search engines that deal with free text. We have developed a search engine that enables querying multiple data sources simultaneously and returns data in a standardized output despite the aforementioned heterogeneity issues between the underlying systems. This application relies mainly on metadata catalogs or indexing databases, ontologies and webservices with virtual globe and AJAX technologies for the graphical user interface. Users can trigger a search of dozens of different parameters over hundreds of thousands of stations from multiple agencies by providing a keyword, a spatial extent, i.e. a bounding box, and a temporal bracket. As part of this development we have also added an environment that allows users to do some of the semantic tagging, i.e. the linkage of a variable name (which can be anything they desire) to defined concepts in the ontology structure which in turn provides the backbone of the search engine.

Heterogeneous Distribution of Chromium on Mercury

NASA Astrophysics Data System (ADS)

Nittler, L. R.; Boujibar, A.; Crapster-Pregont, E.; Frank, E. A.; McCoy, T. J.; McCubbin, F. M.; Starr, R. D.; Vander Kaaden, K. E.; Vorburger, A.; Weider, S. Z.

2018-05-01

Mercury's surface has an average Cr/Si ratio of 0.003 (Cr 800 ppm), with at least a factor of 2 systematic uncertainty. Cr is heterogeneously distributed and correlated with Mg, Ca, S, and Fe and anti-correlated with Al.

A Support Database System for Integrated System Health Management (ISHM)

NASA Technical Reports Server (NTRS)

Schmalzel, John; Figueroa, Jorge F.; Turowski, Mark; Morris, John

2007-01-01

The development, deployment, operation and maintenance of Integrated Systems Health Management (ISHM) applications require the storage and processing of tremendous amounts of low-level data. This data must be shared in a secure and cost-effective manner between developers, and processed within several heterogeneous architectures. Modern database technology allows this data to be organized efficiently, while ensuring the integrity and security of the data. The extensibility and interoperability of the current database technologies also allows for the creation of an associated support database system. A support database system provides additional capabilities by building applications on top of the database structure. These applications can then be used to support the various technologies in an ISHM architecture. This presentation and paper propose a detailed structure and application description for a support database system, called the Health Assessment Database System (HADS). The HADS provides a shared context for organizing and distributing data as well as a definition of the applications that provide the required data-driven support to ISHM. This approach provides another powerful tool for ISHM developers, while also enabling novel functionality. This functionality includes: automated firmware updating and deployment, algorithm development assistance and electronic datasheet generation. The architecture for the HADS has been developed as part of the ISHM toolset at Stennis Space Center for rocket engine testing. A detailed implementation has begun for the Methane Thruster Testbed Project (MTTP) in order to assist in developing health assessment and anomaly detection algorithms for ISHM. The structure of this implementation is shown in Figure 1. The database structure consists of three primary components: the system hierarchy model, the historical data archive and the firmware codebase. The system hierarchy model replicates the physical relationships between system elements to provide the logical context for the database. The historical data archive provides a common repository for sensor data that can be shared between developers and applications. The firmware codebase is used by the developer to organize the intelligent element firmware into atomic units which can be assembled into complete firmware for specific elements.

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

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1992-01-01

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

Biomedical data integration in computational drug design and bioinformatics.

PubMed

Seoane, Jose A; Aguiar-Pulido, Vanessa; Munteanu, Cristian R; Rivero, Daniel; Rabunal, Juan R; Dorado, Julian; Pazos, Alejandro

2013-03-01

In recent years, in the post genomic era, more and more data is being generated by biological high throughput technologies, such as proteomics and transcriptomics. This omics data can be very useful, but the real challenge is to analyze all this data, as a whole, after integrating it. Biomedical data integration enables making queries to different, heterogeneous and distributed biomedical data sources. Data integration solutions can be very useful not only in the context of drug design, but also in biomedical information retrieval, clinical diagnosis, system biology, etc. In this review, we analyze the most common approaches to biomedical data integration, such as federated databases, data warehousing, multi-agent systems and semantic technology, as well as the solutions developed using these approaches in the past few years.

Improving healthcare services using web based platform for management of medical case studies.

PubMed

Ogescu, Cristina; Plaisanu, Claudiu; Udrescu, Florian; Dumitru, Silviu

2008-01-01

The paper presents a web based platform for management of medical cases, support for healthcare specialists in taking the best clinical decision. Research has been oriented mostly on multimedia data management, classification algorithms for querying, retrieving and processing different medical data types (text and images). The medical case studies can be accessed by healthcare specialists and by students as anonymous case studies providing trust and confidentiality in Internet virtual environment. The MIDAS platform develops an intelligent framework to manage sets of medical data (text, static or dynamic images), in order to optimize the diagnosis and the decision process, which will reduce the medical errors and will increase the quality of medical act. MIDAS is an integrated project working on medical information retrieval from heterogeneous, distributed medical multimedia database.

Graph Partitioning for Parallel Applications in Heterogeneous Grid Environments

NASA Technical Reports Server (NTRS)

Bisws, Rupak; Kumar, Shailendra; Das, Sajal K.; Biegel, Bryan (Technical Monitor)

2002-01-01

The problem of partitioning irregular graphs and meshes for parallel computations on homogeneous systems has been extensively studied. However, these partitioning schemes fail when the target system architecture exhibits heterogeneity in resource characteristics. With the emergence of technologies such as the Grid, it is imperative to study the partitioning problem taking into consideration the differing capabilities of such distributed heterogeneous systems. In our model, the heterogeneous system consists of processors with varying processing power and an underlying non-uniform communication network. We present in this paper a novel multilevel partitioning scheme for irregular graphs and meshes, that takes into account issues pertinent to Grid computing environments. Our partitioning algorithm, called MiniMax, generates and maps partitions onto a heterogeneous system with the objective of minimizing the maximum execution time of the parallel distributed application. For experimental performance study, we have considered both a realistic mesh problem from NASA as well as synthetic workloads. Simulation results demonstrate that MiniMax generates high quality partitions for various classes of applications targeted for parallel execution in a distributed heterogeneous environment.

Big Geo Data Management: AN Exploration with Social Media and Telecommunications Open Data

NASA Astrophysics Data System (ADS)

Arias Munoz, C.; Brovelli, M. A.; Corti, S.; Zamboni, G.

2016-06-01

The term Big Data has been recently used to define big, highly varied, complex data sets, which are created and updated at a high speed and require faster processing, namely, a reduced time to filter and analyse relevant data. These data is also increasingly becoming Open Data (data that can be freely distributed) made public by the government, agencies, private enterprises and among others. There are at least two issues that can obstruct the availability and use of Open Big Datasets: Firstly, the gathering and geoprocessing of these datasets are very computationally intensive; hence, it is necessary to integrate high-performance solutions, preferably internet based, to achieve the goals. Secondly, the problems of heterogeneity and inconsistency in geospatial data are well known and affect the data integration process, but is particularly problematic for Big Geo Data. Therefore, Big Geo Data integration will be one of the most challenging issues to solve. With these applications, we demonstrate that is possible to provide processed Big Geo Data to common users, using open geospatial standards and technologies. NoSQL databases like MongoDB and frameworks like RASDAMAN could offer different functionalities that facilitate working with larger volumes and more heterogeneous geospatial data sources.

SU-E-T-626: Accuracy of Dose Calculation Algorithms in MultiPlan Treatment Planning System in Presence of Heterogeneities

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

Moignier, C; Huet, C; Barraux, V

Purpose: Advanced stereotactic radiotherapy (SRT) treatments require accurate dose calculation for treatment planning especially for treatment sites involving heterogeneous patient anatomy. The purpose of this study was to evaluate the accuracy of dose calculation algorithms, Raytracing and Monte Carlo (MC), implemented in the MultiPlan treatment planning system (TPS) in presence of heterogeneities. Methods: First, the LINAC of a CyberKnife radiotherapy facility was modeled with the PENELOPE MC code. A protocol for the measurement of dose distributions with EBT3 films was established and validated thanks to comparison between experimental dose distributions and calculated dose distributions obtained with MultiPlan Raytracing and MCmore » algorithms as well as with the PENELOPE MC model for treatments planned with the homogenous Easycube phantom. Finally, bones and lungs inserts were used to set up a heterogeneous Easycube phantom. Treatment plans with the 10, 7.5 or the 5 mm field sizes were generated in Multiplan TPS with different tumor localizations (in the lung and at the lung/bone/soft tissue interface). Experimental dose distributions were compared to the PENELOPE MC and Multiplan calculations using the gamma index method. Results: Regarding the experiment in the homogenous phantom, 100% of the points passed for the 3%/3mm tolerance criteria. These criteria include the global error of the method (CT-scan resolution, EBT3 dosimetry, LINAC positionning …), and were used afterwards to estimate the accuracy of the MultiPlan algorithms in heterogeneous media. Comparison of the dose distributions obtained in the heterogeneous phantom is in progress. Conclusion: This work has led to the development of numerical and experimental dosimetric tools for small beam dosimetry. Raytracing and MC algorithms implemented in MultiPlan TPS were evaluated in heterogeneous media.« less

Impacts of Streambed Heterogeneity and Anisotropy on Residence Time of Hyporheic Zone.

PubMed

Liu, Suning; Chui, Ting Fong May

2018-05-01

The hyporheic zone (HZ), which is the region beneath or alongside a streambed, plays an important role in the stream's ecology. The duration that a water molecule or a solute remains within the HZ, or residence time (RT), is one of the most common metrics used to evaluate the function of the HZ. The RT is greatly influenced by the streambed's hydraulic conductivity (K), which is intrinsically difficult to characterize due to its heterogeneity and anisotropy. Many laboratory and numerical studies of the HZ have simplified the streambed K to a constant, thus producing RT values that may differ from those gathered from the field. Some studies have considered the heterogeneity of the HZ, but very few have accounted for anisotropy or the natural K distributions typically found in real streambeds. This study developed numerical models in MODFLOW to examine the influence of heterogeneity and anisotropy, and that of the natural K distribution in a streambed, on the RT of the HZ. Heterogeneity and anisotropy were both found to shorten the mean and median RTs while increasing the range of the RTs. Moreover, heterogeneous K fields arranged in a more orderly pattern had longer RTs than those with random K distributions. These results could facilitate the design of streambed K values and distributions to achieve the desired RT during river restoration. They could also assist the translation of results from the more commonly considered homogeneous and/or isotropic conditions into heterogeneous and anisotropic field situations. © 2017, National Ground Water Association.

Iodine nutritional status in Brazil: a meta-analysis of all studies performed in the country pinpoints to an insufficient evaluation and heterogeneity.

PubMed

Campos, Renata de Oliveira; Barreto, Iasmin dos Santos; Maia, Lorena Rejane de Jesus; Rebouças, Sara Cristina Lima; Cerqueira, Taíse Lima de Oliveira; Oliveira, Clotilde Assis; Santos, Carlos Antônio de Souza Teles; Mendes, Carlos Maurício Cardeal; Teixeira, Leonardo Sena Gomes; Ramos, Helton Estrela

2015-02-01

Iodine deficiency disorder (IDD) is the result of an inadequate dietary intake of iodine, which physiological consequences are endemic goiter and thyroid dysfunction. The objective of this study was to a analyze studies that assessed the status of Brazil's population iodine nutrition and IDD prevalence. Systematic review using PRISMA statement. Electronic database: PubMed, Medline, SciELO and Lilacs. Quality of studies: Newcastle-Ottawa Scale. Meta-analysis was carried out with R Core Team Statistical Software, version 3.1.0 (2014). The summary measure (WMD) and its confidence interval (CI) of 95% were calculated. The "Funnel plot" graph assessed publication bias and heterogeneity. Seventeen papers were eligible: pregnant women (2), school children (9), adults/elderly (4) and preschool children/infants (2). Geographic distribution: North (1), Northeast (1), Midwest (2), Southeast (13), South (3). Twenty-three thousand two hundred seventy-two subjects were evaluated between 1997 and 2013 and all have use urinary iodine (UI) measurement. However, only 7 studies could be included in meta-analysis, all from Southeast region. The overall prevalence of IDD in school children in southeast region was 15.3% (95% CI, 13-35%), however this data had an important heterogeneity, expressed by the I2 Statistic of 99.5%. Only few studies have been performed and enrolled populations from south/southeast region of Brazil. The actual IDD prevalence analysis is complex because it was detected bias due influence of individual studies and very high heterogeneity. IDD might still be high in some areas but this remained unknown even after this meta-analysis evaluation. The generation of a national program for analysis of iodine status in all regions is urgently required.

Use of sinkhole and specific capacity distributions to assess vertical gradients in a karst aquifer

USGS Publications Warehouse

McCoy, K.J.; Kozar, M.D.

2008-01-01

The carbonate-rock aquifer in the Great Valley, West Virginia, USA, was evaluated using a database of 687 sinkholes and 350 specific capacity tests to assess structural, lithologic, and topographic influences on the groundwater flow system. The enhanced permeability of the aquifer is characterized in part by the many sinkholes, springs, and solutionally enlarged fractures throughout the valley. Yet, vertical components of subsurface flow in this highly heterogeneous aquifer are currently not well understood. To address this problem, this study examines the apparent relation between geologic features of the aquifer and two spatial indices of enhanced permeability attributed to aquifer karstification: (1) the distribution of sinkholes and (2) the occurrence of wells with relatively high specific capacity. Statistical results indicate that sinkholes (funnel and collapse) occur primarily along cleavage and bedding planes parallel to subparallel to strike where lateral or downward vertical gradients are highest. Conversely, high specific capacity values are common along prominent joints perpendicular or oblique to strike. The similarity of the latter distribution to that of springs suggests these fractures are areas of upward-convergent flow. These differences between sinkhole and high specific capacity distributions suggest vertical flow components are primarily controlled by the orientation of geologic structure and associated subsurface fracturing. ?? 2007 Springer-Verlag.

UMD-USHbases: a comprehensive set of databases to record and analyse pathogenic mutations and unclassified variants in seven Usher syndrome causing genes.

PubMed

Baux, David; Faugère, Valérie; Larrieu, Lise; Le Guédard-Méreuze, Sandie; Hamroun, Dalil; Béroud, Christophe; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

2008-08-01

Using the Universal Mutation Database (UMD) software, we have constructed "UMD-USHbases", a set of relational databases of nucleotide variations for seven genes involved in Usher syndrome (MYO7A, CDH23, PCDH15, USH1C, USH1G, USH3A and USH2A). Mutations in the Usher syndrome type I causing genes are also recorded in non-syndromic hearing loss cases and mutations in USH2A in non-syndromic retinitis pigmentosa. Usher syndrome provides a particular challenge for molecular diagnostics because of the clinical and molecular heterogeneity. As many mutations are missense changes, and all the genes also contain apparently non-pathogenic polymorphisms, well-curated databases are crucial for accurate interpretation of pathogenicity. Tools are provided to assess the pathogenicity of mutations, including conservation of amino acids and analysis of splice-sites. Reference amino acid alignments are provided. Apparently non-pathogenic variants in patients with Usher syndrome, at both the nucleotide and amino acid level, are included. The UMD-USHbases currently contain more than 2,830 entries including disease causing mutations, unclassified variants or non-pathogenic polymorphisms identified in over 938 patients. In addition to data collected from 89 publications, 15 novel mutations identified in our laboratory are recorded in MYO7A (6), CDH23 (8), or PCDH15 (1) genes. Information is given on the relative involvement of the seven genes, the number and distribution of variants in each gene. UMD-USHbases give access to a software package that provides specific routines and optimized multicriteria research and sorting tools. These databases should assist clinicians and geneticists seeking information about mutations responsible for Usher syndrome.

Impact of mechanical heterogeneity on joint density in a welded ignimbrite

NASA Astrophysics Data System (ADS)

Soden, A. M.; Lunn, R. J.; Shipton, Z. K.

2016-08-01

Joints are conduits for groundwater, hydrocarbons and hydrothermal fluids. Robust fluid flow models rely on accurate characterisation of joint networks, in particular joint density. It is generally assumed that the predominant factor controlling joint density in layered stratigraphy is the thickness of the mechanical layer where the joints occur. Mechanical heterogeneity within the layer is considered a lesser influence on joint formation. We analysed the frequency and distribution of joints within a single 12-m thick ignimbrite layer to identify the controls on joint geometry and distribution. The observed joint distribution is not related to the thickness of the ignimbrite layer. Rather, joint initiation, propagation and termination are controlled by the shape, spatial distribution and mechanical properties of fiamme, which are present within the ignimbrite. The observations and analysis presented here demonstrate that models of joint distribution, particularly in thicker layers, that do not fully account for mechanical heterogeneity are likely to underestimate joint density, the spatial variability of joint distribution and the complex joint geometries that result. Consequently, we recommend that characterisation of a layer's compositional and material properties improves predictions of subsurface joint density in rock layers that are mechanically heterogeneous.

Heterogeneous Data Fusion Method to Estimate Travel Time Distributions in Congested Road Networks

PubMed Central

Lam, William H. K.; Li, Qingquan

2017-01-01

Travel times in congested urban road networks are highly stochastic. Provision of travel time distribution information, including both mean and variance, can be very useful for travelers to make reliable path choice decisions to ensure higher probability of on-time arrival. To this end, a heterogeneous data fusion method is proposed to estimate travel time distributions by fusing heterogeneous data from point and interval detectors. In the proposed method, link travel time distributions are first estimated from point detector observations. The travel time distributions of links without point detectors are imputed based on their spatial correlations with links that have point detectors. The estimated link travel time distributions are then fused with path travel time distributions obtained from the interval detectors using Dempster-Shafer evidence theory. Based on fused path travel time distribution, an optimization technique is further introduced to update link travel time distributions and their spatial correlations. A case study was performed using real-world data from Hong Kong and showed that the proposed method obtained accurate and robust estimations of link and path travel time distributions in congested road networks. PMID:29210978

Heterogeneous Data Fusion Method to Estimate Travel Time Distributions in Congested Road Networks.

PubMed

Shi, Chaoyang; Chen, Bi Yu; Lam, William H K; Li, Qingquan

2017-12-06

Travel times in congested urban road networks are highly stochastic. Provision of travel time distribution information, including both mean and variance, can be very useful for travelers to make reliable path choice decisions to ensure higher probability of on-time arrival. To this end, a heterogeneous data fusion method is proposed to estimate travel time distributions by fusing heterogeneous data from point and interval detectors. In the proposed method, link travel time distributions are first estimated from point detector observations. The travel time distributions of links without point detectors are imputed based on their spatial correlations with links that have point detectors. The estimated link travel time distributions are then fused with path travel time distributions obtained from the interval detectors using Dempster-Shafer evidence theory. Based on fused path travel time distribution, an optimization technique is further introduced to update link travel time distributions and their spatial correlations. A case study was performed using real-world data from Hong Kong and showed that the proposed method obtained accurate and robust estimations of link and path travel time distributions in congested road networks.

Models@Home: distributed computing in bioinformatics using a screensaver based approach.

PubMed

Krieger, Elmar; Vriend, Gert

2002-02-01

Due to the steadily growing computational demands in bioinformatics and related scientific disciplines, one is forced to make optimal use of the available resources. A straightforward solution is to build a network of idle computers and let each of them work on a small piece of a scientific challenge, as done by Seti@Home (http://setiathome.berkeley.edu), the world's largest distributed computing project. We developed a generally applicable distributed computing solution that uses a screensaver system similar to Seti@Home. The software exploits the coarse-grained nature of typical bioinformatics projects. Three major considerations for the design were: (1) often, many different programs are needed, while the time is lacking to parallelize them. Models@Home can run any program in parallel without modifications to the source code; (2) in contrast to the Seti project, bioinformatics applications are normally more sensitive to lost jobs. Models@Home therefore includes stringent control over job scheduling; (3) to allow use in heterogeneous environments, Linux and Windows based workstations can be combined with dedicated PCs to build a homogeneous cluster. We present three practical applications of Models@Home, running the modeling programs WHAT IF and YASARA on 30 PCs: force field parameterization, molecular dynamics docking, and database maintenance.

Evaluating Spatial Heterogeneity and Environmental Variability Inferred from Branched Glycerol Dialkyl Glycerol Tetraethers (GDGTs) Distribution in Soils from Valles Caldera, New Mexic

NASA Astrophysics Data System (ADS)

Contreras Quintana, S. H.; Werne, J. P.; Brown, E. T.; Halbur, J.; Sinninghe Damsté, , J.; Schouten, S.; Correa-Metrio, A.; Fawcett, P. J.

2014-12-01

Branched glycerol dialkyl glycerol tetraethers (GDGTs) are recently discovered bacterial membrane lipids, ubiquitously present in peat bogs and soils, as well as in rivers, lakes and lake sediments. Their distribution appears to be controlled mainly by soil pH and annual mean air temperature (MAT) and they have been increasingly used as paleoclimate proxies in sedimentary records. In order to validate their application as paleoclimate proxies, it is essential evaluate the influence of small scale environmental variability on their distribution. Initial application of the original soil-based branched GDGT distribution proxy to lacustrine sediments from Valles Caldera, New Mexico (NM) was promising, producing a viable temperature record spanning two glacial/interglacial cycles. In this study, we assess the influence of analytical and spatial soil heterogeneity on the concentration and distribution of 9 branched GDGTs in soils from Valles Caldera, and show how this variability is propagated to MAT and pH estimates using multiple soil-based branched GDGT transfer functions. Our results show that significant differences in the abundance and distribution of branched GDGTs in soil can be observed even within a small area such as Valles Caldera. Although the original MBT-CBT calibration appears to give robust MAT estimates and the newest calibration provides pH estimates in better agreement with modern local soils in Valles Caldera, the environmental heterogeneity (e.g. vegetation type and soil moisture) appears to affect the precision of MAT and pH estimates. Furthermore, the heterogeneity of soils leads to significant variability among samples taken even from within a square meter. While such soil heterogeneity is not unknown (and is typically controlled for by combining multiple samples), this study quantifies heterogeneity relative to branched GDGT-based proxies for the first time, indicating that care must be taken with samples from heterogeneous soils in MAT and pH reconstructions.

Theoretical foundation for measuring the groundwater age distribution.

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

Gardner, William Payton; Arnold, Bill Walter

2014-01-01

In this study, we use PFLOTRAN, a highly scalable, parallel, flow and reactive transport code to simulate the concentrations of 3H, 3He, CFC-11, CFC-12, CFC-113, SF6, 39Ar, 81Kr, 4He and themean groundwater age in heterogeneous fields on grids with an excess of 10 million nodes. We utilize this computational platform to simulate the concentration of multiple tracers in high-resolution, heterogeneous 2-D and 3-D domains, and calculate tracer-derived ages. Tracer-derived ages show systematic biases toward younger ages when the groundwater age distribution contains water older than the maximum tracer age. The deviation of the tracer-derived age distribution from the true groundwatermore » age distribution increases with increasing heterogeneity of the system. However, the effect of heterogeneity is diminished as the mean travel time gets closer the tracer age limit. Age distributions in 3-D domains differ significantly from 2-D domains. 3D simulations show decreased mean age, and less variance in age distribution for identical heterogeneity statistics. High-performance computing allows for investigation of tracer and groundwater age systematics in high-resolution domains, providing a platform for understanding and utilizing environmental tracer and groundwater age information in heterogeneous 3-D systems. Groundwater environmental tracers can provide important constraints for the calibration of groundwater flow models. Direct simulation of environmental tracer concentrations in models has the additional advantage of avoiding assumptions associated with using calculated groundwater age values. This study quantifies model uncertainty reduction resulting from the addition of environmental tracer concentration data. The analysis uses a synthetic heterogeneous aquifer and the calibration of a flow and transport model using the pilot point method. Results indicate a significant reduction in the uncertainty in permeability with the addition of environmental tracer data, relative to the use of hydraulic measurements alone. Anthropogenic tracers and their decay products, such as CFC11, 3H, and 3He, provide significant constraint oninput permeability values in the model. Tracer data for 39Ar provide even more complete information on the heterogeneity of permeability and variability in the flow system than the anthropogenic tracers, leading to greater parameter uncertainty reduction.« less

Deeply learnt hashing forests for content based image retrieval in prostate MR images

NASA Astrophysics Data System (ADS)

Shah, Amit; Conjeti, Sailesh; Navab, Nassir; Katouzian, Amin

2016-03-01

Deluge in the size and heterogeneity of medical image databases necessitates the need for content based retrieval systems for their efficient organization. In this paper, we propose such a system to retrieve prostate MR images which share similarities in appearance and content with a query image. We introduce deeply learnt hashing forests (DL-HF) for this image retrieval task. DL-HF effectively leverages the semantic descriptiveness of deep learnt Convolutional Neural Networks. This is used in conjunction with hashing forests which are unsupervised random forests. DL-HF hierarchically parses the deep-learnt feature space to encode subspaces with compact binary code words. We propose a similarity preserving feature descriptor called Parts Histogram which is derived from DL-HF. Correlation defined on this descriptor is used as a similarity metric for retrieval from the database. Validations on publicly available multi-center prostate MR image database established the validity of the proposed approach. The proposed method is fully-automated without any user-interaction and is not dependent on any external image standardization like image normalization and registration. This image retrieval method is generalizable and is well-suited for retrieval in heterogeneous databases other imaging modalities and anatomies.

Evolutionary dynamics of social dilemmas in structured heterogeneous populations.

PubMed

Santos, F C; Pacheco, J M; Lenaerts, Tom

2006-02-28

Real populations have been shown to be heterogeneous, in which some individuals have many more contacts than others. This fact contrasts with the traditional homogeneous setting used in studies of evolutionary game dynamics. We incorporate heterogeneity in the population by studying games on graphs, in which the variability in connectivity ranges from single-scale graphs, for which heterogeneity is small and associated degree distributions exhibit a Gaussian tale, to scale-free graphs, for which heterogeneity is large with degree distributions exhibiting a power-law behavior. We study the evolution of cooperation, modeled in terms of the most popular dilemmas of cooperation. We show that, for all dilemmas, increasing heterogeneity favors the emergence of cooperation, such that long-term cooperative behavior easily resists short-term noncooperative behavior. Moreover, we show how cooperation depends on the intricate ties between individuals in scale-free populations.

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

NASA Astrophysics Data System (ADS)

Ghiorso, M. S.

2013-12-01

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

Arsenic metabolism and cancer risk: A meta-analysis.

PubMed

Gamboa-Loira, Brenda; Cebrián, Mariano E; Franco-Marina, Francisco; López-Carrillo, Lizbeth

2017-07-01

To describe the studies that have reported association measures between risk of cancer and the percentage distribution of urinary inorganic arsenic (iAs) metabolites by anatomical site, in non-ecological epidemiological studies. Studies were identified in the PubMed database in the period from 1990 to 2015. Inclusion criteria were: non-ecological epidemiological study, with histologically confirmed cancer cases, reporting the percentage distribution of inorganic arsenic (iAs), monomethylated (MMA) and dimethylated (DMA) metabolites, as well as association measures with confidence intervals (CI) between cancer and %iAs and/or %MMA and/or %DMA. A descriptive meta-analysis was performed by the method of the inverse of the variance for the fixed effects model and the DerSimonian and Laird's method for the random effects model. Heterogeneity was tested using the Q statistic and stratifying for epidemiological design and total As in urine. The possibility of publication bias was assessed through Begg's test. A total of 13 eligible studies were found, most of them were performed in Taiwan and focused on skin and bladder cancer. The positive association between %MMA and various types of cancer was consistent, in contrast to the negative relationship between %DMA and cancer that was inconsistent. The summary risk of bladder (OR=1.79; 95% CI: 1.42, 2.26, n=4 studies) and lung (OR=2.44; 95% CI: 1.57, 3.80, n=2 studies) cancer increased significantly with increasing %MMA, without statistical heterogeneity. In contrast, lung cancer risk was inversely related to %DMA (OR=0.58; 95% CI: 0.36, 0.93, n=2 studies), also without significant heterogeneity. These results were similar after stratifying by epidemiological design and total As in urine. No evidence of publication bias was found. These findings provide additional support that methylation needs to be taken into account when assessing the potential iAs carcinogenicity risk. Copyright © 2017. Published by Elsevier Inc.

The impact of individual-level heterogeneity on estimated infectious disease burden: a simulation study.

PubMed

McDonald, Scott A; Devleesschauwer, Brecht; Wallinga, Jacco

2016-12-08

Disease burden is not evenly distributed within a population; this uneven distribution can be due to individual heterogeneity in progression rates between disease stages. Composite measures of disease burden that are based on disease progression models, such as the disability-adjusted life year (DALY), are widely used to quantify the current and future burden of infectious diseases. Our goal was to investigate to what extent ignoring the presence of heterogeneity could bias DALY computation. Simulations using individual-based models for hypothetical infectious diseases with short and long natural histories were run assuming either "population-averaged" progression probabilities between disease stages, or progression probabilities that were influenced by an a priori defined individual-level frailty (i.e., heterogeneity in disease risk) distribution, and DALYs were calculated. Under the assumption of heterogeneity in transition rates and increasing frailty with age, the short natural history disease model predicted 14% fewer DALYs compared with the homogenous population assumption. Simulations of a long natural history disease indicated that assuming homogeneity in transition rates when heterogeneity was present could overestimate total DALYs, in the present case by 4% (95% quantile interval: 1-8%). The consequences of ignoring population heterogeneity should be considered when defining transition parameters for natural history models and when interpreting the resulting disease burden estimates.

Molecular Tracing of Hepatitis C Virus Genotype 1 Isolates in Iran: A NS5B Phylogenetic Analysis with Systematic Review.

PubMed

Hesamizadeh, Khashayar; Alavian, Seyed Moayed; Najafi Tireh Shabankareh, Azar; Sharafi, Heidar

2016-12-01

Hepatitis C virus (HCV) is characterized by a high degree of genetic heterogeneity and classified into 7 genotypes and different subtypes. It heterogeneously distributed through various risk groups and geographical regions. A well-established phylogenetic relationship can simplify the tracing of HCV hierarchical strata into geographical regions. The current study aimed to find genetic phylogeny of subtypes 1a and 1b of HCV isolates based on NS5B nucleotide sequences in Iran and other members of Eastern Mediterranean regional office of world health organization, as well as other Middle Eastern countries, with a systematic review of available published and unpublished studies. The phylogenetic analyses were performed based on the nucleotide sequences of NS5B gene of HCV genotype 1 (HCV-1), which were registered in the GenBank database. The literature review was performed in two steps: 1) searching studies evaluating the NS5B sequences of HCV-1, on PubMed, Scopus, and Web of Science, and 2) Searching sequences of unpublished studies registered in the GenBank database. In this study, 442 sequences from HCV-1a and 232 from HCV-1b underwent phylogenetic analysis. Phylogenetic analysis of all sequences revealed different clusters in the phylogenetic trees. The results showed that the proportion of HCV-1a and -1b isolates from Iranian patients probably originated from domestic sources. Moreover, the HCV-1b isolates from Iranian patients may have similarities with the European ones. In this study, phylogenetic reconstruction of HCV-1 sequences clearly indicated for molecular tracing and ancestral relationships of the HCV genotypes in Iran, and showed the likelihood of domestic origin for HCV-1a and various origin for HCV-1b.

Multi-heuristic dynamic task allocation using genetic algorithms in a heterogeneous distributed system

PubMed Central

Page, Andrew J.; Keane, Thomas M.; Naughton, Thomas J.

2010-01-01

We present a multi-heuristic evolutionary task allocation algorithm to dynamically map tasks to processors in a heterogeneous distributed system. It utilizes a genetic algorithm, combined with eight common heuristics, in an effort to minimize the total execution time. It operates on batches of unmapped tasks and can preemptively remap tasks to processors. The algorithm has been implemented on a Java distributed system and evaluated with a set of six problems from the areas of bioinformatics, biomedical engineering, computer science and cryptography. Experiments using up to 150 heterogeneous processors show that the algorithm achieves better efficiency than other state-of-the-art heuristic algorithms. PMID:20862190

[Tumor Data Interacted System Design Based on Grid Platform].

PubMed

Liu, Ying; Cao, Jiaji; Zhang, Haowei; Zhang, Ke

2016-06-01

In order to satisfy demands of massive and heterogeneous tumor clinical data processing and the multi-center collaborative diagnosis and treatment for tumor diseases,a Tumor Data Interacted System(TDIS)was established based on grid platform,so that an implementing virtualization platform of tumor diagnosis service was realized,sharing tumor information in real time and carrying on standardized management.The system adopts Globus Toolkit 4.0tools to build the open grid service framework and encapsulats data resources based on Web Services Resource Framework(WSRF).The system uses the middleware technology to provide unified access interface for heterogeneous data interaction,which could optimize interactive process with virtualized service to query and call tumor information resources flexibly.For massive amounts of heterogeneous tumor data,the federated stored and multiple authorized mode is selected as security services mechanism,real-time monitoring and balancing load.The system can cooperatively manage multi-center heterogeneous tumor data to realize the tumor patient data query,sharing and analysis,and compare and match resources in typical clinical database or clinical information database in other service node,thus it can assist doctors in consulting similar case and making up multidisciplinary treatment plan for tumors.Consequently,the system can improve efficiency of diagnosis and treatment for tumor,and promote the development of collaborative tumor diagnosis model.

Influence of the Redundant Verification and the Non-Redundant Verification on the Hydraulic Tomography

NASA Astrophysics Data System (ADS)

Wei, T. B.; Chen, Y. L.; Lin, H. R.; Huang, S. Y.; Yeh, T. C. J.; Wen, J. C.

2016-12-01

In the groundwater study, it estimated the heterogeneous spatial distribution of hydraulic Properties, there were many scholars use to hydraulic tomography (HT) from field site pumping tests to estimate inverse of heterogeneous spatial distribution of hydraulic Properties, to prove the most of most field site aquifer was heterogeneous hydrogeological parameters spatial distribution field. Many scholars had proposed a method of hydraulic tomography to estimate heterogeneous spatial distribution of hydraulic Properties of aquifer, the Huang et al. [2011] was used the non-redundant verification analysis of pumping wells changed, observation wells fixed on the inverse and the forward, to reflect the feasibility of the heterogeneous spatial distribution of hydraulic Properties of field site aquifer of the non-redundant verification analysis on steady-state model.From post literature, finding only in steady state, non-redundant verification analysis of pumping well changed location and observation wells fixed location for inverse and forward. But the studies had not yet pumping wells fixed or changed location, and observation wells fixed location for redundant verification or observation wells change location for non-redundant verification of the various combinations may to explore of influences of hydraulic tomography method. In this study, it carried out redundant verification method and non-redundant verification method for forward to influences of hydraulic tomography method in transient. And it discuss above mentioned in NYUST campus sites the actual case, to prove the effectiveness of hydraulic tomography methods, and confirmed the feasibility on inverse and forward analysis from analysis results.Keywords: Hydraulic Tomography, Redundant Verification, Heterogeneous, Inverse, Forward

Integrating mean and variance heterogeneities to identify differentially expressed genes.

PubMed

Ouyang, Weiwei; An, Qiang; Zhao, Jinying; Qin, Huaizhen

2016-12-06

In functional genomics studies, tests on mean heterogeneity have been widely employed to identify differentially expressed genes with distinct mean expression levels under different experimental conditions. Variance heterogeneity (aka, the difference between condition-specific variances) of gene expression levels is simply neglected or calibrated for as an impediment. The mean heterogeneity in the expression level of a gene reflects one aspect of its distribution alteration; and variance heterogeneity induced by condition change may reflect another aspect. Change in condition may alter both mean and some higher-order characteristics of the distributions of expression levels of susceptible genes. In this report, we put forth a conception of mean-variance differentially expressed (MVDE) genes, whose expression means and variances are sensitive to the change in experimental condition. We mathematically proved the null independence of existent mean heterogeneity tests and variance heterogeneity tests. Based on the independence, we proposed an integrative mean-variance test (IMVT) to combine gene-wise mean heterogeneity and variance heterogeneity induced by condition change. The IMVT outperformed its competitors under comprehensive simulations of normality and Laplace settings. For moderate samples, the IMVT well controlled type I error rates, and so did existent mean heterogeneity test (i.e., the Welch t test (WT), the moderated Welch t test (MWT)) and the procedure of separate tests on mean and variance heterogeneities (SMVT), but the likelihood ratio test (LRT) severely inflated type I error rates. In presence of variance heterogeneity, the IMVT appeared noticeably more powerful than all the valid mean heterogeneity tests. Application to the gene profiles of peripheral circulating B raised solid evidence of informative variance heterogeneity. After adjusting for background data structure, the IMVT replicated previous discoveries and identified novel experiment-wide significant MVDE genes. Our results indicate tremendous potential gain of integrating informative variance heterogeneity after adjusting for global confounders and background data structure. The proposed informative integration test better summarizes the impacts of condition change on expression distributions of susceptible genes than do the existent competitors. Therefore, particular attention should be paid to explicitly exploit the variance heterogeneity induced by condition change in functional genomics analysis.

Confronting the Paradox of Enrichment to the Metacommunity Perspective

PubMed Central

Hauzy, Céline; Nadin, Grégoire; Canard, Elsa; Gounand, Isabelle; Mouquet, Nicolas; Ebenman, Bo

2013-01-01

Resource enrichment can potentially destabilize predator-prey dynamics. This phenomenon historically referred as the "paradox of enrichment" has mostly been explored in spatially homogenous environments. However, many predator-prey communities exchange organisms within spatially heterogeneous networks called metacommunities. This heterogeneity can result from uneven distribution of resources among communities and thus can lead to the spreading of local enrichment within metacommunities. Here, we adapted the original Rosenzweig-MacArthur predator-prey model, built to study the paradox of enrichment, to investigate the effect of regional enrichment and of its spatial distribution on predator-prey dynamics in metacommunities. We found that the potential for destabilization was depending on the connectivity among communities and the spatial distribution of enrichment. In one hand, we found that at low dispersal regional enrichment led to the destabilization of predator-prey dynamics. This destabilizing effect was more pronounced when the enrichment was uneven among communities. In the other hand, we found that high dispersal could stabilize the predator-prey dynamics when the enrichment was spatially heterogeneous. Our results illustrate that the destabilizing effect of enrichment can be dampened when the spatial scale of resource enrichment is lower than that of organismss movements (heterogeneous enrichment). From a conservation perspective, our results illustrate that spatial heterogeneity could decrease the regional extinction risk of species involved in specialized trophic interactions. From the perspective of biological control, our results show that the heterogeneous distribution of pest resource could favor or dampen outbreaks of pests and of their natural enemies, depending on the spatial scale of heterogeneity. PMID:24358242

An empirical likelihood ratio test robust to individual heterogeneity for differential expression analysis of RNA-seq.

PubMed

Xu, Maoqi; Chen, Liang

2018-01-01

The individual sample heterogeneity is one of the biggest obstacles in biomarker identification for complex diseases such as cancers. Current statistical models to identify differentially expressed genes between disease and control groups often overlook the substantial human sample heterogeneity. Meanwhile, traditional nonparametric tests lose detailed data information and sacrifice the analysis power, although they are distribution free and robust to heterogeneity. Here, we propose an empirical likelihood ratio test with a mean-variance relationship constraint (ELTSeq) for the differential expression analysis of RNA sequencing (RNA-seq). As a distribution-free nonparametric model, ELTSeq handles individual heterogeneity by estimating an empirical probability for each observation without making any assumption about read-count distribution. It also incorporates a constraint for the read-count overdispersion, which is widely observed in RNA-seq data. ELTSeq demonstrates a significant improvement over existing methods such as edgeR, DESeq, t-tests, Wilcoxon tests and the classic empirical likelihood-ratio test when handling heterogeneous groups. It will significantly advance the transcriptomics studies of cancers and other complex disease. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals

PubMed Central

You, Leiming; Wu, Jiexin; Feng, Yuchao; Fu, Yonggui; Guo, Yanan; Long, Liyuan; Zhang, Hui; Luan, Yijie; Tian, Peng; Chen, Liangfu; Huang, Guangrui; Huang, Shengfeng; Li, Yuxin; Li, Jie; Chen, Chengyong; Zhang, Yaqing; Chen, Shangwu; Xu, Anlong

2015-01-01

Increasing amounts of genes have been shown to utilize alternative polyadenylation (APA) 3′-processing sites depending on the cell and tissue type and/or physiological and pathological conditions at the time of processing, and the construction of genome-wide database regarding APA is urgently needed for better understanding poly(A) site selection and APA-directed gene expression regulation for a given biology. Here we present a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3′-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3′-untranslated regions (3′-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish. PMID:25378337

Self-concept of left-behind children in China: a systematic review of the literature.

PubMed

Wang, X; Ling, L; Su, H; Cheng, J; Jin, L; Sun, Y-H

2015-05-01

The aim of our study was to systematically review studies which had compared self-concept in left-behind children with the general population of children in China. Relevant studies about self-concept of left-behind children in China published from 2004 to 2014 were sought by searching online databases including Chinese Biological Medicine Database (CBM), Chinese National Knowledge Infrastructure (CNKI), Wanfang Database, Vip Database, PubMed Database, Google Scholar and Web of Science. The methodological quality of the articles was assessed by using Newcastle-Ottawa Scale (NOS). Poled effect size and associated 95% confidence interval (CI) were calculated using the random effects model. Cochrane's Q was used to test for heterogeneity and I(2) index was used to determine the degree of heterogeneity. Nineteen studies involving 7758 left-behind children met the inclusion criteria and 15 studies were included in a meta-analysis. The results indicated that left-behind group had a lower score of self-concept and more psychological problems than the control group. The factors associated with self-concept in left-behind children were gender, age, grade and the relationships with parents, guardians and teachers. Left-behind children had lower self-concept and more mental health problems compared with the general population of children. The development of self-concept may be an important channel for promoting mental health of left-behind children. © 2014 John Wiley & Sons Ltd.

Exploration of Heterogeneity in Distributed Research Network Drug Safety Analyses

ERIC Educational Resources Information Center

Hansen, Richard A.; Zeng, Peng; Ryan, Patrick; Gao, Juan; Sonawane, Kalyani; Teeter, Benjamin; Westrich, Kimberly; Dubois, Robert W.

2014-01-01

Distributed data networks representing large diverse populations are an expanding focus of drug safety research. However, interpreting results is difficult when treatment effect estimates vary across datasets (i.e., heterogeneity). In a previous study, risk estimates were generated for selected drugs and potential adverse outcomes. Analyses were…

Heterogeneous Integration Technology

DTIC Science & Technology

2017-05-19

Distribution A. Approved for public release; distribution unlimited. (APRS-RY-17-0383) Heterogeneous Integration Technology Dr. Burhan...2013 and 2015 [4]. ...................................... 9 Figure 3: 3D integration of similar or diverse technology components follows More Moore and...10 Figure 4: Many different technologies are used in the implementation of modern microelectronics systems can benefit from

DbMap: improving database interoperability issues in medical software using a simple, Java-Xml based solution.

PubMed Central

Karadimas, H.; Hemery, F.; Roland, P.; Lepage, E.

2000-01-01

In medical software development, the use of databases plays a central role. However, most of the databases have heterogeneous encoding and data models. To deal with these variations in the application code directly is error-prone and reduces the potential reuse of the produced software. Several approaches to overcome these limitations have been proposed in the medical database literature, which will be presented. We present a simple solution, based on a Java library, and a central Metadata description file in XML. This development approach presents several benefits in software design and development cycles, the main one being the simplicity in maintenance. PMID:11079915

Heterogeneous distribution of metabolites across plant species

NASA Astrophysics Data System (ADS)

Takemoto, Kazuhiro; Arita, Masanori

2009-07-01

We investigate the distribution of flavonoids, a major category of plant secondary metabolites, across species. Flavonoids are known to show high species specificity, and were once considered as chemical markers for understanding adaptive evolution and characterization of living organisms. We investigate the distribution among species using bipartite networks, and find that two heterogeneous distributions are conserved among several families: the power-law distributions of the number of flavonoids in a species and the number of shared species of a particular flavonoid. In order to explain the possible origin of the heterogeneity, we propose a simple model with, essentially, a single parameter. As a result, we show that two respective power-law statistics emerge from simple evolutionary mechanisms based on a multiplicative process. These findings provide insights into the evolution of metabolite diversity and characterization of living organisms that defy genome sequence analysis for different reasons.

Privacy Preservation in Distributed Subgradient Optimization Algorithms.

PubMed

Lou, Youcheng; Yu, Lean; Wang, Shouyang; Yi, Peng

2017-07-31

In this paper, some privacy-preserving features for distributed subgradient optimization algorithms are considered. Most of the existing distributed algorithms focus mainly on the algorithm design and convergence analysis, but not the protection of agents' privacy. Privacy is becoming an increasingly important issue in applications involving sensitive information. In this paper, we first show that the distributed subgradient synchronous homogeneous-stepsize algorithm is not privacy preserving in the sense that the malicious agent can asymptotically discover other agents' subgradients by transmitting untrue estimates to its neighbors. Then a distributed subgradient asynchronous heterogeneous-stepsize projection algorithm is proposed and accordingly its convergence and optimality is established. In contrast to the synchronous homogeneous-stepsize algorithm, in the new algorithm agents make their optimization updates asynchronously with heterogeneous stepsizes. The introduced two mechanisms of projection operation and asynchronous heterogeneous-stepsize optimization can guarantee that agents' privacy can be effectively protected.

A Grid Metadata Service for Earth and Environmental Sciences

NASA Astrophysics Data System (ADS)

Fiore, Sandro; Negro, Alessandro; Aloisio, Giovanni

2010-05-01

Critical challenges for climate modeling researchers are strongly connected with the increasingly complex simulation models and the huge quantities of produced datasets. Future trends in climate modeling will only increase computational and storage requirements. For this reason the ability to transparently access to both computational and data resources for large-scale complex climate simulations must be considered as a key requirement for Earth Science and Environmental distributed systems. From the data management perspective (i) the quantity of data will continuously increases, (ii) data will become more and more distributed and widespread, (iii) data sharing/federation will represent a key challenging issue among different sites distributed worldwide, (iv) the potential community of users (large and heterogeneous) will be interested in discovery experimental results, searching of metadata, browsing collections of files, compare different results, display output, etc.; A key element to carry out data search and discovery, manage and access huge and distributed amount of data is the metadata handling framework. What we propose for the management of distributed datasets is the GRelC service (a data grid solution focusing on metadata management). Despite the classical approaches, the proposed data-grid solution is able to address scalability, transparency, security and efficiency and interoperability. The GRelC service we propose is able to provide access to metadata stored in different and widespread data sources (relational databases running on top of MySQL, Oracle, DB2, etc. leveraging SQL as query language, as well as XML databases - XIndice, eXist, and libxml2 based documents, adopting either XPath or XQuery) providing a strong data virtualization layer in a grid environment. Such a technological solution for distributed metadata management leverages on well known adopted standards (W3C, OASIS, etc.); (ii) supports role-based management (based on VOMS), which increases flexibility and scalability; (iii) provides full support for Grid Security Infrastructure, which means (authorization, mutual authentication, data integrity, data confidentiality and delegation); (iv) is compatible with existing grid middleware such as gLite and Globus and finally (v) is currently adopted at the Euro-Mediterranean Centre for Climate Change (CMCC - Italy) to manage the entire CMCC data production activity as well as in the international Climate-G testbed.

Data Mining on Distributed Medical Databases: Recent Trends and Future Directions

NASA Astrophysics Data System (ADS)

Atilgan, Yasemin; Dogan, Firat

As computerization in healthcare services increase, the amount of available digital data is growing at an unprecedented rate and as a result healthcare organizations are much more able to store data than to extract knowledge from it. Today the major challenge is to transform these data into useful information and knowledge. It is important for healthcare organizations to use stored data to improve quality while reducing cost. This paper first investigates the data mining applications on centralized medical databases, and how they are used for diagnostic and population health, then introduces distributed databases. The integration needs and issues of distributed medical databases are described. Finally the paper focuses on data mining studies on distributed medical databases.

Prediction of down-gradient impacts of DNAPL source depletion using tracer techniques: Laboratory and modeling validation

NASA Astrophysics Data System (ADS)

Jawitz, J. W.; Basu, N.; Chen, X.

2007-05-01

Interwell application of coupled nonreactive and reactive tracers through aquifer contaminant source zones enables quantitative characterization of aquifer heterogeneity and contaminant architecture. Parameters obtained from tracer tests are presented here in a Lagrangian framework that can be used to predict the dissolution of nonaqueous phase liquid (NAPL) contaminants. Nonreactive tracers are commonly used to provide information about travel time distributions in hydrologic systems. Reactive tracers have more recently been introduced as a tool to quantify the amount of NAPL contaminant present within the tracer swept volume. Our group has extended reactive tracer techniques to also characterize NAPL spatial distribution heterogeneity. By conceptualizing the flow field through an aquifer as a collection of streamtubes, the aquifer hydrodynamic heterogeneities may be characterized by a nonreactive tracer travel time distribution, and NAPL spatial distribution heterogeneity may be similarly described using reactive travel time distributions. The combined statistics of these distributions are used to derive a simple analytical solution for contaminant dissolution. This analytical solution, and the tracer techniques used for its parameterization, were validated both numerically and experimentally. Illustrative applications are presented from numerical simulations using the multiphase flow and transport simulator UTCHEM, and laboratory experiments of surfactant-enhanced NAPL remediation in two-dimensional flow chambers.

Saada: A Generator of Astronomical Database

NASA Astrophysics Data System (ADS)

Michel, L.

2011-11-01

Saada transforms a set of heterogeneous FITS files or VOtables of various categories (images, tables, spectra, etc.) in a powerful database deployed on the Web. Databases are located on your host and stay independent of any external server. This job doesn’t require writing code. Saada can mix data of various categories in multiple collections. Data collections can be linked each to others making relevant browsing paths and allowing data-mining oriented queries. Saada supports 4 VO services (Spectra, images, sources and TAP) . Data collections can be published immediately after the deployment of the Web interface.

High-Resolution Chromosome Ideogram Representation of Currently Recognized Genes for Autism Spectrum Disorders

PubMed Central

Butler, Merlin G.; Rafi, Syed K.; Manzardo, Ann M.

2015-01-01

Recently, autism-related research has focused on the identification of various genes and disturbed pathways causing the genetically heterogeneous group of autism spectrum disorders (ASD). The list of autism-related genes has significantly increased due to better awareness with advances in genetic technology and expanding searchable genomic databases. We compiled a master list of known and clinically relevant autism spectrum disorder genes identified with supporting evidence from peer-reviewed medical literature sources by searching key words related to autism and genetics and from authoritative autism-related public access websites, such as the Simons Foundation Autism Research Institute autism genomic database dedicated to gene discovery and characterization. Our list consists of 792 genes arranged in alphabetical order in tabular form with gene symbols placed on high-resolution human chromosome ideograms, thereby enabling clinical and laboratory geneticists and genetic counsellors to access convenient visual images of the location and distribution of ASD genes. Meaningful correlations of the observed phenotype in patients with suspected/confirmed ASD gene(s) at the chromosome region or breakpoint band site can be made to inform diagnosis and gene-based personalized care and provide genetic counselling for families. PMID:25803107

Production and distribution of scientific and technical databases - Comparison among Japan, US and Europe

NASA Astrophysics Data System (ADS)

Onodera, Natsuo; Mizukami, Masayuki

This paper estimates several quantitative indice on production and distribution of scientific and technical databases based on various recent publications and attempts to compare the indice internationally. Raw data used for the estimation are brought mainly from the Database Directory (published by MITI) for database production and from some domestic and foreign study reports for database revenues. The ratio of the indice among Japan, US and Europe for usage of database is similar to those for general scientific and technical activities such as population and R&D expenditures. But Japanese contributions to production, revenue and over-countory distribution of databases are still lower than US and European countries. International comparison of relative database activities between public and private sectors is also discussed.

Heterogeneous characters modeling of instant message services users’ online behavior

PubMed Central

Fang, Yajun; Horn, Berthold

2018-01-01

Research on temporal characteristics of human dynamics has attracted much attentions for its contribution to various areas such as communication, medical treatment, finance, etc. Existing studies show that the time intervals between two consecutive events present different non-Poisson characteristics, such as power-law, Pareto, bimodal distribution of power-law, exponential distribution, piecewise power-law, et al. With the occurrences of new services, new types of distributions may arise. In this paper, we study the distributions of the time intervals between two consecutive visits to QQ and WeChat service, the top two popular instant messaging services in China, and present a new finding that when the value of statistical unit T is set to 0.001s, the inter-event time distribution follows a piecewise distribution of exponential and power-law, indicating the heterogeneous character of IM services users’ online behavior in different time scales. We infer that the heterogeneous character is related to the communication mechanism of IM and the habits of users. Then we develop a combination model of exponential model and interest model to characterize the heterogeneity. Furthermore, we find that the exponent of the inter-event time distribution of the same service is different in two cities, which is correlated with the popularity of the services. Our research is useful for the application of information diffusion, prediction of economic development of cities, and so on. PMID:29734327

Heterogeneous characters modeling of instant message services users' online behavior.

PubMed

Cui, Hongyan; Li, Ruibing; Fang, Yajun; Horn, Berthold; Welsch, Roy E

2018-01-01

Research on temporal characteristics of human dynamics has attracted much attentions for its contribution to various areas such as communication, medical treatment, finance, etc. Existing studies show that the time intervals between two consecutive events present different non-Poisson characteristics, such as power-law, Pareto, bimodal distribution of power-law, exponential distribution, piecewise power-law, et al. With the occurrences of new services, new types of distributions may arise. In this paper, we study the distributions of the time intervals between two consecutive visits to QQ and WeChat service, the top two popular instant messaging services in China, and present a new finding that when the value of statistical unit T is set to 0.001s, the inter-event time distribution follows a piecewise distribution of exponential and power-law, indicating the heterogeneous character of IM services users' online behavior in different time scales. We infer that the heterogeneous character is related to the communication mechanism of IM and the habits of users. Then we develop a combination model of exponential model and interest model to characterize the heterogeneity. Furthermore, we find that the exponent of the inter-event time distribution of the same service is different in two cities, which is correlated with the popularity of the services. Our research is useful for the application of information diffusion, prediction of economic development of cities, and so on.

A web-based, relational database for studying glaciers in the Italian Alps

NASA Astrophysics Data System (ADS)

Nigrelli, G.; Chiarle, M.; Nuzzi, A.; Perotti, L.; Torta, G.; Giardino, M.

2013-02-01

Glaciers are among the best terrestrial indicators of climate change and thus glacier inventories have attracted a growing, worldwide interest in recent years. In Italy, the first official glacier inventory was completed in 1925 and 774 glacial bodies were identified. As the amount of data continues to increase, and new techniques become available, there is a growing demand for computer tools that can efficiently manage the collected data. The Research Institute for Geo-hydrological Protection of the National Research Council, in cooperation with the Departments of Computer Science and Earth Sciences of the University of Turin, created a database that provides a modern tool for storing, processing and sharing glaciological data. The database was developed according to the need of storing heterogeneous information, which can be retrieved through a set of web search queries. The database's architecture is server-side, and was designed by means of an open source software. The website interface, simple and intuitive, was intended to meet the needs of a distributed public: through this interface, any type of glaciological data can be managed, specific queries can be performed, and the results can be exported in a standard format. The use of a relational database to store and organize a large variety of information about Italian glaciers collected over the last hundred years constitutes a significant step forward in ensuring the safety and accessibility of such data. Moreover, the same benefits also apply to the enhanced operability for handling information in the future, including new and emerging types of data formats, such as geographic and multimedia files. Future developments include the integration of cartographic data, such as base maps, satellite images and vector data. The relational database described in this paper will be the heart of a new geographic system that will merge data, data attributes and maps, leading to a complete description of Italian glacial environments.

Addressing the Heterogeneity of Subject Indexing in the ADS Databases

NASA Astrophysics Data System (ADS)

Dubin, David S.

A drawback of the current document representation scheme in the ADS abstract service is its heterogeneous subject indexing. Several related but inconsistent indexing languages are represented in ADS. A method of reconciling some indexing inconsistencies is described. Using lexical similarity alone, one out of six ADS descriptors can be automatically mapped to some other descriptor. Analysis of postings data can direct administrators to those mergings it is most important to check for errors.

SU-E-T-121: Analyzing the Broadening Effect On the Bragg Peak Due to Heterogeneous Geometries and Implementing User-Routines in the Monte-Carlo Code FLUKA in Order to Reduce Computation Time

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

Baumann, K; Weber, U; Simeonov, Y

2015-06-15

Purpose: Aim of this study was to analyze the modulating, broadening effect on the Bragg Peak due to heterogeneous geometries like multi-wire chambers in the beam path of a particle therapy beam line. The effect was described by a mathematical model which was implemented in the Monte-Carlo code FLUKA via user-routines, in order to reduce the computation time for the simulations. Methods: The depth dose curve of 80 MeV/u C12-ions in a water phantom was calculated using the Monte-Carlo code FLUKA (reference curve). The modulating effect on this dose distribution behind eleven mesh-like foils (periodicity ∼80 microns) occurring in amore » typical set of multi-wire and dose chambers was mathematically described by optimizing a normal distribution so that the reverence curve convoluted with this distribution equals the modulated dose curve. This distribution describes a displacement in water and was transferred in a probability distribution of the thickness of the eleven foils using the water equivalent thickness of the foil’s material. From this distribution the distribution of the thickness of one foil was determined inversely. In FLUKA the heterogeneous foils were replaced by homogeneous foils and a user-routine was programmed that varies the thickness of the homogeneous foils for each simulated particle using this distribution. Results: Using the mathematical model and user-routine in FLUKA the broadening effect could be reproduced exactly when replacing the heterogeneous foils by homogeneous ones. The computation time was reduced by 90 percent. Conclusion: In this study the broadening effect on the Bragg Peak due to heterogeneous structures was analyzed, described by a mathematical model and implemented in FLUKA via user-routines. Applying these routines the computing time was reduced by 90 percent. The developed tool can be used for any heterogeneous structure in the dimensions of microns to millimeters, in principle even for organic materials like lung tissue.« less

Mining of hospital laboratory information systems: a model study defining age- and gender-specific reference intervals and trajectories for plasma creatinine in a pediatric population.

PubMed

Søeby, Karen; Jensen, Peter Bjødstrup; Werge, Thomas; Sørensen, Steen

2015-09-01

The knowledge of physiological fluctuation and variation of even commonly used biochemical quantities in extreme age groups and during development is sparse. This challenges the clinical interpretation and utility of laboratory tests in these age groups. To explore the utility of hospital laboratory data as a source of information, we analyzed enzymatic plasma creatinine as a model analyte in two large pediatric hospital samples. Plasma creatinine measurements from 9700 children aged 0-18 years were obtained from hospital laboratory databases and partitioned into high-resolution gender- and age-groups. Normal probability plots were used to deduce parameters of the normal distributions from healthy creatinine values in the mixed hospital datasets. Furthermore, temporal trajectories were generated from repeated measurements to examine developmental patterns in periods of changing creatinine levels. Creatinine shows great age dependence from birth throughout childhood. We computed and replicated 95% reference intervals in narrow gender and age bins and showed them to be comparable to those determined in healthy population studies. We identified pronounced transitions in creatinine levels at different time points after birth and around the early teens, which challenges the establishment and usefulness of reference intervals in those age groups. The study documents that hospital laboratory data may inform on the developmental aspects of creatinine, on periods with pronounced heterogeneity and valid reference intervals. Furthermore, part of the heterogeneity in creatinine distribution is likely due to differences in biological and chronological age of children and should be considered when using age-specific reference intervals.

Hierarchical Distributed-Lag Models: Exploring Varying Geographic Scale and Magnitude in Associations Between the Built Environment and Health.

PubMed

Baek, Jonggyu; Sanchez-Vaznaugh, Emma V; Sánchez, Brisa N

2016-03-15

It is well known that associations between features of the built environment and health depend on the geographic scale used to construct environmental attributes. In the built environment literature, it has long been argued that geographic scales may vary across study locations. However, this hypothesized variation has not been systematically examined due to a lack of available statistical methods. We propose a hierarchical distributed-lag model (HDLM) for estimating the underlying overall shape of food environment-health associations as a function of distance from locations of interest. This method enables indirect assessment of relevant geographic scales and captures area-level heterogeneity in the magnitudes of associations, along with relevant distances within areas. The proposed model was used to systematically examine area-level variation in the association between availability of convenience stores around schools and children's weights. For this case study, body mass index (weight kg)/height (m)2) z scores (BMIz) for 7th grade children collected via California's 2001-2009 FitnessGram testing program were linked to a commercial database that contained locations of food outlets statewide. Findings suggested that convenience store availability may influence BMIz only in some places and at varying distances from schools. Future research should examine localized environmental or policy differences that may explain the heterogeneity in convenience store-BMIz associations. © The Author 2016. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Small-scale heterogeneity spectra in the Earth mantle resolved by PKP-ab,-bc and -df waves

NASA Astrophysics Data System (ADS)

Zheng, Y.

2016-12-01

Plate tectonics creates heterogeneities at mid ocean ridges and subducts the heterogeneities back to the mantle at subduction zones. Heterogeneities manifest themselves by different densities and seismic wave speeds. The length scales and spatial distribution of the heterogeneities measure the mixing mechanism of the plate tectonics. This information can be mathematically captured as the heterogeneity spatial Fourier spectrum. Since most heterogeneities created are on the order of 10s of km, global seismic tomography is not able to resolve them directly. Here, we use seismic P-waves that transmit through the outer core (phases: PKP-ab and PKP-bc) and through the inner core (PKP-df) to probe the lower-mantle heterogeneities. The differential traveltimes (PKP-ab versus PKP-df; PKP-bc versus PKP-df) are sensitive to lower mantle structures. We have collected more than 10,000 PKP phases recorded by Japan Hi-Net short-period seismic network. We found that the lower mantle was filled with seismic heterogeneities from scale 20km to 200km. The heterogeneity spectrum is similar to an exponential distribution but is more enriched in small-scale heterogeneities at the high-wavenumber end. The spectrum is "red" meaning large scales have more power and heterogeneities show a multiscale nature: small-scale heterogeneities are embedded in large-scale heterogeneities. These small-scale heterogeneities cannot be due to thermal origin and they must be compositional. If all these heterogeneities were located in the D" layer, statistically, it would have a root-mean-square P-wave velocity fluctuation of 1% (i.e., -3% to 3%).

Harvesting implementation for the GI-cat distributed catalog

NASA Astrophysics Data System (ADS)

Boldrini, Enrico; Papeschi, Fabrizio; Bigagli, Lorenzo; Mazzetti, Paolo

2010-05-01

GI-cat framework implements a distributed catalog service supporting different international standards and interoperability arrangements in use by the geoscientific community. The distribution functionality in conjunction with the mediation functionality allows to seamlessly query remote heterogeneous data sources, including OGC Web Services - e.e. OGC CSW, WCS, WFS and WMS, community standards such as UNIDATA THREDDS/OPeNDAP, SeaDataNet CDI (Common Data Index), GBIF (Global Biodiversity Information Facility) services and OpenSearch engines. In the GI-cat modular architecture a distributor component carry out the distribution functionality by query delegation to the mediator components (one for each different data source). Each of these mediator components is able to query a specific data source and convert back the results by mapping of the foreign data model to the GI-cat internal one, based on ISO 19139. In order to cope with deployment scenarios in which local data is expected, an harvesting approach has been experimented. The new strategy comes in addition to the consolidated distributed approach, allowing the user to switch between a remote and a local search at will for each federated resource; this extends GI-cat configuration possibilities. The harvesting strategy is designed in GI-cat by the use at the core of a local cache component, implemented as a native XML database and based on eXist. The different heterogeneous sources are queried for the bulk of available data; this data is then injected into the cache component after being converted to the GI-cat data model. The query and conversion steps are performed by the mediator components that were are part of the GI-cat framework. Afterward each new query can be exercised against local data that have been stored in the cache component. Considering both advantages and shortcomings that affect harvesting and query distribution approaches, it comes out that a user driven tuning is required to take the best of them. This is often related to the specific user scenarios to be implemented. GI-cat proved to be a flexible framework to address user need. The GI-cat configurator tool was updated to make such a tuning possible: each data source can be configured to enable either harvesting or query distribution approaches; in the former case an appropriate harvesting interval can be set.

[The relevance between obstructive sleep apnea hypopnea syndrome andchronic obstructive pulmonary disease in China: A Meta-analysis].

PubMed

Du, G D; Ma, L; Lv, Y H; Huang, L H; Fan, C Y; Xiang, Y; Lei, Q; Hu, R

2016-10-20

Objective: To assess the correlation between obstructive sleep apnea hypopnea syndrome(OSAHS) and chronic obstructive pulmonary disease(COPD). Method: Databases such as Chinese Biomedical Literature Database, PubMed, Chinese Academic Journals full-text database, Wanfang Resource Database and Chongqing VIP have been searched to collect literatures about the relationship between OSAHS and COPD. The literature in conference proceedings and certain unpublished articles were also manually retrieved. RCT conformed to the condition was evaluated according to the standards of literature assessment, and the data has been extracted. The RevMan5.3 software was applied to carry out the same Metaanalysis. Result: Totally 19 articles were included, and Metaanalysis reveal that overlap syndrome(OS) patient's apnea hypopnea index is significantly higher than those of OSAHS patients［WMD=7.56, 95% CI （4.19,10.94）, P <0.01］; The LSaO₂ of OS patients is significantly lower than OSAHS patients［WMD=-10.50, 95% CI (-11.58, -6.08), P <0.01］; OS patients' FEV₁/FVC is significantly lower than COPD patients［WMD=4.65,95% CI （1.15,8.15）, P <0.01］.The results revealed that subgroup analysis according to the sample volume, age, body mass index(BMI) and FEV₁/FVC between OS patients and OSAHS patients has heterogeneity, but when analysis with the score of ESS the heterogeneity does not exist. Further, the subgroup analysis according to the sample volume, BMI, AHI,LSaO₂ and the time of Oxygen is lower than 90%(T90) those index between OS patients and COPD patients has heterogeneity, and the heterogeneity does not exist when subgroup is analyses with neck circumference. The funnel schema was nearly symmetry with little bias. Conclusion: The experimental results indicate that OSAHS is significantly related with COPD, and they may be the mutual risk factor for each other.. Copyright© by the Editorial Department of Journal of Clinical Otorhinolaryngology Head and Neck Surgery.

Influence of permeability on nanoscale zero-valent iron particle transport in saturated homogeneous and heterogeneous porous media.

PubMed

Strutz, Tessa J; Hornbruch, Götz; Dahmke, Andreas; Köber, Ralf

2016-09-01

Nanoscale zero-valent iron (NZVI) particles can be used for in situ groundwater remediation. The spatial particle distribution plays a very important role in successful and efficient remediation, especially in heterogeneous systems. Initial sand permeability (k 0) influences on spatial particle distributions were investigated and quantified in homogeneous and heterogeneous systems within the presented study. Four homogeneously filled column experiments and a heterogeneously filled tank experiment, using different median sand grain diameters (d 50), were performed to determine if NZVI particles were transported into finer sand where contaminants could be trapped. More NZVI particle retention, less particle transport, and faster decrease in k were observed in the column studies using finer sands than in those using coarser sands, reflecting a function of k 0. In heterogeneous media, NZVI particles were initially transported and deposited in coarse sand areas. Increasing the retained NZVI mass (decreasing k in particle deposition areas) caused NZVI particles to also be transported into finer sand areas, forming an area with a relatively homogeneous particle distribution and converged k values despite the different grain sizes present. The deposited-particle surface area contribution to the increasing of the matrix surface area (θ) was one to two orders of magnitude higher for finer than coarser sand. The dependency of θ on d 50 presumably affects simulated k changes and NZVI distributions in numerical simulations of NZVI injections into heterogeneous aquifers. The results implied that NZVI can in principle also penetrate finer layers.

Ventilation heterogeneity measured by multiple breath inert gas testing is not affected by inspired oxygen concentration in healthy humans

PubMed Central

Elliott, Ann R.; Prisk, G. Kim; Darquenne, Chantal

2017-01-01

Multiple breath washout (MBW) and oxygen-enhanced MRI techniques use acute exposure to 100% oxygen to measure ventilation heterogeneity. Implicit is the assumption that breathing 100% oxygen does not induce changes in ventilation heterogeneity; however, this is untested. We hypothesized that ventilation heterogeneity decreases with increasing inspired oxygen concentration in healthy subjects. We performed MBW in 8 healthy subjects (4 women, 4 men; age = 43 ± 15 yr) with normal pulmonary function (FEV1 = 98 ± 6% predicted) using 10% argon as a tracer gas and oxygen concentrations of 12.5%, 21%, or 90%. MBW was performed in accordance with ERS-ATS guidelines. Subjects initially inspired air followed by a wash-in of test gas. Tests were performed in balanced order in triplicate. Gas concentrations were measured at the mouth, and argon signals rescaled to mimic a N2 washout, and analyzed to determine the distribution of specific ventilation (SV). Heterogeneity was characterized by the width of a log-Gaussian fit of the SV distribution and from Sacin and Scond indexes derived from the phase III slope. There were no significant differences in the ventilation heterogeneity due to altered inspired oxygen: histogram width (hypoxia 0.57 ± 0.11, normoxia 0.60 ± 0.08, hyperoxia 0.59 ± 0.09, P = 0.51), Scond (hypoxia 0.014 ± 0.011, normoxia 0.012 ± 0.015, hyperoxia 0.010 ± 0.011, P = 0.34), or Sacin (hypoxia 0.11 ± 0.04, normoxia 0.10 ± 0.03, hyperoxia 0.12 ± 0.03, P = 0.23). Functional residual capacity was increased in hypoxia (P = 0.04) and dead space increased in hyperoxia (P = 0.0001) compared with the other conditions. The acute use of 100% oxygen in MBW or MRI is unlikely to affect ventilation heterogeneity. NEW & NOTEWORTHY Hyperoxia is used to measure the distribution of ventilation in imaging and MBW but may alter the underlying ventilation distribution. We used MBW to evaluate the effect of inspired oxygen concentration on the ventilation distribution using 10% argon as a tracer. Short-duration exposure to hypoxia (12.5% oxygen) and hyperoxia (90% oxygen) during MBW had no significant effect on ventilation heterogeneity, suggesting that hyperoxia can be used to assess the ventilation distribution. PMID:28280107

Ventilation heterogeneity measured by multiple breath inert gas testing is not affected by inspired oxygen concentration in healthy humans.

PubMed

Hopkins, Susan R; Elliott, Ann R; Prisk, G Kim; Darquenne, Chantal

2017-06-01

Multiple breath washout (MBW) and oxygen-enhanced MRI techniques use acute exposure to 100% oxygen to measure ventilation heterogeneity. Implicit is the assumption that breathing 100% oxygen does not induce changes in ventilation heterogeneity; however, this is untested. We hypothesized that ventilation heterogeneity decreases with increasing inspired oxygen concentration in healthy subjects. We performed MBW in 8 healthy subjects (4 women, 4 men; age = 43 ± 15 yr) with normal pulmonary function (FEV 1 = 98 ± 6% predicted) using 10% argon as a tracer gas and oxygen concentrations of 12.5%, 21%, or 90%. MBW was performed in accordance with ERS-ATS guidelines. Subjects initially inspired air followed by a wash-in of test gas. Tests were performed in balanced order in triplicate. Gas concentrations were measured at the mouth, and argon signals rescaled to mimic a N 2 washout, and analyzed to determine the distribution of specific ventilation (SV). Heterogeneity was characterized by the width of a log-Gaussian fit of the SV distribution and from S acin and S cond indexes derived from the phase III slope. There were no significant differences in the ventilation heterogeneity due to altered inspired oxygen: histogram width (hypoxia 0.57 ± 0.11, normoxia 0.60 ± 0.08, hyperoxia 0.59 ± 0.09, P = 0.51), S cond (hypoxia 0.014 ± 0.011, normoxia 0.012 ± 0.015, hyperoxia 0.010 ± 0.011, P = 0.34), or S acin (hypoxia 0.11 ± 0.04, normoxia 0.10 ± 0.03, hyperoxia 0.12 ± 0.03, P = 0.23). Functional residual capacity was increased in hypoxia ( P = 0.04) and dead space increased in hyperoxia ( P = 0.0001) compared with the other conditions. The acute use of 100% oxygen in MBW or MRI is unlikely to affect ventilation heterogeneity. NEW & NOTEWORTHY Hyperoxia is used to measure the distribution of ventilation in imaging and MBW but may alter the underlying ventilation distribution. We used MBW to evaluate the effect of inspired oxygen concentration on the ventilation distribution using 10% argon as a tracer. Short-duration exposure to hypoxia (12.5% oxygen) and hyperoxia (90% oxygen) during MBW had no significant effect on ventilation heterogeneity, suggesting that hyperoxia can be used to assess the ventilation distribution. Copyright © 2017 the American Physiological Society.

Accounting for Heterogeneous-Phase Chemistry in Air Quality Models - Research Needs and Applications

EPA Science Inventory

Understanding the extent to which heterogeneous chemical reactions affect the burden and distribution of atmospheric pollutants is important because heterogeneous surfaces are ubiquitous throughout our environment. They include materials such as aerosol particles, clouds and fog,...

Towards a Heterogeneous, Polystore-like Data Architecture for the US Department of Veteran Affairs (VA) Enterprise Analytics

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

Begoli, Edmon; Bates, Jack; Kistler, Derek E

The Polystore architecture revisits the federated approach to access and querying of the standalone, independent databases in the uniform and optimized fashion, but this time in the context of heterogeneous data and specialized analyses. In the light of this architectural philosophy, and in the light of the major data architecture development efforts at the US Department of Veterans Administration (VA), we discuss the need for the heterogeneous data store consisting of the large relational data warehouse, an image and text datastore, and a peta-scale genomic repository. The VA's heterogeneous datastore would, to a larger or smaller degree, follow the architecturalmore » blueprint proposed by the polystore architecture. To this end, we discuss the current state of the data architecture at VA, architectural alternatives for development of the heterogeneous datastore, the anticipated challenges, and the drawbacks and benefits of adopting the polystore architecture.« less

QuakeSim 2.0

NASA Technical Reports Server (NTRS)

Donnellan, Andrea; Parker, Jay W.; Lyzenga, Gregory A.; Granat, Robert A.; Norton, Charles D.; Rundle, John B.; Pierce, Marlon E.; Fox, Geoffrey C.; McLeod, Dennis; Ludwig, Lisa Grant

2012-01-01

QuakeSim 2.0 improves understanding of earthquake processes by providing modeling tools and integrating model applications and various heterogeneous data sources within a Web services environment. QuakeSim is a multisource, synergistic, data-intensive environment for modeling the behavior of earthquake faults individually, and as part of complex interacting systems. Remotely sensed geodetic data products may be explored, compared with faults and landscape features, mined by pattern analysis applications, and integrated with models and pattern analysis applications in a rich Web-based and visualization environment. Integration of heterogeneous data products with pattern informatics tools enables efficient development of models. Federated database components and visualization tools allow rapid exploration of large datasets, while pattern informatics enables identification of subtle, but important, features in large data sets. QuakeSim is valuable for earthquake investigations and modeling in its current state, and also serves as a prototype and nucleus for broader systems under development. The framework provides access to physics-based simulation tools that model the earthquake cycle and related crustal deformation. Spaceborne GPS and Inter ferometric Synthetic Aperture (InSAR) data provide information on near-term crustal deformation, while paleoseismic geologic data provide longerterm information on earthquake fault processes. These data sources are integrated into QuakeSim's QuakeTables database system, and are accessible by users or various model applications. UAVSAR repeat pass interferometry data products are added to the QuakeTables database, and are available through a browseable map interface or Representational State Transfer (REST) interfaces. Model applications can retrieve data from Quake Tables, or from third-party GPS velocity data services; alternatively, users can manually input parameters into the models. Pattern analysis of GPS and seismicity data has proved useful for mid-term forecasting of earthquakes, and for detecting subtle changes in crustal deformation. The GPS time series analysis has also proved useful as a data-quality tool, enabling the discovery of station anomalies and data processing and distribution errors. Improved visualization tools enable more efficient data exploration and understanding. Tools provide flexibility to science users for exploring data in new ways through download links, but also facilitate standard, intuitive, and routine uses for science users and end users such as emergency responders.

Multiscale characteristics of mechanical and mineralogical heterogeneity using nanoindentation and Maps Mineralogy in Mancos Shale

NASA Astrophysics Data System (ADS)

Yoon, H.; Mook, W. M.; Dewers, T. A.

2017-12-01

Multiscale characteristics of textural and compositional (e.g., clay, cement, organics, etc.) heterogeneity profoundly influence the mechanical properties of shale. In particular, strongly anisotropic (i.e., laminated) heterogeneities are often observed to have a significant influence on hydrological and mechanical properties. In this work, we investigate a sample of the Cretaceous Mancos Shale to explore the importance of lamination, cements, organic content, and the spatial distribution of these characteristics. For compositional and structural characterization, the mineralogical distribution of thin core sample polished by ion-milling is analyzed using QEMSCAN® with MAPS MineralogyTM (developed by FEI Corporoation). Based on mineralogy and organic matter distribution, multi-scale nanoindentation testing was performed to directly link compositional heterogeneity to mechanical properties. With FIB-SEM (3D) and high-magnitude SEM (2D) images, key nanoindentation patterns are analyzed to evaluate elastic and plastic responses. Combined with MAPs Mineralogy data and fine-resolution BSE images, nanoindentation results are explained as a function of compositional and structural heterogeneity. Finite element modeling is used to quantitatively evaluate the link between the heterogeneity and mechanical behavior during nanoindentation. In addition, the spatial distribution of compositional heterogeneity, anisotropic bedding patterns, and mechanical anisotropy are employed as inputs for multiscale brittle fracture simulations using a phase field model. Comparison of experimental and numerical simulations reveal that proper incorporation of additional material information, such as bedding layer thickness and other geometrical attributes of the microstructures, may yield improvements on the numerical predictions of the mesoscale fracture patterns and hence the macroscopic effective toughness. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Speeding-up Bioinformatics Algorithms with Heterogeneous Architectures: Highly Heterogeneous Smith-Waterman (HHeterSW).

PubMed

Gálvez, Sergio; Ferusic, Adis; Esteban, Francisco J; Hernández, Pilar; Caballero, Juan A; Dorado, Gabriel

2016-10-01

The Smith-Waterman algorithm has a great sensitivity when used for biological sequence-database searches, but at the expense of high computing-power requirements. To overcome this problem, there are implementations in literature that exploit the different hardware-architectures available in a standard PC, such as GPU, CPU, and coprocessors. We introduce an application that splits the original database-search problem into smaller parts, resolves each of them by executing the most efficient implementations of the Smith-Waterman algorithms in different hardware architectures, and finally unifies the generated results. Using non-overlapping hardware allows simultaneous execution, and up to 2.58-fold performance gain, when compared with any other algorithm to search sequence databases. Even the performance of the popular BLAST heuristic is exceeded in 78% of the tests. The application has been tested with standard hardware: Intel i7-4820K CPU, Intel Xeon Phi 31S1P coprocessors, and nVidia GeForce GTX 960 graphics cards. An important increase in performance has been obtained in a wide range of situations, effectively exploiting the available hardware.

The Battle Command Sustainment Support System: Initial Analysis Report

DTIC Science & Technology

2016-09-01

diagnostic monitoring, asynchronous commits, and others. The other components of the NEDP include a main forwarding gateway /web server and one or more...NATIONAL ENTERPRISE DATA PORTAL ANALYSIS The NEDP is comprised of an Oracle Database 10g referred to as the National Data Server and several other...data forwarding gateways (DFG). Together, with the Oracle Database 10g, these components provide a heterogeneous data source that aligns various data

Towards Direct Manipulation and Remixing of Massive Data: The EarthServer Approach

NASA Astrophysics Data System (ADS)

Baumann, P.

2012-04-01

Complex analytics on "big data" is one of the core challenges of current Earth science, generating strong requirements for on-demand processing and fil tering of massive data sets. Issues under discussion include flexibility, performance, scalability, and the heterogeneity of the information types invo lved. In other domains, high-level query languages (such as those offered by database systems) have proven successful in the quest for flexible, scalable data access interfaces to massive amounts of data. However, due to the lack of support for many of the Earth science data structures, database systems are only used for registries and catalogs, but not for the bulk of spatio-temporal data. One core information category in this field is given by coverage data. ISO 19123 defines coverages, simplifying, as a representation of a "space-time varying phenomenon". This model can express a large class of Earth science data structures, including rectified and non-rectified rasters, curvilinear grids, point clouds, TINs, general meshes, trajectories, surfaces, and solids. This abstract definition, which is too high-level to establish interoperability, is concretized by the OGC GML 3.2.1 Application Schema for Coverages Standard into an interoperable representation. The OGC Web Coverage Processing Service (WCPS) Standard defines a declarative query language on multi-dimensional raster-type coverages, such as 1D in-situ sensor timeseries, 2D EO imagery, 3D x/y/t image time series and x/y/z geophysical data, 4D x/y/z/t climate and ocean data. Hence, important ingredients for versatile coverage retrieval are given - however, this potential has not been fully unleashed by service architectures up to now. The EU FP7-INFRA project EarthServer, launched in September 2011, aims at enabling standards-based on-demand analytics over the Web for Earth science data based on an integration of W3C XQuery for alphanumeric data and OGC-WCPS for raster data. Ultimately, EarthServer will support all OGC coverage types. The platform used by EarthServer is the rasdaman raster database system. To exploit heterogeneous multi-parallel platforms, automatic request distribution and orchestration is being established. Client toolkits are under development which will allow to quickly compose bespoke interactive clients, ranging from mobile devices over Web clients to high-end immersive virtual reality. The EarthServer platform has been deployed in six large-scale data centres with the aim of setting up Lighthouse Applications addressing all Earth Sciences, including satellite and airborne earth observation as well as use cases from atmosphere, ocean, snow, and ice monitoring, and geology on Earth and Mars. These services, each of which will ultimately host at least 100 TB, will form a peer cloud with distributed query processing for arbitrarily mixing database and in-situ access. With its ability to directly manipulate, analyze and remix massive data, the goal of EarthServer is to lift the data providers' semantic level from data stewardship to service stewardship.

Post-processing of metal matrix composites by friction stir processing

NASA Astrophysics Data System (ADS)

Sharma, Vipin; Singla, Yogesh; Gupta, Yashpal; Raghuwanshi, Jitendra

2018-05-01

In metal matrix composites non-uniform distribution of reinforcement particles resulted in adverse affect on the mechanical properties. It is of great interest to explore post-processing techniques that can eliminate particle distribution heterogeneity. Friction stir processing is a relatively newer technique used for post-processing of metal matrix composites to improve homogeneity in particles distribution. In friction stir processing, synergistic effect of stirring, extrusion and forging resulted in refinement of grains, reduction of reinforcement particles size, uniformity in particles distribution, reduction in microstructural heterogeneity and elimination of defects.

Numerical Model Sensitivity to Heterogeneous Satellite Derived Vegetation Roughness

NASA Technical Reports Server (NTRS)

Jasinski, Michael; Eastman, Joseph; Borak, Jordan

2011-01-01

The sensitivity of a mesoscale weather prediction model to a 1 km satellite-based vegetation roughness initialization is investigated for a domain within the south central United States. Three different roughness databases are employed: i) a control or standard lookup table roughness that is a function only of land cover type, ii) a spatially heterogeneous roughness database, specific to the domain, that was previously derived using a physically based procedure and Moderate Resolution Imaging Spectroradiometer (MODIS) imagery, and iii) a MODIS climatologic roughness database that like (i) is a function only of land cover type, but possesses domain specific mean values from (ii). The model used is the Weather Research and Forecast Model (WRF) coupled to the Community Land Model within the Land Information System (LIS). For each simulation, a statistical comparison is made between modeled results and ground observations within a domain including Oklahoma, Eastern Arkansas, and Northwest Louisiana during a 4-day period within IHOP 2002. Sensitivity analysis compares the impact the three roughness initializations on time-series temperature, precipitation probability of detection (POD), average wind speed, boundary layer height, and turbulent kinetic energy (TKE). Overall, the results indicate that, for the current investigation, replacement of the standard look-up table values with the satellite-derived values statistically improves model performance for most observed variables. Such natural roughness heterogeneity enhances the surface wind speed, PBL height and TKE production up to 10 percent, with a lesser effect over grassland, and greater effect over mixed land cover domains.

WLN's Database: New Directions.

ERIC Educational Resources Information Center

Ziegman, Bruce N.

1988-01-01

Describes features of the Western Library Network's database, including the database structure, authority control, contents, quality control, and distribution methods. The discussion covers changes in distribution necessitated by increasing telecommunications costs and the development of optical data disk products. (CLB)

Characterizing the heterogeneity of tumor tissues from spatially resolved molecular measures

PubMed Central

Zavodszky, Maria I.

2017-01-01

Background Tumor heterogeneity can manifest itself by sub-populations of cells having distinct phenotypic profiles expressed as diverse molecular, morphological and spatial distributions. This inherent heterogeneity poses challenges in terms of diagnosis, prognosis and efficient treatment. Consequently, tools and techniques are being developed to properly characterize and quantify tumor heterogeneity. Multiplexed immunofluorescence (MxIF) is one such technology that offers molecular insight into both inter-individual and intratumor heterogeneity. It enables the quantification of both the concentration and spatial distribution of 60+ proteins across a tissue section. Upon bioimage processing, protein expression data can be generated for each cell from a tissue field of view. Results The Multi-Omics Heterogeneity Analysis (MOHA) tool was developed to compute tissue heterogeneity metrics from MxIF spatially resolved tissue imaging data. This technique computes the molecular state of each cell in a sample based on a pathway or gene set. Spatial states are then computed based on the spatial arrangements of the cells as distinguished by their respective molecular states. MOHA computes tissue heterogeneity metrics from the distributions of these molecular and spatially defined states. A colorectal cancer cohort of approximately 700 subjects with MxIF data is presented to demonstrate the MOHA methodology. Within this dataset, statistically significant correlations were found between the intratumor AKT pathway state diversity and cancer stage and histological tumor grade. Furthermore, intratumor spatial diversity metrics were found to correlate with cancer recurrence. Conclusions MOHA provides a simple and robust approach to characterize molecular and spatial heterogeneity of tissues. Research projects that generate spatially resolved tissue imaging data can take full advantage of this useful technique. The MOHA algorithm is implemented as a freely available R script (see supplementary information). PMID:29190747

Generic Entity Resolution in Relational Databases

NASA Astrophysics Data System (ADS)

Sidló, Csaba István

Entity Resolution (ER) covers the problem of identifying distinct representations of real-world entities in heterogeneous databases. We consider the generic formulation of ER problems (GER) with exact outcome. In practice, input data usually resides in relational databases and can grow to huge volumes. Yet, typical solutions described in the literature employ standalone memory resident algorithms. In this paper we utilize facilities of standard, unmodified relational database management systems (RDBMS) to enhance the efficiency of GER algorithms. We study and revise the problem formulation, and propose practical and efficient algorithms optimized for RDBMS external memory processing. We outline a real-world scenario and demonstrate the advantage of algorithms by performing experiments on insurance customer data.

Counting Patterns in Degenerated Sequences

NASA Astrophysics Data System (ADS)

Nuel, Grégory

Biological sequences like DNA or proteins, are always obtained through a sequencing process which might produce some uncertainty. As a result, such sequences are usually written in a degenerated alphabet where some symbols may correspond to several possible letters (ex: IUPAC DNA alphabet). When counting patterns in such degenerated sequences, the question that naturally arises is: how to deal with degenerated positions ? Since most (usually 99%) of the positions are not degenerated, it is considered harmless to discard the degenerated positions in order to get an observation, but the exact consequences of such a practice are unclear. In this paper, we introduce a rigorous method to take into account the uncertainty of sequencing for biological sequences (DNA, Proteins). We first introduce a Forward-Backward approach to compute the marginal distribution of the constrained sequence and use it both to perform a Expectation-Maximization estimation of parameters, as well as deriving a heterogeneous Markov distribution for the constrained sequence. This distribution is hence used along with known DFA-based pattern approaches to obtain the exact distribution of the pattern count under the constraints. As an illustration, we consider a EST dataset from the EMBL database. Despite the fact that only 1% of the positions in this dataset are degenerated, we show that not taking into account these positions might lead to erroneous observations, further proving the interest of our approach.

Comparative analysis of perioperative complications between a multicenter prospective cervical deformity database and the Nationwide Inpatient Sample database.

PubMed

Passias, Peter G; Horn, Samantha R; Jalai, Cyrus M; Poorman, Gregory; Bono, Olivia J; Ramchandran, Subaraman; Smith, Justin S; Scheer, Justin K; Sciubba, Daniel M; Hamilton, D Kojo; Mundis, Gregory; Oh, Cheongeun; Klineberg, Eric O; Lafage, Virginie; Shaffrey, Christopher I; Ames, Christopher P

2017-11-01

Complication rates for adult cervical deformity are poorly characterized given the complexity and heterogeneity of cases. To compare perioperative complication rates following adult cervical deformity corrective surgery between a prospective multicenter database for patients with cervical deformity (PCD) and the Nationwide Inpatient Sample (NIS). Retrospective review of prospective databases. A total of 11,501 adult patients with cervical deformity (11,379 patients from the NIS and 122 patients from the PCD database). Perioperative medical and surgical complications. The NIS was queried (2001-2013) for cervical deformity discharges for patients ≥18 years undergoing cervical fusions using International Classification of Disease, Ninth Revision (ICD-9) coding. Patients ≥18 years from the PCD database (2013-2015) were selected. Equivalent complications were identified and rates were compared. Bonferroni correction (p<.004) was used for Pearson chi-square. Binary logistic regression was used to evaluate differences in complication rates between databases. A total of 11,379 patients from the NIS database and 122 patiens from the PCD database were identified. Patients from the PCD database were older (62.49 vs. 55.15, p<.001) but displayed similar gender distribution. Intraoperative complication rate was higher in the PCD (39.3%) group than in the NIS (9.2%, p<.001) database. The PCD database had an increased risk of reporting overall complications than the NIS (odds ratio: 2.81, confidence interval: 1.81-4.38). Only device-related complications were greater in the NIS (7.1% vs. 1.1%, p=.007). Patients from the PCD database displayed higher rates of the following complications: peripheral vascular (0.8% vs. 0.1%, p=.001), gastrointestinal (GI) (2.5% vs. 0.2%, p<.001), infection (8.2% vs. 0.5%, p<.001), dural tear (4.1% vs. 0.6%, p<.001), and dysphagia (9.8% vs. 1.9%, p<.001). Genitourinary, wound, and deep veinthrombosis (DVT) complications were similar between databases (p>.004). Based on surgicalapproach, the PCD reported higher GI and neurologic complication rates for combined anterior-posterior procedures (p<.001). For posterior-only procedures, the NIS had more device-related complications (12.4% vs. 0.1%, p=.003), whereas PCD had more infections (9.3% vs. 0.7%, p<.001). Analysis of the surgeon-maintained cervical database revealed higher overall and individual complication rates and higher data granularity. The nationwide database may underestimate complications of patients with adult cervical deformity (ACD) particularly in regard to perioperative surgical details owing to coding and deformity generalizations. The surgeon-maintained database captures the surgical details, but may underestimate some medical complications. Copyright © 2017 Elsevier Inc. All rights reserved.

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

NASA Technical Reports Server (NTRS)

Roussopoulos, N.; Sellis, Timos

1993-01-01

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

Spatial Data Integration Using Ontology-Based Approach

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Formation Learning Control of Multiple Autonomous Underwater Vehicles With Heterogeneous Nonlinear Uncertain Dynamics.

PubMed

Yuan, Chengzhi; Licht, Stephen; He, Haibo

2017-09-26

In this paper, a new concept of formation learning control is introduced to the field of formation control of multiple autonomous underwater vehicles (AUVs), which specifies a joint objective of distributed formation tracking control and learning/identification of nonlinear uncertain AUV dynamics. A novel two-layer distributed formation learning control scheme is proposed, which consists of an upper-layer distributed adaptive observer and a lower-layer decentralized deterministic learning controller. This new formation learning control scheme advances existing techniques in three important ways: 1) the multi-AUV system under consideration has heterogeneous nonlinear uncertain dynamics; 2) the formation learning control protocol can be designed and implemented by each local AUV agent in a fully distributed fashion without using any global information; and 3) in addition to the formation control performance, the distributed control protocol is also capable of accurately identifying the AUVs' heterogeneous nonlinear uncertain dynamics and utilizing experiences to improve formation control performance. Extensive simulations have been conducted to demonstrate the effectiveness of the proposed results.

Towards Semantic e-Science for Traditional Chinese Medicine

PubMed Central

Chen, Huajun; Mao, Yuxin; Zheng, Xiaoqing; Cui, Meng; Feng, Yi; Deng, Shuiguang; Yin, Aining; Zhou, Chunying; Tang, Jinming; Jiang, Xiaohong; Wu, Zhaohui

2007-01-01

Background Recent advances in Web and information technologies with the increasing decentralization of organizational structures have resulted in massive amounts of information resources and domain-specific services in Traditional Chinese Medicine. The massive volume and diversity of information and services available have made it difficult to achieve seamless and interoperable e-Science for knowledge-intensive disciplines like TCM. Therefore, information integration and service coordination are two major challenges in e-Science for TCM. We still lack sophisticated approaches to integrate scientific data and services for TCM e-Science. Results We present a comprehensive approach to build dynamic and extendable e-Science applications for knowledge-intensive disciplines like TCM based on semantic and knowledge-based techniques. The semantic e-Science infrastructure for TCM supports large-scale database integration and service coordination in a virtual organization. We use domain ontologies to integrate TCM database resources and services in a semantic cyberspace and deliver a semantically superior experience including browsing, searching, querying and knowledge discovering to users. We have developed a collection of semantic-based toolkits to facilitate TCM scientists and researchers in information sharing and collaborative research. Conclusion Semantic and knowledge-based techniques are suitable to knowledge-intensive disciplines like TCM. It's possible to build on-demand e-Science system for TCM based on existing semantic and knowledge-based techniques. The presented approach in the paper integrates heterogeneous distributed TCM databases and services, and provides scientists with semantically superior experience to support collaborative research in TCM discipline. PMID:17493289

Spatiotemporal Distribution of β-Amyloid in Alzheimer Disease Is the Result of Heterogeneous Regional Carrying Capacities.

PubMed

Whittington, Alex; Sharp, David J; Gunn, Roger N

2018-05-01

β-amyloid (Aβ) accumulation in the brain is 1 of 2 pathologic hallmarks of Alzheimer disease (AD), and the spatial distribution of Aβ has been studied extensively ex vivo. Methods: We applied mathematical modeling to Aβ in vivo PET imaging data to investigate competing theories of Aβ spread in AD. Results: Our results provided evidence that Aβ accumulation starts in all brain regions simultaneously and that its spatiotemporal distribution is due to heterogeneous regional carrying capacities (regional maximum possible concentration of Aβ) for the aggregated protein rather than to longer-term spreading from seed regions. Conclusion: The in vivo spatiotemporal distribution of Aβ in AD can be mathematically modeled using a logistic growth model in which the Aβ carrying capacity is heterogeneous across the brain but the exponential growth rate and time of half maximal Aβ concentration are constant. © 2018 by the Society of Nuclear Medicine and Molecular Imaging.

Integrating CLIPS applications into heterogeneous distributed systems

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1991-01-01

SOCIAL is an advanced, object-oriented development tool for integrating intelligent and conventional applications across heterogeneous hardware and software platforms. SOCIAL defines a family of 'wrapper' objects called agents, which incorporate predefined capabilities for distributed communication and control. Developers embed applications within agents and establish interactions between distributed agents via non-intrusive message-based interfaces. This paper describes a predefined SOCIAL agent that is specialized for integrating C Language Integrated Production System (CLIPS)-based applications. The agent's high-level Application Programming Interface supports bidirectional flow of data, knowledge, and commands to other agents, enabling CLIPS applications to initiate interactions autonomously, and respond to requests and results from heterogeneous remote systems. The design and operation of CLIPS agents are illustrated with two distributed applications that integrate CLIPS-based expert systems with other intelligent systems for isolating and mapping problems in the Space Shuttle Launch Processing System at the NASA Kennedy Space Center.

Heterogeneous Distributed Computing for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Sunderam, Vaidy S.

1998-01-01

The research supported under this award focuses on heterogeneous distributed computing for high-performance applications, with particular emphasis on computational aerosciences. The overall goal of this project was to and investigate issues in, and develop solutions to, efficient execution of computational aeroscience codes in heterogeneous concurrent computing environments. In particular, we worked in the context of the PVM[1] system and, subsequent to detailed conversion efforts and performance benchmarking, devising novel techniques to increase the efficacy of heterogeneous networked environments for computational aerosciences. Our work has been based upon the NAS Parallel Benchmark suite, but has also recently expanded in scope to include the NAS I/O benchmarks as specified in the NHT-1 document. In this report we summarize our research accomplishments under the auspices of the grant.

Three dimensional simulation of hydrogen chloride and hydrogen fluoride during the Airborne Arctic Stratospheric Expedition

NASA Technical Reports Server (NTRS)

Kaye, Jack A.; Rood, Richard B.; Stolarski, Richard S.; Douglass, Anne R.; Newman, Paul A.; Allen, Dale J.; Larson, Edmund M.; Coffey, Michael T.; Mankin, William G.; Toon, Geoffrey C.

1990-01-01

Simulations of the evolution of stratospheric distributions of hydrogen chloride (HCl) and hydrogen fluoride (HF) have been carried out for the period of the Airborne Arctic Stratospheric Expedition (AASE) with a three-dimensional chemistry-transport model. Simulations were performed assuming only homogeneous gas phase chemistry for HF and both homogeneous gas phase and heterogeneous chemistry for HCl. Results show heterogeneous loss of HCl is needed to provide agreement with infrared column measurements. Estimates of the impact of heterogeneous loss on the global HCl distribution are obtained from the model. Reductions of HCl due to heterogeneous loss are calculated to be localized to regions of high vorticity, even after more than a month of integration.

Toughening by crack bridging in heterogeneous ceramics

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

Curtin, W.A.

1995-05-01

The toughening of a ceramic by crack bridging is considered, including the heterogeneity caused simply by spatial randomness in the bridge locations. The growth of a single planar crack is investigated numerically by representing the microstructure as an array of discrete springs with heterogeneity in the mechanical properties of each spring. The stresses on each microstructural element are determined, for arbitrary configurations of spring properties and heterogeneity, using a lattice Green function technique. For toughening by (heterogeneous) crack bridging for both elastic and Dugdale bridging mechanisms, the following key physical results are found: (1) growing cracks avoid regions which aremore » efficiently bridged, and do not propagate as self-similar penny cracks; (2) crack growth thus proceeds at lower applied stresses in a heterogeneous material than in an ordered material; (3) very little toughening is evident for moderate amounts of crack growth in many cases; and (4) a different R-curve is found for every particular spatial distribution of bridging elements. These results show that material reliability is determined by both the flaw distribution and the ``toughness`` distribution, or local environment, around each flaw. These results also demonstrate that the ``microstructural`` parameters derived from fitting an R-curve to a continuum model may not have an immediate relationship to the actual microstructure; the parameters are ``effective`` parameters that absorb the effects of the heterogeneity. The conceptual issues illuminated by these conclusions must be fully understood and appreciated to further develop microstructure-property relationships in ceramic materials.« less

A Guided Tour of Saada

NASA Astrophysics Data System (ADS)

Michel, L.; Motch, C.; Nguyen Ngoc, H.; Pineau, F. X.

2009-09-01

Saada (http://amwdb.u-strasbg.fr/saada) is a tool for helping astronomers build local archives without writing any code (Michel et al. 2004). Databases created by Saada can host collections of heterogeneous data files. These data collections can also be published in the VO. An overview of the main Saada features is presented in this demo: creation of a basic database, creation of relationships, data searches using SaadaQL, metadata tagging, and use of VO services.

Carrying capacity in a heterogeneous environment with habitat connectivity.

PubMed

Zhang, Bo; Kula, Alex; Mack, Keenan M L; Zhai, Lu; Ryce, Arrix L; Ni, Wei-Ming; DeAngelis, Donald L; Van Dyken, J David

2017-09-01

A large body of theory predicts that populations diffusing in heterogeneous environments reach higher total size than if non-diffusing, and, paradoxically, higher size than in a corresponding homogeneous environment. However, this theory and its assumptions have not been rigorously tested. Here, we extended previous theory to include exploitable resources, proving qualitatively novel results, which we tested experimentally using spatially diffusing laboratory populations of yeast. Consistent with previous theory, we predicted and experimentally observed that spatial diffusion increased total equilibrium population abundance in heterogeneous environments, with the effect size depending on the relationship between r and K. Refuting previous theory, however, we discovered that homogeneously distributed resources support higher total carrying capacity than heterogeneously distributed resources, even with species diffusion. Our results provide rigorous experimental tests of new and old theory, demonstrating how the traditional notion of carrying capacity is ambiguous for populations diffusing in spatially heterogeneous environments. © 2017 John Wiley & Sons Ltd/CNRS.

Carrying capacity in a heterogeneous environment with habitat connectivity

USGS Publications Warehouse

Zhang, Bo; Kula, Alex; Mack, Keenan M.L.; Zhai, Lu; Ryce, Arrix L.; Ni, Wei-Ming; DeAngelis, Donald L.; Van Dyken, J. David

2017-01-01

A large body of theory predicts that populations diffusing in heterogeneous environments reach higher total size than if non-diffusing, and, paradoxically, higher size than in a corresponding homogeneous environment. However, this theory and its assumptions have not been rigorously tested. Here, we extended previous theory to include exploitable resources, proving qualitatively novel results, which we tested experimentally using spatially diffusing laboratory populations of yeast. Consistent with previous theory, we predicted and experimentally observed that spatial diffusion increased total equilibrium population abundance in heterogeneous environments, with the effect size depending on the relationship between r and K. Refuting previous theory, however, we discovered that homogeneously distributed resources support higher total carrying capacity than heterogeneously distributed resources, even with species diffusion. Our results provide rigorous experimental tests of new and old theory, demonstrating how the traditional notion of carrying capacity is ambiguous for populations diffusing in spatially heterogeneous environments.

MalaCards: an integrated compendium for diseases and their annotation

PubMed Central

Rappaport, Noa; Nativ, Noam; Stelzer, Gil; Twik, Michal; Guan-Golan, Yaron; Iny Stein, Tsippi; Bahir, Iris; Belinky, Frida; Morrey, C. Paul; Safran, Marilyn; Lancet, Doron

2013-01-01

Comprehensive disease classification, integration and annotation are crucial for biomedical discovery. At present, disease compilation is incomplete, heterogeneous and often lacking systematic inquiry mechanisms. We introduce MalaCards, an integrated database of human maladies and their annotations, modeled on the architecture and strategy of the GeneCards database of human genes. MalaCards mines and merges 44 data sources to generate a computerized card for each of 16 919 human diseases. Each MalaCard contains disease-specific prioritized annotations, as well as inter-disease connections, empowered by the GeneCards relational database, its searches and GeneDecks set analyses. First, we generate a disease list from 15 ranked sources, using disease-name unification heuristics. Next, we use four schemes to populate MalaCards sections: (i) directly interrogating disease resources, to establish integrated disease names, synonyms, summaries, drugs/therapeutics, clinical features, genetic tests and anatomical context; (ii) searching GeneCards for related publications, and for associated genes with corresponding relevance scores; (iii) analyzing disease-associated gene sets in GeneDecks to yield affiliated pathways, phenotypes, compounds and GO terms, sorted by a composite relevance score and presented with GeneCards links; and (iv) searching within MalaCards itself, e.g. for additional related diseases and anatomical context. The latter forms the basis for the construction of a disease network, based on shared MalaCards annotations, embodying associations based on etiology, clinical features and clinical conditions. This broadly disposed network has a power-law degree distribution, suggesting that this might be an inherent property of such networks. Work in progress includes hierarchical malady classification, ontological mapping and disease set analyses, striving to make MalaCards an even more effective tool for biomedical research. Database URL: http://www.malacards.org/ PMID:23584832

Utilization of Positive and Negative Controls to Examine Comorbid Associations in Observational Database Studies.

PubMed

Desai, Jigar R; Hyde, Craig L; Kabadi, Shaum; St Louis, Matthew; Bonato, Vinicius; Katrina Loomis, A; Galaznik, Aaron; Berger, Marc L

2017-03-01

Opportunities to leverage observational data for precision medicine research are hampered by underlying sources of bias and paucity of methods to handle resulting uncertainty. We outline an approach to account for bias in identifying comorbid associations between 2 rare genetic disorders and type 2 diabetes (T2D) by applying a positive and negative control disease paradigm. Association between 10 common and 2 rare genetic disorders [Hereditary Fructose Intolerance (HFI) and α-1 antitrypsin deficiency] and T2D was compared with the association between T2D and 7 negative control diseases with no established relationship with T2D in 4 observational databases. Negative controls were used to estimate how much bias and variance existed in datasets when no effect should be observed. Unadjusted association for common and rare genetic disorders and T2D was positive and variable in magnitude and distribution in all 4 databases. However, association between negative controls and T2D was 200% greater than expected indicating the magnitude and confidence intervals for comorbid associations are sensitive to systematic bias. A meta-analysis using this method demonstrated a significant association between HFI and T2D but not for α-1 antitrypsin deficiency. For observational studies, when covariate data are limited or ambiguous, positive and negative controls provide a method to account for the broadest level of systematic bias, heterogeneity, and uncertainty. This provides greater confidence in assessing associations between diseases and comorbidities. Using this approach we were able to demonstrate an association between HFI and T2D. Leveraging real-world databases is a promising approach to identify and corroborate potential targets for precision medicine therapies.

Accounting for heterogeneity of nutrient dynamics in riverscapes through spatially distributed models

NASA Astrophysics Data System (ADS)

Wollheim, W. M.; Stewart, R. J.

2011-12-01

Numerous types of heterogeneity exist within river systems, leading to hotspots of nutrient sources, sinks, and impacts embedded within an underlying gradient defined by river size. This heterogeneity influences the downstream propagation of anthropogenic impacts across flow conditions. We applied a river network model to explore how nitrogen saturation at river network scales is influenced by the abundance and distribution of potential nutrient processing hotspots (lakes, beaver ponds, tributary junctions, hyporheic zones) under different flow conditions. We determined that under low flow conditions, whole network nutrient removal is relatively insensitive to the number of hotspots because the underlying river network structure has sufficient nutrient processing capacity. However, hotspots become more important at higher flows and greatly influence the spatial distribution of removal within the network at all flows, suggesting that identification of heterogeneity is critical to develop predictive understanding of nutrient removal processes under changing loading and climate conditions. New temporally intensive data from in situ sensors can potentially help to better understand and constrain these dynamics.

Spatiotemporal Heterogeneity Analysis of Hemorrhagic Fever with Renal Syndrome in China Using Geographically Weighted Regression Models

PubMed Central

Li, Shujuan; Ren, Hongyan; Hu, Wensheng; Lu, Liang; Xu, Xinliang; Zhuang, Dafang; Liu, Qiyong

2014-01-01

Hemorrhagic fever with renal syndrome (HFRS) is an important public health problem in China. The identification of the spatiotemporal pattern of HFRS will provide a foundation for the effective control of the disease. Based on the incidence of HFRS, as well as environmental factors, and social-economic factors of China from 2005–2012, this paper identified the spatiotemporal characteristics of HFRS distribution and the factors that impact this distribution. The results indicate that the spatial distribution of HFRS had a significant, positive spatial correlation. The spatiotemporal heterogeneity was affected by the temperature, precipitation, humidity, NDVI of January, NDVI of August for the previous year, land use, and elevation in 2005–2009. However, these factors did not explain the spatiotemporal heterogeneity of HFRS incidences in 2010–2012. Spatiotemporal heterogeneity of provincial HFRS incidences and its relation to environmental factors would provide valuable information for hygiene authorities to design and implement effective measures for the prevention and control of HFRS in China. PMID:25429681

Performance analysis of static locking in replicated distributed database systems

NASA Technical Reports Server (NTRS)

Kuang, Yinghong; Mukkamala, Ravi

1991-01-01

Data replication and transaction deadlocks can severely affect the performance of distributed database systems. Many current evaluation techniques ignore these aspects, because it is difficult to evaluate through analysis and time consuming to evaluate through simulation. A technique is used that combines simulation and analysis to closely illustrate the impact of deadlock and evaluate performance of replicated distributed database with both shared and exclusive locks.

Characterization of continuously distributed cortical water diffusion rates with a stretched-exponential model.

PubMed

Bennett, Kevin M; Schmainda, Kathleen M; Bennett, Raoqiong Tong; Rowe, Daniel B; Lu, Hanbing; Hyde, James S

2003-10-01

Experience with diffusion-weighted imaging (DWI) shows that signal attenuation is consistent with a multicompartmental theory of water diffusion in the brain. The source of this so-called nonexponential behavior is a topic of debate, because the cerebral cortex contains considerable microscopic heterogeneity and is therefore difficult to model. To account for this heterogeneity and understand its implications for current models of diffusion, a stretched-exponential function was developed to describe diffusion-related signal decay as a continuous distribution of sources decaying at different rates, with no assumptions made about the number of participating sources. DWI experiments were performed using a spin-echo diffusion-weighted pulse sequence with b-values of 500-6500 s/mm(2) in six rats. Signal attenuation curves were fit to a stretched-exponential function, and 20% of the voxels were better fit to the stretched-exponential model than to a biexponential model, even though the latter model had one more adjustable parameter. Based on the calculated intravoxel heterogeneity measure, the cerebral cortex contains considerable heterogeneity in diffusion. The use of a distributed diffusion coefficient (DDC) is suggested to measure mean intravoxel diffusion rates in the presence of such heterogeneity. Copyright 2003 Wiley-Liss, Inc.

Dynamical links between small- and large-scale mantle heterogeneity: Seismological evidence

NASA Astrophysics Data System (ADS)

Frost, Daniel A.; Garnero, Edward J.; Rost, Sebastian

2018-01-01

We identify PKP • PKP scattered waves (also known as P‧ •P‧) from earthquakes recorded at small-aperture seismic arrays at distances less than 65°. P‧ •P‧ energy travels as a PKP wave through the core, up into the mantle, then scatters back down through the core to the receiver as a second PKP. P‧ •P‧ waves are unique in that they allow scattering heterogeneities throughout the mantle to be imaged. We use array-processing methods to amplify low amplitude, coherent scattered energy signals and resolve their incoming direction. We deterministically map scattering heterogeneity locations from the core-mantle boundary to the surface. We use an extensive dataset with sensitivity to a large volume of the mantle and a location method allowing us to resolve and map more heterogeneities than have previously been possible, representing a significant increase in our understanding of small-scale structure within the mantle. Our results demonstrate that the distribution of scattering heterogeneities varies both radially and laterally. Scattering is most abundant in the uppermost and lowermost mantle, and a minimum in the mid-mantle, resembling the radial distribution of tomographically derived whole-mantle velocity heterogeneity. We investigate the spatial correlation of scattering heterogeneities with large-scale tomographic velocities, lateral velocity gradients, the locations of deep-seated hotspots and subducted slabs. In the lowermost 1500 km of the mantle, small-scale heterogeneities correlate with regions of low seismic velocity, high lateral seismic gradient, and proximity to hotspots. In the upper 1000 km of the mantle there is no significant correlation between scattering heterogeneity location and subducted slabs. Between 600 and 900 km depth, scattering heterogeneities are more common in the regions most remote from slabs, and close to hotspots. Scattering heterogeneities show an affinity for regions close to slabs within the upper 200 km of the mantle. The similarity between the distribution of large-scale and small-scale mantle structures suggests a dynamic connection across scales, whereby mantle heterogeneities of all sizes may be directed in similar ways by large-scale convective currents.

Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity.

PubMed

Rubin, Ilan N; Doebeli, Michael

2017-12-21

Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, "bet-hedging" in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into the evolutionary dynamics, effectively guaranteeing eventual branching. Large mutations allow the second order disruptive selection to dominate the first order selection toward phenotypic heterogeneity. Copyright © 2017 Elsevier Ltd. All rights reserved.

REBOCOL (Robotic Calorimetry): An automated NDA (Nondestructive assay) calorimetry and gamma isotopic system

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

Hurd, J.R.; Bonner, C.A.; Ostenak, C.A.

1989-01-01

ROBOCAL, which is presently being developed and tested at Los Alamos National Laboratory, is a full-scale, prototypical robotic system, for remote calorimetric and gamma-ray analysis of special nuclear materials. It integrates a fully automated, multi-drawer, vertical stacker-retriever system for staging unmeasured nuclear materials, and a fully automated gantry robot for computer-based selection and transfer of nuclear materials to calorimetric and gamma-ray measurement stations. Since ROBOCAL is designed for minimal operator intervention, a completely programmed user interface and data-base system are provided to interact with the automated mechanical and assay systems. The assay system is designed to completely integrate calorimetric andmore » gamma-ray data acquisition and to perform state-of-the-art analyses on both homogeneous and heterogeneous distributions of nuclear materials in a wide variety of matrices. 10 refs., 10 figs., 4 tabs.« less

BioMAJ: a flexible framework for databanks synchronization and processing.

PubMed

Filangi, Olivier; Beausse, Yoann; Assi, Anthony; Legrand, Ludovic; Larré, Jean-Marc; Martin, Véronique; Collin, Olivier; Caron, Christophe; Leroy, Hugues; Allouche, David

2008-08-15

Large- and medium-scale computational molecular biology projects require accurate bioinformatics software and numerous heterogeneous biological databanks, which are distributed around the world. BioMAJ provides a flexible, robust, fully automated environment for managing such massive amounts of data. The JAVA application enables automation of the data update cycle process and supervision of the locally mirrored data repository. We have developed workflows that handle some of the most commonly used bioinformatics databases. A set of scripts is also available for post-synchronization data treatment consisting of indexation or format conversion (for NCBI blast, SRS, EMBOSS, GCG, etc.). BioMAJ can be easily extended by personal homemade processing scripts. Source history can be kept via html reports containing statements of locally managed databanks. http://biomaj.genouest.org. BioMAJ is free open software. It is freely available under the CECILL version 2 license.

Architecture Knowledge for Evaluating Scalable Databases

DTIC Science & Technology

2015-01-16

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

Preliminary surficial geologic map database of the Amboy 30 x 60 minute quadrangle, California

USGS Publications Warehouse

Bedford, David R.; Miller, David M.; Phelps, Geoffrey A.

2006-01-01

The surficial geologic map database of the Amboy 30x60 minute quadrangle presents characteristics of surficial materials for an area approximately 5,000 km2 in the eastern Mojave Desert of California. This map consists of new surficial mapping conducted between 2000 and 2005, as well as compilations of previous surficial mapping. Surficial geology units are mapped and described based on depositional process and age categories that reflect the mode of deposition, pedogenic effects occurring post-deposition, and, where appropriate, the lithologic nature of the material. The physical properties recorded in the database focus on those that drive hydrologic, biologic, and physical processes such as particle size distribution (PSD) and bulk density. This version of the database is distributed with point data representing locations of samples for both laboratory determined physical properties and semi-quantitative field-based information. Future publications will include the field and laboratory data as well as maps of distributed physical properties across the landscape tied to physical process models where appropriate. The database is distributed in three parts: documentation, spatial map-based data, and printable map graphics of the database. Documentation includes this file, which provides a discussion of the surficial geology and describes the format and content of the map data, a database 'readme' file, which describes the database contents, and FGDC metadata for the spatial map information. Spatial data are distributed as Arc/Info coverage in ESRI interchange (e00) format, or as tabular data in the form of DBF3-file (.DBF) file formats. Map graphics files are distributed as Postscript and Adobe Portable Document Format (PDF) files, and are appropriate for representing a view of the spatial database at the mapped scale.

Effects of Soil Data and Simulation Unit Resolution on Quantifying Changes of Soil Organic Carbon at Regional Scale with a Biogeochemical Process Model

PubMed Central

Zhang, Liming; Yu, Dongsheng; Shi, Xuezheng; Xu, Shengxiang; Xing, Shihe; Zhao, Yongcong

2014-01-01

Soil organic carbon (SOC) models were often applied to regions with high heterogeneity, but limited spatially differentiated soil information and simulation unit resolution. This study, carried out in the Tai-Lake region of China, defined the uncertainty derived from application of the DeNitrification-DeComposition (DNDC) biogeochemical model in an area with heterogeneous soil properties and different simulation units. Three different resolution soil attribute databases, a polygonal capture of mapping units at 1∶50,000 (P5), a county-based database of 1∶50,000 (C5) and county-based database of 1∶14,000,000 (C14), were used as inputs for regional DNDC simulation. The P5 and C5 databases were combined with the 1∶50,000 digital soil map, which is the most detailed soil database for the Tai-Lake region. The C14 database was combined with 1∶14,000,000 digital soil map, which is a coarse database and is often used for modeling at a national or regional scale in China. The soil polygons of P5 database and county boundaries of C5 and C14 databases were used as basic simulation units. Results project that from 1982 to 2000, total SOC change in the top layer (0–30 cm) of the 2.3 M ha of paddy soil in the Tai-Lake region was +1.48 Tg C, −3.99 Tg C and −15.38 Tg C based on P5, C5 and C14 databases, respectively. With the total SOC change as modeled with P5 inputs as the baseline, which is the advantages of using detailed, polygon-based soil dataset, the relative deviation of C5 and C14 were 368% and 1126%, respectively. The comparison illustrates that DNDC simulation is strongly influenced by choice of fundamental geographic resolution as well as input soil attribute detail. The results also indicate that improving the framework of DNDC is essential in creating accurate models of the soil carbon cycle. PMID:24523922

Distribution of Model-based Multipoint Heterogeneity Lod Scores

PubMed Central

Xing, Chao; Morris, Nathan; Xing, Guan

2011-01-01

The distribution of two-point heterogeneity lod scores (HLOD) has been intensively investigated because the conventional χ2 approximation to the likelihood ratio test is not directly applicable. However, there was no study investigating the distribution of the multipoint HLOD despite its wide application. Here we want to point out that, compared with the two-point HLOD, the multipoint HLOD essentially tests for homogeneity given linkage and follows a relatively simple limiting distribution 12χ02+12χ12, which can be obtained by established statistical theory. We further examine the theoretical result by simulation studies. PMID:21104892

Fine-Scale Habitat Heterogeneity Influences Occupancy in Terrestrial Mammals in a Temperate Region of Australia

PubMed Central

Stirnemann, Ingrid; Mortelliti, Alessio; Gibbons, Philip; Lindenmayer, David B.

2015-01-01

Vegetation heterogeneity is an inherent feature of most ecosystems, characterises the structure of habitat, and is considered an important driver of species distribution patterns. However, quantifying fine-scale heterogeneity of vegetation cover can be time consuming, and therefore it is seldom measured. Here, we determine if heterogeneity is worthwhile measuring, in addition to the amount of cover, when examining species distribution patterns. Further, we investigated the effect of the surrounding landscape heterogeneity on species occupancy. We tested the effect of cover and heterogeneity of trees and shrubs, and the context of the surrounding landscape (number of habitats and distance to an ecotone) on site occupancy of three mammal species (the black wallaby [Wallabia bicolor], the long-nosed bandicoot [Perameles nasuta], and the bush rat [Rattus fuscipes]) within a naturally heterogeneous landscape in a temperate region of Australia. We found that fine-scale heterogeneity of vegetation attributes is an important driver of mammal occurrence of two of these species. Further, we found that, although all three species responded positively to vegetation heterogeneity, different mammals vary in their response to different types of vegetation heterogeneity measurement. For example, the black wallaby responded to the proximity of an ecotone, and the bush rat and the long-nosed bandicoot responded to fine-scale heterogeneity of small tree cover, whereas none of the mammals responded to broad scale heterogeneity (i.e., the number of habitat types). Our results highlight the influence of methodological decisions, such as how heterogeneity vegetation is measured, in quantifying species responses to habitat structures. The findings confirm the importance of choosing meaningful heterogeneity measures when modelling the factors influencing occupancy of the species of interest. PMID:26394327

Design and implementation of a distributed large-scale spatial database system based on J2EE

NASA Astrophysics Data System (ADS)

Gong, Jianya; Chen, Nengcheng; Zhu, Xinyan; Zhang, Xia

2003-03-01

With the increasing maturity of distributed object technology, CORBA, .NET and EJB are universally used in traditional IT field. However, theories and practices of distributed spatial database need farther improvement in virtue of contradictions between large scale spatial data and limited network bandwidth or between transitory session and long transaction processing. Differences and trends among of CORBA, .NET and EJB are discussed in details, afterwards the concept, architecture and characteristic of distributed large-scale seamless spatial database system based on J2EE is provided, which contains GIS client application, web server, GIS application server and spatial data server. Moreover the design and implementation of components of GIS client application based on JavaBeans, the GIS engine based on servlet, the GIS Application server based on GIS enterprise JavaBeans(contains session bean and entity bean) are explained.Besides, the experiments of relation of spatial data and response time under different conditions are conducted, which proves that distributed spatial database system based on J2EE can be used to manage, distribute and share large scale spatial data on Internet. Lastly, a distributed large-scale seamless image database based on Internet is presented.

Comparison of the Frontier Distributed Database Caching System to NoSQL Databases

NASA Astrophysics Data System (ADS)

Dykstra, Dave

2012-12-01

One of the main attractions of non-relational “NoSQL” databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It also compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.

Comparison of the Frontier Distributed Database Caching System to NoSQL Databases

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

Dykstra, Dave

One of the main attractions of non-relational NoSQL databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It alsomore » compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.« less

The ATLAS TAGS database distribution and management - Operational challenges of a multi-terabyte distributed database

NASA Astrophysics Data System (ADS)

Viegas, F.; Malon, D.; Cranshaw, J.; Dimitrov, G.; Nowak, M.; Nairz, A.; Goossens, L.; Gallas, E.; Gamboa, C.; Wong, A.; Vinek, E.

2010-04-01

The TAG files store summary event quantities that allow a quick selection of interesting events. This data will be produced at a nominal rate of 200 Hz, and is uploaded into a relational database for access from websites and other tools. The estimated database volume is 6TB per year, making it the largest application running on the ATLAS relational databases, at CERN and at other voluntary sites. The sheer volume and high rate of production makes this application a challenge to data and resource management, in many aspects. This paper will focus on the operational challenges of this system. These include: uploading the data from files to the CERN's and remote sites' databases; distributing the TAG metadata that is essential to guide the user through event selection; controlling resource usage of the database, from the user query load to the strategy of cleaning and archiving of old TAG data.

Brief Report: Databases in the Asia-Pacific Region: The Potential for a Distributed Network Approach.

PubMed

Lai, Edward Chia-Cheng; Man, Kenneth K C; Chaiyakunapruk, Nathorn; Cheng, Ching-Lan; Chien, Hsu-Chih; Chui, Celine S L; Dilokthornsakul, Piyameth; Hardy, N Chantelle; Hsieh, Cheng-Yang; Hsu, Chung Y; Kubota, Kiyoshi; Lin, Tzu-Chieh; Liu, Yanfang; Park, Byung Joo; Pratt, Nicole; Roughead, Elizabeth E; Shin, Ju-Young; Watcharathanakij, Sawaeng; Wen, Jin; Wong, Ian C K; Yang, Yea-Huei Kao; Zhang, Yinghong; Setoguchi, Soko

2015-11-01

This study describes the availability and characteristics of databases in Asian-Pacific countries and assesses the feasibility of a distributed network approach in the region. A web-based survey was conducted among investigators using healthcare databases in the Asia-Pacific countries. Potential survey participants were identified through the Asian Pharmacoepidemiology Network. Investigators from a total of 11 databases participated in the survey. Database sources included four nationwide claims databases from Japan, South Korea, and Taiwan; two nationwide electronic health records from Hong Kong and Singapore; a regional electronic health record from western China; two electronic health records from Thailand; and cancer and stroke registries from Taiwan. We identified 11 databases with capabilities for distributed network approaches. Many country-specific coding systems and terminologies have been already converted to international coding systems. The harmonization of health expenditure data is a major obstacle for future investigations attempting to evaluate issues related to medical costs.

Performance analysis of static locking in replicated distributed database systems

NASA Technical Reports Server (NTRS)

Kuang, Yinghong; Mukkamala, Ravi

1991-01-01

Data replications and transaction deadlocks can severely affect the performance of distributed database systems. Many current evaluation techniques ignore these aspects, because it is difficult to evaluate through analysis and time consuming to evaluate through simulation. Here, a technique is discussed that combines simulation and analysis to closely illustrate the impact of deadlock and evaluate performance of replicated distributed databases with both shared and exclusive locks.

A Database for Decision-Making in Training and Distributed Learning Technology

DTIC Science & Technology

1998-04-01

developer must answer these questions: ♦ Who will develop the courseware? Should we outsource ? ♦ What media should we use? How much will it cost? ♦ What...to develop , the database can be useful for answering staffing questions and planning transitions to technology- assisted courses. The database...of distributed learning curricula in com- parison to traditional methods. To develop a military-wide distributed learning plan, the existing course

Heterogeneity in the distribution of genetically modified and conventional oilseed rape within fields and seed lots.

PubMed

Begg, Graham S; Elliott, Martin J; Cullen, Danny W; Iannetta, Pietro P M; Squire, Geoff R

2008-10-01

The implementation of co-existence in the commercialisation of GM crops requires GM and non-GM products to be segregated in production and supply. However, maintaining segregation in oilseed rape will be made difficult by the highly persistent nature of this species. An understanding of its population dynamics is needed to predict persistence and develop potential strategies for control, while to ensure segregation is being achieved, the production of GM oilseed rape must be accompanied by the monitoring of GM levels in crop or seed populations. Heterogeneity in the spatial distribution of oilseed rape has the potential to affect both control and monitoring and, although a universal phenomenon in arable weeds and harvested seed lots, spatial heterogeneity in oilseed rape populations remains to be demonstrated and quantified. Here we investigate the distribution of crop and volunteer populations in a commercial field before and during the cultivation of the first conventional oilseed rape (winter) crop since the cultivation of a GM glufosinate-tolerant oilseed rape crop (spring) three years previously. GM presence was detected by ELISA for the PAT protein in each of three morphologically distinguishable phenotypes: autumn germinating crop-type plants (3% GM), autumn-germinating 'regrowths' (72% GM) and spring germinating 'small-type' plants (17% GM). Statistical models (Poisson log-normal and binomial logit-normal) were used to describe the spatial distribution of these populations at multiple spatial scales in the field and of GM presence in the harvested seed lot. Heterogeneity was a consistent feature in the distribution of GM and conventional oilseed rape. Large trends across the field (50 x 400 m) and seed lot (4 x 1.5 x 1.5 m) were observed in addition to small-scale heterogeneity, less than 20 m in the field and 20 cm in the seed lot. The heterogeneity was greater for the 'regrowth' and 'small' phenotypes, which were likely to be volunteers and included most of the GM plants detected, than for the largely non-GM 'crop' phenotype. The implications of the volunteer heterogeneity for field management and GM-sampling are discussed.

Estimating Pore Properties from NMR Relaxation Time Measurements in Heterogeneous Media

NASA Astrophysics Data System (ADS)

Grunewald, E.; Knight, R.

2008-12-01

The link between pore geometry and the nuclear magnetic resonance (NMR) relaxation time T2 is well- established for simple systems but is poorly understood for complex media with heterogeneous pores. Conventional interpretation of NMR relaxation data employs a model of isolated pores in which each hydrogen proton samples only one pore type, and the T2-distribution is directly scaled to estimate a pore-size distribution. During an actual NMR measurement, however, each proton diffuses through a finite volume of the pore network, and so may sample multiple pore types encountered within this diffusion cell. For cases in which heterogeneous pores are strongly coupled by diffusion, the meaning of the T2- distribution is not well understood and further research is required to determine how such measurements should be interpreted. In this study we directly investigate the implications of pore coupling in two groups of laboratory NMR experiments. We conduct two suites of experiments, in which samples are synthesized to exhibit a range of pore coupling strengths using two independent approaches: (a) varying the scale of the diffusion cell and (b) varying the scale over which heterogeneous pores are encountered. In the first set of experiments, we vary the scale of the diffusion cell in silica gels which have a bimodal pore-size distribution comprised of intragrannular micropores and much larger intergrannular pores. The untreated gel exhibits strong pore coupling with a single broad peak observed in the T2-distribution. By treating the gel with varied amounts of paramagnetic iron surface coatings, we decrease the surface relaxation time, T2S, and effectively decrease both the size of the diffusion cell and the degree of pore coupling. As more iron is coated to the grain surfaces, we observe a separation of the broad T2-distribution into two peaks that more accurately represent the true bimodal pore-size distribution. In the second set of experiments, we vary the scale over which heterogeneous pores are encountered in bimodal grain packs of pure quartz (long T2S) and hematite (short T2S). The scale of heterogeneity is varied by changing the mean grain size and relative mineral concentrations. When the mean grain size is small and the mineral concentrations are comparable, the T2-distribution is roughly monomodal indicating strong pore coupling. As the grain size is increased or the mineral concentrations are made increasingly uneven, the T2- distribution develops a bimodal character, more representative of the actual distribution of pore types. Numerical simulations of measurements in both experiment groups allow us to more closely investigate how the relaxing magnetization evolves in both time and space. Collectively, these experiments provide important insights into the effects of pore coupling on NMR measurements in heterogeneous systems and contribute to our ultimate goal of improving the interpretation of these data in complex near-surface sediments.

Querying XML Data with SPARQL

NASA Astrophysics Data System (ADS)

Bikakis, Nikos; Gioldasis, Nektarios; Tsinaraki, Chrisa; Christodoulakis, Stavros

SPARQL is today the standard access language for Semantic Web data. In the recent years XML databases have also acquired industrial importance due to the widespread applicability of XML in the Web. In this paper we present a framework that bridges the heterogeneity gap and creates an interoperable environment where SPARQL queries are used to access XML databases. Our approach assumes that fairly generic mappings between ontology constructs and XML Schema constructs have been automatically derived or manually specified. The mappings are used to automatically translate SPARQL queries to semantically equivalent XQuery queries which are used to access the XML databases. We present the algorithms and the implementation of SPARQL2XQuery framework, which is used for answering SPARQL queries over XML databases.

Lattice Boltzmann Simulation of Electroosmotic Micromixing by Heterogeneous Surface Charge

NASA Astrophysics Data System (ADS)

Tang, G. H.; Wang, F. F.; Tao, W. Q.

Microelectroosmotic flow is usually restricted to low Reynolds number regime, and mixing in these microfluidic systems becomes problematic due to the negligible inertial effects. To gain an improved understanding of mixing enhancement in microchannels patterned with heterogeneous surface charge, the lattice Boltzmann method has been employed to obtain the electric potential distribution in the electrolyte, the flow field, and the species concentration distribution, respectively. The simulation results show that heterogeneous surfaces can significantly disturb the streamlines leading to apparently substantial improvements in mixing. However, the introduction of such a feature can reduce the mass flow rate in the channel. The reduction in flow rate effectively prolongs the available mixing time when the flow passes through the channel and the observed mixing enhancement by heterogeneous surfaces partly results from longer mixing time.

Worldwide increased prevalence of human adenovirus type 3 (HAdV-3) respiratory infections is well correlated with heterogeneous hypervariable regions (HVRs) of hexon.

PubMed

Haque, Ezazul; Banik, Urmila; Monwar, Tahmina; Anthony, Leela; Adhikary, Arun Kumar

2018-01-01

Human adenovirus type 3 (HAdV-3) respiratory infections occurs worldwide in both children and adults, leading to severe morbidity and mortality, particularly in the paediatric age group and especially in neonates. During HAdV infection, neutralizing antibodies are formed against the epitopes located in the hyper variable regions (HVRs) of the hexon protein. These neutralizing antibodies provide protection against reinfection by viruses of the same type. Therefore it is reasonable to speculate that variations of HAdV-3 in the HVRs could impair the immunity acquired by previous infection with a different strain with variation in its HVRs. HAdV-3 has recently become the major agent of acute respiratory infection worldwide, being responsible for 15% to 87% of all adenoviral respiratory infections. However, despite the increased prevalence of HAdV-3 as respiratory pathogen, the diversity of hexon proteins in circulating strains remains unexplored. This study was designed to explore the variation in HVRs of hexon among globally distributed strains of HAdV-3 as well as to discover possible relationship among them, thus possibly shedding light on the cause for the increased prevalence of HAdV-3. In this study, for the first time we analysed the hexon proteins of all 248 available strains of HAdV-3 from the NCBI database and compared them with those of the HAdV-3 prototype (GB stain). We found that the HVRs of HAdV-3 strains circulating worldwide were highly heterogeneous and have been mutating continuously since -their original isolation. Based on their immense heterogeneity, the strains can be categorized into 25 hexon variants (3Hv-1 to 3Hv-25), 4 of which (3Hv-1 to 3Hv-4) comprises 80% of the strains. This heterogeneity may explain why HAdV-3 has become the most prevalent HAdVs type worldwide. The heterogeneity of hexon proteins also shows that the development of a vaccine against HAdV-3 might be challenging. The data on hexon variants provided here may be useful for the future epidemiological study of HAdV-3 infection.

Breast dose in mammography is about 30% lower when realistic heterogeneous glandular distributions are considered

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

Hernandez, Andrew M., E-mail: amhern@ucdavis.edu; Seibert, J. Anthony; Boone, John M.

2015-11-15

Purpose: Current dosimetry methods in mammography assume that the breast is comprised of a homogeneous mixture of glandular and adipose tissues. Three-dimensional (3D) dedicated breast CT (bCT) data sets were used previously to assess the complex anatomical structure within the breast, characterizing the statistical distribution of glandular tissue in the breast. The purpose of this work was to investigate the effect of bCT-derived heterogeneous glandular distributions on dosimetry in mammography. Methods: bCT-derived breast diameters, volumes, and 3D fibroglandular distributions were used to design realistic compressed breast models comprised of heterogeneous distributions of glandular tissue. The bCT-derived glandular distributions were fitmore » to biGaussian functions and used as probability density maps to assign the density distributions within compressed breast models. The MCNPX 2.6.0 Monte Carlo code was used to estimate monoenergetic normalized mean glandular dose “DgN(E)” values in mammography geometry. The DgN(E) values were then weighted by typical mammography x-ray spectra to determine polyenergetic DgN (pDgN) coefficients for heterogeneous (pDgN{sub hetero}) and homogeneous (pDgN{sub homo}) cases. The dependence of estimated pDgN values on phantom size, volumetric glandular fraction (VGF), x-ray technique factors, and location of the heterogeneous glandular distributions was investigated. Results: The pDgN{sub hetero} coefficients were on average 35.3% (SD, 4.1) and 24.2% (SD, 3.0) lower than the pDgN{sub homo} coefficients for the Mo–Mo and W–Rh x-ray spectra, respectively, across all phantom sizes and VGFs when the glandular distributions were centered within the breast phantom in the coronal plane. At constant breast size, increasing VGF from 7.3% to 19.1% lead to a reduction in pDgN{sub hetero} relative to pDgN{sub homo} of 23.6%–27.4% for a W–Rh spectrum. Displacement of the glandular distribution, at a distance equal to 10% of the compressed breast width in the superior and inferior directions, resulted in a 37.3% and a −26.6% change in the pDgN{sub hetero} coefficient, respectively, relative to the centered distribution for the Mo–Mo spectrum. Lateral displacement of the glandular distribution, at a distance equal to 10% of the compressed breast width, resulted in a 1.5% change in the pDgN{sub hetero} coefficient relative to the centered distribution for the W–Rh spectrum. Conclusions: Introducing bCT-derived heterogeneous glandular distributions into mammography phantom design resulted in decreased glandular dose relative to the widely used homogeneous assumption. A homogeneous distribution overestimates the amount of glandular tissue near the entrant surface of the breast, where dose deposition is exponentially higher. While these findings are based on clinically measured distributions of glandular tissue using a large cohort of women, future work is required to improve the classification of glandular distributions based on breast size and overall glandular fraction.« less

A cross-site comparison of methods used for hydrogeologic characterization of the Galena-Platteville aquifer in Illinois and Wisconsin, with examples from selected Superfund sites

USGS Publications Warehouse

Kay, Robert T.; Mills, Patrick C.; Dunning, Charles P.; Yeskis, Douglas J.; Ursic, James R.; Vendl, Mark

2004-01-01

The effectiveness of 28 methods used to characterize the fractured Galena-Platteville aquifer at eight sites in northern Illinois and Wisconsin is evaluated. Analysis of government databases, previous investigations, topographic maps, aerial photographs, and outcrops was essential to understanding the hydrogeology in the area to be investigated. The effectiveness of surface-geophysical methods depended on site geology. Lithologic logging provided essential information for site characterization. Cores were used for stratigraphy and geotechnical analysis. Natural-gamma logging helped identify the effect of lithology on the location of secondary- permeability features. Caliper logging identified large secondary-permeability features. Neutron logs identified trends in matrix porosity. Acoustic-televiewer logs identified numerous secondary-permeability features and their orientation. Borehole-camera logs also identified a number of secondary-permeability features. Borehole ground-penetrating radar identified lithologic and secondary-permeability features. However, the accuracy and completeness of this method is uncertain. Single-point-resistance, density, and normal resistivity logs were of limited use. Water-level and water-quality data identified flow directions and indicated the horizontal and vertical distribution of aquifer permeability and the depth of the permeable features. Temperature, spontaneous potential, and fluid-resistivity logging identified few secondary-permeability features at some sites and several features at others. Flowmeter logging was the most effective geophysical method for characterizing secondary-permeability features. Aquifer tests provided insight into the permeability distribution, identified hydraulically interconnected features, the presence of heterogeneity and anisotropy, and determined effective porosity. Aquifer heterogeneity prevented calculation of accurate hydraulic properties from some tests. Different methods, such as flowmeter logging and slug testing, occasionally produced different interpretations. Aquifer characterization improved with an increase in the number of data points, the period of data collection, and the number of methods used.

Imaging genetics paradigms in depression research: Systematic review and meta-analysis.

PubMed

Pereira, Lícia P; Köhler, Cristiano A; Stubbs, Brendon; Miskowiak, Kamilla W; Morris, Gerwyn; de Freitas, Bárbara P; Thompson, Trevor; Fernandes, Brisa S; Brunoni, André R; Maes, Michael; Pizzagalli, Diego A; Carvalho, André F

2018-05-17

Imaging genetics studies involving participants with major depressive disorder (MDD) have expanded. Nevertheless, findings have been inconsistent. Thus, we conducted a systematic review and meta-analysis of imaging genetics studies that enrolled MDD participants across major databases through June 30th, 2017. Sixty-five studies met eligibility criteria (N = 4034 MDD participants and 3293 controls), and there was substantial between-study variability in the methodological quality of included studies. However, few replicated findings emerged from this literature with only 22 studies providing data for meta-analyses (882 participants with MDD and 616 controls). Total hippocampal volumes did not significantly vary in MDD participants or controls carrying either the BDNF Val66Met 'Met' (386 participants with MDD and 376 controls) or the 5-HTTLPR short 'S' (310 participants with MDD and 230 controls) risk alleles compared to non-carriers. Heterogeneity across studies was explored through meta-regression and subgroup analyses. Gender distribution, the use of medications, segmentation methods used to measure the hippocampus, and age emerged as potential sources of heterogeneity across studies that assessed the association of 5-HTTLPR short 'S' alleles and hippocampal volumes. Our data also suggest that the methodological quality of included studies, publication year, and the inclusion of brain volume as a covariate contributed to the heterogeneity of studies that assessed the association of the BDNF Val66Met 'Met' risk allele and hippocampal volumes. In exploratory voxel-wise meta-analyses, MDD participants carrying the 5-HTTLPR short 'S' allele had white matter microstructural abnormalities predominantly in the corpus callosum, while carriers of the BDNF Val66Met 'Met' allele had larger gray matter volumes and hyperactivation of the right middle frontal gyrus compared to non-carriers. In conclusion, few replicated findings emerged from imaging genetics studies that included participants with MDD. Nevertheless, we explored and identified specific sources of heterogeneity across studies, which could provide insights to enhance the reproducibility of this emerging field. Copyright © 2018 Elsevier Inc. All rights reserved.

The effect of dose heterogeneity on radiation risk in medical imaging.

PubMed

Samei, Ehsan; Li, Xiang; Chen, Baiyu; Reiman, Robert

2013-06-01

The current estimations of risk associated with medical imaging procedures rely on assessing the organ dose via direct measurements or simulation. The dose to each organ is assumed to be homogeneous. To take into account the differences in radiation sensitivities, the mean organ doses are weighted by a corresponding tissue-weighting coefficients provided by ICRP to calculate the effective dose, which has been used as a surrogate of radiation risk. However, those coefficients were derived under the assumption of a homogeneous dose distribution within each organ. That assumption is significantly violated in most medical-imaging procedures. In helical chest CT, for example, superficial organs (e.g. breasts) demonstrate a heterogeneous dose distribution, whereas organs on the peripheries of the irradiation field (e.g. liver) might possess a discontinuous dose profile. Projection radiography and mammography involve an even higher level of organ dose heterogeneity spanning up to two orders of magnitude. As such, mean dose or point measured dose values do not reflect the maximum energy deposited per unit volume of the organ. In this paper, the magnitude of the dose heterogeneity in both CT and projection X-ray imaging was reported, using Monte Carlo methods. The lung dose demonstrated factors of 1.7 and 2.2 difference between the mean and maximum dose for chest CT and radiography, respectively. The corresponding values for the liver were 1.9 and 3.5. For mammography and breast tomosynthesis, the difference between mean glandular dose and maximum glandular dose was 3.1. Risk models based on the mean dose were found to provide a reasonable reflection of cancer risk. However, for leukaemia, they were found to significantly under-represent the risk when the organ dose distribution is heterogeneous. A systematic study is needed to develop a risk model for heterogeneous dose distributions.

Distribution System Upgrade Unit Cost Database

DOE Data Explorer

Horowitz, Kelsey

2017-11-30

This database contains unit cost information for different components that may be used to integrate distributed photovotaic (D-PV) systems onto distribution systems. Some of these upgrades and costs may also apply to integration of other distributed energy resources (DER). Which components are required, and how many of each, is system-specific and should be determined by analyzing the effects of distributed PV at a given penetration level on the circuit of interest in combination with engineering assessments on the efficacy of different solutions to increase the ability of the circuit to host additional PV as desired. The current state of the distribution system should always be considered in these types of analysis. The data in this database was collected from a variety of utilities, PV developers, technology vendors, and published research reports. Where possible, we have included information on the source of each data point and relevant notes. In some cases where data provided is sensitive or proprietary, we were not able to specify the source, but provide other information that may be useful to the user (e.g. year, location where equipment was installed). NREL has carefully reviewed these sources prior to inclusion in this database. Additional information about the database, data sources, and assumptions is included in the "Unit_cost_database_guide.doc" file included in this submission. This guide provides important information on what costs are included in each entry. Please refer to this guide before using the unit cost database for any purpose.

Shock Wave Propagation in Cementitious Materials at Micro/Meso Scales

DTIC Science & Technology

2015-08-31

ABSTRACT 16. SECURITY CLASSIFICATION OF: Shock wave response of heterogeneous materials like cement and concrete is greatly influenced by the...constituents and their statistical distributions. The microstructure of cement is complex due to the presence of unhydrated water, nano /micro pores, and other...heterogeneous materials like cement and concrete is greatly influenced by the constituents and their statistical distributions. The microstructure of cement

Spatial P heterogeneity in forest soil: Influence on microbial P uptake and community structure

NASA Astrophysics Data System (ADS)

Zilla, Thomas; Angulo-Schipper, Bridith; Méndez, Juan Carlos; Dippold, Michaela A.; Kuzyakov, Yakov; Spielvogel, Sandra

2017-04-01

Other than nitrogen, phosphorus (P) is the most important growth limiting nutrient in soils. Yet, little information is available concerning the spatial heterogeneity of P content in forest soils. More so, the effects of a homogeneous vs. heterogeneous soil P distribution on microbial P acquisition and community structure have yet to be determined. Thus, a rhizotron experiment based on a P-deficient forest soil was conducted to investigate competitive P uptake strategies of microbes. F. sylvatica-bearing rhizotrons were labeled with Fe33PO4, a relatively immobile P source native to the study soil. Homogeneous and heterogeneous P patterns were created to study the effects of spatial P heterogeneity on plant and microbial P acquisition. P mobilization by microorganisms was tracked by an improved 33P-PLFA method, linking 33P incorporation in microbes with changes in microbial community structure in soils in situ. The microbial P uptake was enhanced in rhizotrons with high P availability and in those with a patchy P distribution. Characteristic PLFAs indicate a congregation of beech-associated ectomycorrhizal fungi in P-rich patches. These ectomycorrhizal fungi are likely to strongly increase P mobilization from the used Fe33PO4 in high P habitats. In contrast, habitats with low P availability require a more complex microbial community structure without a dominant group to mobilize this inaccessible P source. Therefore, hotspots of P are likely to promote the efforts of fungal hyphae for P mobilization - an effect which decreases with lower P content. Additionally, gram positive and negative bacteria exhibit a vastly higher P uptake under increasingly patchy P distributions. However, they form a smaller portion of the microbial community than in homogeneously P enriched rhizotrons, suggesting that filamentous organisms benefit from the patchy P distribution. Thus, only a heterogeneous P distribution promotes P acquisition of forest microbial communities from mineral P sources with low bioavailability. These novel insights into the effects of spatial P distributions on forest soil community dynamics will hopefully shed further light on microbial P cycling, thereby helping to tackle the impending global P crisis.|

Pore-scale Investigation of Surfactant Induced Mobilization for the Remediation of LNAPL

NASA Astrophysics Data System (ADS)

Ghosh, J.; Tick, G. R.

2011-12-01

The presence of nonaqueous phase liquids within the subsurface can significantly limit the effectiveness of groundwater remediation. Specifically, light nonaqueous phase liquids (LNAPLs) present unique challenges as they can become "smeared" within zones above and below the water table. The aim of this research is to understand the interfacial phenomena at the pore scale influencing residual saturation of LNAPL distribution as function of media heterogeneity and remediation processes from various aquifer systems. A series of columns were packed with three types of unconsolidated sand of increasing heterogeneity in grain size distribution and were established with residual saturations of light and heavy crude oil fractions, respectively. These columns were then subjected to flooding with 0.1% anionic surfactant solution in various episodes to initiate mobilization and enhanced recovery of NAPL phase contamination. Synchrotron X-ray microtomography (SXM) imaging technology was used to study three-dimensional (3-D) distributions of crude-oil-blobs before and after sequential surfactant flooding events. Results showed that LNAPL blob distributions became more heterogeneous after each subsequent surfactant flooding episode for all porous-media systems. NAPL recovery was most effective from the homogenous porous medium whereby 100% recovery resulted after 5 pore volumes (PVs) of flushing. LNAPL within the mildly heterogeneous porous medium produced a limited but consistent reduction in saturation after each surfactant flooding episode (23% and 43% recovery for light and heavy after the 5-PV flood). The highly heterogeneous porous medium showed greater NAPL recovery potential (42% and 16% for light and heavy) only after multiple pore volumes of flushing, at which point the NAPL blobs become fragmented into the smaller fragments in response to the reduced interfacial tension. The heterogeneity of the porous media (i.e. grain-size distribution) was a dominant control on the NAPL-blob-size-distribution trapped as residual saturation. The mobility of the NAPL blobs, as a result of surfactant flooding, was primarily controlled by the relative permeability of the medium and the reduction of interfacial tension between the wetting phase (water) and NAPL phase.

Djeen (Database for Joomla!'s Extensible Engine): a research information management system for flexible multi-technology project administration.

PubMed

Stahl, Olivier; Duvergey, Hugo; Guille, Arnaud; Blondin, Fanny; Vecchio, Alexandre Del; Finetti, Pascal; Granjeaud, Samuel; Vigy, Oana; Bidaut, Ghislain

2013-06-06

With the advance of post-genomic technologies, the need for tools to manage large scale data in biology becomes more pressing. This involves annotating and storing data securely, as well as granting permissions flexibly with several technologies (all array types, flow cytometry, proteomics) for collaborative work and data sharing. This task is not easily achieved with most systems available today. We developed Djeen (Database for Joomla!'s Extensible Engine), a new Research Information Management System (RIMS) for collaborative projects. Djeen is a user-friendly application, designed to streamline data storage and annotation collaboratively. Its database model, kept simple, is compliant with most technologies and allows storing and managing of heterogeneous data with the same system. Advanced permissions are managed through different roles. Templates allow Minimum Information (MI) compliance. Djeen allows managing project associated with heterogeneous data types while enforcing annotation integrity and minimum information. Projects are managed within a hierarchy and user permissions are finely-grained for each project, user and group.Djeen Component source code (version 1.5.1) and installation documentation are available under CeCILL license from http://sourceforge.net/projects/djeen/files and supplementary material.

Djeen (Database for Joomla!’s Extensible Engine): a research information management system for flexible multi-technology project administration

PubMed Central

2013-01-01

Background With the advance of post-genomic technologies, the need for tools to manage large scale data in biology becomes more pressing. This involves annotating and storing data securely, as well as granting permissions flexibly with several technologies (all array types, flow cytometry, proteomics) for collaborative work and data sharing. This task is not easily achieved with most systems available today. Findings We developed Djeen (Database for Joomla!’s Extensible Engine), a new Research Information Management System (RIMS) for collaborative projects. Djeen is a user-friendly application, designed to streamline data storage and annotation collaboratively. Its database model, kept simple, is compliant with most technologies and allows storing and managing of heterogeneous data with the same system. Advanced permissions are managed through different roles. Templates allow Minimum Information (MI) compliance. Conclusion Djeen allows managing project associated with heterogeneous data types while enforcing annotation integrity and minimum information. Projects are managed within a hierarchy and user permissions are finely-grained for each project, user and group. Djeen Component source code (version 1.5.1) and installation documentation are available under CeCILL license from http://sourceforge.net/projects/djeen/files and supplementary material. PMID:23742665

A Comprehensive Database and Analysis Framework To Incorporate Multiscale Data Types and Enable Integrated Analysis of Bioactive Polyphenols.

PubMed

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

2018-03-05

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

Heterogeneous Systems for Information-Variable Environments (HIVE)

DTIC Science & Technology

2017-05-01

ARL-TR-8027 ● May 2017 US Army Research Laboratory Heterogeneous Systems for Information - Variable Environments (HIVE) by Amar...not return it to the originator. ARL-TR-8027 ● May 2017 US Army Research Laboratory Heterogeneous Systems for Information ...Computational and Information Sciences Directorate, ARL Approved for public release; distribution is unlimited. ii REPORT

Direct Breakthrough Curve Prediction From Statistics of Heterogeneous Conductivity Fields

NASA Astrophysics Data System (ADS)

Hansen, Scott K.; Haslauer, Claus P.; Cirpka, Olaf A.; Vesselinov, Velimir V.

2018-01-01

This paper presents a methodology to predict the shape of solute breakthrough curves in heterogeneous aquifers at early times and/or under high degrees of heterogeneity, both cases in which the classical macrodispersion theory may not be applicable. The methodology relies on the observation that breakthrough curves in heterogeneous media are generally well described by lognormal distributions, and mean breakthrough times can be predicted analytically. The log-variance of solute arrival is thus sufficient to completely specify the breakthrough curves, and this is calibrated as a function of aquifer heterogeneity and dimensionless distance from a source plane by means of Monte Carlo analysis and statistical regression. Using the ensemble of simulated groundwater flow and solute transport realizations employed to calibrate the predictive regression, reliability estimates for the prediction are also developed. Additional theoretical contributions include heuristics for the time until an effective macrodispersion coefficient becomes applicable, and also an expression for its magnitude that applies in highly heterogeneous systems. It is seen that the results here represent a way to derive continuous time random walk transition distributions from physical considerations rather than from empirical field calibration.

Slope stability of bioreactor landfills during leachate injection: effects of heterogeneous and anisotropic municipal solid waste conditions.

PubMed

Giri, Rajiv K; Reddy, Krishna R

2014-03-01

In bioreactor landfills, leachate recirculation can significantly affect the stability of landfill slope due to generation and distribution of excessive pore fluid pressures near side slope. The current design and operation of leachate recirculation systems do not consider the effects of heterogeneous and anisotropic nature of municipal solid waste (MSW) and the increased pore gas pressures in landfilled waste caused due to leachate recirculation on the physical stability of landfill slope. In this study, a numerical two-phase flow model (landfill leachate and gas as immiscible phases) was used to investigate the effects of heterogeneous and anisotropic nature of MSW on moisture distribution and pore-water and capillary pressures and their resulting impacts on the stability of a simplified bioreactor landfill during leachate recirculation using horizontal trench system. The unsaturated hydraulic properties of MSW were considered based on the van Genuchten model. The strength reduction technique was used for slope stability analyses as it takes into account of the transient and spatially varying pore-water and gas pressures. It was concluded that heterogeneous and anisotropic MSW with varied unit weight and saturated hydraulic conductivity significantly influenced the moisture distribution and generation and distribution of pore fluid pressures in landfill and considerably reduced the stability of bioreactor landfill slope. It is recommended that heterogeneous and anisotropic MSW must be considered as it provides a more reliable approach for the design and leachate operations in bioreactor landfills.

Are recent empirical directivity models sufficient in capturing near-fault directivity effect?

NASA Astrophysics Data System (ADS)

Chen, Yen-Shin; Cotton, Fabrice; Pagani, Marco; Weatherill, Graeme; Reshi, Owais; Mai, Martin

2017-04-01

It has been widely observed that the ground motion variability in the near field can be significantly higher than that commonly reported in published GMPEs, and this has been suggested to be a consequence of directivity. To capture the spatial variation in ground motion amplitude and frequency caused by the near-fault directivity effect, several models for engineering applications have been developed using empirical or, more recently, the combination of empirical and simulation data. Many research works have indicated that the large velocity pulses mainly observed in the near-field are primarily related to slip heterogeneity (i.e., asperities), suggesting that the slip heterogeneity is a more dominant controlling factor than the rupture velocity or source rise time function. The first generation of broadband directivity models for application in ground motion prediction do not account for heterogeneity of slip and rupture speed. With the increased availability of strong motion recordings (e.g., NGA-West 2 database) in the near-fault region, the directivity models moved from broadband to narrowband models to include the magnitude dependence of the period of the rupture directivity pulses, wherein the pulses are believed to be closely related to the heterogeneity of slip distribution. After decades of directivity models development, does the latest generation of models - i.e. the one including narrowband directivity models - better capture the near-fault directivity effects, particularly in presence of strong slip heterogeneity? To address this question, a set of simulated motions for an earthquake rupture scenario, with various kinematic slip models and hypocenter locations, are used as a basis for a comparison with the directivity models proposed by the NGA-West 2 project for application with ground motion prediction equations incorporating a narrowband directivity model. The aim of this research is to gain better insights on the accuracy of narrowband directivity models under conditions commonly encountered in the real world. Our preliminary result shows that empirical models including directivity factors better predict physics based ground-motion and their spatial variability than classical empirical models. However, the results clearly indicate that it is still a challenge for the directivity models to capture the strong directivity effect if a high level of slip heterogeneity is involved during the source rupture process.

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

PubMed

Chiba, Hirokazu; Nishide, Hiroyo; Uchiyama, Ikuo

2015-01-01

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

Stochastic analysis of the efficiency of coupled hydraulic-physical barriers to contain solute plumes in highly heterogeneous aquifers

NASA Astrophysics Data System (ADS)

Pedretti, Daniele; Masetti, Marco; Beretta, Giovanni Pietro

2017-10-01

The expected long-term efficiency of vertical cutoff walls coupled to pump-and-treat technologies to contain solute plumes in highly heterogeneous aquifers was analyzed. A well-characterized case study in Italy, with a hydrogeological database of 471 results from hydraulic tests performed on the aquifer and the surrounding 2-km-long cement-bentonite (CB) walls, was used to build a conceptual model and assess a representative remediation site adopting coupled technologies. In the studied area, the aquifer hydraulic conductivity Ka [m/d] is log-normally distributed with mean E (Ya) = 0.32 , variance σYa2 = 6.36 (Ya = lnKa) and spatial correlation well described by an exponential isotropic variogram with integral scale less than 1/12 the domain size. The hardened CB wall's hydraulic conductivity, Kw [m/d], displayed strong scaling effects and a lognormal distribution with mean E (Yw) = - 3.43 and σYw2 = 0.53 (Yw =log10Kw). No spatial correlation of Kw was detected. Using this information, conservative transport was simulated across a CB wall in spatially correlated 1-D random Ya fields within a numerical Monte Carlo framework. Multiple scenarios representing different Kw values were tested. A continuous solute source with known concentration and deterministic drains' discharge rates were assumed. The efficiency of the confining system was measured by the probability of exceedance of concentration over a threshold (C∗) at a control section 10 years after the initial solute release. It was found that the stronger the aquifer heterogeneity, the higher the expected efficiency of the confinement system and the lower the likelihood of aquifer pollution. This behavior can be explained because, for the analyzed aquifer conditions, a lower Ka generates more pronounced drawdown in the water table in the proximity of the drain and consequently a higher advective flux towards the confined area, which counteracts diffusive fluxes across the walls. Thus, a higher σYa2 results in a larger amount of low Ka values in the proximity of the drain, and a higher probability of not exceeding C∗ .

A Distributed Transmission Rate Adjustment Algorithm in Heterogeneous CSMA/CA Networks

PubMed Central

Xie, Shuanglong; Low, Kay Soon; Gunawan, Erry

2015-01-01

Distributed transmission rate tuning is important for a wide variety of IEEE 802.15.4 network applications such as industrial network control systems. Such systems often require each node to sustain certain throughput demand in order to guarantee the system performance. It is thus essential to determine a proper transmission rate that can meet the application requirement and compensate for network imperfections (e.g., packet loss). Such a tuning in a heterogeneous network is difficult due to the lack of modeling techniques that can deal with the heterogeneity of the network as well as the network traffic changes. In this paper, a distributed transmission rate tuning algorithm in a heterogeneous IEEE 802.15.4 CSMA/CA network is proposed. Each node uses the results of clear channel assessment (CCA) to estimate the busy channel probability. Then a mathematical framework is developed to estimate the on-going heterogeneous traffics using the busy channel probability at runtime. Finally a distributed algorithm is derived to tune the transmission rate of each node to accurately meet the throughput requirement. The algorithm does not require modifications on IEEE 802.15.4 MAC layer and it has been experimentally implemented and extensively tested using TelosB nodes with the TinyOS protocol stack. The results reveal that the algorithm is accurate and can satisfy the throughput demand. Compared with existing techniques, the algorithm is fully distributed and thus does not require any central coordination. With this property, it is able to adapt to traffic changes and re-adjust the transmission rate to the desired level, which cannot be achieved using the traditional modeling techniques. PMID:25822140

Flow field and dissolved oxygen distributions in the outer channel of the Orbal oxidation ditch by monitor and CFD simulation.

PubMed

Guo, Xuesong; Zhou, Xin; Chen, Qiuwen; Liu, Junxin

2013-04-01

In the Orbal oxidation ditch, denitrification is primarily accomplished in the outer channel. However, the detailed characteristics of the flow field and dissolved oxygen (DO) distribution in the outer channel are not well understood. Therefore, in this study, the flow velocity and DO concentration in the outer channel of an Orbal oxidation ditch system in a wastewater treatment plant in Beijing (China) were monitored under actual operation conditions. The flow field and DO concentration distributions were analyzed by computed fluid dynamic modeling. In situ monitoring and modeling both showed that the flow velocity was heterogeneous in the outer channel. As a result, the DO was also heterogeneously distributed in the outer channel, with concentration gradients occurring along the flow direction as well as in the cross-section. This heterogeneous DO distribution created many anoxic and aerobic zones, which may have facilitated simultaneous nitrification-denitrification in the channel. These findings may provide supporting information for rational optimization of the performance of the Orbal oxidation ditch.

Distribution of model-based multipoint heterogeneity lod scores.

PubMed

Xing, Chao; Morris, Nathan; Xing, Guan

2010-12-01

The distribution of two-point heterogeneity lod scores (HLOD) has been intensively investigated because the conventional χ(2) approximation to the likelihood ratio test is not directly applicable. However, there was no study investigating th e distribution of the multipoint HLOD despite its wide application. Here we want to point out that, compared with the two-point HLOD, the multipoint HLOD essentially tests for homogeneity given linkage and follows a relatively simple limiting distribution ½χ²₀+ ½χ²₁, which can be obtained by established statistical theory. We further examine the theoretical result by simulation studies. © 2010 Wiley-Liss, Inc.

Heterogeneity in ultrathin films simulated by Monte Carlo method

NASA Astrophysics Data System (ADS)

Sun, Jiebing; Hannon, James B.; Kellogg, Gary L.; Pohl, Karsten

2007-03-01

The 3D composition profile of ultra-thin Pd films on Cu(001) has been experimentally determined using low energy electron microscopy (LEEM).^[1] Quantitative measurements of the alloy concentration profile near steps show that the Pd distribution in the 3^rd layer is heterogeneous due to step overgrowth during Pd deposition. Interestingly, the Pd distribution in the 2^nd layer is also heterogeneous, and appears to be correlated with the distribution in the 1^st layer. We describe Monte Carlo simulations that show that correlation is due to Cu-Pd attraction, and that the 2^nd layer Pd is, in fact, laterally equilibrated. By comparing measured and simulated concentration profiles, we can estimate this attraction within a simple bond counting model. [1] J. B. Hannon, J. Sun, K. Pohl, G. L. Kellogg, Phys. Rev. Lett. 96, 246103 (2006)

Distributed heterogeneous inspecting system and its middleware-based solution.

PubMed

Huang, Li-can; Wu, Zhao-hui; Pan, Yun-he

2003-01-01

There are many cases when an organization needs to monitor the data and operations of its supervised departments, especially those departments which are not owned by this organization and are managed by their own information systems. Distributed Heterogeneous Inspecting System (DHIS) is the system an organization uses to monitor its supervised departments by inspecting their information systems. In DHIS, the inspected systems are generally distributed, heterogeneous, and constructed by different companies. DHIS has three key processes-abstracting core data sets and core operation sets, collecting these sets, and inspecting these collected sets. In this paper, we present the concept and mathematical definition of DHIS, a metadata method for solving the interoperability, a security strategy for data transferring, and a middleware-based solution of DHIS. We also describe an example of the inspecting system at WENZHOU custom.

heterogeneous mixture distributions for multi-source extreme rainfall

NASA Astrophysics Data System (ADS)

Ouarda, T.; Shin, J.; Lee, T. S.

2013-12-01

Mixture distributions have been used to model hydro-meteorological variables showing mixture distributional characteristics, e.g. bimodality. Homogeneous mixture (HOM) distributions (e.g. Normal-Normal and Gumbel-Gumbel) have been traditionally applied to hydro-meteorological variables. However, there is no reason to restrict the mixture distribution as the combination of one identical type. It might be beneficial to characterize the statistical behavior of hydro-meteorological variables from the application of heterogeneous mixture (HTM) distributions such as Normal-Gamma. In the present work, we focus on assessing the suitability of HTM distributions for the frequency analysis of hydro-meteorological variables. In the present work, in order to estimate the parameters of HTM distributions, the meta-heuristic algorithm (Genetic Algorithm) is employed to maximize the likelihood function. In the present study, a number of distributions are compared, including the Gamma-Extreme value type-one (EV1) HTM distribution, the EV1-EV1 HOM distribution, and EV1 distribution. The proposed distribution models are applied to the annual maximum precipitation data in South Korea. The Akaike Information Criterion (AIC), the root mean squared errors (RMSE) and the log-likelihood are used as measures of goodness-of-fit of the tested distributions. Results indicate that the HTM distribution (Gamma-EV1) presents the best fitness. The HTM distribution shows significant improvement in the estimation of quantiles corresponding to the 20-year return period. It is shown that extreme rainfall in the coastal region of South Korea presents strong heterogeneous mixture distributional characteristics. Results indicate that HTM distributions are a good alternative for the frequency analysis of hydro-meteorological variables when disparate statistical characteristics are presented.

Heterogeneity of keratin expression and actin distribution in benign and malignant mammary diseases.

PubMed

Wada, T; Yasutomi, M; Yamada, K; Hashimura, K; Kunikata, M; Tanaka, T; Huang, J W; Mori, M

1991-01-01

Immunoreactivity of monoclonal anti-cytokeratin KL1, PKK1, K8.12 and anti-actin antibodies in 101 cases of diseased human breast lesions showed irregular keratin distribution in luminal cells of terminal ductal-lobular unit and basal layer cells of the interlobular and main duct. Actin staining was confined to myoepithelial cells. Benign lesions showed great heterogeneity in luminal cells of the terminal ductal-lobular units. Breast carcinoma showed a reduced staining for keratins, heterogeneity of keratin expression was found in solid tubular carcinoma, and actin was usually absent: however, papillo-ductal or comedo type had actin positive myoepithelial cells around carcinoma foci.

Individual heterogeneity and identifiability in capture-recapture models

USGS Publications Warehouse

Link, W.A.

2004-01-01

Individual heterogeneity in detection probabilities is a far more serious problem for capture-recapture modeling than has previously been recognized. In this note, I illustrate that population size is not an identifiable parameter under the general closed population mark-recapture model Mh. The problem of identifiability is obvious if the population includes individuals with pi = 0, but persists even when it is assumed that individual detection probabilities are bounded away from zero. Identifiability may be attained within parametric families of distributions for pi, but not among parametric families of distributions. Consequently, in the presence of individual heterogeneity in detection probability, capture-recapture analysis is strongly model dependent.

Modeling the heterogeneous catalytic activity of a single nanoparticle using a first passage time distribution formalism

NASA Astrophysics Data System (ADS)

Das, Anusheela; Chaudhury, Srabanti

2015-11-01

Metal nanoparticles are heterogeneous catalysts and have a multitude of non-equivalent, catalytic sites on the nanoparticle surface. The product dissociation step in such reaction schemes can follow multiple pathways. Proposed here for the first time is a completely analytical theoretical framework, based on the first passage time distribution, that incorporates the effect of heterogeneity in nanoparticle catalysis explicitly by considering multiple, non-equivalent catalytic sites on the nanoparticle surface. Our results show that in nanoparticle catalysis, the effect of dynamic disorder is manifested even at limiting substrate concentrations in contrast to an enzyme that has only one well-defined active site.

Chloride Transport in Heterogeneous Formation

NASA Astrophysics Data System (ADS)

Mukherjee, A.; Holt, R. M.

2017-12-01

The chloride mass balance (CMB) is a commonly-used method for estimating groundwater recharge. Observations of the vertical distribution of pore-water chloride are related to the groundwater infiltration rates (i.e. recharge rates). In CMB method, the chloride distribution is attributed mainly to the assumption of one dimensional piston flow. In many places, however, the vertical distribution of chloride will be influenced by heterogeneity, leading to horizontal movement of infiltrating waters. The impact of heterogeneity will be particularly important when recharge is locally focused. When recharge is focused in an area, horizontal movement of chloride-bearing waters, coupled with upward movement driven by evapotranspiration, may lead to chloride bulges that could be misinterpreted if the CMB method is used to estimate recharge. We numerically simulate chloride transport and evaluate the validity of the CMB method in highly heterogeneous systems. This simulation is conducted for the unsaturated zone of Ogallala, Antlers, and Gatuna (OAG) formations in Andrews County, Texas. A two dimensional finite element model will show the movement of chloride through heterogeneous systems. We expect to see chloride bulges not only close to the surface but also at depths characterized by horizontal or upward movement. A comparative study of focused recharge estimates in this study with available recharge data will be presented.

Spatial heterogeneity of plant-soil feedback affects root interactions and interspecific competition.

PubMed

Hendriks, Marloes; Ravenek, Janneke M; Smit-Tiekstra, Annemiek E; van der Paauw, Jan Willem; de Caluwe, Hannie; van der Putten, Wim H; de Kroon, Hans; Mommer, Liesje

2015-08-01

Plant-soil feedback is receiving increasing interest as a factor influencing plant competition and species coexistence in grasslands. However, we do not know how spatial distribution of plant-soil feedback affects plant below-ground interactions. We investigated the way in which spatial heterogeneity of soil biota affects competitive interactions in grassland plant species. We performed a pairwise competition experiment combined with heterogeneous distribution of soil biota using four grassland plant species and their soil biota. Patches were applied as quadrants of 'own' and 'foreign' soils from all plant species in all pairwise combinations. To evaluate interspecific root responses, species-specific root biomass was quantified using real-time PCR. All plant species suffered negative soil feedback, but strength was species-specific, reflected by a decrease in root growth in own compared with foreign soil. Reduction in root growth in own patches by the superior plant competitor provided opportunities for inferior competitors to increase root biomass in these patches. These patterns did not cascade into above-ground effects during our experiment. We show that root distributions can be determined by spatial heterogeneity of soil biota, affecting plant below-ground competitive interactions. Thus, spatial heterogeneity of soil biota may contribute to plant species coexistence in species-rich grasslands. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

XML-based approaches for the integration of heterogeneous bio-molecular data.

PubMed

Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David

2009-10-15

The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

CMO: Cruise Metadata Organizer for JAMSTEC Research Cruises

NASA Astrophysics Data System (ADS)

Fukuda, K.; Saito, H.; Hanafusa, Y.; Vanroosebeke, A.; Kitayama, T.

2011-12-01

JAMSTEC's Data Research Center for Marine-Earth Sciences manages and distributes a wide variety of observational data and samples obtained from JAMSTEC research vessels and deep sea submersibles. Generally, metadata are essential to identify data and samples were obtained. In JAMSTEC, cruise metadata include cruise information such as cruise ID, name of vessel, research theme, and diving information such as dive number, name of submersible and position of diving point. They are submitted by chief scientists of research cruises in the Microsoft Excel° spreadsheet format, and registered into a data management database to confirm receipt of observational data files, cruise summaries, and cruise reports. The cruise metadata are also published via "JAMSTEC Data Site for Research Cruises" within two months after end of cruise. Furthermore, these metadata are distributed with observational data, images and samples via several data and sample distribution websites after a publication moratorium period. However, there are two operational issues in the metadata publishing process. One is that duplication efforts and asynchronous metadata across multiple distribution websites due to manual metadata entry into individual websites by administrators. The other is that differential data types or representation of metadata in each website. To solve those problems, we have developed a cruise metadata organizer (CMO) which allows cruise metadata to be connected from the data management database to several distribution websites. CMO is comprised of three components: an Extensible Markup Language (XML) database, an Enterprise Application Integration (EAI) software, and a web-based interface. The XML database is used because of its flexibility for any change of metadata. Daily differential uptake of metadata from the data management database to the XML database is automatically processed via the EAI software. Some metadata are entered into the XML database using the web-based interface by a metadata editor in CMO as needed. Then daily differential uptake of metadata from the XML database to databases in several distribution websites is automatically processed using a convertor defined by the EAI software. Currently, CMO is available for three distribution websites: "Deep Sea Floor Rock Sample Database GANSEKI", "Marine Biological Sample Database", and "JAMSTEC E-library of Deep-sea Images". CMO is planned to provide "JAMSTEC Data Site for Research Cruises" with metadata in the future.

Streaming data analytics via message passing with application to graph algorithms

DOE PAGES

Plimpton, Steven J.; Shead, Tim

2014-05-06

The need to process streaming data, which arrives continuously at high-volume in real-time, arises in a variety of contexts including data produced by experiments, collections of environmental or network sensors, and running simulations. Streaming data can also be formulated as queries or transactions which operate on a large dynamic data store, e.g. a distributed database. We describe a lightweight, portable framework named PHISH which enables a set of independent processes to compute on a stream of data in a distributed-memory parallel manner. Datums are routed between processes in patterns defined by the application. PHISH can run on top of eithermore » message-passing via MPI or sockets via ZMQ. The former means streaming computations can be run on any parallel machine which supports MPI; the latter allows them to run on a heterogeneous, geographically dispersed network of machines. We illustrate how PHISH can support streaming MapReduce operations, and describe streaming versions of three algorithms for large, sparse graph analytics: triangle enumeration, subgraph isomorphism matching, and connected component finding. Lastly, we also provide benchmark timings for MPI versus socket performance of several kernel operations useful in streaming algorithms.« less

Site occupancy models with heterogeneous detection probabilities

USGS Publications Warehouse

Royle, J. Andrew

2006-01-01

Models for estimating the probability of occurrence of a species in the presence of imperfect detection are important in many ecological disciplines. In these ?site occupancy? models, the possibility of heterogeneity in detection probabilities among sites must be considered because variation in abundance (and other factors) among sampled sites induces variation in detection probability (p). In this article, I develop occurrence probability models that allow for heterogeneous detection probabilities by considering several common classes of mixture distributions for p. For any mixing distribution, the likelihood has the general form of a zero-inflated binomial mixture for which inference based upon integrated likelihood is straightforward. A recent paper by Link (2003, Biometrics 59, 1123?1130) demonstrates that in closed population models used for estimating population size, different classes of mixture distributions are indistinguishable from data, yet can produce very different inferences about population size. I demonstrate that this problem can also arise in models for estimating site occupancy in the presence of heterogeneous detection probabilities. The implications of this are discussed in the context of an application to avian survey data and the development of animal monitoring programs.

Imaging oxygen distribution in marine sediments. The importance of bioturbation and sediment heterogeneity.

PubMed

Pischedda, L; Poggiale, J C; Cuny, P; Gilbert, F

2008-06-01

The influence of sediment oxygen heterogeneity, due to bioturbation, on diffusive oxygen flux was investigated. Laboratory experiments were carried out with 3 macrobenthic species presenting different bioturbation behaviour patterns: the polychaetes Nereis diversicolor and Nereis virens, both constructing ventilated galleries in the sediment column, and the gastropod Cyclope neritea, a burrowing species which does not build any structure. Oxygen two-dimensional distribution in sediments was quantified by means of the optical planar optode technique. Diffusive oxygen fluxes (mean and integrated) and a variability index were calculated on the captured oxygen images. All species increased sediment oxygen heterogeneity compared to the controls without animals. This was particularly noticeable with the polychaetes because of the construction of more or less complex burrows. Integrated diffusive oxygen flux increased with oxygen heterogeneity due to the production of interface available for solute exchanges between overlying water and sediments. This work shows that sediment heterogeneity is an important feature of the control of oxygen exchanges at the sediment-water interface.

SMALL-SCALE AND GLOBAL DYNAMOS AND THE AREA AND FLUX DISTRIBUTIONS OF ACTIVE REGIONS, SUNSPOT GROUPS, AND SUNSPOTS: A MULTI-DATABASE STUDY

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

Muñoz-Jaramillo, Andrés; Windmueller, John C.; Amouzou, Ernest C.

2015-02-10

In this work, we take advantage of 11 different sunspot group, sunspot, and active region databases to characterize the area and flux distributions of photospheric magnetic structures. We find that, when taken separately, different databases are better fitted by different distributions (as has been reported previously in the literature). However, we find that all our databases can be reconciled by the simple application of a proportionality constant, and that, in reality, different databases are sampling different parts of a composite distribution. This composite distribution is made up by linear combination of Weibull and log-normal distributions—where a pure Weibull (log-normal) characterizesmore » the distribution of structures with fluxes below (above) 10{sup 21}Mx (10{sup 22}Mx). Additionally, we demonstrate that the Weibull distribution shows the expected linear behavior of a power-law distribution (when extended to smaller fluxes), making our results compatible with the results of Parnell et al. We propose that this is evidence of two separate mechanisms giving rise to visible structures on the photosphere: one directly connected to the global component of the dynamo (and the generation of bipolar active regions), and the other with the small-scale component of the dynamo (and the fragmentation of magnetic structures due to their interaction with turbulent convection)« less

Using Markov Decision Processes with Heterogeneous Queueing Systems to Examine Military MEDEVAC Dispatching Policies

DTIC Science & Technology

2017-03-23

Air Force Institute of Technology AFIT Scholar Theses and Dissertations 3-23-2017 Using Markov Decision Processes with Heterogeneous Queueing Systems... TECHNOLOGY Wright-Patterson Air Force Base, Ohio DISTRIBUTION STATEMENT A APPROVED FOR PUBLIC RELEASE; DISTRIBUTION UNLIMITED. The views expressed in...POLICIES THESIS Presented to the Faculty Department of Operational Sciences Graduate School of Engineering and Management Air Force Institute of Technology

Bridging the Gap between the Data Base and User in a Distributed Environment.

ERIC Educational Resources Information Center

Howard, Richard D.; And Others

1989-01-01

The distribution of databases physically separates users from those who administer the database and the administrators who perform database administration. By drawing on the work of social scientists in reliability and validity, a set of concepts and a list of questions to ensure data quality were developed. (Author/MLW)

Distributed containment control of heterogeneous fractional-order multi-agent systems with communication delays

NASA Astrophysics Data System (ADS)

Yang, Hongyong; Han, Fujun; Zhao, Mei; Zhang, Shuning; Yue, Jun

2017-08-01

Because many networked systems can only be characterized with fractional-order dynamics in complex environments, fractional-order calculus has been studied deeply recently. When diverse individual features are shown in different agents of networked systems, heterogeneous fractional-order dynamics will be used to describe the complex systems. Based on the distinguishing properties of agents, heterogeneous fractional-order multi-agent systems (FOMAS) are presented. With the supposition of multiple leader agents in FOMAS, distributed containment control of FOMAS is studied in directed weighted topologies. By applying Laplace transformation and frequency domain theory of the fractional-order operator, an upper bound of delays is obtained to ensure containment consensus of delayed heterogenous FOMAS. Consensus results of delayed FOMAS in this paper can be extended to systems with integer-order models. Finally, numerical examples are used to verify our results.

Influence of microscale heterogeneity and microstructure on the tensile behavior of crystalline rocks

NASA Astrophysics Data System (ADS)

Mahabadi, O. K.; Tatone, B. S. A.; Grasselli, G.

2014-07-01

This study investigates the influence of microscale heterogeneity and microcracks on the failure behavior and mechanical response of a crystalline rock. The thin section analysis for obtaining the microcrack density is presented. Using micro X-ray computed tomography (μCT) scanning of failed laboratory specimens, the influence of heterogeneity and, in particular, biotite grains on the brittle fracture of the specimens is discussed and various failure patterns are characterized. Three groups of numerical simulations are presented, which demonstrate the role of microcracks and the influence of μCT-based and stochastically generated phase distributions. The mechanical response, stress distribution, and fracturing process obtained by the numerical simulations are also discussed. The simulation results illustrate that heterogeneity and microcracks should be considered to accurately predict the tensile strength and failure behavior of the sample.

Time scale of dynamic heterogeneity in model ionic liquids and its relation to static length scale and charge distribution.

PubMed

Park, Sang-Won; Kim, Soree; Jung, YounJoon

2015-11-21

We study how dynamic heterogeneity in ionic liquids is affected by the length scale of structural relaxation and the ionic charge distribution by the molecular dynamics simulations performed on two differently charged models of ionic liquid and their uncharged counterpart. In one model of ionic liquid, the charge distribution in the cation is asymmetric, and in the other it is symmetric, while their neutral counterpart has no charge with the ions. It is found that all the models display heterogeneous dynamics, exhibiting subdiffusive dynamics and a nonexponential decay of structural relaxation. We investigate the lifetime of dynamic heterogeneity, τ(dh), in these systems by calculating the three-time correlation functions to find that τ(dh) has in general a power-law behavior with respect to the structural relaxation time, τ(α), i.e., τ(dh) ∝ τ(α)(ζ(dh)). Although the dynamics of the asymmetric-charge model is seemingly more heterogeneous than that of the symmetric-charge model, the exponent is found to be similar, ζ(dh) ≈ 1.2, for all the models studied in this work. The same scaling relation is found regardless of interactions, i.e., with or without Coulomb interaction, and it holds even when the length scale of structural relaxation is long enough to become the Fickian diffusion. This fact indicates that τ(dh) is a distinctive time scale from τ(α), and the dynamic heterogeneity is mainly affected by the short-range interaction and the molecular structure.

Intratumoral heterogeneity on dedicated breast positron emission tomography predicts malignancy grade of breast cancer.

PubMed

Masumoto, Norio; Kadoya, Takayuki; Sasada, Shinsuke; Emi, Akiko; Arihiro, Koji; Okada, Morihito

2018-05-19

Dedicated breast positron emission tomography (DbPET) provides detailed high-resolution images and can detect intratumoral heterogeneity using 18 F-fluorodeoxyglucose (FDG). We aimed to evaluate the correlation between FDG uptake on DbPET and the clinicopathological features of breast cancer, particularly those with an intratumoral heterogeneous distribution of FDG on DbPET. We evaluated 195 consecutive patients with invasive breast cancer who underwent preoperative whole-body PET (WBPET) and DbPET concurrently between January 2016 and March 2017. The relationships between clinicopathological factors and the maximum standard uptake values (SUVmax) of DbPET and WBPET, including clinical stage, nuclear grade, Ki67 proliferation index, estrogen receptor (ER) and human epidermal growth factor receptor type 2 (HER2) statuses, and the intratumoral heterogeneous distribution of FDG on DbPET, were evaluated. The SUVmax of DbPET was significantly correlated with clinical T stage, N stage, nuclear grade, and Ki67 proliferation index (all p < 0.001) as well as the ER (p = 0.006) and HER2 (p = 0.040) statuses. Intratumoral heterogeneous distribution of FDG on DbPET was significantly related with high nuclear grade (p = 0.016) and high Ki67 proliferation index (p = 0.015) but not with clinical T stage, N stage, and ER and HER2 statuses. The SUVmax of DbPET correlates with clinicopathological factors and also WBPET does. In addition, intratumoral heterogeneity on DbPET provides predictive value for malignancy grade and could inform therapeutic decisions.

Device Data Ingestion for Industrial Big Data Platforms with a Case Study †

PubMed Central

Ji, Cun; Shao, Qingshi; Sun, Jiao; Liu, Shijun; Pan, Li; Wu, Lei; Yang, Chenglei

2016-01-01

Despite having played a significant role in the Industry 4.0 era, the Internet of Things is currently faced with the challenge of how to ingest large-scale heterogeneous and multi-type device data. In response to this problem we present a heterogeneous device data ingestion model for an industrial big data platform. The model includes device templates and four strategies for data synchronization, data slicing, data splitting and data indexing, respectively. We can ingest device data from multiple sources with this heterogeneous device data ingestion model, which has been verified on our industrial big data platform. In addition, we present a case study on device data-based scenario analysis of industrial big data. PMID:26927121

Assessing the Implicit Curriculum in Social Work Education: Heterogeneity of Students' Experiences and Impact on Professional Empowerment

ERIC Educational Resources Information Center

Peterson, N. Andrew; Farmer, Antoinette Y.; Donnelly, Louis; Forenza, Brad

2014-01-01

The implicit curriculum, which refers to a student's learning environment, has been described as an essential feature of an integrated professional social work curriculum. Very little is known, however, about the heterogeneity of students' experiences with the implicit curriculum, how this heterogeneity may be distributed across groups of…

A Web-based open-source database for the distribution of hyperspectral signatures

NASA Astrophysics Data System (ADS)

Ferwerda, J. G.; Jones, S. D.; Du, Pei-Jun

2006-10-01

With the coming of age of field spectroscopy as a non-destructive means to collect information on the physiology of vegetation, there is a need for storage of signatures, and, more importantly, their metadata. Without the proper organisation of metadata, the signatures itself become limited. In order to facilitate re-distribution of data, a database for the storage & distribution of hyperspectral signatures and their metadata was designed. The database was built using open-source software, and can be used by the hyperspectral community to share their data. Data is uploaded through a simple web-based interface. The database recognizes major file-formats by ASD, GER and International Spectronics. The database source code is available for download through the hyperspectral.info web domain, and we happily invite suggestion for additions & modification for the database to be submitted through the online forums on the same website.

Health sciences libraries’ subscriptions to journals: expectations of general practice departments and collection-based analysis

PubMed Central

Barreau, David; Bouton, Céline; Renard, Vincent; Fournier, Jean-Pascal

2018-01-01

Objective The aims of this study were to (i) assess the expectations of general practice departments regarding health sciences libraries’ subscriptions to journals and (ii) describe the current general practice journal collections of health sciences libraries. Methods A cross-sectional survey was distributed electronically to the thirty-five university general practice departments in France. General practice departments were asked to list ten journals to which they expected access via the subscriptions of their health sciences libraries. A ranked reference list of journals was then developed. Access to these journals was assessed through a survey sent to all health sciences libraries in France. Adequacy ratios (access/need) were calculated for each journal. Results All general practice departments completed the survey. The total reference list included 44 journals. This list was heterogeneous in terms of indexation/impact factor, language of publication, and scope (e.g., patient care, research, or medical education). Among the first 10 journals listed, La Revue Prescrire (96.6%), La Revue du Praticien–Médecine Générale (90.9%), the British Medical Journal (85.0%), Pédagogie Médicale (70.0%), Exercer (69.7%), and the Cochrane Database of Systematic Reviews (62.5%) had the highest adequacy ratios, whereas Family Practice (4.2%), the British Journal of General Practice (16.7%), Médecine (29.4%), and the European Journal of General Practice (33.3%) had the lowest adequacy ratios. Conclusions General practice departments have heterogeneous expectations in terms of health sciences libraries’ subscriptions to journals. It is important for librarians to understand the heterogeneity of these expectations, as well as local priorities, so that journal access meets users’ needs. PMID:29632446

Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates

PubMed Central

Calderón-Patrón, Jaime M.; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E.; Sánchez-Rojas, Gerardo; Zuria, Iriana

2016-01-01

Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project “Biodiversity in the state of Hidalgo”. Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area. PMID:27500934

Beta Diversity in a Highly Heterogeneous Area: Disentangling Species and Taxonomic Dissimilarity for Terrestrial Vertebrates.

PubMed

Calderón-Patrón, Jaime M; Goyenechea, Irene; Ortiz-Pulido, Raúl; Castillo-Cerón, Jesús; Manriquez, Norma; Ramírez-Bautista, Aurelio; Rojas-Martínez, Alberto E; Sánchez-Rojas, Gerardo; Zuria, Iriana; Moreno, Claudia E

2016-01-01

Quantifying differences in species composition among communities provides important information related to the distribution, conservation and management of biodiversity, especially when two components are recognized: dissimilarity due to turnover, and dissimilarity due to richness differences. The ecoregions in central Mexico, within the Mexican Transition Zone, have outstanding environmental heterogeneity and harbor huge biological richness, besides differences in the origin of the biota. Therefore, biodiversity studies in this area require the use of complementary measures to achieve appropriate information that may help in the design of conservation strategies. In this work we analyze the dissimilarity of terrestrial vertebrates, and the components of turnover and richness differences, among six ecoregions in the state of Hidalgo, central Mexico. We follow two approaches: one based on species level dissimilarity, and the second on taxonomic dissimilarity. We used databases from the project "Biodiversity in the state of Hidalgo". Our results indicate that species dissimilarity is higher than taxonomic dissimilarity, and that turnover contributes more than richness differences, both for species and taxonomic total dissimilarity. Moreover, total dissimilarity, turnover dissimilarity and the dissimilarity due to richness differences were positively related in the four vertebrate groups. Reptiles had the highest values of dissimilarity, followed by mammals, amphibians and birds. For reptiles, birds, and mammals, species turnover was the most important component, while richness differences had a higher contribution for amphibians. The highest values of dissimilarity occurred between environmentally contrasting ecoregions (i.e., tropical and temperate forests), which suggests that environmental heterogeneity and differences in the origin of biotas are key factors driving beta diversity of terrestrial vertebrates among ecoregions in this complex area.

Distributed Database Control and Allocation. Volume 3. Distributed Database System Designer’s Handbook.

DTIC Science & Technology

1983-10-01

Multiversion Data 2-18 2.7.1 Multiversion Timestamping 2-20 2.T.2 Multiversion Looking 2-20 2.8 Combining the Techniques 2-22 3. Database Recovery Algorithms...See rTHEM79, GIFF79] for details. 2.7 Multiversion Data Let us return to a database system model where each logical data item is stored at one DM...In a multiversion database each Write wifxl, produces a new copy (or version) of x, denoted xi. Thus, the value of z is a set of ver- sions. For each

Empirical evidence about inconsistency among studies in a pair‐wise meta‐analysis

PubMed Central

Turner, Rebecca M.; Higgins, Julian P. T.

2015-01-01

This paper investigates how inconsistency (as measured by the I2 statistic) among studies in a meta‐analysis may differ, according to the type of outcome data and effect measure. We used hierarchical models to analyse data from 3873 binary, 5132 continuous and 880 mixed outcome meta‐analyses within the Cochrane Database of Systematic Reviews. Predictive distributions for inconsistency expected in future meta‐analyses were obtained, which can inform priors for between‐study variance. Inconsistency estimates were highest on average for binary outcome meta‐analyses of risk differences and continuous outcome meta‐analyses. For a planned binary outcome meta‐analysis in a general research setting, the predictive distribution for inconsistency among log odds ratios had median 22% and 95% CI: 12% to 39%. For a continuous outcome meta‐analysis, the predictive distribution for inconsistency among standardized mean differences had median 40% and 95% CI: 15% to 73%. Levels of inconsistency were similar for binary data measured by log odds ratios and log relative risks. Fitted distributions for inconsistency expected in continuous outcome meta‐analyses using mean differences were almost identical to those using standardized mean differences. The empirical evidence on inconsistency gives guidance on which outcome measures are most likely to be consistent in particular circumstances and facilitates Bayesian meta‐analysis with an informative prior for heterogeneity. © 2015 The Authors. Research Synthesis Methods published by John Wiley & Sons, Ltd. © 2015 The Authors. Research Synthesis Methods published by John Wiley & Sons, Ltd. PMID:26679486

E-health and healthcare enterprise information system leveraging service-oriented architecture.

PubMed

Hsieh, Sung-Huai; Hsieh, Sheau-Ling; Cheng, Po-Hsun; Lai, Feipei

2012-04-01

To present the successful experiences of an integrated, collaborative, distributed, large-scale enterprise healthcare information system over a wired and wireless infrastructure in National Taiwan University Hospital (NTUH). In order to smoothly and sequentially transfer from the complex relations among the old (legacy) systems to the new-generation enterprise healthcare information system, we adopted the multitier framework based on service-oriented architecture to integrate the heterogeneous systems as well as to interoperate among many other components and multiple databases. We also present mechanisms of a logical layer reusability approach and data (message) exchange flow via Health Level 7 (HL7) middleware, DICOM standard, and the Integrating the Healthcare Enterprise workflow. The architecture and protocols of the NTUH enterprise healthcare information system, especially in the Inpatient Information System (IIS), are discussed in detail. The NTUH Inpatient Healthcare Information System is designed and deployed on service-oriented architecture middleware frameworks. The mechanisms of integration as well as interoperability among the components and the multiple databases apply the HL7 standards for data exchanges, which are embedded in XML formats, and Microsoft .NET Web services to integrate heterogeneous platforms. The preliminary performance of the current operation IIS is evaluated and analyzed to verify the efficiency and effectiveness of the designed architecture; it shows reliability and robustness in the highly demanding traffic environment of NTUH. The newly developed NTUH IIS provides an open and flexible environment not only to share medical information easily among other branch hospitals, but also to reduce the cost of maintenance. The HL7 message standard is widely adopted to cover all data exchanges in the system. All services are independent modules that enable the system to be deployed and configured to the highest degree of flexibility. Furthermore, we can conclude that the multitier Inpatient Healthcare Information System has been designed successfully and in a collaborative manner, based on the index of performance evaluations, central processing unit, and memory utilizations.

Analytics to Better Interpret and Use Large Amounts of Heterogeneous Data

NASA Astrophysics Data System (ADS)

Mathews, T. J.; Baskin, W. E.; Rinsland, P. L.

2014-12-01

Data scientists at NASA's Atmospheric Science Data Center (ASDC) are seasoned software application developers who have worked with the creation, archival, and distribution of large datasets (multiple terabytes and larger). In order for ASDC data scientists to effectively implement the most efficient processes for cataloging and organizing data access applications, they must be intimately familiar with data contained in the datasets with which they are working. Key technologies that are critical components to the background of ASDC data scientists include: large RBMSs (relational database management systems) and NoSQL databases; web services; service-oriented architectures; structured and unstructured data access; as well as processing algorithms. However, as prices of data storage and processing decrease, sources of data increase, and technologies advance - granting more people to access to data at real or near-real time - data scientists are being pressured to accelerate their ability to identify and analyze vast amounts of data. With existing tools this is becoming exceedingly more challenging to accomplish. For example, NASA Earth Science Data and Information System (ESDIS) alone grew from having just over 4PBs of data in 2009 to nearly 6PBs of data in 2011. This amount then increased to roughly10PBs of data in 2013. With data from at least ten new missions to be added to the ESDIS holdings by 2017, the current volume will continue to grow exponentially and drive the need to be able to analyze more data even faster. Though there are many highly efficient, off-the-shelf analytics tools available, these tools mainly cater towards business data, which is predominantly unstructured. Inadvertently, there are very few known analytics tools that interface well to archived Earth science data, which is predominantly heterogeneous and structured. This presentation will identify use cases for data analytics from an Earth science perspective in order to begin to identify specific tools that may be able to address those challenges.

Prognostic Role of Mucin Antigen MUC4 for Cholangiocarcinoma: A Meta-Analysis.

PubMed

Li, Bingmin; Tang, Haowen; Zhang, Aiqun; Dong, Jiahong

2016-01-01

Surgery carries the best hope for cure in the treatment of cholangiocarcinoma (CC), whereas surgical outcome is not fully satisfactory. Bio-molecular markers have been used to improve tumor staging and prognosis prediction. Mucin antigen MUC4 (MUC4) has been implicated as a marker for poor survival in various tumors. However, prognostic significance of MUC4 for patients with CC remains undefined. The aim of the present meta-analysis was to investigate the association between MUC4 expression and overall survival (OS) of patients with resected CC. The meta-analysis was conducted in adherence to the MOOSE guidelines. PubMed, Embase databases, Cochrane Library and the Chinese SinoMed were systematically searched to identify eligible studies from the initiation of the databases to April, 2016. OSs were pooled by using hazard ratio (HR) with corresponding 95% confidence interval (CI). Random effect models were utilized because of the between-study heterogeneities. Five studies reporting on 249 patients were analyzed: 94 (37.75%) were in positive or high expression group and 155 (62.25%) in negative or low expression group. The pooled HR for positive or high expression group was found to be 3.04 (95% CI 2.25-4.12) when compared with negative or low expression group with slight between-study heterogeneities (I2 3.10%, P = 0.39). The result indicated that a positive or high expression level of MUC4 was significantly related to poor survival in patients with resected CC. A commensurate result was identified by sensitivity analysis. The main limitations of the present meta-analysis were the rather small size of the studies included and relatively narrow geographical distribution of population. The result of this meta-analysis indicated that a positive or high expression level of MUC4 was significantly related to poor survival in patients with resected CC.

Prognostic Role of Mucin Antigen MUC4 for Cholangiocarcinoma: A Meta-Analysis

PubMed Central

Zhang, Aiqun; Dong, Jiahong

2016-01-01

Background and Objective Surgery carries the best hope for cure in the treatment of cholangiocarcinoma (CC), whereas surgical outcome is not fully satisfactory. Bio-molecular markers have been used to improve tumor staging and prognosis prediction. Mucin antigen MUC4 (MUC4) has been implicated as a marker for poor survival in various tumors. However, prognostic significance of MUC4 for patients with CC remains undefined. The aim of the present meta-analysis was to investigate the association between MUC4 expression and overall survival (OS) of patients with resected CC. Methods The meta-analysis was conducted in adherence to the MOOSE guidelines. PubMed, Embase databases, Cochrane Library and the Chinese SinoMed were systematically searched to identify eligible studies from the initiation of the databases to April, 2016. OSs were pooled by using hazard ratio (HR) with corresponding 95% confidence interval (CI). Random effect models were utilized because of the between-study heterogeneities. Results Five studies reporting on 249 patients were analyzed: 94 (37.75%) were in positive or high expression group and 155 (62.25%) in negative or low expression group. The pooled HR for positive or high expression group was found to be 3.04 (95% CI 2.25–4.12) when compared with negative or low expression group with slight between-study heterogeneities (I2 3.10%, P = 0.39). The result indicated that a positive or high expression level of MUC4 was significantly related to poor survival in patients with resected CC. A commensurate result was identified by sensitivity analysis. The main limitations of the present meta-analysis were the rather small size of the studies included and relatively narrow geographical distribution of population. Conclusion The result of this meta-analysis indicated that a positive or high expression level of MUC4 was significantly related to poor survival in patients with resected CC. PMID:27305093

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

PubMed

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

2016-01-01

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

Illuminating the Depths of the MagIC (Magnetics Information Consortium) Database

NASA Astrophysics Data System (ADS)

Koppers, A. A. P.; Minnett, R.; Jarboe, N.; Jonestrask, L.; Tauxe, L.; Constable, C.

2015-12-01

The Magnetics Information Consortium (http://earthref.org/MagIC/) is a grass-roots cyberinfrastructure effort envisioned by the paleo-, geo-, and rock magnetic scientific community. Its mission is to archive their wealth of peer-reviewed raw data and interpretations from magnetics studies on natural and synthetic samples. Many of these valuable data are legacy datasets that were never published in their entirety, some resided in other databases that are no longer maintained, and others were never digitized from the field notebooks and lab work. Due to the volume of data collected, most studies, modern and legacy, only publish the interpreted results and, occasionally, a subset of the raw data. MagIC is making an extraordinary effort to archive these data in a single data model, including the raw instrument measurements if possible. This facilitates the reproducibility of the interpretations, the re-interpretation of the raw data as the community introduces new techniques, and the compilation of heterogeneous datasets that are otherwise distributed across multiple formats and physical locations. MagIC has developed tools to assist the scientific community in many stages of their workflow. Contributors easily share studies (in a private mode if so desired) in the MagIC Database with colleagues and reviewers prior to publication, publish the data online after the study is peer reviewed, and visualize their data in the context of the rest of the contributions to the MagIC Database. From organizing their data in the MagIC Data Model with an online editable spreadsheet, to validating the integrity of the dataset with automated plots and statistics, MagIC is continually lowering the barriers to transforming dark data into transparent and reproducible datasets. Additionally, this web application generalizes to other databases in MagIC's umbrella website (EarthRef.org) so that the Geochemical Earth Reference Model (http://earthref.org/GERM/) portal, Seamount Biogeosciences Network (http://earthref.org/SBN/), EarthRef Digital Archive (http://earthref.org/ERDA/) and EarthRef Reference Database (http://earthref.org/ERR/) benefit from its development.

Effect of lithological heterogeneity of bitumen sandstones on SAGD reservoir development

NASA Astrophysics Data System (ADS)

Korolev, E. A.; Usmanov, S. A.; Nikolaev, D. S.; Gabdelvaliyeva, R. R.

2018-05-01

The article describes the heavy oil field developed by the SAGD method. While development planning all the heterogeneity of the reservoir is must be taken into account. The objective of this work is to identify the distribution of lithological heterogeneities and their influence on oil production. For this reason, the studies of core samples were conducted and the heterogeneity was identified. Then properties and approximate geometry of lithological objects were studied. Also the effect of the heterogeneity on the heat propagation and production of fluid were analyzed. In the end, recommendations were made for the study of such heterogeneities on other deposits with similar geology

The Design and Implementation of a Relational to Network Query Translator for a Distributed Database Management System.

DTIC Science & Technology

1985-12-01

RELATIONAL TO NETWORK QUERY TRANSLATOR FOR A DISTRIBUTED DATABASE MANAGEMENT SYSTEM TH ESI S .L Kevin H. Mahoney -- Captain, USAF AFIT/GCS/ENG/85D-7...NETWORK QUERY TRANSLATOR FOR A DISTRIBUTED DATABASE MANAGEMENT SYSTEM - THESIS Presented to the Faculty of the School of Engineering of the Air Force...Institute of Technology Air University In Partial Fulfillment of the Requirements for the Degree of Master of Science in Computer Systems - Kevin H. Mahoney

Visualizing excipient composition and homogeneity of Compound Liquorice Tablets by near-infrared chemical imaging

NASA Astrophysics Data System (ADS)

Wu, Zhisheng; Tao, Ou; Cheng, Wei; Yu, Lu; Shi, Xinyuan; Qiao, Yanjiang

2012-02-01

This study demonstrated that near-infrared chemical imaging (NIR-CI) was a promising technology for visualizing the spatial distribution and homogeneity of Compound Liquorice Tablets. The starch distribution (indirectly, plant extraction) could be spatially determined using basic analysis of correlation between analytes (BACRA) method. The correlation coefficients between starch spectrum and spectrum of each sample were greater than 0.95. Depending on the accurate determination of starch distribution, a method to determine homogeneous distribution was proposed by histogram graph. The result demonstrated that starch distribution in sample 3 was relatively heterogeneous according to four statistical parameters. Furthermore, the agglomerates domain in each tablet was detected using score image layers of principal component analysis (PCA) method. Finally, a novel method named Standard Deviation of Macropixel Texture (SDMT) was introduced to detect agglomerates and heterogeneity based on binary image. Every binary image was divided into different sizes length of macropixel and the number of zero values in each macropixel was counted to calculate standard deviation. Additionally, a curve fitting graph was plotted on the relationship between standard deviation and the size length of macropixel. The result demonstrated the inter-tablet heterogeneity of both starch and total compounds distribution, simultaneously, the similarity of starch distribution and the inconsistency of total compounds distribution among intra-tablet were signified according to the value of slope and intercept parameters in the curve.

Beam angle selection incorporation of anatomical heterogeneities for pencil beam scanning charged-particle therapy

NASA Astrophysics Data System (ADS)

Toramatsu, Chie; Inaniwa, Taku

2016-12-01

In charged particle therapy with pencil beam scanning (PBS), localization of the dose in the Bragg peak makes dose distributions sensitive to lateral tissue heterogeneities. The sensitivity of a PBS plan to lateral tissue heterogeneities can be reduced by selecting appropriate beam angles. The purpose of this study is to develop a fast and accurate method of beam angle selection for PBS. The lateral tissue heterogeneity surrounding the path of the pencil beams at a given angle was quantified with the heterogeneity number representing the variation of the Bragg peak depth across the cross section of the beams using the stopping power ratio of body tissues with respect to water. To shorten the computation time, one-dimensional dose optimization was conducted along the central axis of the pencil beams as they were directed by the scanning magnets. The heterogeneity numbers were derived for all possible beam angles for treatment. The angles leading to the minimum mean heterogeneity number were selected as the optimal beam angle. Three clinical cases of head and neck cancer were used to evaluate the developed method. Dose distributions and their robustness to setup and range errors were evaluated for all tested angles, and their relation to the heterogeneity numbers was investigated. The mean heterogeneity number varied from 1.2 mm-10.6 mm in the evaluated cases. By selecting a field with a low mean heterogeneity number, target dose coverage and robustness against setup and range errors were improved. The developed method is simple, fast, accurate and applicable for beam angle selection in charged particle therapy with PBS.

Oceanic crust recycling and the formation of lower mantle heterogeneity

NASA Astrophysics Data System (ADS)

van Keken, Peter E.; Ritsema, Jeroen; Haugland, Sam; Goes, Saskia; Kaneshima, Satoshi

2016-04-01

The Earth's lower mantle is heterogeneous at multiple scales as demonstrated for example by the degree-2 distribution of LLSVPs seen in global tomography and widespread distribution of small scale heterogeneity as seen in seismic scattering. The origin of this heterogeneity is generally attributed to leftovers from Earth's formation, the recycling of oceanic crust, or a combination thereof. Here we will explore the consequences of long-term oceanic crust extraction and recycling by plate tectonics. We use geodynamical models of mantle convection that simulate plates in an energetically consistent manner. The recycling of oceanic crust over the age of the Earth produces persistent lower mantle heterogeneity while the upper mantle tends to be significantly more homogeneous. We quantitatively compare the predicted heterogeneity to that of the present day Earth by tomographic filtering of the geodynamical models and comparison with S40RTS. We also predict the scattering characteristics from S-P conversions and compare these to global scattering observations. The geophysical comparison shows that lower mantle heterogeneity is likely dominated by long-term oceanic crust recycling. The models also demonstrate reasonable agreement with the geochemically observed spread between HIMU-EM1-DMM in ocean island basalts as well as the long-term gradual depletion of the upper mantle as observed in Lu-Hf systematics.

Predicting Intra-Urban Population Densities in Africa using SAR and Optical Remote Sensing Data

NASA Astrophysics Data System (ADS)

Linard, C.; Steele, J.; Forget, Y.; Lopez, J.; Shimoni, M.

2017-12-01

The population of Africa is predicted to double over the next 40 years, driving profound social, environmental and epidemiological changes within rapidly growing cities. Estimations of within-city variations in population density must be improved in order to take urban heterogeneities into account and better help urban research and decision making, especially for vulnerability and health assessments. Satellite remote sensing offers an effective solution for mapping settlements and monitoring urbanization at different spatial and temporal scales. In Africa, the urban landscape is covered by slums and small houses, where the heterogeneity is high and where the man-made materials are natural. Innovative methods that combine optical and SAR data are therefore necessary for improving settlement mapping and population density predictions. An automatic method was developed to estimate built-up densities using recent and archived optical and SAR data and a multi-temporal database of built-up densities was produced for 48 African cities. Geo-statistical methods were then used to study the relationships between census-derived population densities and satellite-derived built-up attributes. Best predictors were combined in a Random Forest framework in order to predict intra-urban variations in population density in any large African city. Models show significant improvement of our spatial understanding of urbanization and urban population distribution in Africa in comparison to the state of the art.

Distributed Episodic Exploratory Planning (DEEP)

DTIC Science & Technology

2008-12-01

API). For DEEP, Hibernate offered the following advantages: • Abstracts SQL by utilizing HQL so any database with a Java Database Connectivity... Hibernate SQL ICCRTS International Command and Control Research and Technology Symposium JDB Java Distributed Blackboard JDBC Java Database Connectivity...selected because of its opportunistic reasoning capabilities and implemented in Java for platform independence. Java was chosen for ease of

Monte Carlo simulations of product distributions and contained metal estimates

USGS Publications Warehouse

Gettings, Mark E.

2013-01-01

Estimation of product distributions of two factors was simulated by conventional Monte Carlo techniques using factor distributions that were independent (uncorrelated). Several simulations using uniform distributions of factors show that the product distribution has a central peak approximately centered at the product of the medians of the factor distributions. Factor distributions that are peaked, such as Gaussian (normal) produce an even more peaked product distribution. Piecewise analytic solutions can be obtained for independent factor distributions and yield insight into the properties of the product distribution. As an example, porphyry copper grades and tonnages are now available in at least one public database and their distributions were analyzed. Although both grade and tonnage can be approximated with lognormal distributions, they are not exactly fit by them. The grade shows some nonlinear correlation with tonnage for the published database. Sampling by deposit from available databases of grade, tonnage, and geological details of each deposit specifies both grade and tonnage for that deposit. Any correlation between grade and tonnage is then preserved and the observed distribution of grades and tonnages can be used with no assumption of distribution form.

Commensurability and transformations of adsorbed phases on a heterogeneous solid with periodic distribution of surface energy

NASA Astrophysics Data System (ADS)

Cortés, Joaquin; Valencia, Eliana

1997-07-01

Monte Carlo experiments are used to investigate the adsorption of argon on a heterogeneous solid with a periodic distribution of surface energy. A study is made of the relation between the adsorbate molecule's diameter and the distance between the sites of maximum surface energy on the critical temperature, the observed phase changes, and the commensurability of the surface phase structure determined in the simulation.

A loosely coupled framework for terminology controlled distributed EHR search for patient cohort identification in clinical research.

PubMed

Zhao, Lei; Lim Choi Keung, Sarah N; Taweel, Adel; Tyler, Edward; Ogunsina, Ire; Rossiter, James; Delaney, Brendan C; Peterson, Kevin A; Hobbs, F D Richard; Arvanitis, Theodoros N

2012-01-01

Heterogeneous data models and coding schemes for electronic health records present challenges for automated search across distributed data sources. This paper describes a loosely coupled software framework based on the terminology controlled approach to enable the interoperation between the search interface and heterogeneous data sources. Software components interoperate via common terminology service and abstract criteria model so as to promote component reuse and incremental system evolution.

[Mortality by homicides in Colombia, 1998-2012].

PubMed

Chaparro-Narváez, Pablo; Cotes-Cantillo, Karol; León-Quevedo, Willian; Castañeda-Orjuela, Carlos

2016-12-01

Homicide is a universal indicator of social violence with large public health consequences. To describe mortality by homicides and to analyze its trends and geographic distribution in Colombia between 1998 and 2012. We conducted a descriptive study of deaths by homicide in Colombia between 1998 and 2012 using official mortality databases and the population projections of the Departamento Administrativo Nacional de Estadística, DANE. We calculated age- and sex-specific mortality rates, and we analyzed the geographical distribution of mean-adjusted homicide mortality rates at municipal level. Between 1998 and 2012, 331,470 homicides were reported in Colombia. The mean crude rate was 51.5 per 100,000 inhabitants: 95.9 in men and 8.2 in women. Since 2003, a decrease in the number of deaths and rates was observed; 91.9% of the victims were men and the highest mortality rates were reported in the 20-29 years old group. The most frequently involved mechanism was the firearm: Eight of 10 homicides in men, and seven of 10 homicides in women. Out of 1,122 municipalities, 186 were in the highest quintile, accumulating 50.1% of all deaths. In Colombia, homicides have been one of the leading causes of death with a trend towards reduction since 2002. Its geographical distribution has been heterogeneous. To continue addressing this public health issue we must recur to multidisciplinary analytical methodologies for a better understanding of the phenomenon.

Jungle Computing: Distributed Supercomputing Beyond Clusters, Grids, and Clouds

NASA Astrophysics Data System (ADS)

Seinstra, Frank J.; Maassen, Jason; van Nieuwpoort, Rob V.; Drost, Niels; van Kessel, Timo; van Werkhoven, Ben; Urbani, Jacopo; Jacobs, Ceriel; Kielmann, Thilo; Bal, Henri E.

In recent years, the application of high-performance and distributed computing in scientific practice has become increasingly wide spread. Among the most widely available platforms to scientists are clusters, grids, and cloud systems. Such infrastructures currently are undergoing revolutionary change due to the integration of many-core technologies, providing orders-of-magnitude speed improvements for selected compute kernels. With high-performance and distributed computing systems thus becoming more heterogeneous and hierarchical, programming complexity is vastly increased. Further complexities arise because urgent desire for scalability and issues including data distribution, software heterogeneity, and ad hoc hardware availability commonly force scientists into simultaneous use of multiple platforms (e.g., clusters, grids, and clouds used concurrently). A true computing jungle.

Work Coordination Engine

NASA Technical Reports Server (NTRS)

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

2009-01-01

The Work Coordination Engine (WCE) is a Java application integrated into the Service Management Database (SMDB), which coordinates the dispatching and monitoring of a work order system. WCE de-queues work orders from SMDB and orchestrates the dispatching of work to a registered set of software worker applications distributed over a set of local, or remote, heterogeneous computing systems. WCE monitors the execution of work orders once dispatched, and accepts the results of the work order by storing to the SMDB persistent store. The software leverages the use of a relational database, Java Messaging System (JMS), and Web Services using Simple Object Access Protocol (SOAP) technologies to implement an efficient work-order dispatching mechanism capable of coordinating the work of multiple computer servers on various platforms working concurrently on different, or similar, types of data or algorithmic processing. Existing (legacy) applications can be wrapped with a proxy object so that no changes to the application are needed to make them available for integration into the work order system as "workers." WCE automatically reschedules work orders that fail to be executed by one server to a different server if available. From initiation to completion, the system manages the execution state of work orders and workers via a well-defined set of events, states, and actions. It allows for configurable work-order execution timeouts by work-order type. This innovation eliminates a current processing bottleneck by providing a highly scalable, distributed work-order system used to quickly generate products needed by the Deep Space Network (DSN) to support space flight operations. WCE is driven by asynchronous messages delivered via JMS indicating the availability of new work or workers. It runs completely unattended in support of the lights-out operations concept in the DSN.

Management and assimilation of diverse, distributed watershed datasets

NASA Astrophysics Data System (ADS)

Varadharajan, C.; Faybishenko, B.; Versteeg, R.; Agarwal, D.; Hubbard, S. S.; Hendrix, V.

2016-12-01

The U.S. Department of Energy's (DOE) Watershed Function Scientific Focus Area (SFA) seeks to determine how perturbations to mountainous watersheds (e.g., floods, drought, early snowmelt) impact the downstream delivery of water, nutrients, carbon, and metals over seasonal to decadal timescales. We are building a software platform that enables integration of diverse and disparate field, laboratory, and simulation datasets, of various types including hydrological, geological, meteorological, geophysical, geochemical, ecological and genomic datasets across a range of spatial and temporal scales within the Rifle floodplain and the East River watershed, Colorado. We are using agile data management and assimilation approaches, to enable web-based integration of heterogeneous, multi-scale dataSensor-based observations of water-level, vadose zone and groundwater temperature, water quality, meteorology as well as biogeochemical analyses of soil and groundwater samples have been curated and archived in federated databases. Quality Assurance and Quality Control (QA/QC) are performed on priority datasets needed for on-going scientific analyses, and hydrological and geochemical modeling. Automated QA/QC methods are used to identify and flag issues in the datasets. Data integration is achieved via a brokering service that dynamically integrates data from distributed databases via web services, based on user queries. The integrated results are presented to users in a portal that enables intuitive search, interactive visualization and download of integrated datasets. The concepts, approaches and codes being used are shared across various data science components of various large DOE-funded projects such as the Watershed Function SFA, Next Generation Ecosystem Experiment (NGEE) Tropics, Ameriflux/FLUXNET, and Advanced Simulation Capability for Environmental Management (ASCEM), and together contribute towards DOE's cyberinfrastructure for data management and model-data integration.

A Hierarchical and Distributed Approach for Mapping Large Applications to Heterogeneous Grids using Genetic Algorithms

NASA Technical Reports Server (NTRS)

Sanyal, Soumya; Jain, Amit; Das, Sajal K.; Biswas, Rupak

2003-01-01

In this paper, we propose a distributed approach for mapping a single large application to a heterogeneous grid environment. To minimize the execution time of the parallel application, we distribute the mapping overhead to the available nodes of the grid. This approach not only provides a fast mapping of tasks to resources but is also scalable. We adopt a hierarchical grid model and accomplish the job of mapping tasks to this topology using a scheduler tree. Results show that our three-phase algorithm provides high quality mappings, and is fast and scalable.

Heterogeneity of long-history migration predicts emotion recognition accuracy.

PubMed

Wood, Adrienne; Rychlowska, Magdalena; Niedenthal, Paula M

2016-06-01

Recent work (Rychlowska et al., 2015) demonstrated the power of a relatively new cultural dimension, historical heterogeneity, in predicting cultural differences in the endorsement of emotion expression norms. Historical heterogeneity describes the number of source countries that have contributed to a country's present-day population over the last 500 years. People in cultures originating from a large number of source countries may have historically benefited from greater and clearer emotional expressivity, because they lacked a common language and well-established social norms. We therefore hypothesized that in addition to endorsing more expressive display rules, individuals from heterogeneous cultures will also produce facial expressions that are easier to recognize by people from other cultures. By reanalyzing cross-cultural emotion recognition data from 92 papers and 82 cultures, we show that emotion expressions of people from heterogeneous cultures are more easily recognized by observers from other cultures than are the expressions produced in homogeneous cultures. Heterogeneity influences expression recognition rates alongside the individualism-collectivism of the perceivers' culture, as more individualistic cultures were more accurate in emotion judgments than collectivistic cultures. This work reveals the present-day behavioral consequences of long-term historical migration patterns and demonstrates the predictive power of historical heterogeneity. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Heterogeneity Coefficients for Mahalanobis' D as a Multivariate Effect Size.

PubMed

Del Giudice, Marco

2017-01-01

The Mahalanobis distance D is the multivariate generalization of Cohen's d and can be used as a standardized effect size for multivariate differences between groups. An important issue in the interpretation of D is heterogeneity, that is, the extent to which contributions to the overall effect size are concentrated in a small subset of variables rather than evenly distributed across the whole set. Here I present two heterogeneity coefficients for D based on the Gini coefficient, a well-known index of inequality among values of a distribution. I discuss the properties and limitations of the two coefficients and illustrate their use by reanalyzing some published findings from studies of gender differences.

Vaccine effects on heterogeneity in susceptibility and implications for population health management

USGS Publications Warehouse

Langwig, Kate E.; Wargo, Andrew R.; Jones, Darbi R.; Viss, Jessie R.; Rutan, Barbara J.; Egan, Nicholas A.; Sá-Guimarães, Pedro; Min Sun Kim,; Kurath, Gael; Gomes, M. Gabriela M.; Lipsitch, Marc; Bansal, Shweta; Pettigrew, Melinda M.

2017-01-01

Heterogeneity in host susceptibility is a key determinant of infectious disease dynamics but is rarely accounted for in assessment of disease control measures. Understanding how susceptibility is distributed in populations, and how control measures change this distribution, is integral to predicting the course of epidemics with and without interventions. Using multiple experimental and modeling approaches, we show that rainbow trout have relatively homogeneous susceptibility to infection with infectious hematopoietic necrosis virus and that vaccination increases heterogeneity in susceptibility in a nearly all-or-nothing fashion. In a simple transmission model with an R0 of 2, the highly heterogeneous vaccine protection would cause a 35 percentage-point reduction in outbreak size over an intervention inducing homogenous protection at the same mean level. More broadly, these findings provide validation of methodology that can help to reduce biases in predictions of vaccine impact in natural settings and provide insight into how vaccination shapes population susceptibility.

Beyond Cassie equation: Local structure of heterogeneous surfaces determines the contact angles of microdroplets

PubMed Central

Zhang, Bo; Wang, Jianjun; Liu, Zhiping; Zhang, Xianren

2014-01-01

The application of Cassie equation to microscopic droplets is recently under intense debate because the microdroplet dimension is often of the same order of magnitude as the characteristic size of substrate heterogeneities, and the mechanism to describe the contact angle of microdroplets is not clear. By representing real surfaces statistically as an ensemble of patterned surfaces with randomly or regularly distributed heterogeneities (patches), lattice Boltzmann simulations here show that the contact angle of microdroplets has a wide distribution, either continuous or discrete, depending on the patch size. The origin of multiple contact angles observed is ascribed to the contact line pinning effect induced by substrate heterogeneities. We demonstrate that the local feature of substrate structure near the contact line determines the range of contact angles that can be stabilized, while the certain contact angle observed is closely related to the contact line width. PMID:25059292

Simulation study of axial ultrasound transmission in heterogeneous cortical bone model

NASA Astrophysics Data System (ADS)

Takano, Koki; Nagatani, Yoshiki; Matsukawa, Mami

2017-07-01

Ultrasound propagation in a heterogeneous cortical bone was studied. Using a bovine radius, the longitudinal wave velocity distribution in the axial direction was experimentally measured in the MHz range. The bilinear interpolation and piecewise cubic Hermite interpolation methods were applied to create a three-dimensional (3D) precise velocity model of the bone using experimental data. By assuming the uniaxial anisotropy of the bone, the distributions of all elastic moduli of a 3D heterogeneous model were estimated. The elastic finite-difference time-domain method was used to simulate axial ultrasonic wave propagation. The wave propagation in the initial model was compared with that in the thinner model, where the inner part of the cortical bone model was removed. The wave front of the first arriving signal (FAS) slightly depended on the heterogeneity in each model. Owing to the decrease in bone thickness, the propagation behavior also changed and the FAS velocity clearly decreased.

Monte-Carlo model development for evaluation of current clinical target volume definition for heterogeneous and hypoxic glioblastoma.

PubMed

Moghaddasi, L; Bezak, E; Harriss-Phillips, W

2016-05-07

Clinical target volume (CTV) determination may be complex and subjective. In this work a microscopic-scale tumour model was developed to evaluate current CTV practices in glioblastoma multiforme (GBM) external radiotherapy. Previously, a Geant4 cell-based dosimetry model was developed to calculate the dose deposited in individual GBM cells. Microscopic extension probability (MEP) models were then developed using Matlab-2012a. The results of the cell-based dosimetry model and MEP models were combined to calculate survival fractions (SF) for CTV margins of 2.0 and 2.5 cm. In the current work, oxygenation and heterogeneous radiosensitivity profiles were incorporated into the GBM model. The genetic heterogeneity was modelled using a range of α/β values (linear-quadratic model parameters) associated with different GBM cell lines. These values were distributed among the cells randomly, taken from a Gaussian-weighted sample of α/β values. Cellular oxygen pressure was distributed randomly taken from a sample weighted to profiles obtained from literature. Three types of GBM models were analysed: homogeneous-normoxic, heterogeneous-normoxic, and heterogeneous-hypoxic. The SF in different regions of the tumour model and the effect of the CTV margin extension from 2.0-2.5 cm on SFs were investigated for three MEP models. The SF within the beam was increased by up to three and two orders of magnitude following incorporation of heterogeneous radiosensitivities and hypoxia, respectively, in the GBM model. However, the total SF was shown to be overdominated by the presence of tumour cells in the penumbra region and to a lesser extent by genetic heterogeneity and hypoxia. CTV extension by 0.5 cm reduced the SF by a maximum of 78.6  ±  3.3%, 78.5  ±  3.3%, and 77.7  ±  3.1% for homogeneous and heterogeneous-normoxic, and heterogeneous hypoxic GBMs, respectively. Monte-Carlo model was developed to quantitatively evaluate SF for genetically heterogeneous and hypoxic GBM with two CTV margins and three MEP distributions. The results suggest that photon therapy may not provide cure for hypoxic and genetically heterogeneous GBM. However, the extension of the CTV margin by 0.5 cm could be beneficial to delay the recurrence time for this tumour type due to significant increase in tumour cell irradiation.

Micro-scale heterogeneity of soil phosphorus depends on soil substrate and depth

DOE PAGES

Werner, Florian; Mueller, Carsten W.; Thieme, Jurgen; ...

2017-06-09

Soils comprise various heterogeneously distributed pools of lithogenic, free organic, occluded, adsorbed, and precipitated phosphorus (P) forms, which differ depending on soil forming factors. Small-scale heterogeneity of element distributions recently has received increased attention in soil science due to its influence on soil functions and soil fertility. We investigated the micro-scale distribution of total P and different specific P binding forms in aggregates taken from a high-P clay-rich soil and a low-P sandy soil by combining advanced spectrometric and spectroscopic techniques to introduce new insights on P accessibility and availability in soils. Here we show that soil substrate and soilmore » depth determine micro-scale P heterogeneity in soil aggregates. In P-rich areas of all investigated soil aggregates, P was predominantly co-located with aluminium and iron oxides and hydroxides, which are known to strongly adsorb P. Clay minerals were co-located with P only to a lesser extent. In the low-P topsoil aggregate, the majority of the P was bound organically. Aluminium and iron phosphate predominated in the quartz-rich low-P subsoil aggregate. Sorbed and mineral P phases determined P speciation in the high-P top- and subsoil, and apatite was only detected in the high-P subsoil aggregate. Lastly, our results indicate that micro-scale spatial and chemical heterogeneity of P influences P accessibility and bioavailability.« less

Micro-scale heterogeneity of soil phosphorus depends on soil substrate and depth

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

Werner, Florian; Mueller, Carsten W.; Thieme, Jurgen

Soils comprise various heterogeneously distributed pools of lithogenic, free organic, occluded, adsorbed, and precipitated phosphorus (P) forms, which differ depending on soil forming factors. Small-scale heterogeneity of element distributions recently has received increased attention in soil science due to its influence on soil functions and soil fertility. We investigated the micro-scale distribution of total P and different specific P binding forms in aggregates taken from a high-P clay-rich soil and a low-P sandy soil by combining advanced spectrometric and spectroscopic techniques to introduce new insights on P accessibility and availability in soils. Here we show that soil substrate and soilmore » depth determine micro-scale P heterogeneity in soil aggregates. In P-rich areas of all investigated soil aggregates, P was predominantly co-located with aluminium and iron oxides and hydroxides, which are known to strongly adsorb P. Clay minerals were co-located with P only to a lesser extent. In the low-P topsoil aggregate, the majority of the P was bound organically. Aluminium and iron phosphate predominated in the quartz-rich low-P subsoil aggregate. Sorbed and mineral P phases determined P speciation in the high-P top- and subsoil, and apatite was only detected in the high-P subsoil aggregate. Lastly, our results indicate that micro-scale spatial and chemical heterogeneity of P influences P accessibility and bioavailability.« less

Database System Design and Implementation for Marine Air-Traffic-Controller Training

DTIC Science & Technology

2017-06-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. DATABASE SYSTEM DESIGN AND...thesis 4. TITLE AND SUBTITLE DATABASE SYSTEM DESIGN AND IMPLEMENTATION FOR MARINE AIR-TRAFFIC-CONTROLLER TRAINING 5. FUNDING NUMBERS 6. AUTHOR(S...12b. DISTRIBUTION CODE 13. ABSTRACT (maximum 200 words) This project focused on the design , development, and implementation of a centralized

Acknowledging patient heterogeneity in economic evaluation : a systematic literature review.

PubMed

Grutters, Janneke P C; Sculpher, Mark; Briggs, Andrew H; Severens, Johan L; Candel, Math J; Stahl, James E; De Ruysscher, Dirk; Boer, Albert; Ramaekers, Bram L T; Joore, Manuela A

2013-02-01

Patient heterogeneity is the part of variability that can be explained by certain patient characteristics (e.g. age, disease stage). Population reimbursement decisions that acknowledge patient heterogeneity could potentially save money and increase population health. To date, however, economic evaluations pay only limited attention to patient heterogeneity. The objective of the present paper is to provide a comprehensive overview of the current knowledge regarding patient heterogeneity within economic evaluation of healthcare programmes. A systematic literature review was performed to identify methodological papers on the topic of patient heterogeneity in economic evaluation. Data were obtained using a keyword search of the PubMed database and manual searches. Handbooks were also included. Relevant data were extracted regarding potential sources of patient heterogeneity, in which of the input parameters of an economic evaluation these occur, methods to acknowledge patient heterogeneity and specific concerns associated with this acknowledgement. A total of 20 articles and five handbooks were included. The relevant sources of patient heterogeneity (demographics, preferences and clinical characteristics) and the input parameters where they occurred (baseline risk, treatment effect, health state utility and resource utilization) were combined in a framework. Methods were derived for the design, analysis and presentation phases of an economic evaluation. Concerns related mainly to the danger of false-positive results and equity issues. By systematically reviewing current knowledge regarding patient heterogeneity within economic evaluations of healthcare programmes, we provide guidance for future economic evaluations. Guidance is provided on which sources of patient heterogeneity to consider, how to acknowledge them in economic evaluation and potential concerns. The improved acknowledgement of patient heterogeneity in future economic evaluations may well improve the efficiency of healthcare.

A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks.

PubMed

Jambusaria, Ankit; Klomp, Jeff; Hong, Zhigang; Rafii, Shahin; Dai, Yang; Malik, Asrar B; Rehman, Jalees

2018-06-07

The heterogeneity of cells across tissue types represents a major challenge for studying biological mechanisms as well as for therapeutic targeting of distinct tissues. Computational prediction of tissue-specific gene regulatory networks may provide important insights into the mechanisms underlying the cellular heterogeneity of cells in distinct organs and tissues. Using three pathway analysis techniques, gene set enrichment analysis (GSEA), parametric analysis of gene set enrichment (PGSEA), alongside our novel model (HeteroPath), which assesses heterogeneously upregulated and downregulated genes within the context of pathways, we generated distinct tissue-specific gene regulatory networks. We analyzed gene expression data derived from freshly isolated heart, brain, and lung endothelial cells and populations of neurons in the hippocampus, cingulate cortex, and amygdala. In both datasets, we found that HeteroPath segregated the distinct cellular populations by identifying regulatory pathways that were not identified by GSEA or PGSEA. Using simulated datasets, HeteroPath demonstrated robustness that was comparable to what was seen using existing gene set enrichment methods. Furthermore, we generated tissue-specific gene regulatory networks involved in vascular heterogeneity and neuronal heterogeneity by performing motif enrichment of the heterogeneous genes identified by HeteroPath and linking the enriched motifs to regulatory transcription factors in the ENCODE database. HeteroPath assesses contextual bidirectional gene expression within pathways and thus allows for transcriptomic assessment of cellular heterogeneity. Unraveling tissue-specific heterogeneity of gene expression can lead to a better understanding of the molecular underpinnings of tissue-specific phenotypes.

Log-amplitude statistics for Beck-Cohen superstatistics

NASA Astrophysics Data System (ADS)

Kiyono, Ken; Konno, Hidetoshi

2013-05-01

As a possible generalization of Beck-Cohen superstatistical processes, we study non-Gaussian processes with temporal heterogeneity of local variance. To characterize the variance heterogeneity, we define log-amplitude cumulants and log-amplitude autocovariance and derive closed-form expressions of the log-amplitude cumulants for χ2, inverse χ2, and log-normal superstatistical distributions. Furthermore, we show that χ2 and inverse χ2 superstatistics with degree 2 are closely related to an extreme value distribution, called the Gumbel distribution. In these cases, the corresponding superstatistical distributions result in the q-Gaussian distribution with q=5/3 and the bilateral exponential distribution, respectively. Thus, our finding provides a hypothesis that the asymptotic appearance of these two special distributions may be explained by a link with the asymptotic limit distributions involving extreme values. In addition, as an application of our approach, we demonstrated that non-Gaussian fluctuations observed in a stock index futures market can be well approximated by the χ2 superstatistical distribution with degree 2.

The Modelling Analysis of the Response of Convective Transport of Energy and Water to Multiscale Surface Heterogeneity over Tibetan Plateau

NASA Astrophysics Data System (ADS)

SUN, G.; Hu, Z.; Ma, Y.; Ma, W.

2017-12-01

The land-atmospheric interactions over a heterogeneous surface is a tricky issue for accurately understanding the energy-water exchanges between land surface and atmosphere. We investigate the vertical transport of energy and water over a heterogeneous land surface in Tibetan Plateau during the evolution of the convective boundary layer using large eddy simulation (WRF_LES). The surface heterogeneity is created according to remote sensing images from high spatial resolution LandSat ETM+ images. The PBL characteristics over a heterogeneous surface are analyzed in terms of secondary circulations under different background wind conditions based on the horizontal and vertical distribution and evolution of wind. The characteristics of vertical transport of energy and heat over a heterogeneous surface are analyzed in terms of the horizontal distribution as well as temporal evolution of sensible and latent heat fluxes at different heights under different wind conditions on basis of the simulated results from WRF_LES. The characteristics of the heat and water transported into the free atmosphere from surface are also analyzed and quantified according to the simulated results from WRF_LES. The convective transport of energy and water are analyzed according to horizontal and vertical distributions of potential temperature and vapor under different background wind conditions. With the analysis based on the WRF_LES simulation, the performance of PBL schemes of mesoscale simulation (WRF_meso) is evaluated. The comparison between horizontal distribution of vertical fluxes and domain-averaged vertical fluxes of the energy and water in the free atmosphere is used to evaluate the performance of PBL schemes of WRF_meso in the simulation of vertical exchange of energy and water. This is an important variable because only the energy and water transported into free atmosphere is able to influence the regional and even global climate. This work would will be of great significance not only for understanding the land atmosphere interactions over a heterogeneous surface by evaluating and improving the performance PBL schemes in WRF-meso, but also for the understanding the profound effect of Tibetan Plateau on the regional and global climate.

Biological data integration: wrapping data and tools.

PubMed

Lacroix, Zoé

2002-06-01

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

Reduced negativity effect in older adults' memory for emotional pictures: the heterogeneity-homogeneity list paradigm.

PubMed

Grühn, Daniel; Scheibe, Susanne; Baltes, Paul B

2007-09-01

Using the heterogeneity-homogeneity list paradigm, the authors investigated 48 young adults' (20-30 years) and 48 older adults' (65-75 years) recognition memory for emotional pictures. The authors obtained no evidence for a positivity bias in older adults' memory: Age differences were primarily driven by older adults' diminished ability to remember negative pictures. The authors further found a strong effect of list types: Pictures, particularly neutral ones, were better recognized in homogeneous (blocked) lists than in heterogeneous (mixed) ones. Results confirm those of a previous study by D. Grühn, J. Smith, and P. B. Baltes (2005) that used a different type of to-be-remembered material, that is, pictures instead of words. (PsycINFO Database Record (c) 2007 APA, all rights reserved).

A Universal Isotherm Model to Capture Adsorption Uptake and Energy Distribution of Porous Heterogeneous Surface.

PubMed

Ng, Kim Choon; Burhan, Muhammad; Shahzad, Muhammad Wakil; Ismail, Azahar Bin

2017-09-06

The adsorbate-adsorbent thermodynamics are complex as it is influenced by the pore size distributions, surface heterogeneity and site energy distribution, as well as the adsorbate properties. Together, these parameters defined the adsorbate uptake forming the state diagrams, known as the adsorption isotherms, when the sorption site energy on the pore surfaces are favorable. The available adsorption models for describing the vapor uptake or isotherms, hitherto, are individually defined to correlate to a certain type of isotherm patterns. There is yet a universal approach in developing these isotherm models. In this paper, we demonstrate that the characteristics of all sorption isotherm types can be succinctly unified by a revised Langmuir model when merged with the concepts of Homotattic Patch Approximation (HPA) and the availability of multiple sets of site energy accompanied by their respective fractional probability factors. The total uptake (q/q*) at assorted pressure ratios (P/P s ) are inextricably traced to the manner the site energies are spread, either naturally or engineered by scientists, over and across the heterogeneous surfaces. An insight to the porous heterogeneous surface characteristics, in terms of adsorption site availability has been presented, describing the unique behavior of each isotherm type.

Automation of multi-agent control for complex dynamic systems in heterogeneous computational network

NASA Astrophysics Data System (ADS)

Oparin, Gennady; Feoktistov, Alexander; Bogdanova, Vera; Sidorov, Ivan

2017-01-01

The rapid progress of high-performance computing entails new challenges related to solving large scientific problems for various subject domains in a heterogeneous distributed computing environment (e.g., a network, Grid system, or Cloud infrastructure). The specialists in the field of parallel and distributed computing give the special attention to a scalability of applications for problem solving. An effective management of the scalable application in the heterogeneous distributed computing environment is still a non-trivial issue. Control systems that operate in networks, especially relate to this issue. We propose a new approach to the multi-agent management for the scalable applications in the heterogeneous computational network. The fundamentals of our approach are the integrated use of conceptual programming, simulation modeling, network monitoring, multi-agent management, and service-oriented programming. We developed a special framework for an automation of the problem solving. Advantages of the proposed approach are demonstrated on the parametric synthesis example of the static linear regulator for complex dynamic systems. Benefits of the scalable application for solving this problem include automation of the multi-agent control for the systems in a parallel mode with various degrees of its detailed elaboration.

Modeling unobserved sources of heterogeneity in animal abundance using a Dirichlet process prior

USGS Publications Warehouse

Dorazio, R.M.; Mukherjee, B.; Zhang, L.; Ghosh, M.; Jelks, H.L.; Jordan, F.

2008-01-01

In surveys of natural populations of animals, a sampling protocol is often spatially replicated to collect a representative sample of the population. In these surveys, differences in abundance of animals among sample locations may induce spatial heterogeneity in the counts associated with a particular sampling protocol. For some species, the sources of heterogeneity in abundance may be unknown or unmeasurable, leading one to specify the variation in abundance among sample locations stochastically. However, choosing a parametric model for the distribution of unmeasured heterogeneity is potentially subject to error and can have profound effects on predictions of abundance at unsampled locations. In this article, we develop an alternative approach wherein a Dirichlet process prior is assumed for the distribution of latent abundances. This approach allows for uncertainty in model specification and for natural clustering in the distribution of abundances in a data-adaptive way. We apply this approach in an analysis of counts based on removal samples of an endangered fish species, the Okaloosa darter. Results of our data analysis and simulation studies suggest that our implementation of the Dirichlet process prior has several attractive features not shared by conventional, fully parametric alternatives. ?? 2008, The International Biometric Society.

Active in-database processing to support ambient assisted living systems.

PubMed

de Morais, Wagner O; Lundström, Jens; Wickström, Nicholas

2014-08-12

As an alternative to the existing software architectures that underpin the development of smart homes and ambient assisted living (AAL) systems, this work presents a database-centric architecture that takes advantage of active databases and in-database processing. Current platforms supporting AAL systems use database management systems (DBMSs) exclusively for data storage. Active databases employ database triggers to detect and react to events taking place inside or outside of the database. DBMSs can be extended with stored procedures and functions that enable in-database processing. This means that the data processing is integrated and performed within the DBMS. The feasibility and flexibility of the proposed approach were demonstrated with the implementation of three distinct AAL services. The active database was used to detect bed-exits and to discover common room transitions and deviations during the night. In-database machine learning methods were used to model early night behaviors. Consequently, active in-database processing avoids transferring sensitive data outside the database, and this improves performance, security and privacy. Furthermore, centralizing the computation into the DBMS facilitates code reuse, adaptation and maintenance. These are important system properties that take into account the evolving heterogeneity of users, their needs and the devices that are characteristic of smart homes and AAL systems. Therefore, DBMSs can provide capabilities to address requirements for scalability, security, privacy, dependability and personalization in applications of smart environments in healthcare.

Active In-Database Processing to Support Ambient Assisted Living Systems

PubMed Central

de Morais, Wagner O.; Lundström, Jens; Wickström, Nicholas

2014-01-01

As an alternative to the existing software architectures that underpin the development of smart homes and ambient assisted living (AAL) systems, this work presents a database-centric architecture that takes advantage of active databases and in-database processing. Current platforms supporting AAL systems use database management systems (DBMSs) exclusively for data storage. Active databases employ database triggers to detect and react to events taking place inside or outside of the database. DBMSs can be extended with stored procedures and functions that enable in-database processing. This means that the data processing is integrated and performed within the DBMS. The feasibility and flexibility of the proposed approach were demonstrated with the implementation of three distinct AAL services. The active database was used to detect bed-exits and to discover common room transitions and deviations during the night. In-database machine learning methods were used to model early night behaviors. Consequently, active in-database processing avoids transferring sensitive data outside the database, and this improves performance, security and privacy. Furthermore, centralizing the computation into the DBMS facilitates code reuse, adaptation and maintenance. These are important system properties that take into account the evolving heterogeneity of users, their needs and the devices that are characteristic of smart homes and AAL systems. Therefore, DBMSs can provide capabilities to address requirements for scalability, security, privacy, dependability and personalization in applications of smart environments in healthcare. PMID:25120164

Modeling the effects of vegetation heterogeneity on wildland fire behavior

NASA Astrophysics Data System (ADS)

Atchley, A. L.; Linn, R.; Sieg, C.; Middleton, R. S.

2017-12-01

Vegetation structure and densities are known to drive fire-spread rate and burn severity. Many fire-spread models incorporate an average, homogenous fuel density in the model domain to drive fire behavior. However, vegetation communities are rarely homogenous and instead present significant heterogeneous structure and fuel densities in the fires path. This results in observed patches of varied burn severities and mosaics of disturbed conditions that affect ecological recovery and hydrologic response. Consequently, to understand the interactions of fire and ecosystem functions, representations of spatially heterogeneous conditions need to be incorporated into fire models. Mechanistic models of fire disturbance offer insight into how fuel load characterization and distribution result in varied fire behavior. Here we use a physically-based 3D combustion model—FIRETEC—that solves conservation of mass, momentum, energy, and chemical species to compare fire behavior on homogenous representations to a heterogeneous vegetation distribution. Results demonstrate the impact vegetation heterogeneity has on the spread rate, intensity, and extent of simulated wildfires thus providing valuable insight in predicted wildland fire evolution and enhanced ability to estimate wildland fire inputs into regional and global climate models.

Vasomotor tone does not affect perfusion heterogeneity and gas exchange in normal primate lungs during normoxia

NASA Technical Reports Server (NTRS)

Glenny, R. W.; Robertson, H. T.; Hlastala, M. P.

2000-01-01

To determine whether vasoregulation is an important cause of pulmonary perfusion heterogeneity, we measured regional blood flow and gas exchange before and after giving prostacyclin (PGI(2)) to baboons. Four animals were anesthetized with ketamine and mechanically ventilated. Fluorescent microspheres were used to mark regional perfusion before and after PGI(2) infusion. The lungs were subsequently excised, dried inflated, and diced into approximately 2-cm(3) pieces (n = 1,208-1,629 per animal) with the spatial coordinates recorded for each piece. Blood flow to each piece was determined for each condition from the fluorescent signals. Blood flow heterogeneity did not change with PGI(2) infusion. Two other measures of spatial blood flow distribution, the fractal dimension and the spatial correlation, did not change with PGI(2) infusion. Alveolar-arterial O(2) differences did not change with PGI(2) infusion. We conclude that, in normal primate lungs during normoxia, vasomotor tone is not a significant cause of perfusion heterogeneity. Despite the heterogeneous distribution of blood flow, active regulation of regional perfusion is not required for efficient gas exchange.

Overload cascading failure on complex networks with heterogeneous load redistribution

NASA Astrophysics Data System (ADS)

Hou, Yueyi; Xing, Xiaoyun; Li, Menghui; Zeng, An; Wang, Yougui

2017-09-01

Many real systems including the Internet, power-grid and financial networks experience rare but large overload cascading failures triggered by small initial shocks. Many models on complex networks have been developed to investigate this phenomenon. Most of these models are based on the load redistribution process and assume that the load on a failed node shifts to nearby nodes in the networks either evenly or according to the load distribution rule before the cascade. Inspired by the fact that real power-grid tends to place the excess load on the nodes with high remaining capacities, we study a heterogeneous load redistribution mechanism in a simplified sandpile model in this paper. We find that weak heterogeneity in load redistribution can effectively mitigate the cascade while strong heterogeneity in load redistribution may even enlarge the size of the final failure. With a parameter θ to control the degree of the redistribution heterogeneity, we identify a rather robust optimal θ∗ = 1. Finally, we find that θ∗ tends to shift to a larger value if the initial sand distribution is homogeneous.

The relative influence of climate, environmental heterogeneity, and human population on the distribution of vertebrate species richness in south-eastern Spain

NASA Astrophysics Data System (ADS)

Moreno-Rueda, Gregorio; Pizarro, Manuel

2007-07-01

In view of the many factors affect species richness, this study examines the relative influence of environmental heterogeneity, climate, human disturbance and spatial structure with respect to the species-richness distribution of terrestrial vertebrates in an area of south-eastern Spain with a Mediterranean climate. We show that environmental heterogeneity was the primary factor determining species richness (20.3% of variance), with the effect of temperature and precipitation being lower (11.6%). Climate had greater importance in determining the species richness of ectotherms (amphibians and reptiles) than of endotherms (mammals and birds). Species richness had less spatial autocorrelation in mammals and birds than in ectotherms. Also, a positive correlation was found between species richness and human population density, especially in reptiles and mammals. Orders and families more sensitive to human presence, such as snakes, raptors, ungulates, and carnivores, showed no relationship (or a negative one) with the human population. This study highlights the importance of environmental heterogeneity (topographic heterogeneity and habitat diversity) for vertebrate conservation in zones with a Mediterranean climate.

The effect of entrapped nonaqueous phase liquids on tracer transport in heterogeneous porous media: Laboratory experiments at the intermediate scale

USGS Publications Warehouse

Barth, Gilbert R.; Illangasekare, T.H.; Rajaram, H.

2003-01-01

This work considers the applicability of conservative tracers for detecting high-saturation nonaqueous-phase liquid (NAPL) entrapment in heterogeneous systems. For this purpose, a series of experiments and simulations was performed using a two-dimensional heterogeneous system (10??1.2 m), which represents an intermediate scale between laboratory and field scales. Tracer tests performed prior to injecting the NAPL provide the baseline response of the heterogeneous porous medium. Two NAPL spill experiments were performed and the entrapped-NAPL saturation distribution measured in detail using a gamma-ray attenuation system. Tracer tests following each of the NAPL spills produced breakthrough curves (BTCs) reflecting the impact of entrapped NAPL on conservative transport. To evaluate significance, the impact of NAPL entrapment on the conservative-tracer breakthrough curves was compared to simulated breakthrough curve variability for different realizations of the heterogeneous distribution. Analysis of the results reveals that the NAPL entrapment has a significant impact on the temporal moments of conservative-tracer breakthrough curves. ?? 2003 Elsevier B.V. All rights reserved.

Spatial heterogeneity study of vegetation coverage at Heihe River Basin

NASA Astrophysics Data System (ADS)

Wu, Lijuan; Zhong, Bo; Guo, Liyu; Zhao, Xiangwei

2014-11-01

Spatial heterogeneity of the animal-landscape system has three major components: heterogeneity of resource distributions in the physical environment, heterogeneity of plant tissue chemistry, heterogeneity of movement modes by the animal. Furthermore, all three different types of heterogeneity interact each other and can either reinforce or offset one another, thereby affecting system stability and dynamics. In previous studies, the study areas are investigated by field sampling, which costs a large amount of manpower. In addition, uncertain in sampling affects the quality of field data, which leads to unsatisfactory results during the entire study. In this study, remote sensing data is used to guide the sampling for research on heterogeneity of vegetation coverage to avoid errors caused by randomness of field sampling. Semi-variance and fractal dimension analysis are used to analyze the spatial heterogeneity of vegetation coverage at Heihe River Basin. The spherical model with nugget is used to fit the semivariogram of vegetation coverage. Based on the experiment above, it is found, (1)there is a strong correlation between vegetation coverage and distance of vegetation populations within the range of 0-28051.3188m at Heihe River Basin, but the correlation loses suddenly when the distance greater than 28051.3188m. (2)The degree of spatial heterogeneity of vegetation coverage at Heihe River Basin is medium. (3)Spatial distribution variability of vegetation occurs mainly on small scales. (4)The degree of spatial autocorrelation is 72.29% between 25% and 75%, which means that spatial correlation of vegetation coverage at Heihe River Basin is medium high.

Gradually Decreasing Starch Branching Enzyme Expression Is Responsible for the Formation of Heterogeneous Starch Granules1[OPEN

PubMed Central

Hu, Pan; Chen, Zichun

2018-01-01

Rice (Oryza sativa) endosperm is mainly occupied by homogeneous polygonal starch from inside to outside. However, morphologically different (heterogeneous) starches have been identified in some rice mutants. How these heterogeneous starches form remains unknown. A high-amylose rice line (TRS) generated through the antisense inhibition of starch branching synthase I (SBEI) and SBEIIb contains four heterogeneous starches: polygonal, aggregate, elongated, and hollow starch; these starches are regionally distributed in the endosperm from inside to outside. Here, we investigated the relationship between SBE dosage and the morphological architecture of heterogeneous starches in TRS endosperm from the view of the molecular structure of starch. The results indicated that their molecular structures underwent regular changes, including gradually increasing true amylose content but decreasing amylopectin content and gradually increasing the ratio of amylopectin long chain but decreasing the ratio of amylopectin short chain. Granule-bound starch synthase I (GBSSI) amounts in the four heterogeneous starches were not significantly different from each other, but SBEI, SBEIIa, and SBEIIb showed a gradually decreasing trend. Further immunostaining analysis revealed that the gradually decreasing SBEs acting on the formation of the four heterogeneous granules were mainly due to the spatial distribution of the three SBEs in the endosperm. It was suggested that the decreased amylopectin in starch might remove steric hindrance and provide extra space for abundant amylose accumulation when the GBSSI amount was not elevated. Furthermore, extra amylose coupled with altered amylopectin structure possibly led to morphological changes in heterogeneous granules. PMID:29133372

Effects of distributed database modeling on evaluation of transaction rollbacks

NASA Technical Reports Server (NTRS)

Mukkamala, Ravi

1991-01-01

Data distribution, degree of data replication, and transaction access patterns are key factors in determining the performance of distributed database systems. In order to simplify the evaluation of performance measures, database designers and researchers tend to make simplistic assumptions about the system. The effect is studied of modeling assumptions on the evaluation of one such measure, the number of transaction rollbacks, in a partitioned distributed database system. Six probabilistic models and expressions are developed for the numbers of rollbacks under each of these models. Essentially, the models differ in terms of the available system information. The analytical results so obtained are compared to results from simulation. From here, it is concluded that most of the probabilistic models yield overly conservative estimates of the number of rollbacks. The effect of transaction commutativity on system throughout is also grossly undermined when such models are employed.

Effects of distributed database modeling on evaluation of transaction rollbacks

NASA Technical Reports Server (NTRS)

Mukkamala, Ravi

1991-01-01

Data distribution, degree of data replication, and transaction access patterns are key factors in determining the performance of distributed database systems. In order to simplify the evaluation of performance measures, database designers and researchers tend to make simplistic assumptions about the system. Here, researchers investigate the effect of modeling assumptions on the evaluation of one such measure, the number of transaction rollbacks in a partitioned distributed database system. The researchers developed six probabilistic models and expressions for the number of rollbacks under each of these models. Essentially, the models differ in terms of the available system information. The analytical results obtained are compared to results from simulation. It was concluded that most of the probabilistic models yield overly conservative estimates of the number of rollbacks. The effect of transaction commutativity on system throughput is also grossly undermined when such models are employed.

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

PubMed Central

Gioutlakis, Aris; Klapa, Maria I.

2017-01-01

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

The Database Query Support Processor (QSP)

NASA Technical Reports Server (NTRS)

1993-01-01

The number and diversity of databases available to users continues to increase dramatically. Currently, the trend is towards decentralized, client server architectures that (on the surface) are less expensive to acquire, operate, and maintain than information architectures based on centralized, monolithic mainframes. The database query support processor (QSP) effort evaluates the performance of a network level, heterogeneous database access capability. Air Force Material Command's Rome Laboratory has developed an approach, based on ANSI standard X3.138 - 1988, 'The Information Resource Dictionary System (IRDS)' to seamless access to heterogeneous databases based on extensions to data dictionary technology. To successfully query a decentralized information system, users must know what data are available from which source, or have the knowledge and system privileges necessary to find out this information. Privacy and security considerations prohibit free and open access to every information system in every network. Even in completely open systems, time required to locate relevant data (in systems of any appreciable size) would be better spent analyzing the data, assuming the original question was not forgotten. Extensions to data dictionary technology have the potential to more fully automate the search and retrieval for relevant data in a decentralized environment. Substantial amounts of time and money could be saved by not having to teach users what data resides in which systems and how to access each of those systems. Information describing data and how to get it could be removed from the application and placed in a dedicated repository where it belongs. The result simplified applications that are less brittle and less expensive to build and maintain. Software technology providing the required functionality is off the shelf. The key difficulty is in defining the metadata required to support the process. The database query support processor effort will provide quantitative data on the amount of effort required to implement an extended data dictionary at the network level, add new systems, adapt to changing user needs, and provide sound estimates on operations and maintenance costs and savings.

TU-F-18C-05: Evaluation of a Method to Calculate Patient-Oriented MGD Coefficients Using Estimates of Glandular Tissue Distribution

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

Porras-Chaverri, M; University of Costa Rica, San Jose; Galavis, P

Purpose: Evaluate mammographic mean glandular dose (MGD) coefficients for particular known tissue distributions using a novel formalism that incorporates the effect of the heterogeneous glandular tissue distribution, by comparing them with MGD coefficients derived from the corresponding anthropomorphic computer breast phantom. Methods: MGD coefficients were obtained using MCNP5 simulations with the currently used homogeneous assumption and the heterogeneously-layered breast (HLB) geometry and compared against those from the computer phantom (ground truth). The tissue distribution for the HLB geometry was estimated using glandularity map image pairs corrected for the presence of non-glandular fibrous tissue. Heterogeneity of tissue distribution was quantified usingmore » the glandular tissue distribution index, Idist. The phantom had 5 cm compressed breast thickness (MLO and CC views) and 29% whole breast glandular percentage. Results: Differences as high as 116% were found between the MGD coefficients with the homogeneous breast core assumption and those from the corresponding ground truth. Higher differences were found for cases with more heterogeneous distribution of glandular tissue. The Idist for all cases was in the [−0.8{sup −}+0.3] range. The use of the methods presented in this work results in better agreement with ground truth with an improvement as high as 105 pp. The decrease in difference across all phantom cases was in the [9{sup −}105] pp range, dependent on the distribution of glandular tissue and was larger for the cases with the highest Idist values. Conclusion: Our results suggest that the use of corrected glandularity image pairs, as well as the HLB geometry, improves the estimates of MGD conversion coefficients by accounting for the distribution of glandular tissue within the breast. The accuracy of this approach with respect to ground truth is highly dependent on the particular glandular tissue distribution studied. Predrag Bakic discloses current funding from NIH, NSF, and DoD, former funding from Real Time Tomography, LLC and a current research collaboration with Barco and Hologic.« less

Multi-source and ontology-based retrieval engine for maize mutant phenotypes

USDA-ARS?s Scientific Manuscript database

In the midst of this genomics era, major plant genome databases are collecting massive amounts of heterogeneous information, including sequence data, gene product information, images of mutant phenotypes, etc., as well as textual descriptions of many of these entities. While basic browsing and sear...

An Examination of Multi-Tier Designs for Legacy Data Access

DTIC Science & Technology

1997-12-01

heterogeneous relational database management systems. The first test system incorporates a two-tier architecture design using Java, and the second system...employs a three-tier architecture design using Java and CORBA. Data on replication times for the two-tier and three-tier designs are presented

Dynamical consequences of mantle heterogeneity in two-phase models of mid-ocean ridges

NASA Astrophysics Data System (ADS)

Katz, R. F.

2010-12-01

The mid-ocean ridge system, over 50,000 km in length, samples the magmatic products of a large swath of the asthenosphere. It provides our best means to assess the heterogeneity structure of the upper mantle. Interpretation of the diverse array of observations of MOR petrology, geochemistry, tomography, etc requires models that can map heterogeneity structure onto predictions testable by comparison with these observations. I report on progress to this end; in particular, I describe numerical models of coupled magma/mantle dynamics at mid-ocean ridges [1,2]. These models incorporate heterogeneity in terms of a simple, two-component thermochemical system with specified amplitude and spatial distribution. They indicate that mantle heterogeneity has significant fluid-dynamical consequences for both mantle and magmatic flow. Models show that the distribution of enrichment can lead to asymmetry in the strength of upwelling across the ridge-axis and channelised magmatic transport to the axis. Furthermore, heterogeneity can cause off-axis upwelling of partially molten diapirs, trapping of enriched melts off-axis, and re-fertilization of the mantle by pooled and refrozen melts. Predicted consequences of geochemical heterogeneity may also be considered. References: [1] Katz, RF, (2008); Magma dynamics with the Enthalpy Method: Benchmark Solutions and Magmatic Focusing at Mid-ocean Ridges. Journal of Petrology, doi: 10.1093/petrology/egn058. [2] Katz RF, (2010); Porosity-driven convection and asymmetry beneath mid-ocean ridges. Submitted to G3.

Effects of Contaminated Site Age on Dissolution Dynamics

NASA Astrophysics Data System (ADS)

Jawitz, J. W.

2004-12-01

This work presents a streamtube-based analytical approach to evaluate reduction in groundwater contaminant flux resulting from partial mass reduction in a nonaqueous phase liquid (NAPL) source zone. The reduction in contaminant flux, Rj, discharged from the source zone is a remediation performance metric that has a direct effect on the fundamental drivers of remediation: protection of human health risks and the environment. Spatial variability is described within a Lagrangian framework where aquifer hydrodynamic heterogeneities are characterized using nonreactive travel time distributions, while NAPL spatial distribution heterogeneity can be similarly described using reactive travel time distributions. The combined statistics of these distributions are used to evaluate the relationship between reduction in contaminant mass, Rm, and Rj. A portion of the contaminant mass in the source zone is assumed to be removed via in-situ flushing remediation, with the initial and final conditions defined as steady-state natural-gradient groundwater flow through the contaminant source zone. The combined effect of aquifer and NAPL heterogeneities are shown to be captured in a single parameter, reactive travel time variability, that was determined to be the most important factor controlling the relationship between Rm and Rj. Increased values of the following parameters are shown to result in more favorable contaminant elution dynamics (i.e., greater flux reduction for a given reduction in mass): aquifer hydrodynamic heterogeneity, NAPL source zone heterogeneity, positive correlation between travel time and NAPL content, and time since the contamination event. Less favorable elution behavior is shown to result from negative correlations between travel time and NAPL content and rate-limited dissolution. The specific emphasis of this presentation is on the effects of the length of time that has elapsed since the contamination event (site age) on the dissolution dynamics.

Hydration-Dependent Dynamical Modes in Xyloglucan from Molecular Dynamics Simulation of 13C NMR Relaxation Times and Their Distributions.

PubMed

Chen, Pan; Terenzi, Camilla; Furó, István; Berglund, Lars A; Wohlert, Jakob

2018-05-15

Macromolecular dynamics in biological systems, which play a crucial role for biomolecular function and activity at ambient temperature, depend strongly on moisture content. Yet, a generally accepted quantitative model of hydration-dependent phenomena based on local relaxation and diffusive dynamics of both polymer and its adsorbed water is still missing. In this work, atomistic-scale spatial distributions of motional modes are calculated using molecular dynamics simulations of hydrated xyloglucan (XG). These are shown to reproduce experimental hydration-dependent 13 C NMR longitudinal relaxation times ( T 1 ) at room temperature, and relevant features of their broad distributions, which are indicative of locally heterogeneous polymer reorientational dynamics. At low hydration, the self-diffusion behavior of water shows that water molecules are confined to particular locations in the randomly aggregated XG network while the average polymer segmental mobility remains low. Upon increasing water content, the hydration network becomes mobile and fully accessible for individual water molecules, and the motion of hydrated XG segments becomes faster. Yet, the polymer network retains a heterogeneous gel-like structure even at the highest level of hydration. We show that the observed distribution of relaxations times arises from the spatial heterogeneity of chain mobility that in turn is a result of heterogeneous distribution of water-chain and chain-chain interactions. Our findings contribute to the picture of hydration-dependent dynamics in other macromolecules such as proteins, DNA, and synthetic polymers, and hold important implications for the mechanical properties of polysaccharide matrixes in plants and plant-based materials.

Effects of heterogeneous wealth distribution on public cooperation with collective risk

NASA Astrophysics Data System (ADS)

Wang, Jing; Fu, Feng; Wang, Long

2010-07-01

The distribution of wealth among individuals in real society can be well described by the Pareto principle or “80-20 rule.” How does such heterogeneity in initial wealth distribution affect the emergence of public cooperation, when individuals, the rich and the poor, engage in a collective-risk enterprise, not to gain a profit but to avoid a potential loss? Here we address this issue by studying a simple but effective model based on threshold public goods games. We analyze the evolutionary dynamics for two distinct scenarios, respectively: one with fair sharers versus defectors and the other with altruists versus defectors. For both scenarios, particularly, we in detail study the dynamics of the population with dichotomic initial wealth—the rich versus the poor. Moreover, we demonstrate the possible steady compositions of the population and provide the conditions for stability of these steady states. We prove that in a population with heterogeneous wealth distribution, richer individuals are more likely to cooperate than poorer ones. Participants with lower initial wealth may choose to cooperate only if all players richer than them are cooperators. The emergence of pubic cooperation largely relies on rich individuals. Furthermore, whenever the wealth gap between the rich and the poor is sufficiently large, cooperation of a few rich individuals can substantially elevate the overall level of social cooperation, which is in line with the well-known Pareto principle. Our work may offer an insight into the emergence of cooperative behavior in real social situations where heterogeneous distribution of wealth among individual is omnipresent.

[Spatial distribution pattern of Chilo suppressalis analyzed by classical method and geostatistics].

PubMed

Yuan, Zheming; Fu, Wei; Li, Fangyi

2004-04-01

Two original samples of Chilo suppressalis and their grid, random and sequence samples were analyzed by classical method and geostatistics to characterize the spatial distribution pattern of C. suppressalis. The limitations of spatial distribution analysis with classical method, especially influenced by the original position of grid, were summarized rather completely. On the contrary, geostatistics characterized well the spatial distribution pattern, congregation intensity and spatial heterogeneity of C. suppressalis. According to geostatistics, the population was up to Poisson distribution in low density. As for higher density population, its distribution was up to aggregative, and the aggregation intensity and dependence range were 0.1056 and 193 cm, respectively. Spatial heterogeneity was also found in the higher density population. Its spatial correlativity in line direction was more closely than that in row direction, and the dependence ranges in line and row direction were 115 and 264 cm, respectively.

Using PVM to host CLIPS in distributed environments

NASA Technical Reports Server (NTRS)

Myers, Leonard; Pohl, Kym

1994-01-01

It is relatively easy to enhance CLIPS (C Language Integrated Production System) to support multiple expert systems running in a distributed environment with heterogeneous machines. The task is minimized by using the PVM (Parallel Virtual Machine) code from Oak Ridge Labs to provide the distributed utility. PVM is a library of C and FORTRAN subprograms that supports distributive computing on many different UNIX platforms. A PVM deamon is easily installed on each CPU that enters the virtual machine environment. Any user with rsh or rexec access to a machine can use the one PVM deamon to obtain a generous set of distributed facilities. The ready availability of both CLIPS and PVM makes the combination of software particularly attractive for budget conscious experimentation of heterogeneous distributive computing with multiple CLIPS executables. This paper presents a design that is sufficient to provide essential message passing functions in CLIPS and enable the full range of PVM facilities.

Effects of physical and geochemical heterogeneities on mineral transformation and biomass accumulation during biostimulation experiments at Rifle, Colorado.

PubMed

Li, Li; Steefel, Carl I; Kowalsky, Michael B; Englert, Andreas; Hubbard, Susan S

2010-03-01

Electron donor amendment for bioremediation often results in precipitation of secondary minerals and the growth of biomass, both of which can potentially change flow paths and the efficacy of bioremediation. Quantitative estimation of precipitate and biomass distribution has remained challenging, partly due to the intrinsic heterogeneities of natural porous media and the scarcity of field data. In this work, we examine the effects of physical and geochemical heterogeneities on the spatial distributions of mineral precipitates and biomass accumulated during a biostimulation field experiment near Rifle, Colorado. Field bromide breakthrough data were used to infer a heterogeneous distribution of hydraulic conductivity through inverse transport modeling, while the solid phase Fe(III) content was determined by assuming a negative correlation with hydraulic conductivity. Validated by field aqueous geochemical data, reactive transport modeling was used to explicitly keep track of the growth of the biomass and to estimate the spatial distribution of precipitates and biomass. The results show that the maximum mineral precipitation and biomass accumulation occurs in the vicinity of the injection wells, occupying up to 5.4vol.% of the pore space, and is dominated by reaction products of sulfate reduction. Accumulation near the injection wells is not strongly affected by heterogeneities present in the system due to the ubiquitous presence of sulfate in the groundwater. However, accumulation in the down-gradient regions is dominated by the iron-reducing reaction products, whose spatial patterns are strongly controlled by both physical and geochemical heterogeneities. Heterogeneities can lead to localized large accumulation of mineral precipitates and biomass, increasing the possibility of pore clogging. Although ignoring the heterogeneities of the system can lead to adequate prediction of the average behavior of sulfate-reducing related products, it can also lead to an overestimation of the overall accumulation of iron-reducing bacteria, as well as the rate and extent of iron reduction. Surprisingly, the model predicts that the total amount of uranium being reduced in the heterogeneous 2D system was similar to that in the 1D homogeneous system, suggesting that the overall uranium bioremediation efficacy may not be significantly affected by the heterogeneities of Fe(III) content in the down-gradient regions. Rather, the characteristics close to the vicinity of the injection wells might be crucial in determining the overall efficacy of uranium bioremediation. These findings have important implications not only for uranium bioremediation at the Rifle site and for bioremediation of other redox sensitive contaminants at sites with similar characteristics, but also for the development of optimal amendment delivery strategies in other settings. Copyright 2009 Elsevier B.V. All rights reserved.

On the multiple depots vehicle routing problem with heterogeneous fleet capacity and velocity

NASA Astrophysics Data System (ADS)

Hanum, F.; Hartono, A. P.; Bakhtiar, T.

2018-03-01

This current manuscript concerns with the optimization problem arising in a route determination of products distribution. The problem is formulated in the form of multiple depots and time windowed vehicle routing problem with heterogeneous capacity and velocity of fleet. Model includes a number of constraints such as route continuity, multiple depots availability and serving time in addition to generic constraints. In dealing with the unique feature of heterogeneous velocity, we generate a number of velocity profiles along the road segments, which then converted into traveling-time tables. An illustrative example of rice distribution among villages by bureau of logistics is provided. Exact approach is utilized to determine the optimal solution in term of vehicle routes and starting time of service.

Dynamical behavior of susceptible-infected-recovered-susceptible epidemic model on weighted networks

NASA Astrophysics Data System (ADS)

Wu, Qingchu; Zhang, Fei

2018-02-01

We study susceptible-infected-recovered-susceptible epidemic model in weighted, regular, and random complex networks. We institute a pairwise-type mathematical model with a general transmission rate to evaluate the influence of the link-weight distribution on the spreading process. Furthermore, we develop a dimensionality reduction approach to derive the condition for the contagion outbreak. Finally, we analyze the influence of the heterogeneity of weight distribution on the outbreak condition for the scenario with a linear transmission rate. Our theoretical analysis is in agreement with stochastic simulations, showing that the heterogeneity of link-weight distribution can have a significant effect on the epidemic dynamics.

Heterogeneous iris image hallucination using sparse representation on a learned heterogeneous patch dictionary

NASA Astrophysics Data System (ADS)

Li, Yung-Hui; Zheng, Bo-Ren; Ji, Dai-Yan; Tien, Chung-Hao; Liu, Po-Tsun

2014-09-01

Cross sensor iris matching may seriously degrade the recognition performance because of the sensor mis-match problem of iris images between the enrollment and test stage. In this paper, we propose two novel patch-based heterogeneous dictionary learning method to attack this problem. The first method applies the latest sparse representation theory while the second method tries to learn the correspondence relationship through PCA in heterogeneous patch space. Both methods learn the basic atoms in iris textures across different image sensors and build connections between them. After such connections are built, at test stage, it is possible to hallucinate (synthesize) iris images across different sensors. By matching training images with hallucinated images, the recognition rate can be successfully enhanced. The experimental results showed the satisfied results both visually and in terms of recognition rate. Experimenting with an iris database consisting of 3015 images, we show that the EER is decreased 39.4% relatively by the proposed method.

Accounting for heterogeneity in meta-analysis using a multiplicative model-an empirical study.

PubMed

Mawdsley, David; Higgins, Julian P T; Sutton, Alex J; Abrams, Keith R

2017-03-01

In meta-analysis, the random-effects model is often used to account for heterogeneity. The model assumes that heterogeneity has an additive effect on the variance of effect sizes. An alternative model, which assumes multiplicative heterogeneity, has been little used in the medical statistics community, but is widely used by particle physicists. In this paper, we compare the two models using a random sample of 448 meta-analyses drawn from the Cochrane Database of Systematic Reviews. In general, differences in goodness of fit are modest. The multiplicative model tends to give results that are closer to the null, with a narrower confidence interval. Both approaches make different assumptions about the outcome of the meta-analysis. In our opinion, the selection of the more appropriate model will often be guided by whether the multiplicative model's assumption of a single effect size is plausible. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Heterogeneous continuous-time random walks

NASA Astrophysics Data System (ADS)

Grebenkov, Denis S.; Tupikina, Liubov

2018-01-01

We introduce a heterogeneous continuous-time random walk (HCTRW) model as a versatile analytical formalism for studying and modeling diffusion processes in heterogeneous structures, such as porous or disordered media, multiscale or crowded environments, weighted graphs or networks. We derive the exact form of the propagator and investigate the effects of spatiotemporal heterogeneities onto the diffusive dynamics via the spectral properties of the generalized transition matrix. In particular, we show how the distribution of first-passage times changes due to local and global heterogeneities of the medium. The HCTRW formalism offers a unified mathematical language to address various diffusion-reaction problems, with numerous applications in material sciences, physics, chemistry, biology, and social sciences.

Distribution Characteristics of Air-Bone Gaps – Evidence of Bias in Manual Audiometry

PubMed Central

Margolis, Robert H.; Wilson, Richard H.; Popelka, Gerald R.; Eikelboom, Robert H.; Swanepoel, De Wet; Saly, George L.

2015-01-01

Objective Five databases were mined to examine distributions of air-bone gaps obtained by automated and manual audiometry. Differences in distribution characteristics were examined for evidence of influences unrelated to the audibility of test signals. Design The databases provided air- and bone-conduction thresholds that permitted examination of air-bone gap distributions that were free of ceiling and floor effects. Cases with conductive hearing loss were eliminated based on air-bone gaps, tympanometry, and otoscopy, when available. The analysis is based on 2,378,921 threshold determinations from 721,831 subjects from five databases. Results Automated audiometry produced air-bone gaps that were normally distributed suggesting that air- and bone-conduction thresholds are normally distributed. Manual audiometry produced air-bone gaps that were not normally distributed and show evidence of biasing effects of assumptions of expected results. In one database, the form of the distributions showed evidence of inclusion of conductive hearing losses. Conclusions Thresholds obtained by manual audiometry show tester bias effects from assumptions of the patient’s hearing loss characteristics. Tester bias artificially reduces the variance of bone-conduction thresholds and the resulting air-bone gaps. Because the automated method is free of bias from assumptions of expected results, these distributions are hypothesized to reflect the true variability of air- and bone-conduction thresholds and the resulting air-bone gaps. PMID:26627469

Optimizing acupuncture treatment for dry eye syndrome: a systematic review.

PubMed

Kim, Bong Hyun; Kim, Min Hee; Kang, Se Hyun; Nam, Hae Jeong

2018-05-03

In a former meta-analysis review, acupuncture was considered a potentially effective treatment for dry eye syndrome (DES), but there were heterogeneities among the outcomes. We updated the meta-analysis and conducted subgroup analysis to reduce the heterogeneity and suggest the most effective acupuncture method based on clinical trials. We searched for randomized controlled trials (RCTs) in 10 databases (MEDLINE, EMBASE, CENTAL, AMED, SCOPUS, CNKI, Wangfang database, Oriental Medicine Advanced Searching Integrated System (OASIS), Koreamed, J-stage) and searched by hand to compare the effects of acupuncture and artificial tears (AT). We also conducted subgroup analysis by (1) method of intervention (acupuncture only or acupuncture plus AT), (2) intervention frequency (less than 3 times a week or more than 3 times a week), (3) period of treatment (less than 4 weeks or more than 4 weeks), and (4) acupoints (BL1, BL2, ST1, ST2, TE23, Ex-HN5). The Bucher method was used for subgroup comparisons. Nineteen studies with 1126 patients were included. Significant improvements on the Schirmer test (weighted mean difference[WMD], 2.14; 95% confidence interval[CI], 0.93 to 3.34; p = 0.0005) and break up time (BUT) (WMD, 0.98; 95% CI, 0.79 to 1.18; p < 0.00001) were reported. In the subgroup analysis, acupuncture plus AT treatment had a weaker effect in BUT but a stronger effect on the Schirmer test and a better overall effect than acupuncture alone. For treatment duration, treatment longer than 1 month was more effective than shorter treatment. With regard to treatment frequency, treatment less than three times a week was more effective than more frequent treatment. In the acupoint analysis, acupuncture treatment including the BL2 and ST1 acupoints was less effective than treatment that did not include them. None of those factors reduced the heterogeneity. Acupuncture was more effective than AT in treating DES but showed high heterogeneity. Intervention differences did not influence the heterogeneity.

DICOM-compliant PACS with CD-based image archival

NASA Astrophysics Data System (ADS)

Cox, Robert D.; Henri, Christopher J.; Rubin, Richard K.; Bret, Patrice M.

1998-07-01

This paper describes the design and implementation of a low- cost PACS conforming to the DICOM 3.0 standard. The goal was to provide an efficient image archival and management solution on a heterogeneous hospital network as a basis for filmless radiology. The system follows a distributed, client/server model and was implemented at a fraction of the cost of a commercial PACS. It provides reliable archiving on recordable CD and allows access to digital images throughout the hospital and on the Internet. Dedicated servers have been designed for short-term storage, CD-based archival, data retrieval and remote data access or teleradiology. The short-term storage devices provide DICOM storage and query/retrieve services to scanners and workstations and approximately twelve weeks of 'on-line' image data. The CD-based archival and data retrieval processes are fully automated with the exception of CD loading and unloading. The system employs lossless compression on both short- and long-term storage devices. All servers communicate via the DICOM protocol in conjunction with both local and 'master' SQL-patient databases. Records are transferred from the local to the master database independently, ensuring that storage devices will still function if the master database server cannot be reached. The system features rules-based work-flow management and WWW servers to provide multi-platform remote data access. The WWW server system is distributed on the storage, retrieval and teleradiology servers allowing viewing of locally stored image data directly in a WWW browser without the need for data transfer to a central WWW server. An independent system monitors disk usage, processes, network and CPU load on each server and reports errors to the image management team via email. The PACS was implemented using a combination of off-the-shelf hardware, freely available software and applications developed in-house. The system has enabled filmless operation in CT, MR and ultrasound within the radiology department and throughout the hospital. The use of WWW technology has enabled the development of an intuitive we- based teleradiology and image management solution that provides complete access to image data.

Probability density function of non-reactive solute concentration in heterogeneous porous formations.

PubMed

Bellin, Alberto; Tonina, Daniele

2007-10-30

Available models of solute transport in heterogeneous formations lack in providing complete characterization of the predicted concentration. This is a serious drawback especially in risk analysis where confidence intervals and probability of exceeding threshold values are required. Our contribution to fill this gap of knowledge is a probability distribution model for the local concentration of conservative tracers migrating in heterogeneous aquifers. Our model accounts for dilution, mechanical mixing within the sampling volume and spreading due to formation heterogeneity. It is developed by modeling local concentration dynamics with an Ito Stochastic Differential Equation (SDE) that under the hypothesis of statistical stationarity leads to the Beta probability distribution function (pdf) for the solute concentration. This model shows large flexibility in capturing the smoothing effect of the sampling volume and the associated reduction of the probability of exceeding large concentrations. Furthermore, it is fully characterized by the first two moments of the solute concentration, and these are the same pieces of information required for standard geostatistical techniques employing Normal or Log-Normal distributions. Additionally, we show that in the absence of pore-scale dispersion and for point concentrations the pdf model converges to the binary distribution of [Dagan, G., 1982. Stochastic modeling of groundwater flow by unconditional and conditional probabilities, 2, The solute transport. Water Resour. Res. 18 (4), 835-848.], while it approaches the Normal distribution for sampling volumes much larger than the characteristic scale of the aquifer heterogeneity. Furthermore, we demonstrate that the same model with the spatial moments replacing the statistical moments can be applied to estimate the proportion of the plume volume where solute concentrations are above or below critical thresholds. Application of this model to point and vertically averaged bromide concentrations from the first Cape Cod tracer test and to a set of numerical simulations confirms the above findings and for the first time it shows the superiority of the Beta model to both Normal and Log-Normal models in interpreting field data. Furthermore, we show that assuming a-priori that local concentrations are normally or log-normally distributed may result in a severe underestimate of the probability of exceeding large concentrations.

Private database queries based on counterfactual quantum key distribution

NASA Astrophysics Data System (ADS)

Zhang, Jia-Li; Guo, Fen-Zhuo; Gao, Fei; Liu, Bin; Wen, Qiao-Yan

2013-08-01

Based on the fundamental concept of quantum counterfactuality, we propose a protocol to achieve quantum private database queries, which is a theoretical study of how counterfactuality can be employed beyond counterfactual quantum key distribution (QKD). By adding crucial detecting apparatus to the device of QKD, the privacy of both the distrustful user and the database owner can be guaranteed. Furthermore, the proposed private-database-query protocol makes full use of the low efficiency in the counterfactual QKD, and by adjusting the relevant parameters, the protocol obtains excellent flexibility and extensibility.

Geometric heterogeneity of the lattice and its effect on the kinetics phase transitions of surface reactions

NASA Astrophysics Data System (ADS)

Cortés, Joaquín.; Valencia, Eliana

1999-04-01

Two novel phenomena are discussed in this paper. The first one refers to the effect of the catalyst's surface heterogeneity on the smoothing of the first-order transition observed in the ( A+ B2) reaction (ZGB model). The second effect corresponds to obtaining information on the surface heterogeneity from the shape of the transition curve. Two types of heterogeneity were considered: the structure obtained by the random blocking of reactive sites, and the existence of a distribution in independent strips or terraces on the catalyst's surface.

Distributed consensus for discrete-time heterogeneous multi-agent systems

NASA Astrophysics Data System (ADS)

Zhao, Huanyu; Fei, Shumin

2018-06-01

This paper studies the consensus problem for a class of discrete-time heterogeneous multi-agent systems. Two kinds of consensus algorithms will be considered. The heterogeneous multi-agent systems considered are converted into equivalent error systems by a model transformation. Then we analyse the consensus problem of the original systems by analysing the stability problem of the error systems. Some sufficient conditions for consensus of heterogeneous multi-agent systems are obtained by applying algebraic graph theory and matrix theory. Simulation examples are presented to show the usefulness of the results.

Newborn screening healthcare information system based on service-oriented architecture.

PubMed

Hsieh, Sung-Huai; Hsieh, Sheau-Ling; Chien, Yin-Hsiu; Weng, Yung-Ching; Hsu, Kai-Ping; Chen, Chi-Huang; Tu, Chien-Ming; Wang, Zhenyu; Lai, Feipei

2010-08-01

In this paper, we established a newborn screening system under the HL7/Web Services frameworks. We rebuilt the NTUH Newborn Screening Laboratory's original standalone architecture, having various heterogeneous systems operating individually, and restructured it into a Service-Oriented Architecture (SOA), distributed platform for further integrity and enhancements of sample collections, testing, diagnoses, evaluations, treatments or follow-up services, screening database management, as well as collaboration, communication among hospitals; decision supports and improving screening accuracy over the Taiwan neonatal systems are also addressed. In addition, the new system not only integrates the newborn screening procedures among phlebotomy clinics, referral hospitals, as well as the newborn screening center in Taiwan, but also introduces new models of screening procedures for the associated, medical practitioners. Furthermore, it reduces the burden of manual operations, especially the reporting services, those were heavily dependent upon previously. The new system can accelerate the whole procedures effectively and efficiently. It improves the accuracy and the reliability of the screening by ensuring the quality control during the processing as well.

MMA-EoS: A Computational Framework for Mineralogical Thermodynamics

NASA Astrophysics Data System (ADS)

Chust, T. C.; Steinle-Neumann, G.; Dolejš, D.; Schuberth, B. S. A.; Bunge, H.-P.

2017-12-01

We present a newly developed software framework, MMA-EoS, that evaluates phase equilibria and thermodynamic properties of multicomponent systems by Gibbs energy minimization, with application to mantle petrology. The code is versatile in terms of the equation-of-state and mixing properties and allows for the computation of properties of single phases, solution phases, and multiphase aggregates. Currently, the open program distribution contains equation-of-state formulations widely used, that is, Caloric-Murnaghan, Caloric-Modified-Tait, and Birch-Murnaghan-Mie-Grüneisen-Debye models, with published databases included. Through its modular design and easily scripted database, MMA-EoS can readily be extended with new formulations of equations-of-state and changes or extensions to thermodynamic data sets. We demonstrate the application of the program by reproducing and comparing physical properties of mantle phases and assemblages with previously published work and experimental data, successively increasing complexity, up to computing phase equilibria of six-component compositions. Chemically complex systems allow us to trace the budget of minor chemical components in order to explore whether they lead to the formation of new phases or extend stability fields of existing ones. Self-consistently computed thermophysical properties for a homogeneous mantle and a mechanical mixture of slab lithologies show no discernible differences that require a heterogeneous mantle structure as has been suggested previously. Such examples illustrate how thermodynamics of mantle mineralogy can advance the study of Earth's interior.

The Prodiguer Messaging Platform

NASA Astrophysics Data System (ADS)

Denvil, S.; Greenslade, M. A.; Carenton, N.; Levavasseur, G.; Raciazek, J.

2015-12-01

CONVERGENCE is a French multi-partner national project designed to gather HPC and informatics expertise to innovate in the context of running French global climate models with differing grids and at differing resolutions. Efficient and reliable execution of these models and the management and dissemination of model output are some of the complexities that CONVERGENCE aims to resolve.At any one moment in time, researchers affiliated with the Institut Pierre Simon Laplace (IPSL) climate modeling group, are running hundreds of global climate simulations. These simulations execute upon a heterogeneous set of French High Performance Computing (HPC) environments. The IPSL's simulation execution runtime libIGCM (library for IPSL Global Climate Modeling group) has recently been enhanced so as to support hitherto impossible realtime use cases such as simulation monitoring, data publication, metrics collection, simulation control, visualizations … etc. At the core of this enhancement is Prodiguer: an AMQP (Advanced Message Queue Protocol) based event driven asynchronous distributed messaging platform. libIGCM now dispatches copious amounts of information, in the form of messages, to the platform for remote processing by Prodiguer software agents at IPSL servers in Paris. Such processing takes several forms: Persisting message content to database(s); Launching rollback jobs upon simulation failure; Notifying downstream applications; Automation of visualization pipelines; We will describe and/or demonstrate the platform's: Technical implementation; Inherent ease of scalability; Inherent adaptiveness in respect to supervising simulations; Web portal receiving simulation notifications in realtime.

Characterizing pulmonary blood flow distribution measured using arterial spin labeling.

PubMed

Henderson, A Cortney; Prisk, G Kim; Levin, David L; Hopkins, Susan R; Buxton, Richard B

2009-12-01

The arterial spin labeling (ASL) method provides images in which, ideally, the signal intensity of each image voxel is proportional to the local perfusion. For studies of pulmonary perfusion, the relative dispersion (RD, standard deviation/mean) of the ASL signal across a lung section is used as a reliable measure of flow heterogeneity. However, the RD of the ASL signals within the lung may systematically differ from the true RD of perfusion because the ASL image also includes signals from larger vessels, which can reflect the blood volume rather than blood flow if the vessels are filled with tagged blood during the imaging time. Theoretical studies suggest that the pulmonary vasculature exhibits a lognormal distribution for blood flow and thus an appropriate measure of heterogeneity is the geometric standard deviation (GSD). To test whether the ASL signal exhibits a lognormal distribution for pulmonary blood flow, determine whether larger vessels play an important role in the distribution, and extract physiologically relevant measures of heterogeneity from the ASL signal, we quantified the ASL signal before and after an intervention (head-down tilt) in six subjects. The distribution of ASL signal was better characterized by a lognormal distribution than a normal distribution, reducing the mean squared error by 72% (p < 0.005). Head-down tilt significantly reduced the lognormal scale parameter (p = 0.01) but not the shape parameter or GSD. The RD increased post-tilt and remained significantly elevated (by 17%, p < 0.05). Test case results and mathematical simulations suggest that RD is more sensitive than the GSD to ASL signal from tagged blood in larger vessels, a probable explanation of the change in RD without a statistically significant change in GSD. This suggests that the GSD is a useful measure of pulmonary blood flow heterogeneity with the advantage of being less affected by the ASL signal from tagged blood in larger vessels.

Long-term spatial heterogeneity in mallard distribution in the Prairie pothole region

USGS Publications Warehouse

Janke, Adam K.; Anteau, Michael J.; Stafford, Joshua D.

2017-01-01

The Prairie Pothole Region (PPR) of north-central United States and south-central Canada supports greater than half of all breeding mallards (Anas platyrhynchos) annually counted in North America and is the focus of widespread conservation and research efforts. Allocation of conservation resources for this socioeconomically important population would benefit from an understanding of the nature of spatiotemporal variation in distribution of breeding mallards throughout the 850,000 km2 landscape. We used mallard counts from the Waterfowl Breeding Population and Habitat Survey to test for spatial heterogeneity and identify high- and low-abundance regions of breeding mallards over a 50-year time series. We found strong annual spatial heterogeneity in all years: 90% of mallards counted annually were on an average of only 15% of surveyed segments. Using a local indicator of spatial autocorrelation, we found a relatively static distribution of low-count clusters in northern Montana, USA, and southern Alberta, Canada, and a dynamic distribution of high-count clusters throughout the study period. Distribution of high-count clusters shifted southeast from northwestern portions of the PPR in Alberta and western Saskatchewan, Canada, to North and South Dakota, USA, during the latter half of the study period. This spatial redistribution of core mallard breeding populations was likely driven by interactions between environmental variation that created favorable hydrological conditions for wetlands in the eastern PPR and dynamic land-use patterns related to upland cropping practices and government land-retirement programs. Our results highlight an opportunity for prioritizing relatively small regions within the PPR for allocation of wetland and grassland conservation for mallard populations. However, the extensive spatial heterogeneity in core distributions over our study period suggests such spatial prioritization will have to overcome challenges presented by dynamic land-use and climate patterns in the region, and thus merits additional monitoring and empirical research to anticipate future population distribution. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

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

PubMed Central

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

2009-01-01

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

Kinematic evolution of the Maacama Fault Zone, Northern California Coast Ranges

NASA Astrophysics Data System (ADS)

Schroeder, Rick D.

The Maacama Fault Zone (MFZ) is a major component of the Pacific-North American transform boundary in northern California, and its distribution of deformation and kinematic evolution defines that of a young continental transform boundary. The USGS Quaternary database (2010) currently defines the MFZ as a relatively narrow fault zone; however, a cluster analysis of microearthquakes beneath the MFZ defines a wider fault zone, composed of multiple seismogenically active faults. The surface projection of best-fit tabular zones through foci clusters correlates with previously interpreted faults that were assumed inactive. New investigations further delineate faults within the MFZ based on geomorphic features and shallow resistivity surveys, and these faults are interpreted to be part of several active pull-apart fault systems. The location of faults and changes in their geometry in relation to geomorphic features, indicate >8 km of cumulative dextral displacement across the eastern portion of the MFZ at Little Lake Valley, which includes other smaller offsets on fault strands in the valley. Some faults within the MFZ have geometries consistent with reactivated subduction-related reverse faults, and project near outcrops of pre-existing faults, filled with mechanically weak minerals. The mechanical behavior of fault zones is influenced by the spatial distribution and abundance of mechanically weak lithologies and mineralogies within the heterogeneous Franciscan melange that the MFZ displaces. This heterogeneity is characterized near Little Lake Valley (LLV) using remotely sensed data, field mapping, and wellbore data, and is composed of 2--5 km diameter disk-shaped coherent blocks that can be competent and resist deformation. Coherent blocks and the melange that surrounds them are the source for altered minerals that fill portions of fault zones. Mechanically weak minerals in pre-existing fault zones, identified by X-ray diffraction and electron microprobe analyses, are interpreted as a major reason for complex configurations of clusters of microearthquakes and zones of aseismic creep along the MFZ. Analysis of the kinematics of the MFZ and the distribution of its deformation is important because it improves the understanding of young stages of transform system evolution, which has implications that affect issues ranging from seismic hazard to petroleum and minerals exploration around the world.

Federated ontology-based queries over cancer data

PubMed Central

2012-01-01

Background Personalised medicine provides patients with treatments that are specific to their genetic profiles. It requires efficient data sharing of disparate data types across a variety of scientific disciplines, such as molecular biology, pathology, radiology and clinical practice. Personalised medicine aims to offer the safest and most effective therapeutic strategy based on the gene variations of each subject. In particular, this is valid in oncology, where knowledge about genetic mutations has already led to new therapies. Current molecular biology techniques (microarrays, proteomics, epigenetic technology and improved DNA sequencing technology) enable better characterisation of cancer tumours. The vast amounts of data, however, coupled with the use of different terms - or semantic heterogeneity - in each discipline makes the retrieval and integration of information difficult. Results Existing software infrastructures for data-sharing in the cancer domain, such as caGrid, support access to distributed information. caGrid follows a service-oriented model-driven architecture. Each data source in caGrid is associated with metadata at increasing levels of abstraction, including syntactic, structural, reference and domain metadata. The domain metadata consists of ontology-based annotations associated with the structural information of each data source. However, caGrid's current querying functionality is given at the structural metadata level, without capitalising on the ontology-based annotations. This paper presents the design of and theoretical foundations for distributed ontology-based queries over cancer research data. Concept-based queries are reformulated to the target query language, where join conditions between multiple data sources are found by exploiting the semantic annotations. The system has been implemented, as a proof of concept, over the caGrid infrastructure. The approach is applicable to other model-driven architectures. A graphical user interface has been developed, supporting ontology-based queries over caGrid data sources. An extensive evaluation of the query reformulation technique is included. Conclusions To support personalised medicine in oncology, it is crucial to retrieve and integrate molecular, pathology, radiology and clinical data in an efficient manner. The semantic heterogeneity of the data makes this a challenging task. Ontologies provide a formal framework to support querying and integration. This paper provides an ontology-based solution for querying distributed databases over service-oriented, model-driven infrastructures. PMID:22373043

Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load

PubMed Central

Alexander, Helen K.; Mayer, Stephanie I.; Bonhoeffer, Sebastian

2017-01-01

Abstract Mutation rate is a crucial evolutionary parameter that has typically been treated as a constant in population genetic analyses. However, the propensity to mutate is likely to vary among co-existing individuals within a population, due to genetic polymorphisms, heterogeneous environmental influences, and random physiological fluctuations. We review the evidence for mutation rate heterogeneity and explore its consequences by extending classic population genetic models to allow an arbitrary distribution of mutation rate among individuals, either with or without inheritance. With this general new framework, we rigorously establish the effects of heterogeneity at various evolutionary timescales. In a single generation, variation of mutation rate about the mean increases the probability of producing zero or many simultaneous mutations on a genome. Over multiple generations of mutation and selection, heterogeneity accelerates the appearance of both deleterious and beneficial multi-point mutants. At mutation-selection balance, higher-order mutant frequencies are likewise boosted, while lower-order mutants exhibit subtler effects; nonetheless, population mean fitness is always enhanced. We quantify the dependencies on moments of the mutation rate distribution and selection coefficients, and clarify the role of mutation rate inheritance. While typical methods of estimating mutation rate will recover only the population mean, analyses assuming mutation rate is fixed to this mean could underestimate the potential for multi-locus adaptation, including medically relevant evolution in pathogenic and cancerous populations. We discuss the potential to empirically parameterize mutation rate distributions, which have to date hardly been quantified. PMID:27836985

A uniform approach for programming distributed heterogeneous computing systems

PubMed Central

Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas

2014-01-01

Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater’s performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations. PMID:25844015

Vivaldi: A Domain-Specific Language for Volume Processing and Visualization on Distributed Heterogeneous Systems.

PubMed

Choi, Hyungsuk; Choi, Woohyuk; Quan, Tran Minh; Hildebrand, David G C; Pfister, Hanspeter; Jeong, Won-Ki

2014-12-01

As the size of image data from microscopes and telescopes increases, the need for high-throughput processing and visualization of large volumetric data has become more pressing. At the same time, many-core processors and GPU accelerators are commonplace, making high-performance distributed heterogeneous computing systems affordable. However, effectively utilizing GPU clusters is difficult for novice programmers, and even experienced programmers often fail to fully leverage the computing power of new parallel architectures due to their steep learning curve and programming complexity. In this paper, we propose Vivaldi, a new domain-specific language for volume processing and visualization on distributed heterogeneous computing systems. Vivaldi's Python-like grammar and parallel processing abstractions provide flexible programming tools for non-experts to easily write high-performance parallel computing code. Vivaldi provides commonly used functions and numerical operators for customized visualization and high-throughput image processing applications. We demonstrate the performance and usability of Vivaldi on several examples ranging from volume rendering to image segmentation.

A uniform approach for programming distributed heterogeneous computing systems.

PubMed

Grasso, Ivan; Pellegrini, Simone; Cosenza, Biagio; Fahringer, Thomas

2014-12-01

Large-scale compute clusters of heterogeneous nodes equipped with multi-core CPUs and GPUs are getting increasingly popular in the scientific community. However, such systems require a combination of different programming paradigms making application development very challenging. In this article we introduce libWater, a library-based extension of the OpenCL programming model that simplifies the development of heterogeneous distributed applications. libWater consists of a simple interface, which is a transparent abstraction of the underlying distributed architecture, offering advanced features such as inter-context and inter-node device synchronization. It provides a runtime system which tracks dependency information enforced by event synchronization to dynamically build a DAG of commands, on which we automatically apply two optimizations: collective communication pattern detection and device-host-device copy removal. We assess libWater's performance in three compute clusters available from the Vienna Scientific Cluster, the Barcelona Supercomputing Center and the University of Innsbruck, demonstrating improved performance and scaling with different test applications and configurations.

Epidemic spreading on activity-driven networks with attractiveness.

PubMed

Pozzana, Iacopo; Sun, Kaiyuan; Perra, Nicola

2017-10-01

We study SIS epidemic spreading processes unfolding on a recent generalization of the activity-driven modeling framework. In this model of time-varying networks, each node is described by two variables: activity and attractiveness. The first describes the propensity to form connections, while the second defines the propensity to attract them. We derive analytically the epidemic threshold considering the time scale driving the evolution of contacts and the contagion as comparable. The solutions are general and hold for any joint distribution of activity and attractiveness. The theoretical picture is confirmed via large-scale numerical simulations performed considering heterogeneous distributions and different correlations between the two variables. We find that heterogeneous distributions of attractiveness alter the contagion process. In particular, in the case of uncorrelated and positive correlations between the two variables, heterogeneous attractiveness facilitates the spreading. On the contrary, negative correlations between activity and attractiveness hamper the spreading. The results presented contribute to the understanding of the dynamical properties of time-varying networks and their effects on contagion phenomena unfolding on their fabric.

Empirical evidence about inconsistency among studies in a pair-wise meta-analysis.

PubMed

Rhodes, Kirsty M; Turner, Rebecca M; Higgins, Julian P T

2016-12-01

This paper investigates how inconsistency (as measured by the I 2 statistic) among studies in a meta-analysis may differ, according to the type of outcome data and effect measure. We used hierarchical models to analyse data from 3873 binary, 5132 continuous and 880 mixed outcome meta-analyses within the Cochrane Database of Systematic Reviews. Predictive distributions for inconsistency expected in future meta-analyses were obtained, which can inform priors for between-study variance. Inconsistency estimates were highest on average for binary outcome meta-analyses of risk differences and continuous outcome meta-analyses. For a planned binary outcome meta-analysis in a general research setting, the predictive distribution for inconsistency among log odds ratios had median 22% and 95% CI: 12% to 39%. For a continuous outcome meta-analysis, the predictive distribution for inconsistency among standardized mean differences had median 40% and 95% CI: 15% to 73%. Levels of inconsistency were similar for binary data measured by log odds ratios and log relative risks. Fitted distributions for inconsistency expected in continuous outcome meta-analyses using mean differences were almost identical to those using standardized mean differences. The empirical evidence on inconsistency gives guidance on which outcome measures are most likely to be consistent in particular circumstances and facilitates Bayesian meta-analysis with an informative prior for heterogeneity. © 2015 The Authors. Research Synthesis Methods published by John Wiley & Sons, Ltd. © 2015 The Authors. Research Synthesis Methods published by John Wiley & Sons, Ltd. © 2015 The Authors. Research Synthesis Methods published by John Wiley & Sons, Ltd.

ARIANE: integration of information databases within a hospital intranet.

PubMed

Joubert, M; Aymard, S; Fieschi, D; Volot, F; Staccini, P; Robert, J J; Fieschi, M

1998-05-01

Large information systems handle massive volume of data stored in heterogeneous sources. Each server has its own model of representation of concepts with regard to its aims. One of the main problems end-users encounter when accessing different servers is to match their own viewpoint on biomedical concepts with the various representations that are made in the databases servers. The aim of the project ARIANE is to provide end-users with easy-to-use and natural means to access and query heterogeneous information databases. The objectives of this research work consist in building a conceptual interface by means of the Internet technology inside an enterprise Intranet and to propose a method to realize it. This method is based on the knowledge sources provided by the Unified Medical Language System (UMLS) project of the US National Library of Medicine. Experiments concern queries to three different information servers: PubMed, a Medline server of the NLM; Thériaque, a French database on drugs implemented in the Hospital Intranet; and a Web site dedicated to Internet resources in gastroenterology and nutrition, located at the Faculty of Medicine of Nice (France). Accessing to each of these servers is different according to the kind of information delivered and according to the technology used to query it. Dealing with health care professional workstation, the authors introduced in the ARIANE project quality criteria in order to attempt a homogeneous and efficient way to build a query system able to be integrated in existing information systems and to integrate existing and new information sources.

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

PubMed

Ezra Tsur, Elishai

2017-01-01

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

Metagenomic Taxonomy-Guided Database-Searching Strategy for Improving Metaproteomic Analysis.

PubMed

Xiao, Jinqiu; Tanca, Alessandro; Jia, Ben; Yang, Runqing; Wang, Bo; Zhang, Yu; Li, Jing

2018-04-06

Metaproteomics provides a direct measure of the functional information by investigating all proteins expressed by a microbiota. However, due to the complexity and heterogeneity of microbial communities, it is very hard to construct a sequence database suitable for a metaproteomic study. Using a public database, researchers might not be able to identify proteins from poorly characterized microbial species, while a sequencing-based metagenomic database may not provide adequate coverage for all potentially expressed protein sequences. To address this challenge, we propose a metagenomic taxonomy-guided database-search strategy (MT), in which a merged database is employed, consisting of both taxonomy-guided reference protein sequences from public databases and proteins from metagenome assembly. By applying our MT strategy to a mock microbial mixture, about two times as many peptides were detected as with the metagenomic database only. According to the evaluation of the reliability of taxonomic attribution, the rate of misassignments was comparable to that obtained using an a priori matched database. We also evaluated the MT strategy with a human gut microbial sample, and we found 1.7 times as many peptides as using a standard metagenomic database. In conclusion, our MT strategy allows the construction of databases able to provide high sensitivity and precision in peptide identification in metaproteomic studies, enabling the detection of proteins from poorly characterized species within the microbiota.

New model for distributed multimedia databases and its application to networking of museums

NASA Astrophysics Data System (ADS)

Kuroda, Kazuhide; Komatsu, Naohisa; Komiya, Kazumi; Ikeda, Hiroaki

1998-02-01

This paper proposes a new distributed multimedia data base system where the databases storing MPEG-2 videos and/or super high definition images are connected together through the B-ISDN's, and also refers to an example of the networking of museums on the basis of the proposed database system. The proposed database system introduces a new concept of the 'retrieval manager' which functions an intelligent controller so that the user can recognize a set of image databases as one logical database. A user terminal issues a request to retrieve contents to the retrieval manager which is located in the nearest place to the user terminal on the network. Then, the retrieved contents are directly sent through the B-ISDN's to the user terminal from the server which stores the designated contents. In this case, the designated logical data base dynamically generates the best combination of such a retrieving parameter as a data transfer path referring to directly or data on the basis of the environment of the system. The generated retrieving parameter is then executed to select the most suitable data transfer path on the network. Therefore, the best combination of these parameters fits to the distributed multimedia database system.

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

NASA Technical Reports Server (NTRS)

Younger, Herbert; Oreilly, John; Frogner, Bjorn

1994-01-01

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

A Framework for Seamless Interoperation of Heterogeneous Distributed Software Components

DTIC Science & Technology

2005-05-01

interoperability, b) distributed resource discovery, and c) validation of quality requirements. Principles and prototypical systems were created to demonstrate the successful completion of the research.

Optimal File-Distribution in Heterogeneous and Asymmetric Storage Networks

NASA Astrophysics Data System (ADS)

Langner, Tobias; Schindelhauer, Christian; Souza, Alexander

We consider an optimisation problem which is motivated from storage virtualisation in the Internet. While storage networks make use of dedicated hardware to provide homogeneous bandwidth between servers and clients, in the Internet, connections between storage servers and clients are heterogeneous and often asymmetric with respect to upload and download. Thus, for a large file, the question arises how it should be fragmented and distributed among the servers to grant "optimal" access to the contents. We concentrate on the transfer time of a file, which is the time needed for one upload and a sequence of n downloads, using a set of m servers with heterogeneous bandwidths. We assume that fragments of the file can be transferred in parallel to and from multiple servers. This model yields a distribution problem that examines the question of how these fragments should be distributed onto those servers in order to minimise the transfer time. We present an algorithm, called FlowScaling, that finds an optimal solution within running time {O}(m log m). We formulate the distribution problem as a maximum flow problem, which involves a function that states whether a solution with a given transfer time bound exists. This function is then used with a scaling argument to determine an optimal solution within the claimed time complexity.

Initiation and dynamics of a spiral wave around an ionic heterogeneity in a model for human cardiac tissue.

PubMed

Defauw, Arne; Dawyndt, Peter; Panfilov, Alexander V

2013-12-01

In relation to cardiac arrhythmias, heterogeneity of cardiac tissue is one of the most important factors underlying the onset of spiral waves and determining their type. In this paper, we numerically model heterogeneity of realistic size and value and study formation and dynamics of spiral waves around such heterogeneity. We find that the only sustained pattern obtained is a single spiral wave anchored around the heterogeneity. Dynamics of an anchored spiral wave depend on the extent of heterogeneity, and for certain heterogeneity size, we find abrupt regional increase in the period of excitation occurring as a bifurcation. We study factors determining spatial distribution of excitation periods of anchored spiral waves and discuss consequences of such dynamics for cardiac arrhythmias and possibilities for experimental testings of our predictions.

Sources of heterogeneity in case-control studies on associations between statins, ACE-inhibitors, and proton pump inhibitors and risk of pneumonia.

PubMed

de Groot, Mark C H; Klungel, Olaf H; Leufkens, Hubert G M; van Dijk, Liset; Grobbee, Diederick E; van de Garde, Ewoudt M W

2014-10-01

The heterogeneity in case-control studies on the associations between community-acquired pneumonia (CAP) and ACE-inhibitors (ACEi), statins, and proton pump inhibitors (PPI) hampers translation to clinical practice. Our objective is to explore sources of this heterogeneity by applying a common protocol in different data settings. We conducted ten case-control studies using data from five different health care databases. Databases varied on type of patients (hospitalised vs. GP), level of case validity, and mode of exposure ascertainment (prescription or dispensing based). Identified CAP patients and controls were matched on age, gender, and calendar year. Conditional logistic regression was used to calculate odds ratios (OR) for the associations between the drugs of interest and CAP. Associations were adjusted by a common set of potential confounders. Data of 38,742 cases and 118,019 controls were studied. Comparable patterns of variation between case-control studies were observed for ACEi, statins and PPI use and pneumonia risk with adjusted ORs varying from 1.04 to 1.49, 0.82 to 1.50 and 1.16 to 2.71, respectively. Overall, higher ORs were found for hospitalised CAP patients matched to population controls versus GP CAP patients matched to population controls. Prevalence of drug exposure was higher in dispensing data versus prescription data. We show that case-control selection and methods of exposure ascertainment induce bias that cannot be adjusted for and to a considerable extent explain the heterogeneity in results obtained in case-control studies on statins, ACEi and PPIs and CAP. The common protocol approach helps to better understand sources of variation in observational studies.

Dynamic tables: an architecture for managing evolving, heterogeneous biomedical data in relational database management systems.

PubMed

Corwin, John; Silberschatz, Avi; Miller, Perry L; Marenco, Luis

2007-01-01

Data sparsity and schema evolution issues affecting clinical informatics and bioinformatics communities have led to the adoption of vertical or object-attribute-value-based database schemas to overcome limitations posed when using conventional relational database technology. This paper explores these issues and discusses why biomedical data are difficult to model using conventional relational techniques. The authors propose a solution to these obstacles based on a relational database engine using a sparse, column-store architecture. The authors provide benchmarks comparing the performance of queries and schema-modification operations using three different strategies: (1) the standard conventional relational design; (2) past approaches used by biomedical informatics researchers; and (3) their sparse, column-store architecture. The performance results show that their architecture is a promising technique for storing and processing many types of data that are not handled well by the other two semantic data models.

Integrating Scientific Array Processing into Standard SQL

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Bachhuber, Johannes; Baumann, Peter

2014-05-01

We live in a time that is dominated by data. Data storage is cheap and more applications than ever accrue vast amounts of data. Storing the emerging multidimensional data sets efficiently, however, and allowing them to be queried by their inherent structure, is a challenge many databases have to face today. Despite the fact that multidimensional array data is almost always linked to additional, non-array information, array databases have mostly developed separately from relational systems, resulting in a disparity between the two database categories. The current SQL standard and SQL DBMS supports arrays - and in an extension also multidimensional arrays - but does so in a very rudimentary and inefficient way. This poster demonstrates the practicality of an SQL extension for array processing, implemented in a proof-of-concept multi-faceted system that manages a federation of array and relational database systems, providing transparent, efficient and scalable access to the heterogeneous data in them.

A local space time kriging approach applied to a national outpatient malaria data set

NASA Astrophysics Data System (ADS)

Gething, P. W.; Atkinson, P. M.; Noor, A. M.; Gikandi, P. W.; Hay, S. I.; Nixon, M. S.

2007-10-01

Increases in the availability of reliable health data are widely recognised as essential for efforts to strengthen health-care systems in resource-poor settings worldwide. Effective health-system planning requires comprehensive and up-to-date information on a range of health metrics and this requirement is generally addressed by a Health Management Information System (HMIS) that coordinates the routine collection of data at individual health facilities and their compilation into national databases. In many resource-poor settings, these systems are inadequate and national databases often contain only a small proportion of the expected records. In this paper, we take an important health metric in Kenya (the proportion of outpatient treatments for malaria (MP)) from the national HMIS database and predict the values of MP at facilities where monthly records are missing. The available MP data were densely distributed across a spatiotemporal domain and displayed second-order heterogeneity. We used three different kriging methodologies to make cross-validation predictions of MP in order to test the effect on prediction accuracy of (a) the extension of a spatial-only to a space-time prediction approach, and (b) the replacement of a globally stationary with a locally varying random function model. Space-time kriging was found to produce predictions with 98.4% less mean bias and 14.8% smaller mean imprecision than conventional spatial-only kriging. A modification of space-time kriging that allowed space-time variograms to be recalculated for every prediction location within a spatially local neighbourhood resulted in a larger decrease in mean imprecision over ordinary kriging (18.3%) although the mean bias was reduced less (87.5%).

A local space–time kriging approach applied to a national outpatient malaria data set

PubMed Central

Gething, P.W.; Atkinson, P.M.; Noor, A.M.; Gikandi, P.W.; Hay, S.I.; Nixon, M.S.

2007-01-01

Increases in the availability of reliable health data are widely recognised as essential for efforts to strengthen health-care systems in resource-poor settings worldwide. Effective health-system planning requires comprehensive and up-to-date information on a range of health metrics and this requirement is generally addressed by a Health Management Information System (HMIS) that coordinates the routine collection of data at individual health facilities and their compilation into national databases. In many resource-poor settings, these systems are inadequate and national databases often contain only a small proportion of the expected records. In this paper, we take an important health metric in Kenya (the proportion of outpatient treatments for malaria (MP)) from the national HMIS database and predict the values of MP at facilities where monthly records are missing. The available MP data were densely distributed across a spatiotemporal domain and displayed second-order heterogeneity. We used three different kriging methodologies to make cross-validation predictions of MP in order to test the effect on prediction accuracy of (a) the extension of a spatial-only to a space–time prediction approach, and (b) the replacement of a globally stationary with a locally varying random function model. Space–time kriging was found to produce predictions with 98.4% less mean bias and 14.8% smaller mean imprecision than conventional spatial-only kriging. A modification of space–time kriging that allowed space–time variograms to be recalculated for every prediction location within a spatially local neighbourhood resulted in a larger decrease in mean imprecision over ordinary kriging (18.3%) although the mean bias was reduced less (87.5%). PMID:19424510

Integration of Heterogeneous Bibliographic Information through Data Abstractions.

ERIC Educational Resources Information Center

Breazeal, Juliette Ow

This study examines the integration of heterogeneous bibliographic information resources from geographically distributed locations in an automated, unified, and controlled way using abstract data types called "classes" through the Message-Object Model defined in Smalltalk-80 software. The concept of achieving data consistency by…

Image-guided spatial localization of heterogeneous compartments for magnetic resonance

PubMed Central

An, Li; Shen, Jun

2015-01-01

Purpose: Image-guided localization SPectral Localization Achieved by Sensitivity Heterogeneity (SPLASH) allows rapid measurement of signals from irregularly shaped anatomical compartments without using phase encoding gradients. Here, the authors propose a novel method to address the issue of heterogeneous signal distribution within the localized compartments. Methods: Each compartment was subdivided into multiple subcompartments and their spectra were solved by Tikhonov regularization to enforce smoothness within each compartment. The spectrum of a given compartment was generated by combining the spectra of the components of that compartment. The proposed method was first tested using Monte Carlo simulations and then applied to reconstructing in vivo spectra from irregularly shaped ischemic stroke and normal tissue compartments. Results: Monte Carlo simulations demonstrate that the proposed regularized SPLASH method significantly reduces localization and metabolite quantification errors. In vivo results show that the intracompartment regularization results in ∼40% reduction of error in metabolite quantification. Conclusions: The proposed method significantly reduces localization errors and metabolite quantification errors caused by intracompartment heterogeneous signal distribution. PMID:26328977

Vaccine Effects on Heterogeneity in Susceptibility and Implications for Population Health Management

PubMed Central

Wargo, Andrew R.; Jones, Darbi R.; Viss, Jessie R.; Rutan, Barbara J.; Egan, Nicholas A.; Sá-Guimarães, Pedro; Kim, Min Sun; Kurath, Gael; Gomes, M. Gabriela M.

2017-01-01

ABSTRACT Heterogeneity in host susceptibility is a key determinant of infectious disease dynamics but is rarely accounted for in assessment of disease control measures. Understanding how susceptibility is distributed in populations, and how control measures change this distribution, is integral to predicting the course of epidemics with and without interventions. Using multiple experimental and modeling approaches, we show that rainbow trout have relatively homogeneous susceptibility to infection with infectious hematopoietic necrosis virus and that vaccination increases heterogeneity in susceptibility in a nearly all-or-nothing fashion. In a simple transmission model with an R0 of 2, the highly heterogeneous vaccine protection would cause a 35 percentage-point reduction in outbreak size over an intervention inducing homogenous protection at the same mean level. More broadly, these findings provide validation of methodology that can help to reduce biases in predictions of vaccine impact in natural settings and provide insight into how vaccination shapes population susceptibility. PMID:29162706

Heterogeneous distribution of water in the mantle transition zone beneath United States inferred from seismic observations

NASA Astrophysics Data System (ADS)

Wang, Y.; Pavlis, G. L.; Li, M.

2017-12-01

The amount of water in the Earth's deep mantle is critical for the evolution of the solid Earth and the atmosphere. Mineral physics studies have revealed that Wadsleyite and Ringwoodite in the mantle transition zone could store several times the volume of water in the ocean. However, the water content and its distribution in the transition zone remain enigmatic due to lack of direct observations. Here we use seismic data from the full deployment of the Earthscope Transportable Array to produce 3D image of P to S scattering of the mantle transition zone beneath the United States. We compute the image volume from 141,080 pairs of high quality receiver functions defined by the Earthscope Automated Receiver Survey, reprocessed by the generalized iterative deconvolution method and imaged by the plane wave migration method. We find that the transition zone is filled with previously unrecognized small-scale heterogeneities that produce pervasive, negative polarity P to S conversions. Seismic synthetic modeling using a point source simulation method suggests two possible structures for these objects: 1) a set of randomly distributed blobs of slight difference in size, and 2) near vertical diapir structures from small scale convections. Combining with geodynamic simulations, we interpret the observation as compositional heterogeneity from small-scale, low-velocity bodies that are water enriched. Our results indicate there is a heterogeneous distribution of water through the entire mantle transition zone beneath the contiguous United States.

Content Based Image Retrieval based on Wavelet Transform coefficients distribution

PubMed Central

Lamard, Mathieu; Cazuguel, Guy; Quellec, Gwénolé; Bekri, Lynda; Roux, Christian; Cochener, Béatrice

2007-01-01

In this paper we propose a content based image retrieval method for diagnosis aid in medical fields. We characterize images without extracting significant features by using distribution of coefficients obtained by building signatures from the distribution of wavelet transform. The research is carried out by computing signature distances between the query and database images. Several signatures are proposed; they use a model of wavelet coefficient distribution. To enhance results, a weighted distance between signatures is used and an adapted wavelet base is proposed. Retrieval efficiency is given for different databases including a diabetic retinopathy, a mammography and a face database. Results are promising: the retrieval efficiency is higher than 95% for some cases using an optimization process. PMID:18003013

Large epidemic thresholds emerge in heterogeneous networks of heterogeneous nodes

NASA Astrophysics Data System (ADS)

Yang, Hui; Tang, Ming; Gross, Thilo

2015-08-01

One of the famous results of network science states that networks with heterogeneous connectivity are more susceptible to epidemic spreading than their more homogeneous counterparts. In particular, in networks of identical nodes it has been shown that network heterogeneity, i.e. a broad degree distribution, can lower the epidemic threshold at which epidemics can invade the system. Network heterogeneity can thus allow diseases with lower transmission probabilities to persist and spread. However, it has been pointed out that networks in which the properties of nodes are intrinsically heterogeneous can be very resilient to disease spreading. Heterogeneity in structure can enhance or diminish the resilience of networks with heterogeneous nodes, depending on the correlations between the topological and intrinsic properties. Here, we consider a plausible scenario where people have intrinsic differences in susceptibility and adapt their social network structure to the presence of the disease. We show that the resilience of networks with heterogeneous connectivity can surpass those of networks with homogeneous connectivity. For epidemiology, this implies that network heterogeneity should not be studied in isolation, it is instead the heterogeneity of infection risk that determines the likelihood of outbreaks.

Large epidemic thresholds emerge in heterogeneous networks of heterogeneous nodes.

PubMed

Yang, Hui; Tang, Ming; Gross, Thilo

2015-08-21

One of the famous results of network science states that networks with heterogeneous connectivity are more susceptible to epidemic spreading than their more homogeneous counterparts. In particular, in networks of identical nodes it has been shown that network heterogeneity, i.e. a broad degree distribution, can lower the epidemic threshold at which epidemics can invade the system. Network heterogeneity can thus allow diseases with lower transmission probabilities to persist and spread. However, it has been pointed out that networks in which the properties of nodes are intrinsically heterogeneous can be very resilient to disease spreading. Heterogeneity in structure can enhance or diminish the resilience of networks with heterogeneous nodes, depending on the correlations between the topological and intrinsic properties. Here, we consider a plausible scenario where people have intrinsic differences in susceptibility and adapt their social network structure to the presence of the disease. We show that the resilience of networks with heterogeneous connectivity can surpass those of networks with homogeneous connectivity. For epidemiology, this implies that network heterogeneity should not be studied in isolation, it is instead the heterogeneity of infection risk that determines the likelihood of outbreaks.

Platelets Cellular and Functional Characteristics in Patients with Atrial Fibrillation: A Comprehensive Meta-Analysis and Systematic Review

PubMed Central

Weymann, Alexander; Ali-Hasan-Al-Saegh, Sadeq; Sabashnikov, Anton; Popov, Aron-Frederik; Mirhosseini, Seyed Jalil; Nombela-Franco, Luis; Testa, Luca; Lotfaliani, Mohammadreza; Zeriouh, Mohamed; Liu, Tong; Dehghan, Hamidreza; Yavuz, Senol; de Oliveira Sá, Michel Pompeu Barros; Baker, William L.; Jang, Jae-Sik; Gong, Mengqi; Benedetto, Umberto; Dohmen, Pascal M.; D’Ascenzo, Fabrizio; Deshmukh, Abhishek J.; Biondi-Zoccai, Giuseppe; Calkins, Hugh; Stone, Gregg W.

2017-01-01

Background This systematic review with meta-analysis aimed to determine the strength of evidence for evaluating the association of platelet cellular and functional characteristics including platelet count (PC), MPV, platelet distribution width (PDW), platelet factor 4, beta thromboglobulin (BTG), and p-selectin with the occurrence of atrial fibrillation (AF) and consequent stroke. Material/Methods We conducted a meta-analysis of observational studies evaluating platelet characteristics in patients with paroxysmal, persistent and permanent atrial fibrillations. A comprehensive subgroup analysis was performed to explore potential sources of heterogeneity. Results Literature search of all major databases retrieved 1,676 studies. After screening, a total of 73 studies were identified. Pooled analysis showed significant differences in PC (weighted mean difference (WMD)=−26.93 and p<0.001), MPV (WMD=0.61 and p<0.001), PDW (WMD=−0.22 and p=0.002), BTG (WMD=24.69 and p<0.001), PF4 (WMD=4.59 and p<0.001), and p-selectin (WMD=4.90 and p<0.001). Conclusions Platelets play a critical and precipitating role in the occurrence of AF. Whereas distribution width of platelets as well as factors of platelet activity was significantly greater in AF patients compared to SR patients, platelet count was significantly lower in AF patients. PMID:28302997

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies.

PubMed

Solberg, Owen D; Mack, Steven J; Lancaster, Alex K; Single, Richard M; Tsai, Yingssu; Sanchez-Mazas, Alicia; Thomson, Glenys

2008-07-01

This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies

PubMed Central

Solberg, Owen D.; Mack, Steven J.; Lancaster, Alex K.; Single, Richard M.; Tsai, Yingssu; Sanchez-Mazas, Alicia; Thomson, Glenys

2008-01-01

This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 suggest that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online. PMID:18638659

Design considerations, architecture, and use of the Mini-Sentinel distributed data system.

PubMed

Curtis, Lesley H; Weiner, Mark G; Boudreau, Denise M; Cooper, William O; Daniel, Gregory W; Nair, Vinit P; Raebel, Marsha A; Beaulieu, Nicolas U; Rosofsky, Robert; Woodworth, Tiffany S; Brown, Jeffrey S

2012-01-01

We describe the design, implementation, and use of a large, multiorganizational distributed database developed to support the Mini-Sentinel Pilot Program of the US Food and Drug Administration (FDA). As envisioned by the US FDA, this implementation will inform and facilitate the development of an active surveillance system for monitoring the safety of medical products (drugs, biologics, and devices) in the USA. A common data model was designed to address the priorities of the Mini-Sentinel Pilot and to leverage the experience and data of participating organizations and data partners. A review of existing common data models informed the process. Each participating organization designed a process to extract, transform, and load its source data, applying the common data model to create the Mini-Sentinel Distributed Database. Transformed data were characterized and evaluated using a series of programs developed centrally and executed locally by participating organizations. A secure communications portal was designed to facilitate queries of the Mini-Sentinel Distributed Database and transfer of confidential data, analytic tools were developed to facilitate rapid response to common questions, and distributed querying software was implemented to facilitate rapid querying of summary data. As of July 2011, information on 99,260,976 health plan members was included in the Mini-Sentinel Distributed Database. The database includes 316,009,067 person-years of observation time, with members contributing, on average, 27.0 months of observation time. All data partners have successfully executed distributed code and returned findings to the Mini-Sentinel Operations Center. This work demonstrates the feasibility of building a large, multiorganizational distributed data system in which organizations retain possession of their data that are used in an active surveillance system. Copyright © 2012 John Wiley & Sons, Ltd.

A geometric exploration of stress in deformed liquid foams

NASA Astrophysics Data System (ADS)

Evans, Myfanwy E.; Schröder-Turk, Gerd E.; Kraynik, Andrew M.

2017-03-01

We explore an alternate way of looking at the rheological response of a yield stress fluid: using discrete geometry to probe the heterogeneous distribution of stress in soap froth. We present quasi-static, uniaxial, isochoric compression and extension of three-dimensional random monodisperse soap froth in periodic boundary conditions and examine the stress and geometry that result. The stress and shape anisotropy of individual cells is quantified by Q, a scalar measure derived from the interface tensor that gauges each cell’s contribution to the global stress. Cumulatively, the spatial distribution of highly deformed cells allows us to examine how stress is internally distributed. The topology of highly deformed cells, how they arrange relative to one another in space, gives insight into the heterogeneous distribution of stress.

Geo-Semantic Framework for Integrating Long-Tail Data and Model Resources for Advancing Earth System Science

NASA Astrophysics Data System (ADS)

Elag, M.; Kumar, P.

2014-12-01

Often, scientists and small research groups collect data, which target to address issues and have limited geographic or temporal range. A large number of such collections together constitute a large database that is of immense value to Earth Science studies. Complexity of integrating these data include heterogeneity in dimensions, coordinate systems, scales, variables, providers, users and contexts. They have been defined as long-tail data. Similarly, we use "long-tail models" to characterize a heterogeneous collection of models and/or modules developed for targeted problems by individuals and small groups, which together provide a large valuable collection. Complexity of integrating across these models include differing variable names and units for the same concept, model runs at different time steps and spatial resolution, use of differing naming and reference conventions, etc. Ability to "integrate long-tail models and data" will provide an opportunity for the interoperability and reusability of communities' resources, where not only models can be combined in a workflow, but each model will be able to discover and (re)use data in application specific context of space, time and questions. This capability is essential to represent, understand, predict, and manage heterogeneous and interconnected processes and activities by harnessing the complex, heterogeneous, and extensive set of distributed resources. Because of the staggering production rate of long-tail models and data resulting from the advances in computational, sensing, and information technologies, an important challenge arises: how can geoinformatics bring together these resources seamlessly, given the inherent complexity among model and data resources that span across various domains. We will present a semantic-based framework to support integration of "long-tail" models and data. This builds on existing technologies including: (i) SEAD (Sustainable Environmental Actionable Data) which supports curation and preservation of long-tail data during its life-cycle; (ii) BrownDog, which enhances the machine interpretability of large unstructured and uncurated data; and (iii) CSDMS (Community Surface Dynamics Modeling System), which "componentizes" models by providing plug-and-play environment for models integration.

Integrating a local database into the StarView distributed user interface

NASA Technical Reports Server (NTRS)

Silberberg, D. P.

1992-01-01

A distributed user interface to the Space Telescope Data Archive and Distribution Service (DADS) known as StarView is being developed. The DADS architecture consists of the data archive as well as a relational database catalog describing the archive. StarView is a client/server system in which the user interface is the front-end client to the DADS catalog and archive servers. Users query the DADS catalog from the StarView interface. Query commands are transmitted via a network and evaluated by the database. The results are returned via the network and are displayed on StarView forms. Based on the results, users decide which data sets to retrieve from the DADS archive. Archive requests are packaged by StarView and sent to DADS, which returns the requested data sets to the users. The advantages of distributed client/server user interfaces over traditional one-machine systems are well known. Since users run software on machines separate from the database, the overall client response time is much faster. Also, since the server is free to process only database requests, the database response time is much faster. Disadvantages inherent in this architecture are slow overall database access time due to the network delays, lack of a 'get previous row' command, and that refinements of a previously issued query must be submitted to the database server, even though the domain of values have already been returned by the previous query. This architecture also does not allow users to cross correlate DADS catalog data with other catalogs. Clearly, a distributed user interface would be more powerful if it overcame these disadvantages. A local database is being integrated into StarView to overcome these disadvantages. When a query is made through a StarView form, which is often composed of fields from multiple tables, it is translated to an SQL query and issued to the DADS catalog. At the same time, a local database table is created to contain the resulting rows of the query. The returned rows are displayed on the form as well as inserted into the local database table. Identical results are produced by reissuing the query to either the DADS catalog or to the local table. Relational databases do not provide a 'get previous row' function because of the inherent complexity of retrieving previous rows of multiple-table joins. However, since this function is easily implemented on a single table, StarView uses the local table to retrieve the previous row. Also, StarView issues subsequent query refinements to the local table instead of the DADS catalog, eliminating the network transmission overhead. Finally, other catalogs can be imported into the local database for cross correlation with local tables. Overall, it is believe that this is a more powerful architecture for distributed, database user interfaces.

Evaluating the assumption of power-law late time scaling of breakthrough curves in highly heterogeneous media

NASA Astrophysics Data System (ADS)

Pedretti, Daniele

2017-04-01

Power-law (PL) distributions are widely adopted to define the late-time scaling of solute breakthrough curves (BTCs) during transport experiments in highly heterogeneous media. However, from a statistical perspective, distinguishing between a PL distribution and another tailed distribution is difficult, particularly when a qualitative assessment based on visual analysis of double-logarithmic plotting is used. This presentation aims to discuss the results from a recent analysis where a suite of statistical tools was applied to evaluate rigorously the scaling of BTCs from experiments that generate tailed distributions typically described as PL at late time. To this end, a set of BTCs from numerical simulations in highly heterogeneous media were generated using a transition probability approach (T-PROGS) coupled to a finite different numerical solver of the flow equation (MODFLOW) and a random walk particle tracking approach for Lagrangian transport (RW3D). The T-PROGS fields assumed randomly distributed hydraulic heterogeneities with long correlation scales creating solute channeling and anomalous transport. For simplicity, transport was simulated as purely advective. This combination of tools generates strongly non-symmetric BTCs visually resembling PL distributions at late time when plotted in double log scales. Unlike other combination of modeling parameters and boundary conditions (e.g. matrix diffusion in fractures), at late time no direct link exists between the mathematical functions describing scaling of these curves and physical parameters controlling transport. The results suggest that the statistical tests fail to describe the majority of curves as PL distributed. Moreover, they suggest that PL or lognormal distributions have the same likelihood to represent parametrically the shape of the tails. It is noticeable that forcing a model to reproduce the tail as PL functions results in a distribution of PL slopes comprised between 1.2 and 4, which are the typical values observed during field experiments. We conclude that care must be taken when defining a BTC late time distribution as a power law function. Even though the estimated scaling factors are found to fall in traditional ranges, the actual distribution controlling the scaling of concentration may different from a power-law function, with direct consequences for instance for the selection of effective parameters in upscaling modeling solutions.

Heterogeneity of Chlorinity distribution within gas hydrate reservoir at Daini-Atsumi knoll, based on logging data analysis

NASA Astrophysics Data System (ADS)

Suzuki, K.; Takayama, T.; Fujii, T.

2016-12-01

We will present possible heterogeneity of pore-water salinity within methane hydrate reservoir of Daini-Atsumi knoll, on the basis of Logging-while-drilling (LWD) data and several kind of wire-line logging dataset. The LWD and the wire-line logging had been carried out during 2012 to 2013, before/after the first offshore gas-production-test from marine-methane-hydrate reservoir at Daini-Atsumi Knoll along the northeast Nankai trough. Several data from the logging, especially data from the reservoir saturation tool; RST, gave us some possible interpretation for heterogeneity distribution of chlorinity within the methane-hydrate reservoir. The computed pore-water chlorinity could be interpreted as condense of chlorinity at gas-hydrate formation. This year, we drilled several number of wells at Daini-Atsumi Knoll, again for next gas production test, and we have also found out possibility of chlorinity heterogeneity from LWD data of Neutron-capture cross section; i.e. Sigma. The distribution of chlorinity within gas-hydrate reservoir may help our understanding of gas hydrate-crystallization and/or dissociation in turbidite reservoir at Daini-Atsumi Knoll. This research is conducted as a part of the Research Consortium for Methane Hydrate Resource in Japan (MH21 Research consortium).

A new approach to interpretation of heterogeneity of fluorescence decay in complex biological systems

NASA Astrophysics Data System (ADS)

Wlodarczyk, Jakub; Kierdaszuk, Borys

2005-08-01

Decays of tyrosine fluorescence in protein-ligand complexes are described by a model of continuous distribution of fluorescence lifetimes. Resulted analytical power-like decay function provides good fits to highly complex fluorescence kinetics. Moreover, this is a manifestation of so-called Tsallis q-exponential function, which is suitable for description of the systems with long-range interactions, memory effect, as well as with fluctuations of the characteristic lifetime of fluorescence. The proposed decay functions were applied to analysis of fluorescence decays of tyrosine in a protein, i.e. the enzyme purine nucleoside phosphorylase from E. coli (the product of the deoD gene), free in aqueous solution and in a complex with formycin A (an inhibitor) and orthophosphate (a co-substrate). The power-like function provides new information about enzyme-ligand complex formation based on the physically justified heterogeneity parameter directly related to the lifetime distribution. A measure of the heterogeneity parameter in the enzyme systems is provided by a variance of fluorescence lifetime distribution. The possible number of deactivation channels and excited state mean lifetime can be easily derived without a priori knowledge of the complexity of studied system. Moreover, proposed model is simpler then traditional multi-exponential one, and better describes heterogeneous nature of studied systems.

Heat and mass transport during a groundwater replenishment trial in a highly heterogeneous aquifer

NASA Astrophysics Data System (ADS)

Seibert, Simone; Prommer, Henning; Siade, Adam; Harris, Brett; Trefry, Mike; Martin, Michael

2014-12-01

Changes in subsurface temperature distribution resulting from the injection of fluids into aquifers may impact physiochemical and microbial processes as well as basin resource management strategies. We have completed a 2 year field trial in a hydrogeologically and geochemically heterogeneous aquifer below Perth, Western Australia in which highly treated wastewater was injected for large-scale groundwater replenishment. During the trial, chloride and temperature data were collected from conventional monitoring wells and by time-lapse temperature logging. We used a joint inversion of these solute tracer and temperature data to parameterize a numerical flow and multispecies transport model and to analyze the solute and heat propagation characteristics that prevailed during the trial. The simulation results illustrate that while solute transport is largely confined to the most permeable lithological units, heat transport was also affected by heat exchange with lithological units that have a much lower hydraulic conductivity. Heat transfer by heat conduction was found to significantly influence the complex temporal and spatial temperature distribution, especially with growing radial distance and in aquifer sequences with a heterogeneous hydraulic conductivity distribution. We attempted to estimate spatially varying thermal transport parameters during the data inversion to illustrate the anticipated correlations of these parameters with lithological heterogeneities, but estimates could not be uniquely determined on the basis of the collected data.

Microbial micropatches within microbial hotspots.

PubMed

Dann, Lisa M; McKerral, Jody C; Smith, Renee J; Tobe, Shanan S; Paterson, James S; Seymour, Justin R; Oliver, Rod L; Mitchell, James G

2018-01-01

The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have 'hotspots' of high abundance, and 'coldspots' of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur.

Synchronization in networks with heterogeneous coupling delays

NASA Astrophysics Data System (ADS)

Otto, Andreas; Radons, Günter; Bachrathy, Dániel; Orosz, Gábor

2018-01-01

Synchronization in networks of identical oscillators with heterogeneous coupling delays is studied. A decomposition of the network dynamics is obtained by block diagonalizing a newly introduced adjacency lag operator which contains the topology of the network as well as the corresponding coupling delays. This generalizes the master stability function approach, which was developed for homogenous delays. As a result the network dynamics can be analyzed by delay differential equations with distributed delay, where different delay distributions emerge for different network modes. Frequency domain methods are used for the stability analysis of synchronized equilibria and synchronized periodic orbits. As an example, the synchronization behavior in a system of delay-coupled Hodgkin-Huxley neurons is investigated. It is shown that the parameter regions where synchronized periodic spiking is unstable expand when increasing the delay heterogeneity.

Access Selection Algorithm of Heterogeneous Wireless Networks for Smart Distribution Grid Based on Entropy-Weight and Rough Set

NASA Astrophysics Data System (ADS)

Xiang, Min; Qu, Qinqin; Chen, Cheng; Tian, Li; Zeng, Lingkang

2017-11-01

To improve the reliability of communication service in smart distribution grid (SDG), an access selection algorithm based on dynamic network status and different service types for heterogeneous wireless networks was proposed. The network performance index values were obtained in real time by multimode terminal and the variation trend of index values was analyzed by the growth matrix. The index weights were calculated by entropy-weight and then modified by rough set to get the final weights. Combining the grey relational analysis to sort the candidate networks, and the optimum communication network is selected. Simulation results show that the proposed algorithm can implement dynamically access selection in heterogeneous wireless networks of SDG effectively and reduce the network blocking probability.

Mass and charge distributions of amyloid fibers involved in neurodegenerative diseases: mapping heterogeneity and polymorphism† †Electronic supplementary information (ESI) available: Experimental section and supplementary figures. See DOI: 10.1039/c7sc04542e

PubMed Central

Pansieri, Jonathan; Halim, Mohammad A.; Vendrely, Charlotte; Dumoulin, Mireille; Legrand, François; Sallanon, Marcelle Moulin; Chierici, Sabine; Denti, Simona; Dagany, Xavier; Dugourd, Philippe; Marquette, Christel

2018-01-01

Heterogeneity and polymorphism are generic features of amyloid fibers with some important effects on the related disease development. We report here the characterization, by charge detection mass spectrometry, of amyloid fibers made of three polypeptides involved in neurodegenerative diseases: Aβ1–42 peptide, tau and α-synuclein. Beside the mass of individual fibers, this technique enables to characterize the heterogeneity and the polymorphism of the population. In the case of Aβ1–42 peptide and tau protein, several coexisting species could be distinguished and characterized. In the case of α-synuclein, we show how the polymorphism affects the mass and charge distributions. PMID:29732065

A Secure Scheme for Distributed Consensus Estimation against Data Falsification in Heterogeneous Wireless Sensor Networks.

PubMed

Mi, Shichao; Han, Hui; Chen, Cailian; Yan, Jian; Guan, Xinping

2016-02-19

Heterogeneous wireless sensor networks (HWSNs) can achieve more tasks and prolong the network lifetime. However, they are vulnerable to attacks from the environment or malicious nodes. This paper is concerned with the issues of a consensus secure scheme in HWSNs consisting of two types of sensor nodes. Sensor nodes (SNs) have more computation power, while relay nodes (RNs) with low power can only transmit information for sensor nodes. To address the security issues of distributed estimation in HWSNs, we apply the heterogeneity of responsibilities between the two types of sensors and then propose a parameter adjusted-based consensus scheme (PACS) to mitigate the effect of the malicious node. Finally, the convergence property is proven to be guaranteed, and the simulation results validate the effectiveness and efficiency of PACS.

Poster - Thur Eve - 69: Electron beam dosimetry in heterogeneous phantoms using the MAGIC normoxic polymer gel.

PubMed

Nedaie, H A; Ghahraman, A R; Bolouri, B; Arbabi, A

2012-07-01

Recently, radiation sensitive polymer gels are being used as a reliable dosimetry method for three-dimensional (3D) verification of radiation doses in clinical use. Some properties of gel dosimeters have made them useful in verifying complex situations in electron therapy. The aim of this study was to experimentally evaluate the influence of tissue inhomogeneities on electron beam dose distributions by use of polymer gel dosimetry. Another purpose was to evaluate the appropriateness of polymer gels for electron beam dosimetry applications. A cylindrical phantom filled with MAGIC polymer gel with a polyacrilic wall (ρ = 1.18 g.cm -3 ) was placed in a Perspex water-filled tank exactly underneath the bone inhomogeneity region .Then, the slab phantom was irradiated with a dose of 5Gy of 8MeV electrons to measure the dose distribution beyond the heterogeneity region. Afterwards, another cylindrical gel phantom similar to the above was used and irradiated with the same dose of 15 MeV electrons to measure the dose distribution beyond the same heterogeneity region. The same mentioned setup was repeated for measurement of the dose distribution beneath the air heterogeneity and homogenous phantom. The results of gel dosimetry under bone inhomogeneity have shown a reduction in dose. This is related to the high mass stopping and mass scattering powers of bone tissue. In addition, dose enhancement is seen laterally near the bone-tissue interface, due to increased side scattering of electrons. Hot and cold scatter lobes under heterogeneity regions are other effects that can be seen. The results of gel dosimetry under the air inhomogeneity have shown an increase in dose. This is related to the low mass stopping and mass scattering powers of the air cavity. When a high energy beam passes through a low-density medium or an air cavity, electronic equilibrium is lost along the central axis of the beam .The dose rebuild up is a consequence of this electronic disequilibrium. An overall good agreement was found between measurements with gel and with a diode detector for the single beam experiment. Electron dose distributions are significantly altered in the presence of tissue inhomogeneities such as bone and air cavities which are related to mass stopping and mass scattering powers of heterogeneous materials. © 2012 American Association of Physicists in Medicine.

[Geostatistics analyzing to cause of formation of circle distribution of plant communities in Horqin Sandy Land].

PubMed

He, Xingdong; Gao, Yubao; Zhao, Wenzhi; Cong, Zili

2004-09-01

Investigation results in the present study showed that plant communities took typical concentric circles distribution patterns along habitat gradient from top, slope to interdune on a few large fixed dunes in middle part of Korqin Sandy Land. In order to explain this phenomenon, analysis of water content and its spatial heterogeneity in sand layers on different locations of dunes was conducted. In these dunes, water contents in sand layers of the tops were lower than those of the slopes; both of them were lower than those of the interdunes. According to the results of geostatistics analysis, whether shifting dune or fixed dune, spatial heterogeneity of water contents in sand layers took on regular changes, such as ratios between nugget and sill and ranges reduced gradually, fractal dimension increased gradually, the regular changes of these parameters indicated that random spatial heterogeneity reduced gradually, and autocorrelation spatial heterogeneity increased gradually from the top, the slope to the interdune. The regular changes of water contents in sand layers and their spatial heterogeneity of different locations of the dunes, thus, might be an important cause resulted in the formation of the concentric circles patterns of the plant communities on these fixed dunes.

A theoretical framework for determining cerebral vascular function and heterogeneity from dynamic susceptibility contrast MRI.

PubMed

Digernes, Ingrid; Bjørnerud, Atle; Vatnehol, Svein Are S; Løvland, Grete; Courivaud, Frédéric; Vik-Mo, Einar; Meling, Torstein R; Emblem, Kyrre E

2017-06-01

Mapping the complex heterogeneity of vascular tissue in the brain is important for understanding cerebrovascular disease. In this translational study, we build on previous work using vessel architectural imaging (VAI) and present a theoretical framework for determining cerebral vascular function and heterogeneity from dynamic susceptibility contrast magnetic resonance imaging (MRI). Our tissue model covers realistic structural architectures for vessel branching and orientations, as well as a range of hemodynamic scenarios for blood flow, capillary transit times and oxygenation. In a typical image voxel, our findings show that the apparent MRI relaxation rates are independent of the mean vessel orientation and that the vortex area, a VAI-based parameter, is determined by the relative oxygen saturation level and the vessel branching of the tissue. Finally, in both simulated and patient data, we show that the relative distributions of the vortex area parameter as a function of capillary transit times show unique characteristics in normal-appearing white and gray matter tissue, whereas tumour-voxels in comparison display a heterogeneous distribution. Collectively, our study presents a comprehensive framework that may serve as a roadmap for in vivo and per-voxel determination of vascular status and heterogeneity in cerebral tissue.

Numerical analysis of mixing enhancement for micro-electroosmotic flow

NASA Astrophysics Data System (ADS)

Tang, G. H.; He, Y. L.; Tao, W. Q.

2010-05-01

Micro-electroosmotic flow is usually slow with negligible inertial effects and diffusion-based mixing can be problematic. To gain an improved understanding of electroosmotic mixing in microchannels, a numerical study has been carried out for channels patterned with wall blocks, and channels patterned with heterogeneous surfaces. The lattice Boltzmann method has been employed to obtain the external electric field, electric potential distribution in the electrolyte, the flow field, and the species concentration distribution within the same framework. The simulation results show that wall blocks and heterogeneous surfaces can significantly disturb the streamlines by fluid folding and stretching leading to apparently substantial improvements in mixing. However, the results show that the introduction of such features can substantially reduce the mass flow rate and thus effectively prolongs the available mixing time when the flow passes through the channel. This is a non-negligible factor on the effectiveness of the observed improvements in mixing efficiency. Compared with the heterogeneous surface distribution, the wall block cases can achieve more effective enhancement in the same mixing time. In addition, the field synergy theory is extended to analyze the mixing enhancement in electroosmotic flow. The distribution of the local synergy angle in the channel aids to evaluate the effectiveness of enhancement method.

Distributional behavior of diffusion coefficients obtained by single trajectories in annealed transit time model

NASA Astrophysics Data System (ADS)

Akimoto, Takuma; Yamamoto, Eiji

2016-12-01

Local diffusion coefficients in disordered systems such as spin glass systems and living cells are highly heterogeneous and may change over time. Such a time-dependent and spatially heterogeneous environment results in irreproducibility of single-particle-tracking measurements. Irreproducibility of time-averaged observables has been theoretically studied in the context of weak ergodicity breaking in stochastic processes. Here, we provide rigorous descriptions of equilibrium and non-equilibrium diffusion processes for the annealed transit time model, which is a heterogeneous diffusion model in living cells. We give analytical solutions for the mean square displacement (MSD) and the relative standard deviation of the time-averaged MSD for equilibrium and non-equilibrium situations. We find that the time-averaged MSD grows linearly with time and that the time-averaged diffusion coefficients are intrinsically random (irreproducible) even in the long-time measurements in non-equilibrium situations. Furthermore, the distribution of the time-averaged diffusion coefficients converges to a universal distribution in the sense that it does not depend on initial conditions. Our findings pave the way for a theoretical understanding of distributional behavior of the time-averaged diffusion coefficients in disordered systems.

Experimental techniques and computational methods toward the estimation of the effective two-phase flow coefficients and multi-scale heterogeneities of soils

NASA Astrophysics Data System (ADS)

Tsakiroglou, C. D.; Aggelopoulos, C. A.; Sygouni, V.

2009-04-01

A hierarchical, network-type, dynamic simulator of the immiscible displacement of water by oil in heterogeneous porous media is developed to simulate the rate-controlled displacement of two fluids at the soil column scale. A cubic network is constructed, where each node is assigned a permeability which is chosen randomly from a distribution function. The intensity of heterogeneities is quantified by the width of the permeability distribution function. The capillary pressure at each node is calculated by combining a generalized Leverett J-function with a Corey type model. Information about the heterogeneity of soils at the pore network scale is obtained by combining mercury intrusion porosimetry (MIP) data with back-scattered scanning electron microscope (BSEM) images [1]. In order to estimate the two-phase flow properties of nodes (relative permeability and capillary pressure functions, permeability distribution function) immiscible and miscible displacement experiments are performed on undisturbed soil columns. The transient responses of measured variables (pressure drop, fluid saturation averaged over five successive segments, solute concentration averaged over three cross-sections) are fitted with models accounting for the preferential flow paths at the micro- (multi-region model) and macro-scale (multi flowpath model) because of multi-scale heterogeneities [2,3]. Simulating the immiscible displacement of water by oil (drainage) in a large netork, at each time step, the fluid saturation and pressure of each node are calculated formulating mass balances at each node, accounting for capillary, viscous and gravity forces, and solving the system of coupled equations. At each iteration of the algorithm, the pressure drop is so selected that the total flow rate of the injected fluid is kept constant. The dynamic large-scale network simulator is used (1) to examine the sensitivity of the transient responses of the axial distribution of fluid saturation and total pressure drop across the network to the permeability distribution function, spatial correlations of permeability, and capillary number, and (2) to estimate the effective (up-scaled) relative permeability functions at the soil column scale. In an attempt to clarify potential effects of the permeability distribution and spatial permeability correlations on the transient responses of the pressure drop across a soil column, signal analysis with wavelets is performed [4] on experimental and simulated results. The transient variation of signal energy and frequency of pressure drop fluctuations at the wavelet domain are correlated with macroscopic properties such as the effective water and oil relative permeabilities of the porous medium, and microscopic properties such as the variation of the permeability distribution of oil-occupied nodes. Toward the solution of the inverse problem, a general procedure is suggested to identify macro-heterogeneities from the fast analysis of pressure drop signals. References 1. Tsakiroglou, C.D. and M.A. Ioannidis, "Dual porosity modeling of the pore structure and transport properties of a contaminated soil", Eur. J. Soil Sci., 59, 744-761 (2008). 2. Aggelopoulos, C.A., and C.D. Tsakiroglou, "Quantifying the Soil Heterogeneity from Solute Dispersion Experiments", Geoderma, 146, 412-424 (2008). 3. Aggelopoulos, C.A., and C.D. Tsakiroglou, "A multi-flow path approach to model immiscible displacement in undisturbed heterogeneous soil columns", J. Contam. Hydrol., in press (2009). 4. Sygouni, V., C.D. Tsakiroglou, and A.C. Payatakes, "Using wavelets to characterize the wettability of porous materials", Phys. Rev. E, 76, 056304 (2007).

Mr-Moose: An advanced SED-fitting tool for heterogeneous multi-wavelength datasets

NASA Astrophysics Data System (ADS)

Drouart, G.; Falkendal, T.

2018-04-01

We present the public release of Mr-Moose, a fitting procedure that is able to perform multi-wavelength and multi-object spectral energy distribution (SED) fitting in a Bayesian framework. This procedure is able to handle a large variety of cases, from an isolated source to blended multi-component sources from an heterogeneous dataset (i.e. a range of observation sensitivities and spectral/spatial resolutions). Furthermore, Mr-Moose handles upper-limits during the fitting process in a continuous way allowing models to be gradually less probable as upper limits are approached. The aim is to propose a simple-to-use, yet highly-versatile fitting tool fro handling increasing source complexity when combining multi-wavelength datasets with fully customisable filter/model databases. The complete control of the user is one advantage, which avoids the traditional problems related to the "black box" effect, where parameter or model tunings are impossible and can lead to overfitting and/or over-interpretation of the results. Also, while a basic knowledge of Python and statistics is required, the code aims to be sufficiently user-friendly for non-experts. We demonstrate the procedure on three cases: two artificially-generated datasets and a previous result from the literature. In particular, the most complex case (inspired by a real source, combining Herschel, ALMA and VLA data) in the context of extragalactic SED fitting, makes Mr-Moose a particularly-attractive SED fitting tool when dealing with partially blended sources, without the need for data deconvolution.

Probing Seismically Melting Induced Mantle Heterogeneities in Thermal-chemical Convection Models

NASA Astrophysics Data System (ADS)

Heck, H. V.; Davies, H.; Nowacki, A.; Wookey, J. M.

2015-12-01

Two regions at the base of the Earth's mantle (the Large Low-Shear Velocity Provinces) pose a fundamental problem in understanding large-scale mantle dynamics and history. Are they dense piles of (possibly primordial) material separated from mantle circulation, or large-scale thermal features which are part of global mantle convection? Or some combination of the two? We use our numerical 3D spherical mantle convection code to perform simulations of the Earths mantle dynamical evolution. We drive the surface velocity of the model according to 200 Ma plate motion reconstructions, to arrive at Earth-like structures in the mantle at present day. Variations in bulk chemistry will be tracked in two ways: 1) by starting the calculations with a (primordial) dense layer at the base of the mantle, and 2) by tracking basalt fraction which is fractionated upon melting close to the surface. The resulting distribution of chemical heterogeneity and temperature will be converted to seismic velocities. This will be done with a thermodynamical database (Stixrude & Lithgow-Bertelloni, GJI, 2005, 2011), allowing us to compare the model with previous observations of triplications and waveform complexity near the margins of the LLSVPs. These observations have been taken as proof that strong chemical variations are present; our simulations can be used to show whether this is true, or if purely thermal convection can also cause these features. We simulate finite-frequency, 3D seismograms at ~5 s period and compare these with previous studies.

Process evaluation distributed system

NASA Technical Reports Server (NTRS)

Moffatt, Christopher L. (Inventor)

2006-01-01

The distributed system includes a database server, an administration module, a process evaluation module, and a data display module. The administration module is in communication with the database server for providing observation criteria information to the database server. The process evaluation module is in communication with the database server for obtaining the observation criteria information from the database server and collecting process data based on the observation criteria information. The process evaluation module utilizes a personal digital assistant (PDA). A data display module in communication with the database server, including a website for viewing collected process data in a desired metrics form, the data display module also for providing desired editing and modification of the collected process data. The connectivity established by the database server to the administration module, the process evaluation module, and the data display module, minimizes the requirement for manual input of the collected process data.

Tracer test modeling for characterizing heterogeneity and local scale residence time distribution in an artificial recharge site.

NASA Astrophysics Data System (ADS)

Valhondo, Cristina; Martinez-Landa, Lurdes; Carrera, Jesús; Hidalgo, Juan J.; Ayora, Carlos

2017-04-01

Artificial recharge of aquifers (AR) is a standard technique to replenish and enhance groundwater resources, that have widely been used due to the increasing demand of quality water. AR through infiltration basins consists on infiltrate surface water, that might be affected in more or less degree by treatment plant effluents, runoff and others undesirables water sources, into an aquifer. The water quality enhances during the passage through the soil and organic matter, nutrients, organic contaminants, and bacteria are reduced mainly due to biodegradation and adsorption. Therefore, one of the goals of AR is to ensure a good quality status of the aquifer even if lesser quality water is used for recharge. Understand the behavior and transport of the potential contaminants is essential for an appropriate management of the artificial recharge system. The knowledge of the flux distribution around the recharge system and the relationship between the recharge system and the aquifer (area affected by the recharge, mixing ratios of recharged and native groundwater, travel times) is essential to achieve this goal. Evaluate the flux distribution is not always simple because the complexity and heterogeneity of natural systems. Indeed, it is not so much regulate by hydraulic conductivity of the different geological units as by their continuity and inter-connectivity particularly in the vertical direction. In summary for an appropriate management of an artificial recharge system it is needed to acknowledge the heterogeneity of the media. Aiming at characterizing the residence time distribution (RTDs) of a pilot artificial recharge system and the extent to which heterogeneity affects RTDs, we performed and evaluated a pulse injection tracer test. The artificial recharge system was simulated as a multilayer model which was used to evaluate the measured breakthrough curves at six monitoring points. Flow and transport parameters were calibrated under two hypotheses. The first hypothesis considered a homogeneous medium where flow and transport parameters were constant for all layers. The second hypothesis considered heterogeneous media and thus parameters were different for each layer. Heterogeneous model yielded to a better fit, measured as root mean square weighted error, of the measured tracer breakthrough curves. Both homogeneous and heterogeneous models reproduce the long tails observed in some observation points implying that the broad RTDs are caused not only by heterogeneity but also by the mean flow structure. We contend that it is this broad RTD, together with the sequence of redox states produced by our reactive layer, what explains the excellent behavior of the system in removing recalcitrant organic micropollutants.

Influence of snowpack and melt energy heterogeneity on snow cover depletion and snowmelt runoff simulation in a cold mountain environment

NASA Astrophysics Data System (ADS)

DeBeer, Chris M.; Pomeroy, John W.

2017-10-01

The spatial heterogeneity of mountain snow cover and ablation is important in controlling patterns of snow cover depletion (SCD), meltwater production, and runoff, yet is not well-represented in most large-scale hydrological models and land surface schemes. Analyses were conducted in this study to examine the influence of various representations of snow cover and melt energy heterogeneity on both simulated SCD and stream discharge from a small alpine basin in the Canadian Rocky Mountains. Simulations were performed using the Cold Regions Hydrological Model (CRHM), where point-scale snowmelt computations were made using a snowpack energy balance formulation and applied to spatial frequency distributions of snow water equivalent (SWE) on individual slope-, aspect-, and landcover-based hydrological response units (HRUs) in the basin. Hydrological routines were added to represent the vertical and lateral transfers of water through the basin and channel system. From previous studies it is understood that the heterogeneity of late winter SWE is a primary control on patterns of SCD. The analyses here showed that spatial variation in applied melt energy, mainly due to differences in net radiation, has an important influence on SCD at multiple scales and basin discharge, and cannot be neglected without serious error in the prediction of these variables. A single basin SWE distribution using the basin-wide mean SWE (SWE ‾) and coefficient of variation (CV; standard deviation/mean) was found to represent the fine-scale spatial heterogeneity of SWE sufficiently well. Simulations that accounted for differences in (SWE ‾) among HRUs but neglected the sub-HRU heterogeneity of SWE were found to yield similar discharge results as simulations that included this heterogeneity, while SCD was poorly represented, even at the basin level. Finally, applying point-scale snowmelt computations based on a single SWE depth for each HRU (thereby neglecting spatial differences in internal snowpack energetics over the distributions) was found to yield similar SCD and discharge results as simulations that resolved internal energy differences. Spatial/internal snowpack melt energy effects are more pronounced at times earlier in spring before the main period of snowmelt and SCD, as shown in previously published work. The paper discusses the importance of these findings as they apply to the warranted complexity of snowmelt process simulation in cold mountain environments, and shows how the end-of-winter SWE distribution represents an effective means of resolving snow cover heterogeneity at multiple scales for modelling, even in steep and complex terrain.

Database Search Strategies & Tips. Reprints from the Best of "ONLINE" [and]"DATABASE."

ERIC Educational Resources Information Center

Online, Inc., Weston, CT.

Reprints of 17 articles presenting strategies and tips for searching databases online appear in this collection, which is one in a series of volumes of reprints from "ONLINE" and "DATABASE" magazines. Edited for information professionals who use electronically distributed databases, these articles address such topics as: (1)…

Statistical parameters of random heterogeneity estimated by analysing coda waves based on finite difference method

NASA Astrophysics Data System (ADS)

Emoto, K.; Saito, T.; Shiomi, K.

2017-12-01

Short-period (<1 s) seismograms are strongly affected by small-scale (<10 km) heterogeneities in the lithosphere. In general, short-period seismograms are analysed based on the statistical method by considering the interaction between seismic waves and randomly distributed small-scale heterogeneities. Statistical properties of the random heterogeneities have been estimated by analysing short-period seismograms. However, generally, the small-scale random heterogeneity is not taken into account for the modelling of long-period (>2 s) seismograms. We found that the energy of the coda of long-period seismograms shows a spatially flat distribution. This phenomenon is well known in short-period seismograms and results from the scattering by small-scale heterogeneities. We estimate the statistical parameters that characterize the small-scale random heterogeneity by modelling the spatiotemporal energy distribution of long-period seismograms. We analyse three moderate-size earthquakes that occurred in southwest Japan. We calculate the spatial distribution of the energy density recorded by a dense seismograph network in Japan at the period bands of 8-16 s, 4-8 s and 2-4 s and model them by using 3-D finite difference (FD) simulations. Compared to conventional methods based on statistical theories, we can calculate more realistic synthetics by using the FD simulation. It is not necessary to assume a uniform background velocity, body or surface waves and scattering properties considered in general scattering theories. By taking the ratio of the energy of the coda area to that of the entire area, we can separately estimate the scattering and the intrinsic absorption effects. Our result reveals the spectrum of the random inhomogeneity in a wide wavenumber range including the intensity around the corner wavenumber as P(m) = 8πε2a3/(1 + a2m2)2, where ε = 0.05 and a = 3.1 km, even though past studies analysing higher-frequency records could not detect the corner. Finally, we estimate the intrinsic attenuation by modelling the decay rate of the energy. The method proposed in this study is suitable for quantifying the statistical properties of long-wavelength subsurface random inhomogeneity, which leads the way to characterizing a wider wavenumber range of spectra, including the corner wavenumber.

Optimization of light source parameters in the photodynamic therapy of heterogeneous prostate

NASA Astrophysics Data System (ADS)

Li, Jun; Altschuler, Martin D.; Hahn, Stephen M.; Zhu, Timothy C.

2008-08-01

The three-dimensional (3D) heterogeneous distributions of optical properties in a patient prostate can now be measured in vivo. Such data can be used to obtain a more accurate light-fluence kernel. (For specified sources and points, the kernel gives the fluence delivered to a point by a source of unit strength.) In turn, the kernel can be used to solve the inverse problem that determines the source strengths needed to deliver a prescribed photodynamic therapy (PDT) dose (or light-fluence) distribution within the prostate (assuming uniform drug concentration). We have developed and tested computational procedures to use the new heterogeneous data to optimize delivered light-fluence. New problems arise, however, in quickly obtaining an accurate kernel following the insertion of interstitial light sources and data acquisition. (1) The light-fluence kernel must be calculated in 3D and separately for each light source, which increases kernel size. (2) An accurate kernel for light scattering in a heterogeneous medium requires ray tracing and volume partitioning, thus significant calculation time. To address these problems, two different kernels were examined and compared for speed of creation and accuracy of dose. Kernels derived more quickly involve simpler algorithms. Our goal is to achieve optimal dose planning with patient-specific heterogeneous optical data applied through accurate kernels, all within clinical times. The optimization process is restricted to accepting the given (interstitially inserted) sources, and determining the best source strengths with which to obtain a prescribed dose. The Cimmino feasibility algorithm is used for this purpose. The dose distribution and source weights obtained for each kernel are analyzed. In clinical use, optimization will also be performed prior to source insertion to obtain initial source positions, source lengths and source weights, but with the assumption of homogeneous optical properties. For this reason, we compare the results from heterogeneous optical data with those obtained from average homogeneous optical properties. The optimized treatment plans are also compared with the reference clinical plan, defined as the plan with sources of equal strength, distributed regularly in space, which delivers a mean value of prescribed fluence at detector locations within the treatment region. The study suggests that comprehensive optimization of source parameters (i.e. strengths, lengths and locations) is feasible, thus allowing acceptable dose coverage in a heterogeneous prostate PDT within the time constraints of the PDT procedure.

Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis

PubMed Central

Gan, Mingyu; Liu, Qingyun; Yang, Chongguang; Gao, Qian; Luo, Tao

2016-01-01

Mixed infection by multiple Mycobacterium tuberculosis (MTB) strains is associated with poor treatment outcome of tuberculosis (TB). Traditional genotyping methods have been used to detect mixed infections of MTB, however, their sensitivity and resolution are limited. Deep whole-genome sequencing (WGS) has been proved highly sensitive and discriminative for studying population heterogeneity of MTB. Here, we developed a phylogenetic-based method to detect MTB mixed infections using WGS data. We collected published WGS data of 782 global MTB strains from public database. We called homogeneous and heterogeneous single nucleotide variations (SNVs) of individual strains by mapping short reads to the ancestral MTB reference genome. We constructed a phylogenomic database based on 68,639 homogeneous SNVs of 652 MTB strains. Mixed infections were determined if multiple evolutionary paths were identified by mapping the SNVs of individual samples to the phylogenomic database. By simulation, our method could specifically detect mixed infections when the sequencing depth of minor strains was as low as 1× coverage, and when the genomic distance of two mixed strains was as small as 16 SNVs. By applying our methods to all 782 samples, we detected 47 mixed infections and 45 of them were caused by locally endemic strains. The results indicate that our method is highly sensitive and discriminative for identifying mixed infections from deep WGS data of MTB isolates. PMID:27391214

Resources | Division of Cancer Prevention

Cancer.gov

Manual of Operations Version 3, 12/13/2012 (PDF, 162KB) Database Sources Consortium for Functional Glycomics databases Design Studies Related to the Development of Distributed, Web-based European Carbohydrate Databases (EUROCarbDB) |

Density-based clustering analyses to identify heterogeneous cellular sub-populations

NASA Astrophysics Data System (ADS)

Heaster, Tiffany M.; Walsh, Alex J.; Landman, Bennett A.; Skala, Melissa C.

2017-02-01

Autofluorescence microscopy of NAD(P)H and FAD provides functional metabolic measurements at the single-cell level. Here, density-based clustering algorithms were applied to metabolic autofluorescence measurements to identify cell-level heterogeneity in tumor cell cultures. The performance of the density-based clustering algorithm, DENCLUE, was tested in samples with known heterogeneity (co-cultures of breast carcinoma lines). DENCLUE was found to better represent the distribution of cell clusters compared to Gaussian mixture modeling. Overall, DENCLUE is a promising approach to quantify cell-level heterogeneity, and could be used to understand single cell population dynamics in cancer progression and treatment.

Evaluation of material heterogeneity dosimetric effects using radiochromic film for COMS eye plaques loaded with {sup 125}I seeds (model I25.S16)

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

Acar, Hilal; Chiu-Tsao, Sou-Tung; Oezbay, Ismail

Purpose: (1) To measure absolute dose distributions in eye phantom for COMS eye plaques with {sup 125}I seeds (model I25.S16) using radiochromic EBT film dosimetry. (2) To determine the dose correction function for calculations involving the TG-43 formalism to account for the presence of the COMS eye plaque using Monte Carlo (MC) method specific to this seed model. (3) To test the heterogeneous dose calculation accuracy of the new version of Plaque Simulator (v5.3.9) against the EBT film data for this seed model. Methods: Using EBT film, absolute doses were measured for {sup 125}I seeds (model I25.S16) in COMS eyemore » plaques (1) along the plaque's central axis for (a) uniformly loaded plaques (14-20 mm in diameter) and (b) a 20 mm plaque with single seed, and (2) in off-axis direction at depths of 5 and 12 mm for all four plaque sizes. The EBT film calibration was performed at {sup 125}I photon energy. MC calculations using MCNP5 code for a single seed at the center of a 20 mm plaque in homogeneous water and polystyrene medium were performed. The heterogeneity dose correction function was determined from the MC calculations. These function values at various depths were entered into PS software (v5.3.9) to calculate the heterogeneous dose distributions for the uniformly loaded plaques (of all four sizes). The dose distributions with homogeneous water assumptions were also calculated using PS for comparison. The EBT film measured absolute dose rate values (film) were compared with those calculated using PS with homogeneous assumption (PS Homo) and heterogeneity correction (PS Hetero). The values of dose ratio (film/PS Homo) and (film/PS Hetero) were obtained. Results: The central axis depth dose rate values for a single seed in 20 mm plaque measured using EBT film and calculated with MCNP5 code (both in ploystyrene phantom) were compared, and agreement within 9% was found. The dose ratio (film/PS Homo) values were substantially lower than unity (mostly between 0.8 and 0.9) for all four plaque sizes, indicating dose reduction by COMS plaque compared with homogeneous assumption. The dose ratio (film/PS Hetero) values were close to unity, indicating the PS Hetero calculations agree with those from the film study. Conclusions: Substantial heterogeneity effect on the {sup 125}I dose distributions in an eye phantom for COMS plaques was verified using radiochromic EBT film dosimetry. The calculated doses for uniformly loaded plaques using PS with heterogeneity correction option enabled were corroborated by the EBT film measurement data. Radiochromic EBT film dosimetry is feasible in measuring absolute dose distributions in eye phantom for COMS eye plaques loaded with single or multiple {sup 125}I seeds. Plaque Simulator is a viable tool for the calculation of dose distributions if one understands its limitations and uses the proper heterogeneity correction feature.« less

PLMItRNA, a database on the heterogeneous genetic origin of mitochondrial tRNA genes and tRNAs in photosynthetic eukaryotes.

PubMed

Rainaldi, Guglielmo; Volpicella, Mariateresa; Licciulli, Flavio; Liuni, Sabino; Gallerani, Raffaele; Ceci, Luigi R

2003-01-01

The updated version of PLMItRNA reports information and multialignments on 609 genes and 34 tRNA molecules active in the mitochondria of Viridiplantae (27 Embryophyta and 10 Chlorophyta), and photosynthetic algae (one Cryptophyta, four Rhodophyta and two Stramenopiles). Colour-code based tables reporting the different genetic origin of identified genes allow hyper-textual link to single entries. Promoter sequences identified for tRNA genes in the mitochondrial genomes of Angiospermae are also reported. The PLMItRNA database is accessible at http://bighost.area.ba.cnr.it/PLMItRNA/.

Analysis and Design of a Distributed System for Management and Distribution of Natural Language Assertions

DTIC Science & Technology

2010-09-01

5 2. SCIL Architecture ...............................................................................6 3. Assertions...137 x THIS PAGE INTENTIONALLY LEFT BLANK xi LIST OF FIGURES Figure 1. SCIL architecture...Database Connectivity LAN Local Area Network ODBC Open Database Connectivity SCIL Social-Cultural Content in Language UMD

DataHub knowledge based assistance for science visualization and analysis using large distributed databases

NASA Technical Reports Server (NTRS)

Handley, Thomas H., Jr.; Collins, Donald J.; Doyle, Richard J.; Jacobson, Allan S.

1991-01-01

Viewgraphs on DataHub knowledge based assistance for science visualization and analysis using large distributed databases. Topics covered include: DataHub functional architecture; data representation; logical access methods; preliminary software architecture; LinkWinds; data knowledge issues; expert systems; and data management.

Spatially correlated heterogeneous aspirations to enhance network reciprocity

NASA Astrophysics Data System (ADS)

Tanimoto, Jun; Nakata, Makoto; Hagishima, Aya; Ikegaya, Naoki

2012-02-01

Perc & Wang demonstrated that aspiring to be the fittest under conditions of pairwise strategy updating enhances network reciprocity in structured populations playing 2×2 Prisoner's Dilemma games (Z. Wang, M. Perc, Aspiring to the fittest and promoted of cooperation in the Prisoner's Dilemma game, Physical Review E 82 (2010) 021115; M. Perc, Z. Wang, Heterogeneous aspiration promotes cooperation in the Prisoner's Dilemma game, PLOS one 5 (12) (2010) e15117). Through numerical simulations, this paper shows that network reciprocity is even greater if heterogeneous aspirations are imposed. We also suggest why heterogeneous aspiration fosters network reciprocity. It distributes strategy updating speed among agents in a manner that fortifies the initially allocated cooperators' clusters against invasion. This finding prompted us to further enhance the usual heterogeneous aspiration cases for heterogeneous network topologies. We find that a negative correlation between degree and aspiration level does extend cooperation among heterogeneously structured agents.

Experiments and Analysis on a Computer Interface to an Information-Retrieval Network.

ERIC Educational Resources Information Center

Marcus, Richard S.; Reintjes, J. Francis

A primary goal of this project was to develop an interface that would provide direct access for inexperienced users to existing online bibliographic information retrieval networks. The experiment tested the concept of a virtual-system mode of access to a network of heterogeneous interactive retrieval systems and databases. An experimental…

The Status of Literacy of Sustainable Agriculture in Iran: A Systematic Review

ERIC Educational Resources Information Center

Vaninee, Hassan Sadough; Veisi, Hadi; Gorbani, Shiva; Falsafi, Peyman; Liaghati, Houman

2016-01-01

This study analyzes heterogeneous research with a focus on the knowledge, attitude, and behavior of farmers and the components of sustainable agriculture literacy through an interdisciplinary, systematic literature review for the time frame from 1996 to 2013. The major research databases were searched and 170 papers were identified. Paper…

Acupuncture for Children with Autism Spectrum Disorders: A Systematic Review of Randomized Clinical Trials

ERIC Educational Resources Information Center

Lee, Myeong Soo; Choi, Tae-Young; Shin, Byung-Cheul; Ernst, Edzard

2012-01-01

This study aimed to assess the effectiveness of acupuncture as a treatment for autism spectrum disorders (ASD). We searched the literature using 15 databases. Eleven randomized clinical trials (RCTs) met our inclusion criteria. Most had significant methodological weaknesses. The studies' statistical and clinical heterogeneity prevented us from…

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

NASA Astrophysics Data System (ADS)

Howe, B.; Halperin, D.

2014-12-01

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

Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes

PubMed Central

Pantazatos, Spiro P.; Li, Jianrong; Pavlidis, Paul; Lussier, Yves A.

2009-01-01

An approach towards heterogeneous neuroscience dataset integration is proposed that uses Natural Language Processing (NLP) and a knowledge-based phenotype organizer system (PhenOS) to link ontology-anchored terms to underlying data from each database, and then maps these terms based on a computable model of disease (SNOMED CT®). The approach was implemented using sample datasets from fMRIDC, GEO, The Whole Brain Atlas and Neuronames, and allowed for complex queries such as “List all disorders with a finding site of brain region X, and then find the semantically related references in all participating databases based on the ontological model of the disease or its anatomical and morphological attributes”. Precision of the NLP-derived coding of the unstructured phenotypes in each dataset was 88% (n = 50), and precision of the semantic mapping between these terms across datasets was 98% (n = 100). To our knowledge, this is the first example of the use of both semantic decomposition of disease relationships and hierarchical information found in ontologies to integrate heterogeneous phenotypes across clinical and molecular datasets. PMID:20495688

Key drivers for market penetration of biosimilars in Europe.

PubMed

Rémuzat, Cécile; Dorey, Julie; Cristeau, Olivier; Ionescu, Dan; Radière, Guerric; Toumi, Mondher

2017-01-01

Background & Objectives : Potential drivers and barriers of biosimilar uptake were mainly analysed through qualitative approaches. The study objective was to conduct a quantitative analysis and identify drivers of biosimilar uptake of all available biosimilars in the European Union (EU). Methods : A three-step process was established to identify key drivers for the uptake of biosimilars in the top 10 EU member states (MS) pharmaceutical markets (Belgium, France, Germany, Greece, Hungary, Italy, Poland, Spain, Sweden, and the UK): (1) literature review to identify incentive policies in place to enhance biosimilars adoption; (2) assessment of biosimilar market dynamics based on database analysis; (3) regression model analysis on price using the following explicative variables: incentive policies; price difference between the biosimilar and the originator product; distribution channel; generic uptake and generic price cut; pharmaceutical expenditure per capita; and market competition. Results : At the study cut-off date, 20 biosimilars were available on the market. Incentive policies applied to biosimilars were found to be heterogeneous across countries, and uptakes of biosimilars were also very heterogeneous between different therapeutic classes and countries. Results from the model demonstrated that incentive policies and the date of first biosimilar market entry were correlated to biosimilar uptake. Pharmaceutical expenditure per capita and the highest generic uptake were inversely correlated with biosimilar uptake. Average generic price discount over originator and the number of biosimilars showed a trend toward statistical significance for correlation with biosimilar uptake, but did not reach the significance threshold. Biosimilar price discount over original biologic price, the number of analogues, and the distribution channel were not correlated with the biosimilar uptake. Conclusions : Understanding drivers of biosimilar uptake becomes a critical issue to inform policy decision-makers. This study showed that incentive policies to enhance uptake remain an important driver of biosimilar penetration, while biosimilar price discounts have no impact. Future research is warranted when the biosimilar market gains maturity.

Key drivers for market penetration of biosimilars in Europe

PubMed Central

Rémuzat, Cécile; Dorey, Julie; Cristeau, Olivier; Ionescu, Dan; Radière, Guerric; Toumi, Mondher

2017-01-01

ABSTRACT Background & Objectives: Potential drivers and barriers of biosimilar uptake were mainly analysed through qualitative approaches. The study objective was to conduct a quantitative analysis and identify drivers of biosimilar uptake of all available biosimilars in the European Union (EU). Methods: A three-step process was established to identify key drivers for the uptake of biosimilars in the top 10 EU member states (MS) pharmaceutical markets (Belgium, France, Germany, Greece, Hungary, Italy, Poland, Spain, Sweden, and the UK): (1) literature review to identify incentive policies in place to enhance biosimilars adoption; (2) assessment of biosimilar market dynamics based on database analysis; (3) regression model analysis on price using the following explicative variables: incentive policies; price difference between the biosimilar and the originator product; distribution channel; generic uptake and generic price cut; pharmaceutical expenditure per capita; and market competition. Results: At the study cut-off date, 20 biosimilars were available on the market. Incentive policies applied to biosimilars were found to be heterogeneous across countries, and uptakes of biosimilars were also very heterogeneous between different therapeutic classes and countries. Results from the model demonstrated that incentive policies and the date of first biosimilar market entry were correlated to biosimilar uptake. Pharmaceutical expenditure per capita and the highest generic uptake were inversely correlated with biosimilar uptake. Average generic price discount over originator and the number of biosimilars showed a trend toward statistical significance for correlation with biosimilar uptake, but did not reach the significance threshold. Biosimilar price discount over original biologic price, the number of analogues, and the distribution channel were not correlated with the biosimilar uptake. Conclusions: Understanding drivers of biosimilar uptake becomes a critical issue to inform policy decision-makers. This study showed that incentive policies to enhance uptake remain an important driver of biosimilar penetration, while biosimilar price discounts have no impact. Future research is warranted when the biosimilar market gains maturity. PMID:28265349

The Heterogeneous Impacts of Business Cycles on Educational Attainment

ERIC Educational Resources Information Center

Boffy-Ramirez, Ernest

2017-01-01

This study examines the impact of fluctuations in the unemployment rate before high school graduation on educational attainment measured 30 years later. I find evidence that important heterogeneity is masked by estimating average effects across the ability distribution. Using data from the 1979 National Longitudinal Survey of Youth, this analysis…

Examining the influence of heterogeneous porosity fields on conservative solute transport

USGS Publications Warehouse

Hu, B.X.; Meerschaert, M.M.; Barrash, W.; Hyndman, D.W.; He, C.; Li, X.; Guo, Laodong

2009-01-01

It is widely recognized that groundwater flow and solute transport in natural media are largely controlled by heterogeneities. In the last three decades, many studies have examined the effects of heterogeneous hydraulic conductivity fields on flow and transport processes, but there has been much less attention to the influence of heterogeneous porosity fields. In this study, we use porosity and particle size measurements from boreholes at the Boise Hydrogeophysical Research Site (BHRS) to evaluate the importance of characterizing the spatial structure of porosity and grain size data for solute transport modeling. Then we develop synthetic hydraulic conductivity fields based on relatively simple measurements of porosity from borehole logs and grain size distributions from core samples to examine and compare the characteristics of tracer transport through these fields with and without inclusion of porosity heterogeneity. In particular, we develop horizontal 2D realizations based on data from one of the less heterogeneous units at the BHRS to examine effects where spatial variations in hydraulic parameters are not large. The results indicate that the distributions of porosity and the derived hydraulic conductivity in the study unit resemble fractal normal and lognormal fields respectively. We numerically simulate solute transport in stochastic fields and find that spatial variations in porosity have significant effects on the spread of an injected tracer plume including a significant delay in simulated tracer concentration histories.

SIMBAD quality-control

NASA Technical Reports Server (NTRS)

Lesteven, Soizick

1992-01-01

The astronomical database SIMBAD developed at the Centre de donnees astronomiques de Strasbourg presently contains 760,000 objects (stellar and non-stellar). It has the unique characteristic of being structured specifically for astronomical objects. All types of heterogeneous data (bibliographic references, measurements, and sets of identification) are connected with each object. The attributes that define quality of the database include the following. Reliability: cross-identification should not rely upon just exact values object coordinates. It also means that information attached to one simple object should be consistent. The existing data must be controlled in order to start with a reliable base and to cross-identify new data assuring the quality as data grows. Exhaustivity: delays between publication of new informations and their inclusion in the database should be as short as possible. The integrity of the database has to be maintained as data accumulates. Taking the amount of data into consideration and the rate of new data production, it is necessary to use automatic methods. One of the possibilities is to use multivariate data analysis. The factor-space is a n-dimensional relevancy space which is described by the n-axes representing a set of n subject matter headings; the words and phrases can be used to scale the axes and the documents are then a vector average of the terms within them. The application reported herein is based on the NASA-STI bibliographical database. The selected data concern astronomy, astrophysics, and space radiation (102,963 references from 1975 to 1991 included 8070 keywords). The F-space is built from this bibliographical data. By comparing the F-space position obtained from the NASA-STI keywords with the F-space position obtained from the SIMBAD references, the authors will be able to show whether it is possible to retrieve information with a restricted set of words only. If the comparison is valid, this will be a way to enter bibliographic information in the SIMBAD quality control process. Furthermore, it is possible to connect the physical measurements of stars from SIMBAD to literature concerning these stars from the NASA-STI abstracts. The physical properties of stars (e.g. UBV colors) are not randomly distributed. Stars are distributed among different clusters in a physical parameter space. The authors will show that there are some relations between this classification and the literature concerning these objects clusters in a factor space. They will investigate the nature of the relationship between the SIMBAD measurements and the bibliography. These would be new relationships that are not pre-established by an astronomer. In addition, the bibliography could be neutral information that can be used in combination with the measured parameters.

Tempest: Accelerated MS/MS database search software for heterogeneous computing platforms

PubMed Central

Adamo, Mark E.; Gerber, Scott A.

2017-01-01

MS/MS database search algorithms derive a set of candidate peptide sequences from in-silico digest of a protein sequence database, and compute theoretical fragmentation patterns to match these candidates against observed MS/MS spectra. The original Tempest publication described these operations mapped to a CPU-GPU model, in which the CPU generates peptide candidates that are asynchronously sent to a discrete GPU to be scored against experimental spectra in parallel (Milloy et al., 2012). The current version of Tempest expands this model, incorporating OpenCL to offer seamless parallelization across multicore CPUs, GPUs, integrated graphics chips, and general-purpose coprocessors. Three protocols describe how to configure and run a Tempest search, including discussion of how to leverage Tempest's unique feature set to produce optimal results. PMID:27603022

Robust scalable stabilisability conditions for large-scale heterogeneous multi-agent systems with uncertain nonlinear interactions: towards a distributed computing architecture

NASA Astrophysics Data System (ADS)

Manfredi, Sabato

2016-06-01

Large-scale dynamic systems are becoming highly pervasive in their occurrence with applications ranging from system biology, environment monitoring, sensor networks, and power systems. They are characterised by high dimensionality, complexity, and uncertainty in the node dynamic/interactions that require more and more computational demanding methods for their analysis and control design, as well as the network size and node system/interaction complexity increase. Therefore, it is a challenging problem to find scalable computational method for distributed control design of large-scale networks. In this paper, we investigate the robust distributed stabilisation problem of large-scale nonlinear multi-agent systems (briefly MASs) composed of non-identical (heterogeneous) linear dynamical systems coupled by uncertain nonlinear time-varying interconnections. By employing Lyapunov stability theory and linear matrix inequality (LMI) technique, new conditions are given for the distributed control design of large-scale MASs that can be easily solved by the toolbox of MATLAB. The stabilisability of each node dynamic is a sufficient assumption to design a global stabilising distributed control. The proposed approach improves some of the existing LMI-based results on MAS by both overcoming their computational limits and extending the applicative scenario to large-scale nonlinear heterogeneous MASs. Additionally, the proposed LMI conditions are further reduced in terms of computational requirement in the case of weakly heterogeneous MASs, which is a common scenario in real application where the network nodes and links are affected by parameter uncertainties. One of the main advantages of the proposed approach is to allow to move from a centralised towards a distributed computing architecture so that the expensive computation workload spent to solve LMIs may be shared among processors located at the networked nodes, thus increasing the scalability of the approach than the network size. Finally, a numerical example shows the applicability of the proposed method and its advantage in terms of computational complexity when compared with the existing approaches.

Upscaling heterogeneity in aquifer reactivity via exposure-time concept: forward model.

PubMed

Seeboonruang, Uma; Ginn, Timothy R

2006-03-20

Reactive properties of aquifer solid phase materials play an important role in solute fate and transport in the natural subsurface on time scales ranging from years in contaminant remediation to millennia in dynamics of aqueous geochemistry. Quantitative tools for dealing with the impact of natural heterogeneity in solid phase reactivity on solute fate and transport are limited. Here we describe the use of a structural variable to keep track of solute flux exposure to reactive surfaces. With this approach, we develop a non-reactive tracer model that is useful for determining the signature of multi-scale reactive solid heterogeneity in terms of solute flux distributions at the field scale, given realizations of three-dimensional reactive site density fields. First, a governing Eulerian equation for the non-reactive tracer model is determined by an upscaling technique in which it is found that the exposure time of solution to reactive surface areas evolves via both a macroscopic velocity and a macroscopic dispersion in the artificial dimension of exposure time. Second, we focus on the Lagrangian approach in the context of a streamtube ensemble and demonstrate the use of the distribution of solute flux over the exposure time dimension in modeling two-dimensional transport of a solute undergoing simplified linear reversible reactions, in hypothetical conditions following prior laboratory experiments. The distribution of solute flux over exposure time in a given case is a signature of the impact of heterogeneous aquifer reactivity coupled with a particular physical heterogeneity, boundary conditions, and hydraulic gradient. Rigorous application of this approach in a simulation sense is limited here to linear kinetically controlled reactions.

An open, object-based modeling approach for simulating subsurface heterogeneity

NASA Astrophysics Data System (ADS)

Bennett, J.; Ross, M.; Haslauer, C. P.; Cirpka, O. A.

2017-12-01

Characterization of subsurface heterogeneity with respect to hydraulic and geochemical properties is critical in hydrogeology as their spatial distribution controls groundwater flow and solute transport. Many approaches of characterizing subsurface heterogeneity do not account for well-established geological concepts about the deposition of the aquifer materials; those that do (i.e. process-based methods) often require forcing parameters that are difficult to derive from site observations. We have developed a new method for simulating subsurface heterogeneity that honors concepts of sequence stratigraphy, resolves fine-scale heterogeneity and anisotropy of distributed parameters, and resembles observed sedimentary deposits. The method implements a multi-scale hierarchical facies modeling framework based on architectural element analysis, with larger features composed of smaller sub-units. The Hydrogeological Virtual Reality simulator (HYVR) simulates distributed parameter models using an object-based approach. Input parameters are derived from observations of stratigraphic morphology in sequence type-sections. Simulation outputs can be used for generic simulations of groundwater flow and solute transport, and for the generation of three-dimensional training images needed in applications of multiple-point geostatistics. The HYVR algorithm is flexible and easy to customize. The algorithm was written in the open-source programming language Python, and is intended to form a code base for hydrogeological researchers, as well as a platform that can be further developed to suit investigators' individual needs. This presentation will encompass the conceptual background and computational methods of the HYVR algorithm, the derivation of input parameters from site characterization, and the results of groundwater flow and solute transport simulations in different depositional settings.

Recharge heterogeneity and high intensity rainfall events increase contamination risk for Mediterranean groundwater resources

NASA Astrophysics Data System (ADS)

Hartmann, Andreas; Jasechko, Scott; Gleeson, Tom; Wada, Yoshihide; Andreo, Bartolomé; Barberá, Juan Antonio; Brielmann, Heike; Charlier, Jean-Baptiste; Darling, George; Filippini, Maria; Garvelmann, Jakob; Goldscheider, Nico; Kralik, Martin; Kunstmann, Harald; Ladouche, Bernard; Lange, Jens; Mudarra, Matías; Francisco Martín, José; Rimmer, Alon; Sanchez, Damián; Stumpp, Christine; Wagener, Thorsten

2017-04-01

Karst develops through the dissolution of carbonate rock and results in pronounced spatiotemporal heterogeneity of hydrological processes. Karst groundwater in Europe is a major source of fresh water contributing up to half of the total drinking water supply in some countries like Austria or Slovenia. Previous work showed that karstic recharge processes enhance and alter the sensitivity of recharge to climate variability. The enhanced preferential flow from the surface to the aquifer may be followed by enhanced risk of groundwater contamination. In this study we assess the contamination risk of karst aquifers over Europe and the Mediterranean using simulated transit time distributions. Using a new type of semi-distributed model that considers the spatial heterogeneity of karst hydraulic properties, we were able to simulate karstic groundwater recharge including its heterogeneous spatiotemporal dynamics. The model is driven by gridded daily climate data from the Global Land Data Assimilation System (GLDAS). Transit time distributions are calculated using virtual tracer experiments. We evaluated our simulations by independent information on transit times derived from observed time series of water isotopes of >70 karst springs over Europe. The simulations indicate that, compared to humid, mountain and desert regions, the Mediterranean region shows a stronger risk of contamination in Europe because preferential flow processes are most pronounced given thin soil layers and the seasonal abundance of high intensity rainfall events in autumn and winter. Our modelling approach includes strong simplifications and its results cannot easily be generalized but it still highlights that the combined effects of variable climate and heterogeneous catchment properties constitute a strong risk on water quality.

Heterogeneous distribution of alectinib in neuroblastoma xenografts revealed by matrix-assisted laser desorption ionization mass spectrometry imaging: a pilot study.

PubMed

Ryu, Shoraku; Hayashi, Mitsuhiro; Aikawa, Hiroaki; Okamoto, Isamu; Fujiwara, Yasuhiro; Hamada, Akinobu

2018-01-01

The penetration of the anaplastic lymphoma kinase (ALK) inhibitor alectinib in neuroblastomas and the relationship between alectinib and ALK expression are unknown. The aim of this study was to perform a quantitative investigation of the inter- and intra-tumoural distribution of alectinib in different neuroblastoma xenograft models using matrix-assisted laser desorption ionization MS imaging (MALDI-MSI). The distribution of alectinib in NB1 (ALK amplification) and SK-N-FI (ALK wild-type) xenograft tissues was analysed using MALDI-MSI. The abundance of alectinib in tumours and intra-tumoural areas was quantified using ion signal intensities from MALDI-MSI after normalization by correlation with LC-MS/MS. The distribution of alectinib was heterogeneous in neuroblastomas. The penetration of alectinib was not significantly different between ALK amplification and ALK wide-type tissues using both LC-MS/MS concentrations and MSI intensities. Normalization with an internal standard increased the quantitative property of MSI by adjusting for the ion suppression effect. The distribution of alectinib in different intra-tumoural areas can alternatively be quantified from MS images by correlation with LC-MS/MS. The penetration of alectinib into tumour tissues may not be homogenous or influenced by ALK expression in the early period after single-dose administration. MALDI-MSI may prove to be a valuable pharmaceutical method for elucidating the mechanism of action of drugs by clarifying their microscopic distribution in heterogeneous tissues. © 2017 The British Pharmacological Society.

Transport lattice models of heat transport in skin with spatially heterogeneous, temperature-dependent perfusion.

PubMed

Gowrishankar, T R; Stewart, Donald A; Martin, Gregory T; Weaver, James C

2004-11-17

Investigation of bioheat transfer problems requires the evaluation of temporal and spatial distributions of temperature. This class of problems has been traditionally addressed using the Pennes bioheat equation. Transport of heat by conduction, and by temperature-dependent, spatially heterogeneous blood perfusion is modeled here using a transport lattice approach. We represent heat transport processes by using a lattice that represents the Pennes bioheat equation in perfused tissues, and diffusion in nonperfused regions. The three layer skin model has a nonperfused viable epidermis, and deeper regions of dermis and subcutaneous tissue with perfusion that is constant or temperature-dependent. Two cases are considered: (1) surface contact heating and (2) spatially distributed heating. The model is relevant to the prediction of the transient and steady state temperature rise for different methods of power deposition within the skin. Accumulated thermal damage is estimated by using an Arrhenius type rate equation at locations where viable tissue temperature exceeds 42 degrees C. Prediction of spatial temperature distributions is also illustrated with a two-dimensional model of skin created from a histological image. The transport lattice approach was validated by comparison with an analytical solution for a slab with homogeneous thermal properties and spatially distributed uniform sink held at constant temperatures at the ends. For typical transcutaneous blood gas sensing conditions the estimated damage is small, even with prolonged skin contact to a 45 degrees C surface. Spatial heterogeneity in skin thermal properties leads to a non-uniform temperature distribution during a 10 GHz electromagnetic field exposure. A realistic two-dimensional model of the skin shows that tissue heterogeneity does not lead to a significant local temperature increase when heated by a hot wire tip. The heat transport system model of the skin was solved by exploiting the mathematical analogy between local thermal models and local electrical (charge transport) models, thereby allowing robust, circuit simulation software to obtain solutions to Kirchhoff's laws for the system model. Transport lattices allow systematic introduction of realistic geometry and spatially heterogeneous heat transport mechanisms. Local representations for both simple, passive functions and more complex local models can be easily and intuitively included into the system model of a tissue.

Is the co-seismic slip distribution fractal?

NASA Astrophysics Data System (ADS)

Milliner, Christopher; Sammis, Charles; Allam, Amir; Dolan, James

2015-04-01

Co-seismic along-strike slip heterogeneity is widely observed for many surface-rupturing earthquakes as revealed by field and high-resolution geodetic methods. However, this co-seismic slip variability is currently a poorly understood phenomenon. Key unanswered questions include: What are the characteristics and underlying causes of along-strike slip variability? Do the properties of slip variability change from fault-to-fault, along-strike or at different scales? We cross-correlate optical, pre- and post-event air photos using the program COSI-Corr to measure the near-field, surface deformation pattern of the 1992 Mw 7.3 Landers and 1999 Mw 7.1 Hector Mine earthquakes in high-resolution. We produce the co-seismic slip profiles of both events from over 1,000 displacement measurements and observe consistent along-strike slip variability. Although the observed slip heterogeneity seems apparently complex and disordered, a spectral analysis reveals that the slip distributions are indeed self-affine fractal i.e., slip exhibits a consistent degree of irregularity at all observable length scales, with a 'short-memory' and is not random. We find a fractal dimension of 1.58 and 1.75 for the Landers and Hector Mine earthquakes, respectively, indicating that slip is more heterogeneous for the Hector Mine event. Fractal slip is consistent with both dynamic and quasi-static numerical simulations that use non-planar faults, which in turn causes heterogeneous along-strike stress, and we attribute the observed fractal slip to fault surfaces of fractal roughness. As fault surfaces are known to smooth over geologic time due to abrasional wear and fracturing, we also test whether the fractal properties of slip distributions alters between earthquakes from immature to mature fault systems. We will present results that test this hypothesis by using the optical image correlation technique to measure historic, co-seismic slip distributions of earthquakes from structurally mature, large cumulative displacement faults and compare these slip distributions to those from immature fault systems. Our results have fundamental implications for an understanding of slip heterogeneity and the behavior of the rupture process.

Toward unification of taxonomy databases in a distributed computer environment

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

Kitakami, Hajime; Tateno, Yoshio; Gojobori, Takashi

1994-12-31

All the taxonomy databases constructed with the DNA databases of the international DNA data banks are powerful electronic dictionaries which aid in biological research by computer. The taxonomy databases are, however not consistently unified with a relational format. If we can achieve consistent unification of the taxonomy databases, it will be useful in comparing many research results, and investigating future research directions from existent research results. In particular, it will be useful in comparing relationships between phylogenetic trees inferred from molecular data and those constructed from morphological data. The goal of the present study is to unify the existent taxonomymore » databases and eliminate inconsistencies (errors) that are present in them. Inconsistencies occur particularly in the restructuring of the existent taxonomy databases, since classification rules for constructing the taxonomy have rapidly changed with biological advancements. A repair system is needed to remove inconsistencies in each data bank and mismatches among data banks. This paper describes a new methodology for removing both inconsistencies and mismatches from the databases on a distributed computer environment. The methodology is implemented in a relational database management system, SYBASE.« less

Multiphase flow modeling of a crude-oil spill site with a bimodal permeability distribution

USGS Publications Warehouse

Dillard, Leslie A.; Essaid, Hedeff I.; Herkelrath, William N.

1997-01-01

Fluid saturation, particle-size distribution, and porosity measurements were obtained from 269 core samples collected from six boreholes along a 90-m transect at a subregion of a crude-oil spill site, the north pool, near Bemidji, Minnesota. The oil saturation data, collected 11 years after the spill, showed an irregularly shaped oil body that appeared to be affected by sediment spatial variability. The particle-size distribution data were used to estimate the permeability (k) and retention curves for each sample. An additional 344 k estimates were obtained from samples previously collected at the north pool. The 613 k estimates were distributed bimodal lognormally with the two population distributions corresponding to the two predominant lithologies: a coarse glacial outwash deposit and fine-grained interbedded lenses. A two-step geostatistical approach was used to generate a conditioned realization of k representing the bimodal heterogeneity. A cross-sectional multiphase flow model was used to simulate the flow of oil and water in the presence of air along the north pool transect for an 11-year period. The inclusion of a representation of the bimodal aquifer heterogeneity was crucial for reproduction of general features of the observed oil body. If the bimodal heterogeneity was characterized, hysteresis did not have to be incorporated into the model because a hysteretic effect was produced by the sediment spatial variability. By revising the relative permeability functional relation, an improved reproduction of the observed oil saturation distribution was achieved. The inclusion of water table fluctuations in the model did not significantly affect the simulated oil saturation distribution.

Chemical and mineralogical heterogeneities of weathered igneous profiles: implications for landslide investigations

NASA Astrophysics Data System (ADS)

Duzgoren-Aydin, N. S.; Aydin, A.

2006-05-01

Landslides in tropical and sub-tropical regions are generally associated with weathered rock profiles which often possess chemical and mineralogical heterogeneities at material- and mineral-scales. Such heterogeneities reach a climax by the occurrences of oxyhydroxide- and clay-rich zones. Weakness and low permeability of these zones makes them ideal for the development of slip zones along which landslides take place. This paper describes the nature and distribution of chemical and mineralogical heterogeneities within weathered profiles developed from felsic igneous rocks in Hong Kong. It sets out the use of integrated geochemical and mineralogical studies to improve understanding of the development of critical heterogeneities and hence to predict their types and presence in a given weathered profile.

Submillimeter-scale heterogeneity of labile phosphorus in sediments characterized by diffusive gradients in thin films and spatial analysis.

PubMed

Meng, Yuting; Ding, Shiming; Gong, Mengdan; Chen, Musong; Wang, Yan; Fan, Xianfang; Shi, Lei; Zhang, Chaosheng

2018-03-01

Sediments have a heterogeneous distribution of labile redox-sensitive elements due to a drastic downward transition from oxic to anoxic condition as a result of organic matter degradation. Characterization of the heterogeneous nature of sediments is vital for understanding of small-scale biogeochemical processes. However, there are limited reports on the related specialized methodology. In this study, the monthly distributions of labile phosphorus (P), a redox-sensitive limiting nutrient, were measured in the eutrophic Lake Taihu by Zr-oxide diffusive gradients in thin films (Zr-oxide DGT) on a two-dimensional (2D) submillimeter level. Geographical information system (GIS) techniques were used to visualize the labile P distribution at such a micro-scale, showing that the DGT-labile P was low in winter and high in summer. Spatial analysis methods, including semivariogram and Moran's I, were used to quantify the spatial variation of DGT-labile P. The distribution of DGT-labile P had clear submillimeter-scale spatial patterns with significant spatial autocorrelation during the whole year and displayed seasonal changes. High values of labile P with strong spatial variation were observed in summer, while low values of labile P with relatively uniform spatial patterns were detected in winter, demonstrating the strong influences of temperature on the mobility and spatial distribution of P in sediment profiles. Copyright © 2017 Elsevier Ltd. All rights reserved.

Why are most aquatic plants widely distributed? Dispersal, clonal growth and small-scale heterogeneity in a stressful environment

NASA Astrophysics Data System (ADS)

Santamaría, Luis

2002-06-01

Non-marine aquatic vascular plants generally show broad distributional ranges. Climatic factors seem to have limited effects on their distributions, besides the determination of major disjunctions (tropical-temperate-subarctic). Dispersal should have been frequent enough to assure the quick colonisation of extensive areas following glacial retreat, but dispersal limitation is still apparent in areas separated by geographic barriers. Aquatic vascular plants also show limited taxonomic differentiation and low within-species genetic variation. Variation within populations is particularly low, but variation among populations seems to be relatively high, mainly due to the persistence of long-lived clones. Ecotypic differentiation is often related to factors that constrain clonal reproduction (salinity and ephemeral inundation). Inland aquatic habitats are heterogeneous environments, but this heterogeneity largely occurs at relatively small scales (within waterbodies and among neighbouring ones). They also represent a stressful environment for plants, characterised by low carbon availability, shaded conditions, sediment anoxia, mechanical damage by currents and waves, significant restrictions to sexual reproduction, and sometimes also osmotic stress and limited nutrient supply. I propose that the generality of broad distributions and low differentiation among the inland aquatic flora is best explained by a combination of: (1) selection for stress-tolerant taxa with broad tolerance ranges. (2) The selective advantages provided by clonal growth and multiplication, which increases plant tolerance to stress, genet survivorship and population viability. (3) Long-distance dispersal of sexual propagules and high local dispersal of asexual clones. (4) The generality of broad plastic responses, promoted by the combination of clonal growth, high local dispersal, small-scale spatial heterogeneity and temporal variability.

Experimental consideration of capillary chromatography based on tube radial distribution of ternary mixture carrier solvents under laminar flow conditions.

PubMed

Jinno, Naoya; Hashimoto, Masahiko; Tsukagoshi, Kazuhiko

2011-01-01

A capillary chromatography system has been developed based on the tube radial distribution of the carrier solvents using an open capillary tube and a water-acetonitrile-ethyl acetate mixture carrier solution. This tube radial distribution chromatography (TRDC) system works under laminar flow conditions. In this study, a phase diagram for the ternary mixture carrier solvents of water, acetonitrile, and ethyl acetate was constructed. The phase diagram that included a boundary curve between homogeneous and heterogeneous solutions was considered together with the component ratios of the solvents in the homogeneous carrier solutions required for the TRDC system. It was found that the TRDC system performed well with homogeneous solutions having component ratios of the solvents that were positioned near the homogeneous-heterogeneous solution boundary of the phase diagram. For preparing the carrier solutions of water-hydrophilic/hydrophobic organic solvents for the TRDC system, we used for the first time methanol, ethanol, 1,4-dioxane, and 1-propanol, instead of acetonitrile (hydrophilic organic solvent), as well as chloroform and 1-butanol, instead of ethyl acetate (hydrophobic organic solvent). The homogeneous ternary mixture carrier solutions were prepared near the homogeneous-heterogeneous solution boundary. Analyte mixtures of 2,6-naphthalenedisulfonic acid and 1-naphthol were separated with the TRDC system using these homogeneous ternary mixture carrier solutions. The pressure change in the capillary tube under laminar flow conditions might alter the carrier solution from homogeneous in the batch vessel to heterogeneous, thus affecting the tube radial distribution of the solvents in the capillary tube.

Design of special purpose database for credit cooperation bank business processing network system

NASA Astrophysics Data System (ADS)

Yu, Yongling; Zong, Sisheng; Shi, Jinfa

2011-12-01

With the popularization of e-finance in the city, the construction of e-finance is transfering to the vast rural market, and quickly to develop in depth. Developing the business processing network system suitable for the rural credit cooperative Banks can make business processing conveniently, and have a good application prospect. In this paper, We analyse the necessity of adopting special purpose distributed database in Credit Cooperation Band System, give corresponding distributed database system structure , design the specical purpose database and interface technology . The application in Tongbai Rural Credit Cooperatives has shown that system has better performance and higher efficiency.

Effects of geometric modulation and surface potential heterogeneity on electrokinetic flow and solute transport in a microchannel

NASA Astrophysics Data System (ADS)

Bera, Subrata; Bhattacharyya, S.

2017-12-01

A numerical investigation is performed on the electroosmotic flow (EOF) in a surface-modulated microchannel to induce enhanced solute mixing. The channel wall is modulated by placing surface-mounted obstacles of trigonometric shape along which the surface potential is considered to be different from the surface potential of the homogeneous part of the wall. The characteristics of the electrokinetic flow are governed by the Laplace equation for the distribution of external electric potential; the Poisson equation for the distribution of induced electric potential; the Nernst-Planck equations for the distribution of ions; and the Navier-Stokes equations for fluid flow simultaneously. These nonlinear coupled set of governing equations are solved numerically by a control volume method over the staggered system. The influence of the geometric modulation of the surface, surface potential heterogeneity and the bulk ionic concentration on the EOF is analyzed. Vortical flow develops near a surface modulation, and it becomes stronger when the surface potential of the modulated region is in opposite sign to the surface potential of the homogeneous part of the channel walls. Vortical flow also depends on the Debye length when the Debye length is in the order of the channel height. Pressure drop along the channel length is higher for a ribbed wall channel compared to the grooved wall case. The pressure drop decreases with the increase in the amplitude for a grooved channel, but increases for a ribbed channel. The mixing index is quantified through the standard deviation of the solute distribution. Our results show that mixing index is higher for the ribbed channel compared to the grooved channel with heterogeneous surface potential. The increase in potential heterogeneity in the modulated region also increases the mixing index in both grooved and ribbed channels. However, the mixing performance, which is the ratio of the mixing index to pressure drop, reduces with the rise in the surface potential heterogeneity.

Effects of geometric modulation and surface potential heterogeneity on electrokinetic flow and solute transport in a microchannel

NASA Astrophysics Data System (ADS)

Bera, Subrata; Bhattacharyya, S.

2018-04-01

A numerical investigation is performed on the electroosmotic flow (EOF) in a surface-modulated microchannel to induce enhanced solute mixing. The channel wall is modulated by placing surface-mounted obstacles of trigonometric shape along which the surface potential is considered to be different from the surface potential of the homogeneous part of the wall. The characteristics of the electrokinetic flow are governed by the Laplace equation for the distribution of external electric potential; the Poisson equation for the distribution of induced electric potential; the Nernst-Planck equations for the distribution of ions; and the Navier-Stokes equations for fluid flow simultaneously. These nonlinear coupled set of governing equations are solved numerically by a control volume method over the staggered system. The influence of the geometric modulation of the surface, surface potential heterogeneity and the bulk ionic concentration on the EOF is analyzed. Vortical flow develops near a surface modulation, and it becomes stronger when the surface potential of the modulated region is in opposite sign to the surface potential of the homogeneous part of the channel walls. Vortical flow also depends on the Debye length when the Debye length is in the order of the channel height. Pressure drop along the channel length is higher for a ribbed wall channel compared to the grooved wall case. The pressure drop decreases with the increase in the amplitude for a grooved channel, but increases for a ribbed channel. The mixing index is quantified through the standard deviation of the solute distribution. Our results show that mixing index is higher for the ribbed channel compared to the grooved channel with heterogeneous surface potential. The increase in potential heterogeneity in the modulated region also increases the mixing index in both grooved and ribbed channels. However, the mixing performance, which is the ratio of the mixing index to pressure drop, reduces with the rise in the surface potential heterogeneity.

Vaccine Effects on Heterogeneity in Susceptibility and Implications for Population Health Management.

PubMed

Langwig, Kate E; Wargo, Andrew R; Jones, Darbi R; Viss, Jessie R; Rutan, Barbara J; Egan, Nicholas A; Sá-Guimarães, Pedro; Kim, Min Sun; Kurath, Gael; Gomes, M Gabriela M; Lipsitch, Marc

2017-11-21

Heterogeneity in host susceptibility is a key determinant of infectious disease dynamics but is rarely accounted for in assessment of disease control measures. Understanding how susceptibility is distributed in populations, and how control measures change this distribution, is integral to predicting the course of epidemics with and without interventions. Using multiple experimental and modeling approaches, we show that rainbow trout have relatively homogeneous susceptibility to infection with infectious hematopoietic necrosis virus and that vaccination increases heterogeneity in susceptibility in a nearly all-or-nothing fashion. In a simple transmission model with an R 0 of 2, the highly heterogeneous vaccine protection would cause a 35 percentage-point reduction in outbreak size over an intervention inducing homogenous protection at the same mean level. More broadly, these findings provide validation of methodology that can help to reduce biases in predictions of vaccine impact in natural settings and provide insight into how vaccination shapes population susceptibility. IMPORTANCE Differences among individuals influence transmission and spread of infectious diseases as well as the effectiveness of control measures. Control measures, such as vaccines, may provide leaky protection, protecting all hosts to an identical degree, or all-or-nothing protection, protecting some hosts completely while leaving others completely unprotected. This distinction can have a dramatic influence on disease dynamics, yet this distribution of protection is frequently unaccounted for in epidemiological models and estimates of vaccine efficacy. Here, we apply new methodology to experimentally examine host heterogeneity in susceptibility and mode of vaccine action as distinct components influencing disease outcome. Through multiple experiments and new modeling approaches, we show that the distribution of vaccine effects can be robustly estimated. These results offer new experimental and inferential methodology that can improve predictions of vaccine effectiveness and have broad applicability to human, wildlife, and ecosystem health. Copyright © 2017 Langwig et al.

Dietary choline and betaine intakes vary in an adult multiethnic population.

PubMed

Yonemori, Kim M; Lim, Unhee; Koga, Karin R; Wilkens, Lynne R; Au, Donna; Boushey, Carol J; Le Marchand, Loïc; Kolonel, Laurence N; Murphy, Suzanne P

2013-06-01

Choline and betaine are important nutrients for human health, but reference food composition databases for these nutrients became available only recently. We tested the feasibility of using these databases to estimate dietary choline and betaine intakes among ethnically diverse adults who participated in the Multiethnic Cohort (MEC) Study. Of the food items (n = 965) used to quantify intakes for the MEC FFQ, 189 items were exactly matched with items in the USDA Database for the Choline Content of Common Foods for total choline, choline-containing compounds, and betaine, and 547 items were matched to the USDA National Nutrient Database for Standard Reference for total choline (n = 547) and 148 for betaine. When a match was not found, choline and betaine values were imputed based on the same food with a different form (124 food items for choline, 300 for choline compounds, 236 for betaine), a similar food (n = 98, 284, and 227, respectively) or the closest item in the same food category (n = 6, 191, and 157, respectively), or the values were assumed to be zero (n = 1, 1, and 8, respectively). The resulting mean intake estimates for choline and betaine among 188,147 MEC participants (aged 45-75) varied by sex (372 and 154 mg/d in men, 304 and 128 mg/d in women, respectively; P-heterogeneity < 0.0001) and by race/ethnicity among Caucasians, African Americans, Japanese Americans, Latinos, and Native Hawaiians (P-heterogeneity < 0.0001), largely due to the variation in energy intake. Our findings demonstrate the feasibility of assessing choline and betaine intake and characterize the variation in intake that exists in a multiethnic population.

Dietary Choline and Betaine Intakes Vary in an Adult Multiethnic Population123

PubMed Central

Yonemori, Kim M.; Lim, Unhee; Koga, Karin R.; Wilkens, Lynne R.; Au, Donna; Boushey, Carol J.; Le Marchand, Loïc; Kolonel, Laurence N.; Murphy, Suzanne P.

2013-01-01

Choline and betaine are important nutrients for human health, but reference food composition databases for these nutrients became available only recently. We tested the feasibility of using these databases to estimate dietary choline and betaine intakes among ethnically diverse adults who participated in the Multiethnic Cohort (MEC) Study. Of the food items (n = 965) used to quantify intakes for the MEC FFQ, 189 items were exactly matched with items in the USDA Database for the Choline Content of Common Foods for total choline, choline-containing compounds, and betaine, and 547 items were matched to the USDA National Nutrient Database for Standard Reference for total choline (n = 547) and 148 for betaine. When a match was not found, choline and betaine values were imputed based on the same food with a different form (124 food items for choline, 300 for choline compounds, 236 for betaine), a similar food (n = 98, 284, and 227, respectively) or the closest item in the same food category (n = 6, 191, and 157, respectively), or the values were assumed to be zero (n = 1, 1, and 8, respectively). The resulting mean intake estimates for choline and betaine among 188,147 MEC participants (aged 45–75) varied by sex (372 and 154 mg/d in men, 304 and 128 mg/d in women, respectively; P-heterogeneity < 0.0001) and by race/ethnicity among Caucasians, African Americans, Japanese Americans, Latinos, and Native Hawaiians (P-heterogeneity < 0.0001), largely due to the variation in energy intake. Our findings demonstrate the feasibility of assessing choline and betaine intake and characterize the variation in intake that exists in a multiethnic population. PMID:23616508

Meta-analysis on the effectiveness of team-based learning on medical education in China.

PubMed

Chen, Minjian; Ni, Chunhui; Hu, Yanhui; Wang, Meilin; Liu, Lu; Ji, Xiaoming; Chu, Haiyan; Wu, Wei; Lu, Chuncheng; Wang, Shouyu; Wang, Shoulin; Zhao, Liping; Li, Zhong; Zhu, Huijuan; Wang, Jianming; Xia, Yankai; Wang, Xinru

2018-04-10

Team-based learning (TBL) has been adopted as a new medical pedagogical approach in China. However, there are no studies or reviews summarizing the effectiveness of TBL on medical education. This study aims to obtain an overall estimation of the effectiveness of TBL on outcomes of theoretical teaching of medical education in China. We retrieved the studies from inception through December, 2015. Chinese National Knowledge Infrastructure, Chinese Biomedical Literature Database, Chinese Wanfang Database, Chinese Scientific Journal Database, PubMed, EMBASE and Cochrane Database were searched. The quality of included studies was assessed by the Newcastle-Ottawa scale. Standardized mean difference (SMD) was applied for the estimation of the pooled effects. Heterogeneity assumption was detected by I 2 statistics, and was further explored by meta-regression analysis. A total of 13 articles including 1545 participants eventually entered into the meta-analysis. The quality scores of these studies ranged from 6 to 10. Altogether, TBL significantly increased students' theoretical examination scores when compared with lecture-based learning (LBL) (SMD = 2.46, 95% CI: 1.53-3.40). Additionally, TBL significantly increased students' learning attitude (SMD = 3.23, 95% CI: 2.27-4.20), and learning skill (SMD = 2.70, 95% CI: 1.33-4.07). The meta-regression results showed that randomization, education classification and gender diversity were the factors that caused heterogeneity. TBL in theoretical teaching of medical education seems to be more effective than LBL in improving the knowledge, attitude and skill of students in China, providing evidence for the implement of TBL in medical education in China. The medical schools should implement TBL with the consideration on the practical teaching situations such as students' education level.

PDXliver: a database of liver cancer patient derived xenograft mouse models.

PubMed

He, Sheng; Hu, Bo; Li, Chao; Lin, Ping; Tang, Wei-Guo; Sun, Yun-Fan; Feng, Fang-You-Min; Guo, Wei; Li, Jia; Xu, Yang; Yao, Qian-Lan; Zhang, Xin; Qiu, Shuang-Jian; Zhou, Jian; Fan, Jia; Li, Yi-Xue; Li, Hong; Yang, Xin-Rong

2018-05-09

Liver cancer is the second leading cause of cancer-related deaths and characterized by heterogeneity and drug resistance. Patient-derived xenograft (PDX) models have been widely used in cancer research because they reproduce the characteristics of original tumors. However, the current studies of liver cancer PDX mice are scattered and the number of available PDX models are too small to represent the heterogeneity of liver cancer patients. To improve this situation and to complement available PDX models related resources, here we constructed a comprehensive database, PDXliver, to integrate and analyze liver cancer PDX models. Currently, PDXliver contains 116 PDX models from Chinese liver cancer patients, 51 of them were established by the in-house PDX platform and others were curated from the public literatures. These models are annotated with complete information, including clinical characteristics of patients, genome-wide expression profiles, germline variations, somatic mutations and copy number alterations. Analysis of expression subtypes and mutated genes show that PDXliver represents the diversity of human patients. Another feature of PDXliver is storing drug response data of PDX mice, which makes it possible to explore the association between molecular profiles and drug sensitivity. All data can be accessed via the Browse and Search pages. Additionally, two tools are provided to interactively visualize the omics data of selected PDXs or to compare two groups of PDXs. As far as we known, PDXliver is the first public database of liver cancer PDX models. We hope that this comprehensive resource will accelerate the utility of PDX models and facilitate liver cancer research. The PDXliver database is freely available online at: http://www.picb.ac.cn/PDXliver/.

Experimental evaluation of dynamic data allocation strategies in a distributed database with changing workloads

NASA Technical Reports Server (NTRS)

Brunstrom, Anna; Leutenegger, Scott T.; Simha, Rahul

1995-01-01

Traditionally, allocation of data in distributed database management systems has been determined by off-line analysis and optimization. This technique works well for static database access patterns, but is often inadequate for frequently changing workloads. In this paper we address how to dynamically reallocate data for partionable distributed databases with changing access patterns. Rather than complicated and expensive optimization algorithms, a simple heuristic is presented and shown, via an implementation study, to improve system throughput by 30 percent in a local area network based system. Based on artificial wide area network delays, we show that dynamic reallocation can improve system throughput by a factor of two and a half for wide area networks. We also show that individual site load must be taken into consideration when reallocating data, and provide a simple policy that incorporates load in the reallocation decision.

Field Test of Enhanced Remedial Amendment Delivery Using a Shear-Thinning Fluid

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

Truex, Michael J.; Vermeul, Vincent R.; Adamson, David

2015-03-01

Heterogeneity of hydraulic properties in aquifers may lead to contaminants residing in lower-permeability zones where it is difficult to deliver remediation amendments using conventional injection processes. The focus of this effort is to examine use of a shear-thinning fluid (STF) to improve the uniformity of remedial amendment distribution within a heterogeneous aquifer. Previous studies have demonstrated the significant potential of STFs for improving remedial amendment delivery in heterogeneous aquifers, but quantitative evaluation of these improvements from field applications are lacking. A field-scale test was conducted that compares data from successive injection of a tracer in water followed by injection ofmore » a tracer in a STF to evaluate the impact of the STF on tracer distribution uniformity in the presence of permeability contrasts within the targeted injection zone. Data from tracer breakthrough at multiple depth-discrete monitoring intervals and electrical resistivity tomography showed that inclusion of STF in the injection solution slowed movement in high-permeability pathways, improved delivery of amendment to low-permeability materials, and resulted in better uniformity in injected fluid distribution within the targeted treatment zone.« less

Modeling the Impact of Heterogeneous Spatial Distribution of Soil Microbes on Pesticide Biodegradation at the Centimeter Scale

NASA Astrophysics Data System (ADS)

Babey, T.; De Dreuzy, J. R.; Pinheiro, M.; Garnier, P.; Vieublé-Gonod, L.; Rapaport, A.

2015-12-01

Micro-organisms and substrates may be heterogeneously distributed in soils. This repartition as well as transport mechanisms bringing them into contact are expected to impact the biodegradation rates. Pinheiro et al [2015] have measured in cm-large reconstructed soil cores the fate of an injection of 2,4-D pesticide for different injection conditions and initial distributions of soil pesticide degraders. Through the calibration of a reactive transport model of these experiments, we show that: i) biodegradation of diffusion-controlled pesticide fluxes is favored by a high Damköhler number (high reaction rate compared to flux rate); ii) abiotic sorption processes are negligible and do not interact strongly with biodegradation; iii) biodegradation is primarily governed by the initial repartition of pesticide and degraders for diffusion-controlled transport, as diffusion greatly limits the flux of pesticide reaching the microbial hotspot due to dilution. These results suggest that for biodegradation to be substantial, a spatial heterogeneity in the repartition of microbes and substrate has to be associated with intermittent and fast transport processes to mix them.

A Modified Distributed Bees Algorithm for Multi-Sensor Task Allocation.

PubMed

Tkach, Itshak; Jevtić, Aleksandar; Nof, Shimon Y; Edan, Yael

2018-03-02

Multi-sensor systems can play an important role in monitoring tasks and detecting targets. However, real-time allocation of heterogeneous sensors to dynamic targets/tasks that are unknown a priori in their locations and priorities is a challenge. This paper presents a Modified Distributed Bees Algorithm (MDBA) that is developed to allocate stationary heterogeneous sensors to upcoming unknown tasks using a decentralized, swarm intelligence approach to minimize the task detection times. Sensors are allocated to tasks based on sensors' performance, tasks' priorities, and the distances of the sensors from the locations where the tasks are being executed. The algorithm was compared to a Distributed Bees Algorithm (DBA), a Bees System, and two common multi-sensor algorithms, market-based and greedy-based algorithms, which were fitted for the specific task. Simulation analyses revealed that MDBA achieved statistically significant improved performance by 7% with respect to DBA as the second-best algorithm, and by 19% with respect to Greedy algorithm, which was the worst, thus indicating its fitness to provide solutions for heterogeneous multi-sensor systems.

A Modified Distributed Bees Algorithm for Multi-Sensor Task Allocation †

PubMed Central

Nof, Shimon Y.; Edan, Yael

2018-01-01

Multi-sensor systems can play an important role in monitoring tasks and detecting targets. However, real-time allocation of heterogeneous sensors to dynamic targets/tasks that are unknown a priori in their locations and priorities is a challenge. This paper presents a Modified Distributed Bees Algorithm (MDBA) that is developed to allocate stationary heterogeneous sensors to upcoming unknown tasks using a decentralized, swarm intelligence approach to minimize the task detection times. Sensors are allocated to tasks based on sensors’ performance, tasks’ priorities, and the distances of the sensors from the locations where the tasks are being executed. The algorithm was compared to a Distributed Bees Algorithm (DBA), a Bees System, and two common multi-sensor algorithms, market-based and greedy-based algorithms, which were fitted for the specific task. Simulation analyses revealed that MDBA achieved statistically significant improved performance by 7% with respect to DBA as the second-best algorithm, and by 19% with respect to Greedy algorithm, which was the worst, thus indicating its fitness to provide solutions for heterogeneous multi-sensor systems. PMID:29498683

The role of local heterogeneity in transport through steep hillslopes.

NASA Astrophysics Data System (ADS)

Fiori, A.; Russo, D.

2009-04-01

A stochastic model is developed for the analysis of the travel time distribution in a hillslope. The latter is represented as a system made up from a highly permeable soil underlain by a less permeable subsoil or bedrock. The heterogeneous hydraulic conductivity K is described as a stationary random space function. The travel time distribution is obtained through a stochastic Lagrangian model of transport, after adopting a first order approximation in the logconductivity variance. The results show that the travel time pdf pertaining to the soil is power-law, with exponent variable between -1 and -0.5; the behavior is mainly determined by unsaturated transport. The subsoil is mainly responsible for the tail of the travel time distribution. Analysis of the first and second moments of travel time show that the spreading of solute is controlled by the variations in the flow-paths (geomorphological dispersion), which depend on the hillslope geometry. Conversely, the contribution of the K heterogeneity to spreading appears as less relevant. The model is tested against a detailed three-dimensional numerical simulation with reasonably good agreement.

A knowledge-based system for patient image pre-fetching in heterogeneous database environments--modeling, design, and evaluation.

PubMed

Wei, C P; Hu, P J; Sheng, O R

2001-03-01

When performing primary reading on a newly taken radiological examination, a radiologist often needs to reference relevant prior images of the same patient for confirmation or comparison purposes. Support of such image references is of clinical importance and may have significant effects on radiologists' examination reading efficiency, service quality, and work satisfaction. To effectively support such image reference needs, we proposed and developed a knowledge-based patient image pre-fetching system, addressing several challenging requirements of the application that include representation and learning of image reference heuristics and management of data-intensive knowledge inferencing. Moreover, the system demands an extensible and maintainable architecture design capable of effectively adapting to a dynamic environment characterized by heterogeneous and autonomous data source systems. In this paper, we developed a synthesized object-oriented entity- relationship model, a conceptual model appropriate for representing radiologists' prior image reference heuristics that are heuristic oriented and data intensive. We detailed the system architecture and design of the knowledge-based patient image pre-fetching system. Our architecture design is based on a client-mediator-server framework, capable of coping with a dynamic environment characterized by distributed, heterogeneous, and highly autonomous data source systems. To adapt to changes in radiologists' patient prior image reference heuristics, ID3-based multidecision-tree induction and CN2-based multidecision induction learning techniques were developed and evaluated. Experimentally, we examined effects of the pre-fetching system we created on radiologists' examination readings. Preliminary results show that the knowledge-based patient image pre-fetching system more accurately supports radiologists' patient prior image reference needs than the current practice adopted at the study site and that radiologists may become more efficient, consultatively effective, and better satisfied when supported by the pre-fetching system than when relying on the study site's pre-fetching practice.

WebGIS based on semantic grid model and web services

NASA Astrophysics Data System (ADS)

Zhang, WangFei; Yue, CaiRong; Gao, JianGuo

2009-10-01

As the combination point of the network technology and GIS technology, WebGIS has got the fast development in recent years. With the restriction of Web and the characteristics of GIS, traditional WebGIS has some prominent problems existing in development. For example, it can't accomplish the interoperability of heterogeneous spatial databases; it can't accomplish the data access of cross-platform. With the appearance of Web Service and Grid technology, there appeared great change in field of WebGIS. Web Service provided an interface which can give information of different site the ability of data sharing and inter communication. The goal of Grid technology was to make the internet to a large and super computer, with this computer we can efficiently implement the overall sharing of computing resources, storage resource, data resource, information resource, knowledge resources and experts resources. But to WebGIS, we only implement the physically connection of data and information and these is far from the enough. Because of the different understanding of the world, following different professional regulations, different policies and different habits, the experts in different field will get different end when they observed the same geographic phenomenon and the semantic heterogeneity produced. Since these there are large differences to the same concept in different field. If we use the WebGIS without considering of the semantic heterogeneity, we will answer the questions users proposed wrongly or we can't answer the questions users proposed. To solve this problem, this paper put forward and experienced an effective method of combing semantic grid and Web Services technology to develop WebGIS. In this paper, we studied the method to construct ontology and the method to combine Grid technology and Web Services and with the detailed analysis of computing characteristics and application model in the distribution of data, we designed the WebGIS query system driven by ontology based on Grid technology and Web Services.

Soil organic carbon content assessment in a heterogeneous landscape: comparison of digital soil mapping and visible and near Infrared spectroscopy approaches

NASA Astrophysics Data System (ADS)

Michot, Didier; Fouad, Youssef; Pascal, Pichelin; Viaud, Valérie; Soltani, Inès; Walter, Christian

2017-04-01

This study aims are: i) to assess SOC content distribution according to the global soil map (GSM) project recommendations in a heterogeneous landscape ; ii) to compare the prediction performance of digital soil mapping (DSM) and visible-near infrared (Vis-NIR) spectroscopy approaches. The study area of 140 ha, located at Plancoët, surrounds the unique mineral spring water of Brittany (Western France). It's a hillock characterized by a heterogeneous landscape mosaic with different types of forest, permanent pastures and wetlands along a small coastal river. We acquired two independent datasets: j) 50 points selected using a conditioned Latin hypercube sampling (cLHS); jj) 254 points corresponding to the GSM grid. Soil samples were collected in three layers (0-5, 20-25 and 40-50cm) for both sampling strategies. SOC content was only measured in cLHS soil samples, while Vis-NIR spectra were measured on all the collected samples. For the DSM approach, a machine-learning algorithm (Cubist) was applied on the cLHS calibration data to build rule-based models linking soil carbon content in the different layers with environmental covariates, derived from digital elevation model, geological variables, land use data and existing large scale soil maps. For the spectroscopy approach, we used two calibration datasets: k) the local cLHS ; kk) a subset selected from the regional spectral database of Brittany after a PCA with a hierarchical clustering analysis and spiked by local cLHS spectra. The PLS regression algorithm with "leave-one-out" cross validation was performed for both calibration datasets. SOC contents for the 3 layers of the GSM grid were predicted using the different approaches and were compared with each other. Their prediction performance was evaluated by the following parameters: R2, RMSE and RPD. Both approaches led to satisfactory predictions for SOC content with an advantage for the spectral approach, particularly as regards the pertinence of the variation range.

Microbial micropatches within microbial hotspots

PubMed Central

Smith, Renee J.; Tobe, Shanan S.; Paterson, James S.; Seymour, Justin R.; Oliver, Rod L.; Mitchell, James G.

2018-01-01

The spatial distributions of organism abundance and diversity are often heterogeneous. This includes the sub-centimetre distributions of microbes, which have ‘hotspots’ of high abundance, and ‘coldspots’ of low abundance. Previously we showed that 300 μl abundance hotspots, coldspots and background regions were distinct at all taxonomic levels. Here we build on these results by showing taxonomic micropatches within these 300 μl microscale hotspots, coldspots and background regions at the 1 μl scale. This heterogeneity among 1 μl subsamples was driven by heightened abundance of specific genera. The micropatches were most pronounced within hotspots. Micropatches were dominated by Pseudomonas, Bacteroides, Parasporobacterium and Lachnospiraceae incertae sedis, with Pseudomonas and Bacteroides being responsible for a shift in the most dominant genera in individual hotspot subsamples, representing up to 80.6% and 47.3% average abundance, respectively. The presence of these micropatches implies the ability these groups have to create, establish themselves in, or exploit heterogeneous microenvironments. These genera are often particle-associated, from which we infer that these micropatches are evidence for sub-millimetre aggregates and the aquatic polymer matrix. These findings support the emerging paradigm that the microscale distributions of planktonic microbes are numerically and taxonomically heterogeneous at scales of millimetres and less. We show that microscale microbial hotspots have internal structure within which specific local nutrient exchanges and cellular interactions might occur. PMID:29787564